The Sarcoma Journal

Aberrations in oncogenic pathways and immune modulation influence treatment response in patients with metastatic leiomyosarcoma or liposarcoma, based on an analysis of whole-exome sequencing of tumor samples from patients in a completed phase 3 randomized trial comparing trabectedin and dacarbazine.

In that trial, trabectedin benefit was mostly seen in patients with leiomyosarcoma, as well as in patients with myxoid/round cell sarcomas, and less so in those with dedifferentiated and pleomorphic liposarcomas.

Gurpreet Kapoor, PhD, of LabConnect, Seattle, and colleagues examined aberrations in oncogenic pathways (DNA damage response, PI3K, MDM2-p53) and in immune modulation and then correlated the genomic aberrations with prospective data on clinical outcomes in the trial.

For the study, presented at the annual meeting of the American Society of Clinical Oncology in Chicago, archival tumor samples were collected from 456 of the 518 patients; 180 had uterine leiomyosarcomas, 149 had nonuterine leiomyosarcomas, 66 had dedifferentiated liposarcomas, 46 had myxoid liposarcomas, and 15 had pleomorphic liposarcomas.

Peripheral blood samples from a subset of 346 patients were also analyzed as matched normal to filter noise from nonpathogenic variants in the whole-exome sequencing.

Consistent with sarcoma data from The Cancer Genome Atlas, frequent homozygous gene deletions with relatively low mutational load were noted in these leiomyosarcoma and liposarcoma samples. TP53 and RB1 alterations were more frequent in leiomyosarcomas than in liposarcomas and were not associated with clinical outcomes. Analyses of 103 DNA damage-response genes found somatic alterations exceeded 20% across subtypes and correlated with improved progression-free survival in only uterine leiomyosarcomas (hazard ratio, 0.63; P = .03).

Genomic alterations in PI3K pathway genes were noted in 30% of myxoid liposarcomas and were associated with a worse rate of progression-free survival (HR, 3.0; P = .045).

A trend towards better overall survival was noted in dedifferentiated liposarcoma patients with MDM2 amplification as compared with normal MDM2 copy number.

Certain subtype-specific genomic aberrations in immune modulation pathways were associated with worse clinical outcomes in patients with uterine leiomyosarcoma or dedifferentiated liposarcoma. Alterations in immune suppressors were associated with improved clinical outcomes in nonuterine leiomyosarcomas and alterations in lipid metabolism were associated with improved clinical outcomes in dedifferentiated liposarcomas.

The invited discussant for the study, Mark Andrew Dickson, MD, of Memorial Sloan Kettering Cancer Center, New York, noted that “the real take-home here is that the TMBs (tumor mutation burdens) are relatively low across all of the L-type sarcomas.

“The pattern and prevalence of genomic aberrations that we’re seeing in this cohort of patients prospectively analyzed on a clinical trial are consistent with prior reports. ... including CDK4 and MDM2 in dedifferentiated liposarcoma, PI3-kinase in some myxoid/round cells, p53 in leiomyosarcoma and liposarcoma, and so on.”

Generally, tumor mutation burden is low in L-type sarcomas, and there are some intriguing associations with benefit to therapies, such as PI3-kinase pathway and potential resistance to trabectedin and high tumor mutation burden and potential sensitivity to trabectedin, that need to be explored and validated in another larger cohort, he said.

“I also am increasingly coming to terms with the fact that the tumors like leiomyosarcoma, which have low tumor mutation burden, and which so far have proven fairly immune to immunotherapy, based on all of the negative PD-1 data that we’ve seen, and that also have recurrent, relatively unactionable mutations, like p53 and Rb, remain very difficult to treat,” Dr. Dickson concluded.

mdales@mdedge.com

SOURCE: Kapoor G et al. ASCO 2018, Abstract 11513.

Aberrations in oncogenic pathways and immune modulation influence treatment response in patients with metastatic leiomyosarcoma or liposarcoma, based on an analysis of whole-exome sequencing of tumor samples from patients in a completed phase 3 randomized trial comparing trabectedin and dacarbazine.

In that trial, trabectedin benefit was mostly seen in patients with leiomyosarcoma, as well as in patients with myxoid/round cell sarcomas, and less so in those with dedifferentiated and pleomorphic liposarcomas.

Gurpreet Kapoor, PhD, of LabConnect, Seattle, and colleagues examined aberrations in oncogenic pathways (DNA damage response, PI3K, MDM2-p53) and in immune modulation and then correlated the genomic aberrations with prospective data on clinical outcomes in the trial.

For the study, presented at the annual meeting of the American Society of Clinical Oncology in Chicago, archival tumor samples were collected from 456 of the 518 patients; 180 had uterine leiomyosarcomas, 149 had nonuterine leiomyosarcomas, 66 had dedifferentiated liposarcomas, 46 had myxoid liposarcomas, and 15 had pleomorphic liposarcomas.

Peripheral blood samples from a subset of 346 patients were also analyzed as matched normal to filter noise from nonpathogenic variants in the whole-exome sequencing.

Consistent with sarcoma data from The Cancer Genome Atlas, frequent homozygous gene deletions with relatively low mutational load were noted in these leiomyosarcoma and liposarcoma samples. TP53 and RB1 alterations were more frequent in leiomyosarcomas than in liposarcomas and were not associated with clinical outcomes. Analyses of 103 DNA damage-response genes found somatic alterations exceeded 20% across subtypes and correlated with improved progression-free survival in only uterine leiomyosarcomas (hazard ratio, 0.63; P = .03).

Genomic alterations in PI3K pathway genes were noted in 30% of myxoid liposarcomas and were associated with a worse rate of progression-free survival (HR, 3.0; P = .045).

A trend towards better overall survival was noted in dedifferentiated liposarcoma patients with MDM2 amplification as compared with normal MDM2 copy number.

Certain subtype-specific genomic aberrations in immune modulation pathways were associated with worse clinical outcomes in patients with uterine leiomyosarcoma or dedifferentiated liposarcoma. Alterations in immune suppressors were associated with improved clinical outcomes in nonuterine leiomyosarcomas and alterations in lipid metabolism were associated with improved clinical outcomes in dedifferentiated liposarcomas.

The invited discussant for the study, Mark Andrew Dickson, MD, of Memorial Sloan Kettering Cancer Center, New York, noted that “the real take-home here is that the TMBs (tumor mutation burdens) are relatively low across all of the L-type sarcomas.

“The pattern and prevalence of genomic aberrations that we’re seeing in this cohort of patients prospectively analyzed on a clinical trial are consistent with prior reports. ... including CDK4 and MDM2 in dedifferentiated liposarcoma, PI3-kinase in some myxoid/round cells, p53 in leiomyosarcoma and liposarcoma, and so on.”

Generally, tumor mutation burden is low in L-type sarcomas, and there are some intriguing associations with benefit to therapies, such as PI3-kinase pathway and potential resistance to trabectedin and high tumor mutation burden and potential sensitivity to trabectedin, that need to be explored and validated in another larger cohort, he said.

“I also am increasingly coming to terms with the fact that the tumors like leiomyosarcoma, which have low tumor mutation burden, and which so far have proven fairly immune to immunotherapy, based on all of the negative PD-1 data that we’ve seen, and that also have recurrent, relatively unactionable mutations, like p53 and Rb, remain very difficult to treat,” Dr. Dickson concluded.

mdales@mdedge.com

SOURCE: Kapoor G et al. ASCO 2018, Abstract 11513.

Aberrations in oncogenic pathways and immune modulation influence treatment response in patients with metastatic leiomyosarcoma or liposarcoma, based on an analysis of whole-exome sequencing of tumor samples from patients in a completed phase 3 randomized trial comparing trabectedin and dacarbazine.

In that trial, trabectedin benefit was mostly seen in patients with leiomyosarcoma, as well as in patients with myxoid/round cell sarcomas, and less so in those with dedifferentiated and pleomorphic liposarcomas.

Gurpreet Kapoor, PhD, of LabConnect, Seattle, and colleagues examined aberrations in oncogenic pathways (DNA damage response, PI3K, MDM2-p53) and in immune modulation and then correlated the genomic aberrations with prospective data on clinical outcomes in the trial.

For the study, presented at the annual meeting of the American Society of Clinical Oncology in Chicago, archival tumor samples were collected from 456 of the 518 patients; 180 had uterine leiomyosarcomas, 149 had nonuterine leiomyosarcomas, 66 had dedifferentiated liposarcomas, 46 had myxoid liposarcomas, and 15 had pleomorphic liposarcomas.

Peripheral blood samples from a subset of 346 patients were also analyzed as matched normal to filter noise from nonpathogenic variants in the whole-exome sequencing.

Consistent with sarcoma data from The Cancer Genome Atlas, frequent homozygous gene deletions with relatively low mutational load were noted in these leiomyosarcoma and liposarcoma samples. TP53 and RB1 alterations were more frequent in leiomyosarcomas than in liposarcomas and were not associated with clinical outcomes. Analyses of 103 DNA damage-response genes found somatic alterations exceeded 20% across subtypes and correlated with improved progression-free survival in only uterine leiomyosarcomas (hazard ratio, 0.63; P = .03).

Genomic alterations in PI3K pathway genes were noted in 30% of myxoid liposarcomas and were associated with a worse rate of progression-free survival (HR, 3.0; P = .045).

A trend towards better overall survival was noted in dedifferentiated liposarcoma patients with MDM2 amplification as compared with normal MDM2 copy number.

Certain subtype-specific genomic aberrations in immune modulation pathways were associated with worse clinical outcomes in patients with uterine leiomyosarcoma or dedifferentiated liposarcoma. Alterations in immune suppressors were associated with improved clinical outcomes in nonuterine leiomyosarcomas and alterations in lipid metabolism were associated with improved clinical outcomes in dedifferentiated liposarcomas.

The invited discussant for the study, Mark Andrew Dickson, MD, of Memorial Sloan Kettering Cancer Center, New York, noted that “the real take-home here is that the TMBs (tumor mutation burdens) are relatively low across all of the L-type sarcomas.

“The pattern and prevalence of genomic aberrations that we’re seeing in this cohort of patients prospectively analyzed on a clinical trial are consistent with prior reports. ... including CDK4 and MDM2 in dedifferentiated liposarcoma, PI3-kinase in some myxoid/round cells, p53 in leiomyosarcoma and liposarcoma, and so on.”

Generally, tumor mutation burden is low in L-type sarcomas, and there are some intriguing associations with benefit to therapies, such as PI3-kinase pathway and potential resistance to trabectedin and high tumor mutation burden and potential sensitivity to trabectedin, that need to be explored and validated in another larger cohort, he said.

“I also am increasingly coming to terms with the fact that the tumors like leiomyosarcoma, which have low tumor mutation burden, and which so far have proven fairly immune to immunotherapy, based on all of the negative PD-1 data that we’ve seen, and that also have recurrent, relatively unactionable mutations, like p53 and Rb, remain very difficult to treat,” Dr. Dickson concluded.

mdales@mdedge.com

SOURCE: Kapoor G et al. ASCO 2018, Abstract 11513.

The U.S. Food and Drug Administration has lifted the partial clinical hold on trials of tazemetostat, an EZH2 inhibitor being developed to treat solid tumors and lymphomas, according to a press release from the drug’s developer Epizyme.

jensmith@mdedge.com

The U.S. Food and Drug Administration has lifted the partial clinical hold on trials of tazemetostat, an EZH2 inhibitor being developed to treat solid tumors and lymphomas, according to a press release from the drug’s developer Epizyme.

jensmith@mdedge.com

The U.S. Food and Drug Administration has lifted the partial clinical hold on trials of tazemetostat, an EZH2 inhibitor being developed to treat solid tumors and lymphomas, according to a press release from the drug’s developer Epizyme.

jensmith@mdedge.com

A combination of trabectedin and the PARP inhibitor olaparib may be a safe and effective therapy for patients with sarcoma, the recent TOMAS trial found.

High PARP1 expression was associated with treatment response, reported Giovanni Grignani, MD, of the Medical Oncology_Sarcoma Unit at Istituto di Ricovero e Cura a Carattere Scientifico in Candiolo, Italy, and his colleagues.

PARP inhibitors prevent repair of DNA damage, suggesting potential synergisms with DNA-damaging anticancer agents. Preclinical models support this strategy; however, clinical trials have found that toxicities restrict doses below antitumor activity levels.

“In view of these findings, trabectedin could be an ideal drug to use in combination with PARP1/2 inhibitors for two reasons: its favourable haemopoietic toxicity profile and its unique mechanisms of action,” the authors wrote in The Lancet Oncology. Trabectedin bends the minor groove of DNA toward the major groove, which activates PARP1 in an attempt to repair the damage. Preclinical trials showed that a PARP inhibitor such as olaparib would block this PARP1 activation, ultimately resulting in a more robust response than with either drug alone.

The phase 1b, open-label TOMAS trial involved 50 patients with sarcoma who had experienced disease progression after standard therapy. The study was divided into two cohorts: dose-escalation and dose-expansion. Patients received a median of four cycles of therapy with a median follow-up of 10 months (some patients are still undergoing treatment). The primary endpoint was maximum tolerated dose. The investigators also evaluated pharmacokinetics, pharmacodynamics, and various response measures.

Although adverse events occurred, these were manageable, and the authors concluded that the combination is safe for further investigation. The most common grade 3 or higher adverse events were lymphopenia (64%), neutropenia (62%), thrombocytopenia (28%), anemia (26%), hypophosphatemia (40%), and alanine aminotransferase elevation (18%). The maximum tolerated dose (recommended phase 2 dose) was olaparib 150 mg twice daily and trabectedin 1.1 mg/m² every 3 weeks.

“These doses allowed us to minimize the need for dose reductions and continue treatment for as long as tumour control was maintained,” the authors wrote. Previous treatments impacted tolerability. The researchers noted that “patients who had received more than two lines of therapy had a higher risk of developing dose-limiting toxicities than those patients who had been treated with only one line of therapy.”

Overall, 14% of patients responded to therapy. Six-month progression-free survival was more common in patients with soft tissue sarcoma (38%) than other tumor types. More patients with high PARP1 expression achieved 6-month PFS compared with patients who had low PARP1 expression (59% vs. 8%; P = .01).

“The combination of olaparib and trabectedin exploits the potential of two different first-in-class drugs and shows tolerability and activity in homologous repair-proficient tumors,” the authors concluded.

They are planning two phase 2 studies in the future; one “comparing trabectedin alone versus the combination of trabectedin and olaparib, stratifying patients according to PARP1 expression,” and an “after-platinum-failure study of patients with ovarian cancer regardless of patients’ BRCA1/2 and BRCAness status.”

The TOMAS trial was funded by the Italian Association for Cancer Research, the Foundation for Research on Musculoskeletal and Rare Tumors, the Italian Ministry of Health, and PharmaMar. The authors reported compensation from Lilly, Novartis, Bayer, Eisai, Amgen, and others.

SOURCE: Grignani et al. Lancet Oncol. 2018 Sep 11. doi: 10.1016/S1470-2045(18)30438-8.

A combination of trabectedin and the PARP inhibitor olaparib may be a safe and effective therapy for patients with sarcoma, the recent TOMAS trial found.

High PARP1 expression was associated with treatment response, reported Giovanni Grignani, MD, of the Medical Oncology_Sarcoma Unit at Istituto di Ricovero e Cura a Carattere Scientifico in Candiolo, Italy, and his colleagues.

PARP inhibitors prevent repair of DNA damage, suggesting potential synergisms with DNA-damaging anticancer agents. Preclinical models support this strategy; however, clinical trials have found that toxicities restrict doses below antitumor activity levels.

“In view of these findings, trabectedin could be an ideal drug to use in combination with PARP1/2 inhibitors for two reasons: its favourable haemopoietic toxicity profile and its unique mechanisms of action,” the authors wrote in The Lancet Oncology. Trabectedin bends the minor groove of DNA toward the major groove, which activates PARP1 in an attempt to repair the damage. Preclinical trials showed that a PARP inhibitor such as olaparib would block this PARP1 activation, ultimately resulting in a more robust response than with either drug alone.

The phase 1b, open-label TOMAS trial involved 50 patients with sarcoma who had experienced disease progression after standard therapy. The study was divided into two cohorts: dose-escalation and dose-expansion. Patients received a median of four cycles of therapy with a median follow-up of 10 months (some patients are still undergoing treatment). The primary endpoint was maximum tolerated dose. The investigators also evaluated pharmacokinetics, pharmacodynamics, and various response measures.

Although adverse events occurred, these were manageable, and the authors concluded that the combination is safe for further investigation. The most common grade 3 or higher adverse events were lymphopenia (64%), neutropenia (62%), thrombocytopenia (28%), anemia (26%), hypophosphatemia (40%), and alanine aminotransferase elevation (18%). The maximum tolerated dose (recommended phase 2 dose) was olaparib 150 mg twice daily and trabectedin 1.1 mg/m² every 3 weeks.

“These doses allowed us to minimize the need for dose reductions and continue treatment for as long as tumour control was maintained,” the authors wrote. Previous treatments impacted tolerability. The researchers noted that “patients who had received more than two lines of therapy had a higher risk of developing dose-limiting toxicities than those patients who had been treated with only one line of therapy.”

Overall, 14% of patients responded to therapy. Six-month progression-free survival was more common in patients with soft tissue sarcoma (38%) than other tumor types. More patients with high PARP1 expression achieved 6-month PFS compared with patients who had low PARP1 expression (59% vs. 8%; P = .01).

“The combination of olaparib and trabectedin exploits the potential of two different first-in-class drugs and shows tolerability and activity in homologous repair-proficient tumors,” the authors concluded.

They are planning two phase 2 studies in the future; one “comparing trabectedin alone versus the combination of trabectedin and olaparib, stratifying patients according to PARP1 expression,” and an “after-platinum-failure study of patients with ovarian cancer regardless of patients’ BRCA1/2 and BRCAness status.”

The TOMAS trial was funded by the Italian Association for Cancer Research, the Foundation for Research on Musculoskeletal and Rare Tumors, the Italian Ministry of Health, and PharmaMar. The authors reported compensation from Lilly, Novartis, Bayer, Eisai, Amgen, and others.

SOURCE: Grignani et al. Lancet Oncol. 2018 Sep 11. doi: 10.1016/S1470-2045(18)30438-8.

A combination of trabectedin and the PARP inhibitor olaparib may be a safe and effective therapy for patients with sarcoma, the recent TOMAS trial found.

High PARP1 expression was associated with treatment response, reported Giovanni Grignani, MD, of the Medical Oncology_Sarcoma Unit at Istituto di Ricovero e Cura a Carattere Scientifico in Candiolo, Italy, and his colleagues.

PARP inhibitors prevent repair of DNA damage, suggesting potential synergisms with DNA-damaging anticancer agents. Preclinical models support this strategy; however, clinical trials have found that toxicities restrict doses below antitumor activity levels.

“In view of these findings, trabectedin could be an ideal drug to use in combination with PARP1/2 inhibitors for two reasons: its favourable haemopoietic toxicity profile and its unique mechanisms of action,” the authors wrote in The Lancet Oncology. Trabectedin bends the minor groove of DNA toward the major groove, which activates PARP1 in an attempt to repair the damage. Preclinical trials showed that a PARP inhibitor such as olaparib would block this PARP1 activation, ultimately resulting in a more robust response than with either drug alone.

The phase 1b, open-label TOMAS trial involved 50 patients with sarcoma who had experienced disease progression after standard therapy. The study was divided into two cohorts: dose-escalation and dose-expansion. Patients received a median of four cycles of therapy with a median follow-up of 10 months (some patients are still undergoing treatment). The primary endpoint was maximum tolerated dose. The investigators also evaluated pharmacokinetics, pharmacodynamics, and various response measures.

Although adverse events occurred, these were manageable, and the authors concluded that the combination is safe for further investigation. The most common grade 3 or higher adverse events were lymphopenia (64%), neutropenia (62%), thrombocytopenia (28%), anemia (26%), hypophosphatemia (40%), and alanine aminotransferase elevation (18%). The maximum tolerated dose (recommended phase 2 dose) was olaparib 150 mg twice daily and trabectedin 1.1 mg/m² every 3 weeks.

“These doses allowed us to minimize the need for dose reductions and continue treatment for as long as tumour control was maintained,” the authors wrote. Previous treatments impacted tolerability. The researchers noted that “patients who had received more than two lines of therapy had a higher risk of developing dose-limiting toxicities than those patients who had been treated with only one line of therapy.”

Overall, 14% of patients responded to therapy. Six-month progression-free survival was more common in patients with soft tissue sarcoma (38%) than other tumor types. More patients with high PARP1 expression achieved 6-month PFS compared with patients who had low PARP1 expression (59% vs. 8%; P = .01).

“The combination of olaparib and trabectedin exploits the potential of two different first-in-class drugs and shows tolerability and activity in homologous repair-proficient tumors,” the authors concluded.

They are planning two phase 2 studies in the future; one “comparing trabectedin alone versus the combination of trabectedin and olaparib, stratifying patients according to PARP1 expression,” and an “after-platinum-failure study of patients with ovarian cancer regardless of patients’ BRCA1/2 and BRCAness status.”

The TOMAS trial was funded by the Italian Association for Cancer Research, the Foundation for Research on Musculoskeletal and Rare Tumors, the Italian Ministry of Health, and PharmaMar. The authors reported compensation from Lilly, Novartis, Bayer, Eisai, Amgen, and others.

SOURCE: Grignani et al. Lancet Oncol. 2018 Sep 11. doi: 10.1016/S1470-2045(18)30438-8.

A novel method for detection of translocations appears to be superior to conventional molecular assays in the evaluation of bone and soft tissue tumor samples, according to researchers.

The technique of anchored multiplex polymerase chain reaction (AMP)–based targeted next-generation sequencing (NGS) had a failure rate of 14% but, nonetheless, worked favorably when compared with conventional techniques, which were associated with several false positives in this study, the researchers reported in the Journal of Molecular Diagnostics.

Two new fusion partners for the USP6 gene were found using AMP-based targeted NGS in this study, which thus contributed to the “further unraveling of the molecular landscape” for these tumors, added corresponding author Judith V.M.G. Bovée, MD, PhD, of the department of pathology at Leiden (the Netherlands) University Medical Center and her colleagues.

While the genetics of bone and soft tissue tumors have diagnostic value in clinical practice, standard fluorescence in situ hybridization (FISH) and reverse transcriptase PCR are associated with several drawbacks, such as a high false negative rate in the case of FISH, Dr. Bovée and her coauthors wrote.

Accordingly, the researchers evaluated the applicability of a targeted sequencing assay (Archer FusionPlex Sarcoma kit, which was developed by ArcherDX) aimed at 26 genes relevant to bone and soft tissue tumor diagnostics.

Besides allowing for assessment of multiple target genes in a single assay, this technique circumvents the need to know both fusion partners for translocation detection, which opens up the possibility of identifying novel or rare fusion partners, investigators noted.

AMP-based targeted NGS was used to evaluate 81 bone and soft tissue tumor samples, and of those, 48 cases showed a fusion. For the remaining 33 cases in which no fusion was detected, 22 were considered truly negative because samples met all criteria for good quality, while the remaining 11 (14%) were considered not reliable because of insufficient quality, investigators reported.

The samples were also evaluated through use of FISH, reverse transcriptase PCR, or both in 58 cases and use of immunohistochemistry in 16 cases; for the remaining seven cases, no assay or immunohistochemistry could be applied because of a lack of availability, according to investigators.

Among the 48 entities that were fusion-positive according to AMP-based targeted NGS, 29 were validated using standard molecular assays, and of those, 25 had concordant results. Further analysis of the four discordant cases with a third independent technique confirmed the AMP-based targeted NGS findings, according to the published report.

Among the 22 fusion-negative high-quality samples, 19 were validated using FISH, and one case was found to be discordant; however, despite use of a third independent technique, this discrepancy could not be resolved, investigators said.

The AMP-based targeted NGS technique identified COL1A1 and SEC31A as novel fusion partners for USP6 in two cases of nodular fasciitis. Those fusion partners had been previously described in aneurysmal bone cysts, according to investigators.

Despite the promising results for the novel assay, conventional methods were sufficient in this study to confirm translocations in straightforward cases and ordinary rearrangements, according to the investigators.

“Both reverse transcription PCR and FISH are not only quick and easy to conduct but are also of low cost and high analytical validity and accuracy, which make them attractive methods,” they wrote.

The work by Dr. Bovée and her colleagues was supported by Leiden University Medical Center. The department of pathology and the department of cell and chemical biology at the medical center receive royalty payments from Kreatech/Leica, which provided a COL1A1/PDGFB fusion probe used in the research.

SOURCE: Lam SW et al. J Mol Diagn. 2018 Aug 20;20(5):653-63.

A novel method for detection of translocations appears to be superior to conventional molecular assays in the evaluation of bone and soft tissue tumor samples, according to researchers.

The technique of anchored multiplex polymerase chain reaction (AMP)–based targeted next-generation sequencing (NGS) had a failure rate of 14% but, nonetheless, worked favorably when compared with conventional techniques, which were associated with several false positives in this study, the researchers reported in the Journal of Molecular Diagnostics.

Two new fusion partners for the USP6 gene were found using AMP-based targeted NGS in this study, which thus contributed to the “further unraveling of the molecular landscape” for these tumors, added corresponding author Judith V.M.G. Bovée, MD, PhD, of the department of pathology at Leiden (the Netherlands) University Medical Center and her colleagues.

While the genetics of bone and soft tissue tumors have diagnostic value in clinical practice, standard fluorescence in situ hybridization (FISH) and reverse transcriptase PCR are associated with several drawbacks, such as a high false negative rate in the case of FISH, Dr. Bovée and her coauthors wrote.

Accordingly, the researchers evaluated the applicability of a targeted sequencing assay (Archer FusionPlex Sarcoma kit, which was developed by ArcherDX) aimed at 26 genes relevant to bone and soft tissue tumor diagnostics.

Besides allowing for assessment of multiple target genes in a single assay, this technique circumvents the need to know both fusion partners for translocation detection, which opens up the possibility of identifying novel or rare fusion partners, investigators noted.

AMP-based targeted NGS was used to evaluate 81 bone and soft tissue tumor samples, and of those, 48 cases showed a fusion. For the remaining 33 cases in which no fusion was detected, 22 were considered truly negative because samples met all criteria for good quality, while the remaining 11 (14%) were considered not reliable because of insufficient quality, investigators reported.

The samples were also evaluated through use of FISH, reverse transcriptase PCR, or both in 58 cases and use of immunohistochemistry in 16 cases; for the remaining seven cases, no assay or immunohistochemistry could be applied because of a lack of availability, according to investigators.

Among the 48 entities that were fusion-positive according to AMP-based targeted NGS, 29 were validated using standard molecular assays, and of those, 25 had concordant results. Further analysis of the four discordant cases with a third independent technique confirmed the AMP-based targeted NGS findings, according to the published report.

Among the 22 fusion-negative high-quality samples, 19 were validated using FISH, and one case was found to be discordant; however, despite use of a third independent technique, this discrepancy could not be resolved, investigators said.

The AMP-based targeted NGS technique identified COL1A1 and SEC31A as novel fusion partners for USP6 in two cases of nodular fasciitis. Those fusion partners had been previously described in aneurysmal bone cysts, according to investigators.

Despite the promising results for the novel assay, conventional methods were sufficient in this study to confirm translocations in straightforward cases and ordinary rearrangements, according to the investigators.

“Both reverse transcription PCR and FISH are not only quick and easy to conduct but are also of low cost and high analytical validity and accuracy, which make them attractive methods,” they wrote.

The work by Dr. Bovée and her colleagues was supported by Leiden University Medical Center. The department of pathology and the department of cell and chemical biology at the medical center receive royalty payments from Kreatech/Leica, which provided a COL1A1/PDGFB fusion probe used in the research.

SOURCE: Lam SW et al. J Mol Diagn. 2018 Aug 20;20(5):653-63.

A novel method for detection of translocations appears to be superior to conventional molecular assays in the evaluation of bone and soft tissue tumor samples, according to researchers.

The technique of anchored multiplex polymerase chain reaction (AMP)–based targeted next-generation sequencing (NGS) had a failure rate of 14% but, nonetheless, worked favorably when compared with conventional techniques, which were associated with several false positives in this study, the researchers reported in the Journal of Molecular Diagnostics.

Two new fusion partners for the USP6 gene were found using AMP-based targeted NGS in this study, which thus contributed to the “further unraveling of the molecular landscape” for these tumors, added corresponding author Judith V.M.G. Bovée, MD, PhD, of the department of pathology at Leiden (the Netherlands) University Medical Center and her colleagues.

While the genetics of bone and soft tissue tumors have diagnostic value in clinical practice, standard fluorescence in situ hybridization (FISH) and reverse transcriptase PCR are associated with several drawbacks, such as a high false negative rate in the case of FISH, Dr. Bovée and her coauthors wrote.

Accordingly, the researchers evaluated the applicability of a targeted sequencing assay (Archer FusionPlex Sarcoma kit, which was developed by ArcherDX) aimed at 26 genes relevant to bone and soft tissue tumor diagnostics.

Besides allowing for assessment of multiple target genes in a single assay, this technique circumvents the need to know both fusion partners for translocation detection, which opens up the possibility of identifying novel or rare fusion partners, investigators noted.

AMP-based targeted NGS was used to evaluate 81 bone and soft tissue tumor samples, and of those, 48 cases showed a fusion. For the remaining 33 cases in which no fusion was detected, 22 were considered truly negative because samples met all criteria for good quality, while the remaining 11 (14%) were considered not reliable because of insufficient quality, investigators reported.

The samples were also evaluated through use of FISH, reverse transcriptase PCR, or both in 58 cases and use of immunohistochemistry in 16 cases; for the remaining seven cases, no assay or immunohistochemistry could be applied because of a lack of availability, according to investigators.

Among the 48 entities that were fusion-positive according to AMP-based targeted NGS, 29 were validated using standard molecular assays, and of those, 25 had concordant results. Further analysis of the four discordant cases with a third independent technique confirmed the AMP-based targeted NGS findings, according to the published report.

Among the 22 fusion-negative high-quality samples, 19 were validated using FISH, and one case was found to be discordant; however, despite use of a third independent technique, this discrepancy could not be resolved, investigators said.

The AMP-based targeted NGS technique identified COL1A1 and SEC31A as novel fusion partners for USP6 in two cases of nodular fasciitis. Those fusion partners had been previously described in aneurysmal bone cysts, according to investigators.

Despite the promising results for the novel assay, conventional methods were sufficient in this study to confirm translocations in straightforward cases and ordinary rearrangements, according to the investigators.

“Both reverse transcription PCR and FISH are not only quick and easy to conduct but are also of low cost and high analytical validity and accuracy, which make them attractive methods,” they wrote.

The work by Dr. Bovée and her colleagues was supported by Leiden University Medical Center. The department of pathology and the department of cell and chemical biology at the medical center receive royalty payments from Kreatech/Leica, which provided a COL1A1/PDGFB fusion probe used in the research.

SOURCE: Lam SW et al. J Mol Diagn. 2018 Aug 20;20(5):653-63.

The investigational drug selinexor appears to be improving progression-free survival in patients with advanced dedifferentiated liposarcoma, based on phase 2 results from the randomized, placebo-controlled SEAL study.

But the statistical significance of the improvements varied depending on whether progression-free survival (PFS) was assessed by the World Health Organization criteria, which looks at two-dimensional measurements of these irregular three-dimensional objects, or RECIST v1.1 criteria, which only looks at a unidimensional measure, reported Mrinal M. Gounder, MD, of Memorial Sloan Kettering Cancer Center, New York, at the annual meeting of the American Society of Clinical Oncology. When tumor response was based on WHO criteria, there was no difference in median PFS for the 24 patients on active therapy (1.4 months) and the 27 patients on placebo (1.8 months). By RECIST v1.1 criteria, however, median PFS was 5.6 months with selinexor.

Dedifferentiated liposarcoma is incurable, and palliative therapies are associated with an overall survival of 11-20 months in these patients. Selinexor is an oral selective inhibitor of exportin-1 which exports proteins from the nucleus into the cytoplasm. The drug appears to prevent p53 from leaving the nucleus, thereby protecting it from overexpressed MDM2, which is a negative regulator of p53, but the drug might have other potential mechanisms of action.

The double-blind study included 56 evaluable patients who had progressive dedifferentiated liposarcoma and had received at least one prior systemic therapy. Patients’ median age was 61 years and they had received a median of two prior therapies. Patients were randomized to get either 60 mg of selinexor (26 patients) or placebo (30 patients) twice weekly until their disease progressed or they were no longer able to tolerate therapy. Patients whose disease progressed on placebo (24 patients) were allowed to cross over to open-label selinexor therapy.

Treatments were unblinded for 51 of the patients, 24 on selinexor and 27 on placebo. Disease progression as confirmed by Independent Central Radiological Review using WHO criteria was the main reason for ending blinded treatment.

Grade 1/2 adverse events for selinexor versus placebo, respectively, were nausea (85% vs. 31%), anorexia (62% vs. 14%), and fatigue (58% vs. 45%). The comparable rates of grade 3/4 adverse events were hyponatremia (15% vs. 0%), anemia (15% vs. 7%), and thrombocytopenia (12% vs. 0%). Selinexor dose was reduced because of adverse events in 12 patients.

In a discussion of the study’s implications, Mark Andrew Dickson, MD, also of Memorial Sloan Kettering Cancer Center, called the adverse events profile “mostly manageable but predictable grade 1/2 adverse events ... and median progression-free survival of 5 and a half months is quite encouraging.

“Changing response assessment method midtrial in a study with progression-free survival as the primary endpoint is obviously problematic, but it also highlights how difficult it is to measure three-dimensional tumors like complex retroperitoneal liposarcomas, which move and change and grow and shrink over time,” he said. “And I would conclude that RECIST is probably the worst method of tumor assessment for sarcoma, except for all the other methods of tumor assessment.”

To illustrate the difficulty of measuring tumor response, Dr. Dickson presented examples of different tumor shapes and scenarios where one method would indicate tumor progression and the other would indicate stable disease.

“There can be differences between the two methods in how progression responds and is determined. And you can do this experiment with a number of different shapes and find scenarios where one method would call it progression at a different time than the other. So this is really critically important when we look at the results of the clinical trial, because it was designed to look at WHO PFS. And you can see that, based on that, there was no significant difference between the selinexor and placebo arm,” he said.

Additionally, he reviewed cases from the study where “either way you measure this, you can see that [the] tumor is getting smaller over time,” as well as cases where the tumor grew in patients on placebo first, but decreased in size after switching to the active therapy.

“The improvement in progression-free survival is promising and ... selinexor probably does have activity in dediff lipo compared to historical data,” said Dr. Dickson, adding that he looks forward to selinexor progressing to a randomized, phase 3 trial and “seeing those data perhaps next year.”

Dr. Gounder disclosed financial relationships with multiple drug companies including Karyopharm Therapeutics, the maker of selinexor. Dr. Dickson disclosed a consult or adviser role with Celgene and research funding from Eli Lilly.

SOURCE: Gounder M et al. ASCO 2018, Abstract 11512.

The investigational drug selinexor appears to be improving progression-free survival in patients with advanced dedifferentiated liposarcoma, based on phase 2 results from the randomized, placebo-controlled SEAL study.

But the statistical significance of the improvements varied depending on whether progression-free survival (PFS) was assessed by the World Health Organization criteria, which looks at two-dimensional measurements of these irregular three-dimensional objects, or RECIST v1.1 criteria, which only looks at a unidimensional measure, reported Mrinal M. Gounder, MD, of Memorial Sloan Kettering Cancer Center, New York, at the annual meeting of the American Society of Clinical Oncology. When tumor response was based on WHO criteria, there was no difference in median PFS for the 24 patients on active therapy (1.4 months) and the 27 patients on placebo (1.8 months). By RECIST v1.1 criteria, however, median PFS was 5.6 months with selinexor.

Dedifferentiated liposarcoma is incurable, and palliative therapies are associated with an overall survival of 11-20 months in these patients. Selinexor is an oral selective inhibitor of exportin-1 which exports proteins from the nucleus into the cytoplasm. The drug appears to prevent p53 from leaving the nucleus, thereby protecting it from overexpressed MDM2, which is a negative regulator of p53, but the drug might have other potential mechanisms of action.

The double-blind study included 56 evaluable patients who had progressive dedifferentiated liposarcoma and had received at least one prior systemic therapy. Patients’ median age was 61 years and they had received a median of two prior therapies. Patients were randomized to get either 60 mg of selinexor (26 patients) or placebo (30 patients) twice weekly until their disease progressed or they were no longer able to tolerate therapy. Patients whose disease progressed on placebo (24 patients) were allowed to cross over to open-label selinexor therapy.

Treatments were unblinded for 51 of the patients, 24 on selinexor and 27 on placebo. Disease progression as confirmed by Independent Central Radiological Review using WHO criteria was the main reason for ending blinded treatment.

Grade 1/2 adverse events for selinexor versus placebo, respectively, were nausea (85% vs. 31%), anorexia (62% vs. 14%), and fatigue (58% vs. 45%). The comparable rates of grade 3/4 adverse events were hyponatremia (15% vs. 0%), anemia (15% vs. 7%), and thrombocytopenia (12% vs. 0%). Selinexor dose was reduced because of adverse events in 12 patients.

In a discussion of the study’s implications, Mark Andrew Dickson, MD, also of Memorial Sloan Kettering Cancer Center, called the adverse events profile “mostly manageable but predictable grade 1/2 adverse events ... and median progression-free survival of 5 and a half months is quite encouraging.

“Changing response assessment method midtrial in a study with progression-free survival as the primary endpoint is obviously problematic, but it also highlights how difficult it is to measure three-dimensional tumors like complex retroperitoneal liposarcomas, which move and change and grow and shrink over time,” he said. “And I would conclude that RECIST is probably the worst method of tumor assessment for sarcoma, except for all the other methods of tumor assessment.”

To illustrate the difficulty of measuring tumor response, Dr. Dickson presented examples of different tumor shapes and scenarios where one method would indicate tumor progression and the other would indicate stable disease.

“There can be differences between the two methods in how progression responds and is determined. And you can do this experiment with a number of different shapes and find scenarios where one method would call it progression at a different time than the other. So this is really critically important when we look at the results of the clinical trial, because it was designed to look at WHO PFS. And you can see that, based on that, there was no significant difference between the selinexor and placebo arm,” he said.

Additionally, he reviewed cases from the study where “either way you measure this, you can see that [the] tumor is getting smaller over time,” as well as cases where the tumor grew in patients on placebo first, but decreased in size after switching to the active therapy.

“The improvement in progression-free survival is promising and ... selinexor probably does have activity in dediff lipo compared to historical data,” said Dr. Dickson, adding that he looks forward to selinexor progressing to a randomized, phase 3 trial and “seeing those data perhaps next year.”

Dr. Gounder disclosed financial relationships with multiple drug companies including Karyopharm Therapeutics, the maker of selinexor. Dr. Dickson disclosed a consult or adviser role with Celgene and research funding from Eli Lilly.

SOURCE: Gounder M et al. ASCO 2018, Abstract 11512.

The investigational drug selinexor appears to be improving progression-free survival in patients with advanced dedifferentiated liposarcoma, based on phase 2 results from the randomized, placebo-controlled SEAL study.

But the statistical significance of the improvements varied depending on whether progression-free survival (PFS) was assessed by the World Health Organization criteria, which looks at two-dimensional measurements of these irregular three-dimensional objects, or RECIST v1.1 criteria, which only looks at a unidimensional measure, reported Mrinal M. Gounder, MD, of Memorial Sloan Kettering Cancer Center, New York, at the annual meeting of the American Society of Clinical Oncology. When tumor response was based on WHO criteria, there was no difference in median PFS for the 24 patients on active therapy (1.4 months) and the 27 patients on placebo (1.8 months). By RECIST v1.1 criteria, however, median PFS was 5.6 months with selinexor.

Dedifferentiated liposarcoma is incurable, and palliative therapies are associated with an overall survival of 11-20 months in these patients. Selinexor is an oral selective inhibitor of exportin-1 which exports proteins from the nucleus into the cytoplasm. The drug appears to prevent p53 from leaving the nucleus, thereby protecting it from overexpressed MDM2, which is a negative regulator of p53, but the drug might have other potential mechanisms of action.

The double-blind study included 56 evaluable patients who had progressive dedifferentiated liposarcoma and had received at least one prior systemic therapy. Patients’ median age was 61 years and they had received a median of two prior therapies. Patients were randomized to get either 60 mg of selinexor (26 patients) or placebo (30 patients) twice weekly until their disease progressed or they were no longer able to tolerate therapy. Patients whose disease progressed on placebo (24 patients) were allowed to cross over to open-label selinexor therapy.

Treatments were unblinded for 51 of the patients, 24 on selinexor and 27 on placebo. Disease progression as confirmed by Independent Central Radiological Review using WHO criteria was the main reason for ending blinded treatment.

Grade 1/2 adverse events for selinexor versus placebo, respectively, were nausea (85% vs. 31%), anorexia (62% vs. 14%), and fatigue (58% vs. 45%). The comparable rates of grade 3/4 adverse events were hyponatremia (15% vs. 0%), anemia (15% vs. 7%), and thrombocytopenia (12% vs. 0%). Selinexor dose was reduced because of adverse events in 12 patients.

In a discussion of the study’s implications, Mark Andrew Dickson, MD, also of Memorial Sloan Kettering Cancer Center, called the adverse events profile “mostly manageable but predictable grade 1/2 adverse events ... and median progression-free survival of 5 and a half months is quite encouraging.

“Changing response assessment method midtrial in a study with progression-free survival as the primary endpoint is obviously problematic, but it also highlights how difficult it is to measure three-dimensional tumors like complex retroperitoneal liposarcomas, which move and change and grow and shrink over time,” he said. “And I would conclude that RECIST is probably the worst method of tumor assessment for sarcoma, except for all the other methods of tumor assessment.”

To illustrate the difficulty of measuring tumor response, Dr. Dickson presented examples of different tumor shapes and scenarios where one method would indicate tumor progression and the other would indicate stable disease.

“There can be differences between the two methods in how progression responds and is determined. And you can do this experiment with a number of different shapes and find scenarios where one method would call it progression at a different time than the other. So this is really critically important when we look at the results of the clinical trial, because it was designed to look at WHO PFS. And you can see that, based on that, there was no significant difference between the selinexor and placebo arm,” he said.

Additionally, he reviewed cases from the study where “either way you measure this, you can see that [the] tumor is getting smaller over time,” as well as cases where the tumor grew in patients on placebo first, but decreased in size after switching to the active therapy.

“The improvement in progression-free survival is promising and ... selinexor probably does have activity in dediff lipo compared to historical data,” said Dr. Dickson, adding that he looks forward to selinexor progressing to a randomized, phase 3 trial and “seeing those data perhaps next year.”

Dr. Gounder disclosed financial relationships with multiple drug companies including Karyopharm Therapeutics, the maker of selinexor. Dr. Dickson disclosed a consult or adviser role with Celgene and research funding from Eli Lilly.

SOURCE: Gounder M et al. ASCO 2018, Abstract 11512.

Chromoplexy, a sudden burst of complex, loop-like gene rearrangements that gives rise to a fusion gene, appears to be associated with aggressive Ewing sarcomas, based on a study of 124 tumors reported in Science.

Ewing sarcomas with complex karyotypes are associated with a poorer prognosis compared with those with simpler karyotypes. The new findings show that these complex karyotypes are the product of chromoplexy, and that chromoplexy-generated fusions arise early, giving rise to both primary and relapse Ewing sarcoma tumors, which can continue to evolve in parallel.

Analysis of the sequence context surrounding chromoplexy breaks may provide clues and potentially point to a therapeutic vulnerability that could be used to treat Ewing sarcomas. Further, given the preference of chromoplexy events for transcriptionally active regions, Ewing sarcomas arising from chromoplexy may be responsive to immune checkpoint inhibition.

In a study of the whole genomes of 124 Ewing sarcomas, chromoplexy rather than simple reciprocal translocations defined the gene fusions seen in 52 tumors (42%). Ewing sarcoma involves fusions between EWSR1, a gene encoding an RNA binding protein, and E26 transformation-specific (ETS) transcription factors.

“Our analyses reveal rearrangement bursts (chromoplectic loops) as a source of gene fusion in human bone and soft tissue tumors. Ewing sarcomas with complex karyotypes are associated with a poorer prognosis than those with simpler karyotypes, and here we show chromoplexy as the mechanism in 42% of tumors. It is possible that the chromoplectic tumor’s additional gene disruptions and fusions contribute to the difference in patient survival,” wrote Nathaniel D. Anderson of the Hospital for Sick Children, Toronto, and the University of Toronto, and his colleagues.

Standard reciprocal translocations involve DNA breaks in two fusion partners. Chromoplexy involves three or more breakpoints in the genome. A loop pattern emerges as these three or more broken chromosome ends are forced to find a new partner. The result is the formation of functional EWSR1-FLI1 or EWSR1-ERG fusions that, upon expression, provide a selective growth or survival advantage

The researchers found that the loop rearrangements always contained the disease-defining fusion at the center, but they disrupted multiple additional genes. The loops occurred preferentially in early replicating and transcriptionally active genomic regions.

They found similar loops forming canonical fusions in three other sarcoma types.

“Our whole-genome sequence data support a model in which there is an early clone of (Ewing sarcoma), containing EWSR1-ETS and chromoplexy, arising at least 1 year before diagnosis, which gives rise to both the primary and metastatic or relapse tumors. Whether the bursts ... are chance events or driven by specific mutational processes, akin to the RAG machinery operative in leukemia, remains to be established. As an increasing and diverse number of tumor genome sequences become available, we may be able to define further rearrangement processes that underlie fusion genes and thus unravel the causes of fusion-driven human cancers,” the researchers wrote.

The clinical features and demographics of the study patients were typical of Ewing sarcoma patients. Average patient age at diagnosis was 14.8 years (2.8 to 36.6 years); the male to female ratio was 1.38:1; and 14 patients had relapsed, with 13 having died from their disease.

About half of fusions between the EWS RNA binding protein 1 (EWSR1) gene on chromosome 22 and an E26 transformation-specific (ETS) family transcription factor gene, either FLI1 at 11q24 or ERG at 21q11 arose via chromoplexy.

mdales@mdedge.com

SOURCE: Anderson et al. Science 2018 Aug 31. doi: 10.1126/science.aam8419.

Chromoplexy, a sudden burst of complex, loop-like gene rearrangements that gives rise to a fusion gene, appears to be associated with aggressive Ewing sarcomas, based on a study of 124 tumors reported in Science.

Ewing sarcomas with complex karyotypes are associated with a poorer prognosis compared with those with simpler karyotypes. The new findings show that these complex karyotypes are the product of chromoplexy, and that chromoplexy-generated fusions arise early, giving rise to both primary and relapse Ewing sarcoma tumors, which can continue to evolve in parallel.

Analysis of the sequence context surrounding chromoplexy breaks may provide clues and potentially point to a therapeutic vulnerability that could be used to treat Ewing sarcomas. Further, given the preference of chromoplexy events for transcriptionally active regions, Ewing sarcomas arising from chromoplexy may be responsive to immune checkpoint inhibition.

In a study of the whole genomes of 124 Ewing sarcomas, chromoplexy rather than simple reciprocal translocations defined the gene fusions seen in 52 tumors (42%). Ewing sarcoma involves fusions between EWSR1, a gene encoding an RNA binding protein, and E26 transformation-specific (ETS) transcription factors.

“Our analyses reveal rearrangement bursts (chromoplectic loops) as a source of gene fusion in human bone and soft tissue tumors. Ewing sarcomas with complex karyotypes are associated with a poorer prognosis than those with simpler karyotypes, and here we show chromoplexy as the mechanism in 42% of tumors. It is possible that the chromoplectic tumor’s additional gene disruptions and fusions contribute to the difference in patient survival,” wrote Nathaniel D. Anderson of the Hospital for Sick Children, Toronto, and the University of Toronto, and his colleagues.

Standard reciprocal translocations involve DNA breaks in two fusion partners. Chromoplexy involves three or more breakpoints in the genome. A loop pattern emerges as these three or more broken chromosome ends are forced to find a new partner. The result is the formation of functional EWSR1-FLI1 or EWSR1-ERG fusions that, upon expression, provide a selective growth or survival advantage

The researchers found that the loop rearrangements always contained the disease-defining fusion at the center, but they disrupted multiple additional genes. The loops occurred preferentially in early replicating and transcriptionally active genomic regions.

They found similar loops forming canonical fusions in three other sarcoma types.

“Our whole-genome sequence data support a model in which there is an early clone of (Ewing sarcoma), containing EWSR1-ETS and chromoplexy, arising at least 1 year before diagnosis, which gives rise to both the primary and metastatic or relapse tumors. Whether the bursts ... are chance events or driven by specific mutational processes, akin to the RAG machinery operative in leukemia, remains to be established. As an increasing and diverse number of tumor genome sequences become available, we may be able to define further rearrangement processes that underlie fusion genes and thus unravel the causes of fusion-driven human cancers,” the researchers wrote.

The clinical features and demographics of the study patients were typical of Ewing sarcoma patients. Average patient age at diagnosis was 14.8 years (2.8 to 36.6 years); the male to female ratio was 1.38:1; and 14 patients had relapsed, with 13 having died from their disease.

About half of fusions between the EWS RNA binding protein 1 (EWSR1) gene on chromosome 22 and an E26 transformation-specific (ETS) family transcription factor gene, either FLI1 at 11q24 or ERG at 21q11 arose via chromoplexy.

mdales@mdedge.com

SOURCE: Anderson et al. Science 2018 Aug 31. doi: 10.1126/science.aam8419.

Chromoplexy, a sudden burst of complex, loop-like gene rearrangements that gives rise to a fusion gene, appears to be associated with aggressive Ewing sarcomas, based on a study of 124 tumors reported in Science.

Ewing sarcomas with complex karyotypes are associated with a poorer prognosis compared with those with simpler karyotypes. The new findings show that these complex karyotypes are the product of chromoplexy, and that chromoplexy-generated fusions arise early, giving rise to both primary and relapse Ewing sarcoma tumors, which can continue to evolve in parallel.

Analysis of the sequence context surrounding chromoplexy breaks may provide clues and potentially point to a therapeutic vulnerability that could be used to treat Ewing sarcomas. Further, given the preference of chromoplexy events for transcriptionally active regions, Ewing sarcomas arising from chromoplexy may be responsive to immune checkpoint inhibition.

In a study of the whole genomes of 124 Ewing sarcomas, chromoplexy rather than simple reciprocal translocations defined the gene fusions seen in 52 tumors (42%). Ewing sarcoma involves fusions between EWSR1, a gene encoding an RNA binding protein, and E26 transformation-specific (ETS) transcription factors.

“Our analyses reveal rearrangement bursts (chromoplectic loops) as a source of gene fusion in human bone and soft tissue tumors. Ewing sarcomas with complex karyotypes are associated with a poorer prognosis than those with simpler karyotypes, and here we show chromoplexy as the mechanism in 42% of tumors. It is possible that the chromoplectic tumor’s additional gene disruptions and fusions contribute to the difference in patient survival,” wrote Nathaniel D. Anderson of the Hospital for Sick Children, Toronto, and the University of Toronto, and his colleagues.

Standard reciprocal translocations involve DNA breaks in two fusion partners. Chromoplexy involves three or more breakpoints in the genome. A loop pattern emerges as these three or more broken chromosome ends are forced to find a new partner. The result is the formation of functional EWSR1-FLI1 or EWSR1-ERG fusions that, upon expression, provide a selective growth or survival advantage

The researchers found that the loop rearrangements always contained the disease-defining fusion at the center, but they disrupted multiple additional genes. The loops occurred preferentially in early replicating and transcriptionally active genomic regions.

They found similar loops forming canonical fusions in three other sarcoma types.

“Our whole-genome sequence data support a model in which there is an early clone of (Ewing sarcoma), containing EWSR1-ETS and chromoplexy, arising at least 1 year before diagnosis, which gives rise to both the primary and metastatic or relapse tumors. Whether the bursts ... are chance events or driven by specific mutational processes, akin to the RAG machinery operative in leukemia, remains to be established. As an increasing and diverse number of tumor genome sequences become available, we may be able to define further rearrangement processes that underlie fusion genes and thus unravel the causes of fusion-driven human cancers,” the researchers wrote.

The clinical features and demographics of the study patients were typical of Ewing sarcoma patients. Average patient age at diagnosis was 14.8 years (2.8 to 36.6 years); the male to female ratio was 1.38:1; and 14 patients had relapsed, with 13 having died from their disease.

About half of fusions between the EWS RNA binding protein 1 (EWSR1) gene on chromosome 22 and an E26 transformation-specific (ETS) family transcription factor gene, either FLI1 at 11q24 or ERG at 21q11 arose via chromoplexy.

mdales@mdedge.com

SOURCE: Anderson et al. Science 2018 Aug 31. doi: 10.1126/science.aam8419.

The rarity and complexities of bone and soft tissue sarcomas pose a major challenge to effective treatment. Historically, there has been a blanket approach to treatment, but more recently that has begun to change thanks to genome profiling studies and novel clinical trial strategies. Here, we discuss the resulting enrichment of the therapeutic armamentarium with molecularly targeted and immune therapies.

A challenging tumor type

Sarcomas are a large group of histologically diverse cancers that arise in the mesenchymal cells. They can be broadly divided into bone and soft tissue sarcomas (STS) but are further subdivided according to the type of cell from which they derive; osteosarcomas in the bone, rhabdomyosarcomas in the skeletal muscle, liposarcomas in the fat tissues, leiomyosarcomas in the smooth muscle, and chondrosarcomas in the cartilaginous tissue, for example.

Each sarcoma subtype itself encompasses a range of different cancers with unique biology. Under the umbrella of liposarcoma, for example, are well/dedifferentiated liposarcomas and myxoid liposarcomas, which have very different pathologies and clinical courses.

As a whole, sarcomas are extremely rare tumors, accounting for less than 1% of all adult cancers, although they disproportionately affect children and young adults, with a prevalence closer to 15%.^1,2 Certain sarcoma subtypes are exceptionally rare, with only a few cases diagnosed worldwide each year, whereas liposarcomas are at the other end of the spectrum, comprising the most common form of STS (Figure 1).³

Magic bullet for GIST

Despite their clear heterogeneity and complexity, sarcomas have tended to be treated as a single entity. Chemotherapy has played a central role in the treatment of advanced sarcomas and continues to do so, with 2 newer drugs approved by the United States Food and Drug Administration (FDA) in the past several years.^6,7

The development of targeted therapy, on the other hand, for the most part proved unsuccessful. In general, studies examining the somatic mutation landscape in sarcomas found very few that were highly recurrent. The exception was gastrointestinal stromal tumors (GIST), which represent around 8% of STS.⁸ Frequent mutations in several highly targetable tyrosine kinases, notably KIT, which is mutated in around 85% of cases,⁹ and platelet-derived growth factor receptor alpha (PDGFRα) were identified in these tumors.¹⁰This prompted the development of tyrosine kinase inhibitors (TKIs), targeting these and other kinases, for the treatment of patients with GIST, and culminated in the approval of imatinib for this indication in 2002. This revolutionized the treatment of GIST, which had a poor prognosis and were resistant to chemotherapy, extending median overall survival in patients with metastatic disease almost to 5 years.^11-13

Imatinib was also shown to benefit patients with surgically resectable disease and was subsequently approved in the adjuvant setting in 2008. A recent trial demonstrated that 3-year continuation of adjuvant imatinib resulted in a significantly longer progression-free survival (PFS) compared with 1 year of adjuvant imatinib, and even longer time periods are now being evaluated.^14,15 The TKIs sunitinib and regorafenib have also been approved for the treatment of patients who become resistant to imatinib.^16,17 Avapritinib, a newer, more specific inhibitor of KIT is also being evaluated in patients with GIST (Table).

Long-sought success for STS

Sunitinib and regorafenib include PDGFRα and the vascular endothelial growth factor receptors (VEGFRs) among their targets, receptors that play crucial roles in the formation of new blood vessels (angiogenesis). Many types of non-GIST sarcomas have been shown to be highly vascularized and express high levels of both of those receptors and other angiogenic proteins, which sparked interest in the development of multitargeted TKIs and other anti-angiogenic drugs in patients with STS.¹⁸

In 2012, pazopanib became the first FDA-approved molecularly targeted therapy for the treatment of non-GIST sarcomas. Approval in the second-line setting was based on the demonstration of a 3-month improvement in PFS compared with placebo.¹⁹ Four years later, the monoclonal antibody olaratumab, a more specific inhibitor of PDGFRα, was approved in combination with doxorubicin, marking the first front-line approval for more than 4 decades.²⁰Numerous other anti-angiogenic drugs continue to be evaluated for the treatment of advanced STS. Among them, anlotinib is being tested in phase 3 clinical trials, and results from the ALTER0203 trial were presented at the 2018 annual meeting of the American Society of Clinical Oncology (ASCO).²¹ After failure of chemotherapy, 223 patients were randomly assigned to receive either anlotinib or placebo. Anlotinib significantly improved median PFS across all patients, compared with placebo (6.27 vs 1.4 months, respectively; hazard ratio [HR], 0.33; P < .0001), but was especially effective in patients with alveolar soft part sarcoma (ASPS; mPFS: 18.2 vs 3 months) and was well tolerated.²¹

Sarcoma secrets revealed

Advancements in genome sequencing technologies have made it possible to interrogate the molecular underpinnings of sarcomas in greater detail. However, their rarity presents a significant technical challenge, with a dearth of samples available for genomic testing. Large-scale worldwide collaborative efforts have facilitated the collection of sufficiently large patient populations to provide statistically robust data in many cases. The Cancer Genome Atlas has established a rare tumor characterization project to facilitate the genomic sequencing of rare cancer types like sarcomas.

Genome sequencing studies have revealed 2 types of sarcomas: those with relatively stable genomes and few molecular alterations, exemplified by Ewing sarcoma, which has a mutational load of 0.15 mutations/Megabase (Mb); and those that are much more complex with frequent somatic mutations, the prime example being leiomyosarcoma. The latter are characterized by mutations in the TP53 gene, dubbed the “guardian of the genome” for its essential role in genome stability.

The 2 types are likely to require very different therapeutic strategies. Although genomically complex tumors offer up lots of potential targets for therapy, they also display significant heterogeneity and it can be challenging to find a shared target across different tumor samples. The p53 protein would make a logical target but, to date, tumor suppressor proteins are not readily druggable.

The most common type of molecular alterations in sarcomas are chromosomal translocations, where part of a chromosome breaks off and becomes reattached to another chromosome. This can result in the formation of a gene fusion when parts of 2 different genes are brought together in a way in which the genetic code can still be read, leading to the formation of a fusion protein with altered activity.^22-25

In sarcomas, these chromosomal translocations predominantly involve genes encoding transcription factors and the gene fusion results in their aberrant expression and activation of the transcriptional programs that they regulate.

Ewing sarcoma is a prime example of a sarcoma that is defined by chromosomal translocations. Most often, the resulting gene fusions occur between members of theten-eleven translocation (TET) family of RNA-binding proteins and the E26 transformation-specific (ETS) family of transcription factors. The most common fusion is between the EWSR1 and FLI1 genes, observed in between 85% and 90% of cases.

Significant efforts have been made to target EWSR1-FLI1. Since direct targeting of transcription factors is challenging, those efforts focused on targeting the aberrant transcriptional programs that they initiate. A major downstream target is the insulin-like growth factor receptor 1 (IGF1R) and numerous IGF1R inhibitors were developed and tested in patients with Ewing sarcoma, but unfortunately success was limited. Attention turned to the mammalian target of rapamycin (mTOR) as a potential mechanism of resistance to IGF1R inhibitors and explanation for the limited responses. Clinical trials combining mTOR and IGF1R inhibitors also proved unsuccessful.²⁶

Although overall these trials were deemed failures, they were notable for the dramatic responses that were seen in 1 or 2 patients. Researchers are probing these “exceptional responses” using novel N-of-1 clinical trial designs that focus on a single patient (Figure 2).^27-30 More recently, the first drug to specifically target the EWSR1-FLI1 fusion protein was developed. TK216 binds to the fusion protein and prevents it from binding to RNA helicase A, thereby blocking its function.³¹

Another type of gene fusion, involving the neurotrophic tropomyosin receptor kinase (NTRK) genes, has recently come into the spotlight for the treatment of lung cancer. According to a recent study, NTRK fusions may also be common in sarcomas. They were observed in 8% of patients with breast sarcomas, 5% with fibrosarcomas, and 5% with stomach or small intestine sarcomas.³²

The NTRK genes encode TRK proteins and several small molecule inhibitors of TRK have been developed to treat patients with NTRK fusion-positive cancers. Another novel clinical trial design – the basket trial – is being used to test these inhibitors. This type of trial uses a tumor-agnostic approach, recruiting patients with all different histological subtypes of cancer that are unified by the shared presence of a specific molecular alteration.³³

Repurposing gynecologic cancer drugs

More recently, a third group of sarcomas was categorized, with intermediate genomic complexity. These tumors, including well/dedifferentiated liposarcomas, were characterized by amplifications of chromosome 12, involving genes such as cyclin-dependent kinase 4 (CDK4). In fact, more than 90% of patients with well/dedifferentiated sarcomas display CDK4 amplification, making it a logical therapeutic target.³⁶

CDK4 encodes CDK4 protein, a cell cycle-associated protein that regulates the transition from G1-S phase, known as the restriction point, beyond which the cell commits to undergoing mitosis. Aberrant expression of CDK4 in cancer drives the hallmark process of unchecked cellular proliferation.

Some small molecule CDK4/6 inhibitors have been developed and have shown significant promise in the treatment of breast cancer. They are also being evaluatedin patients with sarcoma whose tumors display CDK4 overexpression. In a recently published phase 2 trial of palbociclib in 60 patients with well/dedifferentiated liposarcomas, there was 1 CR.³⁷

Another group of drugs that has advanced the treatment of gynecologic cancers comprises the poly (ADP-ribose) polymerase (PARP) inhibitors. In this context, PARP inhibitors are used in patients with mutations in the breast cancer susceptibility genes, BRCA1/2. The BRCA and PARP proteins are both involved in DNA repair pathways and the inhibition of PARP in patients who already have a defective BRCA pathway renders a lethal double blow to the cancer cell. According to the Broad Institute Cancer Cell Line Encyclopedia, Ewing sarcomas express high levels of the PARP1 enzyme, which could render them sensitive to PARP inhibition. Preclinical studies seemed to confirm that sensitivity, however, so far this has yet to translate into success in clinical trials, with no objective responses observed as yet.³⁸
 

Expanding the field

Other treatment strategies being tested in patients with sarcoma are moving the field beyond conventional targeted therapies. There has been substantial focus in recent years on epigenetic alterations and their potential role in the development of cancer. Epigenetics is the secondary layer of regulation that acts on the genome and directs the spatial and temporal expression of genes.

Both DNA and the histone proteins they are packaged up with to form chromatin in nondividing cells can be modified by the attachment of chemical groups, such as acetyl and methyl groups, which can alter access to the DNA for transcription.

EZH2 is an enzyme that participates in histone methylation and thereby regulates transcriptional repression. Some types of sarcoma are characterized by a loss of expression of the INI1 gene, also known as SMARCB1. The INI1 protein is part of a chromatin remodeling complex that relieves transcriptional repression and when INI1 is lost, cells become dependent upon EZH2.³⁹Clinical trials of the EZH2 inhibitor tazemetostat are ongoing in several types of sarcoma. Results from a phase 2 study in adults with INI1-negative tumors were presented at ASCO in 2017. Among 31 patients treated with 800 mg tazemetostat in continuous 28-day cycles, mPFS was 5.7 months, disease control rate was 10%, and confirmed overall response rate was 13%. The FDA has granted tazemetostat orphan drug designation in this indication.⁴⁰A pediatric basket trial of tazemetostat is also ongoing, but the FDA recently placed it under a clinical hold as a result of a safety update from the trial in which a pediatric patient with advanced poorly differentiated chordoma developed a secondary T-cell lymphoma.⁴¹

Targeting the unique metabolism of sarcomas may offer a promising therapeutic strategy, although this is in the preliminary stages of evaluation. A recent study showed that the expression of the argininosuccinate synthase 1 enzyme, which is involved in the generation of arginine through the urea cycle, was lost in up to 90% of STS. A pegylated arginine deaminase (ADI-PEG20), is being evaluated in a phase 2 clinical trial.⁴²

Finally, the concept of using immunotherapy to boost the anti-tumor immune response is also being examined in sarcomas. A significant number of cases of STS, osteosarcoma and GIST have been shown to express programmed cell death protein-ligand 1, therefore the use of immune checkpoint inhibitors that block this ligand or its receptor and help to reactive tumor-infiltrating T cells, could be a beneficial strategy.

Limited activity has been observed in studies conducted to date, however combination therapies, especially with inhibitors of the indoleamine 2,3-dioxygenase (IDO) enzyme, which plays a key role in immunosuppression, could help to harness the power of these drugs. Studies have suggested that sarcomas may be infiltrated by immunosuppressive macrophages that express IDO.⁴³

It is generally believed that immunotherapy is most effective in tumors that are highly mutated because that allows a large number of cancer antigens to provoke an anti-tumor immune response. However, a single highly expressed antigen can also be strongly immunogenic. Synovial sarcomas have a relatively low mutational burden but they do express high levels of the cancer testis antigen NY-ESO-1.

NY-ESO-1 has provided a useful target for the development of adoptive cell therapies and vaccines for the treatment of sarcomas. CMB305 is an NY-ESO-1 vaccine that also incorporates a toll-like receptor 4 agonist. It is being evaluated in the phase 3 Synovate study as maintenance monotherapy in patients with locally advanced, unresectable or metastatic synovial sarcoma. In a phase 1 study, at a median follow-up of just under 18 months, the median OS for all 25 patients was 23.7 months.⁴⁴

The rarity and complexities of bone and soft tissue sarcomas pose a major challenge to effective treatment. Historically, there has been a blanket approach to treatment, but more recently that has begun to change thanks to genome profiling studies and novel clinical trial strategies. Here, we discuss the resulting enrichment of the therapeutic armamentarium with molecularly targeted and immune therapies.

A challenging tumor type

Sarcomas are a large group of histologically diverse cancers that arise in the mesenchymal cells. They can be broadly divided into bone and soft tissue sarcomas (STS) but are further subdivided according to the type of cell from which they derive; osteosarcomas in the bone, rhabdomyosarcomas in the skeletal muscle, liposarcomas in the fat tissues, leiomyosarcomas in the smooth muscle, and chondrosarcomas in the cartilaginous tissue, for example.

Each sarcoma subtype itself encompasses a range of different cancers with unique biology. Under the umbrella of liposarcoma, for example, are well/dedifferentiated liposarcomas and myxoid liposarcomas, which have very different pathologies and clinical courses.

As a whole, sarcomas are extremely rare tumors, accounting for less than 1% of all adult cancers, although they disproportionately affect children and young adults, with a prevalence closer to 15%.^1,2 Certain sarcoma subtypes are exceptionally rare, with only a few cases diagnosed worldwide each year, whereas liposarcomas are at the other end of the spectrum, comprising the most common form of STS (Figure 1).³

Magic bullet for GIST

Despite their clear heterogeneity and complexity, sarcomas have tended to be treated as a single entity. Chemotherapy has played a central role in the treatment of advanced sarcomas and continues to do so, with 2 newer drugs approved by the United States Food and Drug Administration (FDA) in the past several years.^6,7

The development of targeted therapy, on the other hand, for the most part proved unsuccessful. In general, studies examining the somatic mutation landscape in sarcomas found very few that were highly recurrent. The exception was gastrointestinal stromal tumors (GIST), which represent around 8% of STS.⁸ Frequent mutations in several highly targetable tyrosine kinases, notably KIT, which is mutated in around 85% of cases,⁹ and platelet-derived growth factor receptor alpha (PDGFRα) were identified in these tumors.¹⁰This prompted the development of tyrosine kinase inhibitors (TKIs), targeting these and other kinases, for the treatment of patients with GIST, and culminated in the approval of imatinib for this indication in 2002. This revolutionized the treatment of GIST, which had a poor prognosis and were resistant to chemotherapy, extending median overall survival in patients with metastatic disease almost to 5 years.^11-13

Imatinib was also shown to benefit patients with surgically resectable disease and was subsequently approved in the adjuvant setting in 2008. A recent trial demonstrated that 3-year continuation of adjuvant imatinib resulted in a significantly longer progression-free survival (PFS) compared with 1 year of adjuvant imatinib, and even longer time periods are now being evaluated.^14,15 The TKIs sunitinib and regorafenib have also been approved for the treatment of patients who become resistant to imatinib.^16,17 Avapritinib, a newer, more specific inhibitor of KIT is also being evaluated in patients with GIST (Table).

Long-sought success for STS

Sunitinib and regorafenib include PDGFRα and the vascular endothelial growth factor receptors (VEGFRs) among their targets, receptors that play crucial roles in the formation of new blood vessels (angiogenesis). Many types of non-GIST sarcomas have been shown to be highly vascularized and express high levels of both of those receptors and other angiogenic proteins, which sparked interest in the development of multitargeted TKIs and other anti-angiogenic drugs in patients with STS.¹⁸

In 2012, pazopanib became the first FDA-approved molecularly targeted therapy for the treatment of non-GIST sarcomas. Approval in the second-line setting was based on the demonstration of a 3-month improvement in PFS compared with placebo.¹⁹ Four years later, the monoclonal antibody olaratumab, a more specific inhibitor of PDGFRα, was approved in combination with doxorubicin, marking the first front-line approval for more than 4 decades.²⁰Numerous other anti-angiogenic drugs continue to be evaluated for the treatment of advanced STS. Among them, anlotinib is being tested in phase 3 clinical trials, and results from the ALTER0203 trial were presented at the 2018 annual meeting of the American Society of Clinical Oncology (ASCO).²¹ After failure of chemotherapy, 223 patients were randomly assigned to receive either anlotinib or placebo. Anlotinib significantly improved median PFS across all patients, compared with placebo (6.27 vs 1.4 months, respectively; hazard ratio [HR], 0.33; P < .0001), but was especially effective in patients with alveolar soft part sarcoma (ASPS; mPFS: 18.2 vs 3 months) and was well tolerated.²¹

Sarcoma secrets revealed

Advancements in genome sequencing technologies have made it possible to interrogate the molecular underpinnings of sarcomas in greater detail. However, their rarity presents a significant technical challenge, with a dearth of samples available for genomic testing. Large-scale worldwide collaborative efforts have facilitated the collection of sufficiently large patient populations to provide statistically robust data in many cases. The Cancer Genome Atlas has established a rare tumor characterization project to facilitate the genomic sequencing of rare cancer types like sarcomas.

Genome sequencing studies have revealed 2 types of sarcomas: those with relatively stable genomes and few molecular alterations, exemplified by Ewing sarcoma, which has a mutational load of 0.15 mutations/Megabase (Mb); and those that are much more complex with frequent somatic mutations, the prime example being leiomyosarcoma. The latter are characterized by mutations in the TP53 gene, dubbed the “guardian of the genome” for its essential role in genome stability.

The 2 types are likely to require very different therapeutic strategies. Although genomically complex tumors offer up lots of potential targets for therapy, they also display significant heterogeneity and it can be challenging to find a shared target across different tumor samples. The p53 protein would make a logical target but, to date, tumor suppressor proteins are not readily druggable.

The most common type of molecular alterations in sarcomas are chromosomal translocations, where part of a chromosome breaks off and becomes reattached to another chromosome. This can result in the formation of a gene fusion when parts of 2 different genes are brought together in a way in which the genetic code can still be read, leading to the formation of a fusion protein with altered activity.^22-25

In sarcomas, these chromosomal translocations predominantly involve genes encoding transcription factors and the gene fusion results in their aberrant expression and activation of the transcriptional programs that they regulate.

Ewing sarcoma is a prime example of a sarcoma that is defined by chromosomal translocations. Most often, the resulting gene fusions occur between members of theten-eleven translocation (TET) family of RNA-binding proteins and the E26 transformation-specific (ETS) family of transcription factors. The most common fusion is between the EWSR1 and FLI1 genes, observed in between 85% and 90% of cases.

Significant efforts have been made to target EWSR1-FLI1. Since direct targeting of transcription factors is challenging, those efforts focused on targeting the aberrant transcriptional programs that they initiate. A major downstream target is the insulin-like growth factor receptor 1 (IGF1R) and numerous IGF1R inhibitors were developed and tested in patients with Ewing sarcoma, but unfortunately success was limited. Attention turned to the mammalian target of rapamycin (mTOR) as a potential mechanism of resistance to IGF1R inhibitors and explanation for the limited responses. Clinical trials combining mTOR and IGF1R inhibitors also proved unsuccessful.²⁶

Although overall these trials were deemed failures, they were notable for the dramatic responses that were seen in 1 or 2 patients. Researchers are probing these “exceptional responses” using novel N-of-1 clinical trial designs that focus on a single patient (Figure 2).^27-30 More recently, the first drug to specifically target the EWSR1-FLI1 fusion protein was developed. TK216 binds to the fusion protein and prevents it from binding to RNA helicase A, thereby blocking its function.³¹

Another type of gene fusion, involving the neurotrophic tropomyosin receptor kinase (NTRK) genes, has recently come into the spotlight for the treatment of lung cancer. According to a recent study, NTRK fusions may also be common in sarcomas. They were observed in 8% of patients with breast sarcomas, 5% with fibrosarcomas, and 5% with stomach or small intestine sarcomas.³²

The NTRK genes encode TRK proteins and several small molecule inhibitors of TRK have been developed to treat patients with NTRK fusion-positive cancers. Another novel clinical trial design – the basket trial – is being used to test these inhibitors. This type of trial uses a tumor-agnostic approach, recruiting patients with all different histological subtypes of cancer that are unified by the shared presence of a specific molecular alteration.³³

Repurposing gynecologic cancer drugs

More recently, a third group of sarcomas was categorized, with intermediate genomic complexity. These tumors, including well/dedifferentiated liposarcomas, were characterized by amplifications of chromosome 12, involving genes such as cyclin-dependent kinase 4 (CDK4). In fact, more than 90% of patients with well/dedifferentiated sarcomas display CDK4 amplification, making it a logical therapeutic target.³⁶

CDK4 encodes CDK4 protein, a cell cycle-associated protein that regulates the transition from G1-S phase, known as the restriction point, beyond which the cell commits to undergoing mitosis. Aberrant expression of CDK4 in cancer drives the hallmark process of unchecked cellular proliferation.

Some small molecule CDK4/6 inhibitors have been developed and have shown significant promise in the treatment of breast cancer. They are also being evaluatedin patients with sarcoma whose tumors display CDK4 overexpression. In a recently published phase 2 trial of palbociclib in 60 patients with well/dedifferentiated liposarcomas, there was 1 CR.³⁷

Another group of drugs that has advanced the treatment of gynecologic cancers comprises the poly (ADP-ribose) polymerase (PARP) inhibitors. In this context, PARP inhibitors are used in patients with mutations in the breast cancer susceptibility genes, BRCA1/2. The BRCA and PARP proteins are both involved in DNA repair pathways and the inhibition of PARP in patients who already have a defective BRCA pathway renders a lethal double blow to the cancer cell. According to the Broad Institute Cancer Cell Line Encyclopedia, Ewing sarcomas express high levels of the PARP1 enzyme, which could render them sensitive to PARP inhibition. Preclinical studies seemed to confirm that sensitivity, however, so far this has yet to translate into success in clinical trials, with no objective responses observed as yet.³⁸
 

Expanding the field

Other treatment strategies being tested in patients with sarcoma are moving the field beyond conventional targeted therapies. There has been substantial focus in recent years on epigenetic alterations and their potential role in the development of cancer. Epigenetics is the secondary layer of regulation that acts on the genome and directs the spatial and temporal expression of genes.

Both DNA and the histone proteins they are packaged up with to form chromatin in nondividing cells can be modified by the attachment of chemical groups, such as acetyl and methyl groups, which can alter access to the DNA for transcription.

EZH2 is an enzyme that participates in histone methylation and thereby regulates transcriptional repression. Some types of sarcoma are characterized by a loss of expression of the INI1 gene, also known as SMARCB1. The INI1 protein is part of a chromatin remodeling complex that relieves transcriptional repression and when INI1 is lost, cells become dependent upon EZH2.³⁹Clinical trials of the EZH2 inhibitor tazemetostat are ongoing in several types of sarcoma. Results from a phase 2 study in adults with INI1-negative tumors were presented at ASCO in 2017. Among 31 patients treated with 800 mg tazemetostat in continuous 28-day cycles, mPFS was 5.7 months, disease control rate was 10%, and confirmed overall response rate was 13%. The FDA has granted tazemetostat orphan drug designation in this indication.⁴⁰A pediatric basket trial of tazemetostat is also ongoing, but the FDA recently placed it under a clinical hold as a result of a safety update from the trial in which a pediatric patient with advanced poorly differentiated chordoma developed a secondary T-cell lymphoma.⁴¹

Targeting the unique metabolism of sarcomas may offer a promising therapeutic strategy, although this is in the preliminary stages of evaluation. A recent study showed that the expression of the argininosuccinate synthase 1 enzyme, which is involved in the generation of arginine through the urea cycle, was lost in up to 90% of STS. A pegylated arginine deaminase (ADI-PEG20), is being evaluated in a phase 2 clinical trial.⁴²

Finally, the concept of using immunotherapy to boost the anti-tumor immune response is also being examined in sarcomas. A significant number of cases of STS, osteosarcoma and GIST have been shown to express programmed cell death protein-ligand 1, therefore the use of immune checkpoint inhibitors that block this ligand or its receptor and help to reactive tumor-infiltrating T cells, could be a beneficial strategy.

Limited activity has been observed in studies conducted to date, however combination therapies, especially with inhibitors of the indoleamine 2,3-dioxygenase (IDO) enzyme, which plays a key role in immunosuppression, could help to harness the power of these drugs. Studies have suggested that sarcomas may be infiltrated by immunosuppressive macrophages that express IDO.⁴³

It is generally believed that immunotherapy is most effective in tumors that are highly mutated because that allows a large number of cancer antigens to provoke an anti-tumor immune response. However, a single highly expressed antigen can also be strongly immunogenic. Synovial sarcomas have a relatively low mutational burden but they do express high levels of the cancer testis antigen NY-ESO-1.

NY-ESO-1 has provided a useful target for the development of adoptive cell therapies and vaccines for the treatment of sarcomas. CMB305 is an NY-ESO-1 vaccine that also incorporates a toll-like receptor 4 agonist. It is being evaluated in the phase 3 Synovate study as maintenance monotherapy in patients with locally advanced, unresectable or metastatic synovial sarcoma. In a phase 1 study, at a median follow-up of just under 18 months, the median OS for all 25 patients was 23.7 months.⁴⁴

The rarity and complexities of bone and soft tissue sarcomas pose a major challenge to effective treatment. Historically, there has been a blanket approach to treatment, but more recently that has begun to change thanks to genome profiling studies and novel clinical trial strategies. Here, we discuss the resulting enrichment of the therapeutic armamentarium with molecularly targeted and immune therapies.

A challenging tumor type

Sarcomas are a large group of histologically diverse cancers that arise in the mesenchymal cells. They can be broadly divided into bone and soft tissue sarcomas (STS) but are further subdivided according to the type of cell from which they derive; osteosarcomas in the bone, rhabdomyosarcomas in the skeletal muscle, liposarcomas in the fat tissues, leiomyosarcomas in the smooth muscle, and chondrosarcomas in the cartilaginous tissue, for example.

Each sarcoma subtype itself encompasses a range of different cancers with unique biology. Under the umbrella of liposarcoma, for example, are well/dedifferentiated liposarcomas and myxoid liposarcomas, which have very different pathologies and clinical courses.

As a whole, sarcomas are extremely rare tumors, accounting for less than 1% of all adult cancers, although they disproportionately affect children and young adults, with a prevalence closer to 15%.^1,2 Certain sarcoma subtypes are exceptionally rare, with only a few cases diagnosed worldwide each year, whereas liposarcomas are at the other end of the spectrum, comprising the most common form of STS (Figure 1).³

Magic bullet for GIST

Despite their clear heterogeneity and complexity, sarcomas have tended to be treated as a single entity. Chemotherapy has played a central role in the treatment of advanced sarcomas and continues to do so, with 2 newer drugs approved by the United States Food and Drug Administration (FDA) in the past several years.^6,7

The development of targeted therapy, on the other hand, for the most part proved unsuccessful. In general, studies examining the somatic mutation landscape in sarcomas found very few that were highly recurrent. The exception was gastrointestinal stromal tumors (GIST), which represent around 8% of STS.⁸ Frequent mutations in several highly targetable tyrosine kinases, notably KIT, which is mutated in around 85% of cases,⁹ and platelet-derived growth factor receptor alpha (PDGFRα) were identified in these tumors.¹⁰This prompted the development of tyrosine kinase inhibitors (TKIs), targeting these and other kinases, for the treatment of patients with GIST, and culminated in the approval of imatinib for this indication in 2002. This revolutionized the treatment of GIST, which had a poor prognosis and were resistant to chemotherapy, extending median overall survival in patients with metastatic disease almost to 5 years.^11-13

Imatinib was also shown to benefit patients with surgically resectable disease and was subsequently approved in the adjuvant setting in 2008. A recent trial demonstrated that 3-year continuation of adjuvant imatinib resulted in a significantly longer progression-free survival (PFS) compared with 1 year of adjuvant imatinib, and even longer time periods are now being evaluated.^14,15 The TKIs sunitinib and regorafenib have also been approved for the treatment of patients who become resistant to imatinib.^16,17 Avapritinib, a newer, more specific inhibitor of KIT is also being evaluated in patients with GIST (Table).

Long-sought success for STS

Sunitinib and regorafenib include PDGFRα and the vascular endothelial growth factor receptors (VEGFRs) among their targets, receptors that play crucial roles in the formation of new blood vessels (angiogenesis). Many types of non-GIST sarcomas have been shown to be highly vascularized and express high levels of both of those receptors and other angiogenic proteins, which sparked interest in the development of multitargeted TKIs and other anti-angiogenic drugs in patients with STS.¹⁸

In 2012, pazopanib became the first FDA-approved molecularly targeted therapy for the treatment of non-GIST sarcomas. Approval in the second-line setting was based on the demonstration of a 3-month improvement in PFS compared with placebo.¹⁹ Four years later, the monoclonal antibody olaratumab, a more specific inhibitor of PDGFRα, was approved in combination with doxorubicin, marking the first front-line approval for more than 4 decades.²⁰Numerous other anti-angiogenic drugs continue to be evaluated for the treatment of advanced STS. Among them, anlotinib is being tested in phase 3 clinical trials, and results from the ALTER0203 trial were presented at the 2018 annual meeting of the American Society of Clinical Oncology (ASCO).²¹ After failure of chemotherapy, 223 patients were randomly assigned to receive either anlotinib or placebo. Anlotinib significantly improved median PFS across all patients, compared with placebo (6.27 vs 1.4 months, respectively; hazard ratio [HR], 0.33; P < .0001), but was especially effective in patients with alveolar soft part sarcoma (ASPS; mPFS: 18.2 vs 3 months) and was well tolerated.²¹

Sarcoma secrets revealed

Advancements in genome sequencing technologies have made it possible to interrogate the molecular underpinnings of sarcomas in greater detail. However, their rarity presents a significant technical challenge, with a dearth of samples available for genomic testing. Large-scale worldwide collaborative efforts have facilitated the collection of sufficiently large patient populations to provide statistically robust data in many cases. The Cancer Genome Atlas has established a rare tumor characterization project to facilitate the genomic sequencing of rare cancer types like sarcomas.

Genome sequencing studies have revealed 2 types of sarcomas: those with relatively stable genomes and few molecular alterations, exemplified by Ewing sarcoma, which has a mutational load of 0.15 mutations/Megabase (Mb); and those that are much more complex with frequent somatic mutations, the prime example being leiomyosarcoma. The latter are characterized by mutations in the TP53 gene, dubbed the “guardian of the genome” for its essential role in genome stability.

The 2 types are likely to require very different therapeutic strategies. Although genomically complex tumors offer up lots of potential targets for therapy, they also display significant heterogeneity and it can be challenging to find a shared target across different tumor samples. The p53 protein would make a logical target but, to date, tumor suppressor proteins are not readily druggable.

The most common type of molecular alterations in sarcomas are chromosomal translocations, where part of a chromosome breaks off and becomes reattached to another chromosome. This can result in the formation of a gene fusion when parts of 2 different genes are brought together in a way in which the genetic code can still be read, leading to the formation of a fusion protein with altered activity.^22-25

In sarcomas, these chromosomal translocations predominantly involve genes encoding transcription factors and the gene fusion results in their aberrant expression and activation of the transcriptional programs that they regulate.

Ewing sarcoma is a prime example of a sarcoma that is defined by chromosomal translocations. Most often, the resulting gene fusions occur between members of theten-eleven translocation (TET) family of RNA-binding proteins and the E26 transformation-specific (ETS) family of transcription factors. The most common fusion is between the EWSR1 and FLI1 genes, observed in between 85% and 90% of cases.

Significant efforts have been made to target EWSR1-FLI1. Since direct targeting of transcription factors is challenging, those efforts focused on targeting the aberrant transcriptional programs that they initiate. A major downstream target is the insulin-like growth factor receptor 1 (IGF1R) and numerous IGF1R inhibitors were developed and tested in patients with Ewing sarcoma, but unfortunately success was limited. Attention turned to the mammalian target of rapamycin (mTOR) as a potential mechanism of resistance to IGF1R inhibitors and explanation for the limited responses. Clinical trials combining mTOR and IGF1R inhibitors also proved unsuccessful.²⁶

Although overall these trials were deemed failures, they were notable for the dramatic responses that were seen in 1 or 2 patients. Researchers are probing these “exceptional responses” using novel N-of-1 clinical trial designs that focus on a single patient (Figure 2).^27-30 More recently, the first drug to specifically target the EWSR1-FLI1 fusion protein was developed. TK216 binds to the fusion protein and prevents it from binding to RNA helicase A, thereby blocking its function.³¹

Another type of gene fusion, involving the neurotrophic tropomyosin receptor kinase (NTRK) genes, has recently come into the spotlight for the treatment of lung cancer. According to a recent study, NTRK fusions may also be common in sarcomas. They were observed in 8% of patients with breast sarcomas, 5% with fibrosarcomas, and 5% with stomach or small intestine sarcomas.³²

The NTRK genes encode TRK proteins and several small molecule inhibitors of TRK have been developed to treat patients with NTRK fusion-positive cancers. Another novel clinical trial design – the basket trial – is being used to test these inhibitors. This type of trial uses a tumor-agnostic approach, recruiting patients with all different histological subtypes of cancer that are unified by the shared presence of a specific molecular alteration.³³

Repurposing gynecologic cancer drugs

More recently, a third group of sarcomas was categorized, with intermediate genomic complexity. These tumors, including well/dedifferentiated liposarcomas, were characterized by amplifications of chromosome 12, involving genes such as cyclin-dependent kinase 4 (CDK4). In fact, more than 90% of patients with well/dedifferentiated sarcomas display CDK4 amplification, making it a logical therapeutic target.³⁶

CDK4 encodes CDK4 protein, a cell cycle-associated protein that regulates the transition from G1-S phase, known as the restriction point, beyond which the cell commits to undergoing mitosis. Aberrant expression of CDK4 in cancer drives the hallmark process of unchecked cellular proliferation.

Some small molecule CDK4/6 inhibitors have been developed and have shown significant promise in the treatment of breast cancer. They are also being evaluatedin patients with sarcoma whose tumors display CDK4 overexpression. In a recently published phase 2 trial of palbociclib in 60 patients with well/dedifferentiated liposarcomas, there was 1 CR.³⁷

Another group of drugs that has advanced the treatment of gynecologic cancers comprises the poly (ADP-ribose) polymerase (PARP) inhibitors. In this context, PARP inhibitors are used in patients with mutations in the breast cancer susceptibility genes, BRCA1/2. The BRCA and PARP proteins are both involved in DNA repair pathways and the inhibition of PARP in patients who already have a defective BRCA pathway renders a lethal double blow to the cancer cell. According to the Broad Institute Cancer Cell Line Encyclopedia, Ewing sarcomas express high levels of the PARP1 enzyme, which could render them sensitive to PARP inhibition. Preclinical studies seemed to confirm that sensitivity, however, so far this has yet to translate into success in clinical trials, with no objective responses observed as yet.³⁸
 

Expanding the field

Other treatment strategies being tested in patients with sarcoma are moving the field beyond conventional targeted therapies. There has been substantial focus in recent years on epigenetic alterations and their potential role in the development of cancer. Epigenetics is the secondary layer of regulation that acts on the genome and directs the spatial and temporal expression of genes.

Both DNA and the histone proteins they are packaged up with to form chromatin in nondividing cells can be modified by the attachment of chemical groups, such as acetyl and methyl groups, which can alter access to the DNA for transcription.

EZH2 is an enzyme that participates in histone methylation and thereby regulates transcriptional repression. Some types of sarcoma are characterized by a loss of expression of the INI1 gene, also known as SMARCB1. The INI1 protein is part of a chromatin remodeling complex that relieves transcriptional repression and when INI1 is lost, cells become dependent upon EZH2.³⁹Clinical trials of the EZH2 inhibitor tazemetostat are ongoing in several types of sarcoma. Results from a phase 2 study in adults with INI1-negative tumors were presented at ASCO in 2017. Among 31 patients treated with 800 mg tazemetostat in continuous 28-day cycles, mPFS was 5.7 months, disease control rate was 10%, and confirmed overall response rate was 13%. The FDA has granted tazemetostat orphan drug designation in this indication.⁴⁰A pediatric basket trial of tazemetostat is also ongoing, but the FDA recently placed it under a clinical hold as a result of a safety update from the trial in which a pediatric patient with advanced poorly differentiated chordoma developed a secondary T-cell lymphoma.⁴¹

Targeting the unique metabolism of sarcomas may offer a promising therapeutic strategy, although this is in the preliminary stages of evaluation. A recent study showed that the expression of the argininosuccinate synthase 1 enzyme, which is involved in the generation of arginine through the urea cycle, was lost in up to 90% of STS. A pegylated arginine deaminase (ADI-PEG20), is being evaluated in a phase 2 clinical trial.⁴²

Finally, the concept of using immunotherapy to boost the anti-tumor immune response is also being examined in sarcomas. A significant number of cases of STS, osteosarcoma and GIST have been shown to express programmed cell death protein-ligand 1, therefore the use of immune checkpoint inhibitors that block this ligand or its receptor and help to reactive tumor-infiltrating T cells, could be a beneficial strategy.

Limited activity has been observed in studies conducted to date, however combination therapies, especially with inhibitors of the indoleamine 2,3-dioxygenase (IDO) enzyme, which plays a key role in immunosuppression, could help to harness the power of these drugs. Studies have suggested that sarcomas may be infiltrated by immunosuppressive macrophages that express IDO.⁴³

It is generally believed that immunotherapy is most effective in tumors that are highly mutated because that allows a large number of cancer antigens to provoke an anti-tumor immune response. However, a single highly expressed antigen can also be strongly immunogenic. Synovial sarcomas have a relatively low mutational burden but they do express high levels of the cancer testis antigen NY-ESO-1.

NY-ESO-1 has provided a useful target for the development of adoptive cell therapies and vaccines for the treatment of sarcomas. CMB305 is an NY-ESO-1 vaccine that also incorporates a toll-like receptor 4 agonist. It is being evaluated in the phase 3 Synovate study as maintenance monotherapy in patients with locally advanced, unresectable or metastatic synovial sarcoma. In a phase 1 study, at a median follow-up of just under 18 months, the median OS for all 25 patients was 23.7 months.⁴⁴

CHICAGO – Single-agent lurbinectedin (PM1183, Zepsyre) showed “encouraging” activity against advanced Ewing’s Sarcoma in previously treated adults, results of a phase 2 study indicated.

Among 28 adults with Ewing’s sarcoma (ES) that had relapsed after up to two prior lines of therapy, treatment with lurbinectedin was associated with five partial responses and six cases of stable disease, reported Vivek Subbiah, MD, from the University of Texas MD Anderson Cancer Center in Houston and his colleagues.

“Treatment in combination with other agents is warranted in this patient population,” they wrote in a poster presented at the annual meeting of the American Society of Clinical Oncology.

Lurbinectedin’s mechanism of action is through blocking DNA transcription and inducing DNA double-strand breaks, which leads to programmed cell death.

“Moreover, in sarcomas associated with translocations, such as ES, in which the translocation produces a fusion protein that acts as a deregulated transcription factor, lurbinectedin might interfere with the binding of this protein to specific DNA promoters and thus with the synthesis of downstream proteins,” the investigators wrote.

This agent is being investigated against ES as part of a phase 2 basket trial, which is testing the drug against a variety of malignancies. The ES cohort in this study included 15 adults who had received up to two prior chemotherapy regimens. The trial rules called for recruitment of a minimum of 10 more patients if at least one of the first 15 had a confirmed response. There were two responses among the 15 patients, leading to an expansion cohort with 13 patients, for a total of 28 in the current analysis.

The median patient age was 33 years (range, 18-74 years). The majority of patients had good performance status, with Eastern Cooperative Oncology Group scores of 0 (11 patients) or 1 (15 patients); one patient had an ECOG PS score of 2, and one had unknown status.

All but one patient had received a minimum of two prior lines of therapy.

The patients were treated with lurbinectedin 3.2 mg/m² in a 1-hour infusion on day 1 of every 21-day cycle, with the longest duration of therapy out to 14 cycles.

Among 25 evaluable patients, eight had tumor shrinkage, ranging from less than 5% (two patients) to more than 45% (four patients).

Median progression-free survival (PFS) was 2.7 months. The 4-month PFS rate was 42.9%, and the 6-month rates was 21.4%.

A total of 11 patients had some clinical benefit, including five partial responses and six cases of stable disease.

Grade 3 or 4 treatment-related adverse events included febrile neutropenia (two events grade 3 and two grade 4), anemia (five events, all grade 3), neutropenia (five grade 3 and 10 grade 4), thrombocytopenia (four grade 3 events), and elevated alanine aminotransferase levels (two grade 3 events).

Myelosuppression was transient and manageable with granulocyte colony-stimulating factor, the investigators said.

The study was supported by PharmaMar. Dr. Subbiah disclosed travel, accommodations, and/or expenses from the company and from Bayer; a consulting or advisory role with MedImmune; and institutional research funding from PharmaMar and multiple other companies.

SOURCE: Subbiah V et al. ASCO 2018, Abstract 11519.

CHICAGO – Single-agent lurbinectedin (PM1183, Zepsyre) showed “encouraging” activity against advanced Ewing’s Sarcoma in previously treated adults, results of a phase 2 study indicated.

Among 28 adults with Ewing’s sarcoma (ES) that had relapsed after up to two prior lines of therapy, treatment with lurbinectedin was associated with five partial responses and six cases of stable disease, reported Vivek Subbiah, MD, from the University of Texas MD Anderson Cancer Center in Houston and his colleagues.

“Treatment in combination with other agents is warranted in this patient population,” they wrote in a poster presented at the annual meeting of the American Society of Clinical Oncology.

Lurbinectedin’s mechanism of action is through blocking DNA transcription and inducing DNA double-strand breaks, which leads to programmed cell death.

“Moreover, in sarcomas associated with translocations, such as ES, in which the translocation produces a fusion protein that acts as a deregulated transcription factor, lurbinectedin might interfere with the binding of this protein to specific DNA promoters and thus with the synthesis of downstream proteins,” the investigators wrote.

This agent is being investigated against ES as part of a phase 2 basket trial, which is testing the drug against a variety of malignancies. The ES cohort in this study included 15 adults who had received up to two prior chemotherapy regimens. The trial rules called for recruitment of a minimum of 10 more patients if at least one of the first 15 had a confirmed response. There were two responses among the 15 patients, leading to an expansion cohort with 13 patients, for a total of 28 in the current analysis.

The median patient age was 33 years (range, 18-74 years). The majority of patients had good performance status, with Eastern Cooperative Oncology Group scores of 0 (11 patients) or 1 (15 patients); one patient had an ECOG PS score of 2, and one had unknown status.

All but one patient had received a minimum of two prior lines of therapy.

The patients were treated with lurbinectedin 3.2 mg/m² in a 1-hour infusion on day 1 of every 21-day cycle, with the longest duration of therapy out to 14 cycles.

Among 25 evaluable patients, eight had tumor shrinkage, ranging from less than 5% (two patients) to more than 45% (four patients).

Median progression-free survival (PFS) was 2.7 months. The 4-month PFS rate was 42.9%, and the 6-month rates was 21.4%.

A total of 11 patients had some clinical benefit, including five partial responses and six cases of stable disease.

Grade 3 or 4 treatment-related adverse events included febrile neutropenia (two events grade 3 and two grade 4), anemia (five events, all grade 3), neutropenia (five grade 3 and 10 grade 4), thrombocytopenia (four grade 3 events), and elevated alanine aminotransferase levels (two grade 3 events).

Myelosuppression was transient and manageable with granulocyte colony-stimulating factor, the investigators said.

The study was supported by PharmaMar. Dr. Subbiah disclosed travel, accommodations, and/or expenses from the company and from Bayer; a consulting or advisory role with MedImmune; and institutional research funding from PharmaMar and multiple other companies.

SOURCE: Subbiah V et al. ASCO 2018, Abstract 11519.

CHICAGO – Single-agent lurbinectedin (PM1183, Zepsyre) showed “encouraging” activity against advanced Ewing’s Sarcoma in previously treated adults, results of a phase 2 study indicated.

Among 28 adults with Ewing’s sarcoma (ES) that had relapsed after up to two prior lines of therapy, treatment with lurbinectedin was associated with five partial responses and six cases of stable disease, reported Vivek Subbiah, MD, from the University of Texas MD Anderson Cancer Center in Houston and his colleagues.

“Treatment in combination with other agents is warranted in this patient population,” they wrote in a poster presented at the annual meeting of the American Society of Clinical Oncology.

Lurbinectedin’s mechanism of action is through blocking DNA transcription and inducing DNA double-strand breaks, which leads to programmed cell death.

“Moreover, in sarcomas associated with translocations, such as ES, in which the translocation produces a fusion protein that acts as a deregulated transcription factor, lurbinectedin might interfere with the binding of this protein to specific DNA promoters and thus with the synthesis of downstream proteins,” the investigators wrote.

This agent is being investigated against ES as part of a phase 2 basket trial, which is testing the drug against a variety of malignancies. The ES cohort in this study included 15 adults who had received up to two prior chemotherapy regimens. The trial rules called for recruitment of a minimum of 10 more patients if at least one of the first 15 had a confirmed response. There were two responses among the 15 patients, leading to an expansion cohort with 13 patients, for a total of 28 in the current analysis.

The median patient age was 33 years (range, 18-74 years). The majority of patients had good performance status, with Eastern Cooperative Oncology Group scores of 0 (11 patients) or 1 (15 patients); one patient had an ECOG PS score of 2, and one had unknown status.

All but one patient had received a minimum of two prior lines of therapy.

The patients were treated with lurbinectedin 3.2 mg/m² in a 1-hour infusion on day 1 of every 21-day cycle, with the longest duration of therapy out to 14 cycles.

Among 25 evaluable patients, eight had tumor shrinkage, ranging from less than 5% (two patients) to more than 45% (four patients).

Median progression-free survival (PFS) was 2.7 months. The 4-month PFS rate was 42.9%, and the 6-month rates was 21.4%.

A total of 11 patients had some clinical benefit, including five partial responses and six cases of stable disease.

Grade 3 or 4 treatment-related adverse events included febrile neutropenia (two events grade 3 and two grade 4), anemia (five events, all grade 3), neutropenia (five grade 3 and 10 grade 4), thrombocytopenia (four grade 3 events), and elevated alanine aminotransferase levels (two grade 3 events).

Myelosuppression was transient and manageable with granulocyte colony-stimulating factor, the investigators said.

The study was supported by PharmaMar. Dr. Subbiah disclosed travel, accommodations, and/or expenses from the company and from Bayer; a consulting or advisory role with MedImmune; and institutional research funding from PharmaMar and multiple other companies.

SOURCE: Subbiah V et al. ASCO 2018, Abstract 11519.

CHICAGO – Patients with high-risk soft-tissue sarcomas identified by patient data and a risk calculator had significantly better overall and disease-free survival when they were treated with adjuvant doxorubicin and ifosfamide, a retrospective analysis from a randomized clinical trial showed.

The findings suggest that future clinical trials for sarcoma therapies may need to focus on specific risk categories, investigators said.

Among 290 patients with soft tissues sarcomas (STS) of the trunk wall or extremities, adjuvant chemotherapy with doxorubicin, ifosfamide, mesna, and lenograstim more than halved the risk of death for patients determined by the nomogram to have a low probability of 10-year overall survival, reported Sandro Pasquali, MD, from the Fondazione IRCCS Istituto Nazionale dei Tumori in Milan, and his colleagues.

“These findings interpret conflicting results of randomized controlled trials on perioperative chemotherapy in STS showing that inclusion of low-risk tumors have diluted the effect of chemotherapy leading to negative results and small study effect in meta-analysis,” they wrote in a poster presented at the annual meeting of the American Society of Clinical Oncology.

The clinical trial in question, EORTC-STBSG 62931, results of which were published in 2012 in The Lancet Oncology, was technically a failure, because it did not show a significant benefit of adjuvant chemotherapy vs. observation in patients with STS.

To see whether adjuvant chemotherapy may have benefited select patients, the investigators calculated 10-year probabilities of overall survival (P-OS) for 290 patients with STS of the trunk wall or extremities out of the total trial cohort of 351 patients. The P-OS for each of three categories – low (51% or less), intermediate (52%-66%), and high (67% or greater) – was calculated using individual patient data and the freely available smartphone-based nomogram Sarculator (available in the Apple App Store and Google Play).

They calculated disease-free survival at the study median follow-up of 8 years.

The tumor histologies included malignant fibrous histiocytoma/undifferentiated pleomorphic sarcoma, liposarcoma, leiomyosarcoma, rhabdomyosarcoma, angiosarcoma, synovial sarcoma, malignant peripheral nerve sheath tumor, and others.

A total of 52 patients were in the low P-OS group, including 24 treated with observation, and 28 with adjuvant chemotherapy. Respective numbers for the intermediate and high P-OS categories were 34/34, and 90/80.

The investigators found that for patients in the low P-OS group, adjuvant chemotherapy cut the risk of death by slightly more than half, with a hazard ratio of 0.46 (P = .033). In contrast, there were no significant differences in the risk of death for patients at either intermediate or high probability of 10 year OS (HR, 1.00 and 1.08, respectively; P values not significant).

Similarly, adjuvant chemotherapy cut the risk of disease progression by the same amount, with an HR of 0.46 (P = .021), whereas there was no additional benefit among patients at either intermediate or high probability of 10-year OS (HR 0.74 and 0.90; P values were not significant).

The absolute risk reduction for adjuvant chemotherapy was 21% (8-yr disease-free survival of 34% for adjuvant chemotherapy vs. 13% for observation), with a number needed to treated of 4.76.

The study was supported by the European Organization for Research and Treatment of Cancer. Dr. Pasquali reported having no conflicts of interest.
 

SOURCE: Pasquali S et al. ASCO 2018, Abstract 115118.
 

CHICAGO – Patients with high-risk soft-tissue sarcomas identified by patient data and a risk calculator had significantly better overall and disease-free survival when they were treated with adjuvant doxorubicin and ifosfamide, a retrospective analysis from a randomized clinical trial showed.

The findings suggest that future clinical trials for sarcoma therapies may need to focus on specific risk categories, investigators said.

Among 290 patients with soft tissues sarcomas (STS) of the trunk wall or extremities, adjuvant chemotherapy with doxorubicin, ifosfamide, mesna, and lenograstim more than halved the risk of death for patients determined by the nomogram to have a low probability of 10-year overall survival, reported Sandro Pasquali, MD, from the Fondazione IRCCS Istituto Nazionale dei Tumori in Milan, and his colleagues.

“These findings interpret conflicting results of randomized controlled trials on perioperative chemotherapy in STS showing that inclusion of low-risk tumors have diluted the effect of chemotherapy leading to negative results and small study effect in meta-analysis,” they wrote in a poster presented at the annual meeting of the American Society of Clinical Oncology.

The clinical trial in question, EORTC-STBSG 62931, results of which were published in 2012 in The Lancet Oncology, was technically a failure, because it did not show a significant benefit of adjuvant chemotherapy vs. observation in patients with STS.

To see whether adjuvant chemotherapy may have benefited select patients, the investigators calculated 10-year probabilities of overall survival (P-OS) for 290 patients with STS of the trunk wall or extremities out of the total trial cohort of 351 patients. The P-OS for each of three categories – low (51% or less), intermediate (52%-66%), and high (67% or greater) – was calculated using individual patient data and the freely available smartphone-based nomogram Sarculator (available in the Apple App Store and Google Play).

They calculated disease-free survival at the study median follow-up of 8 years.

The tumor histologies included malignant fibrous histiocytoma/undifferentiated pleomorphic sarcoma, liposarcoma, leiomyosarcoma, rhabdomyosarcoma, angiosarcoma, synovial sarcoma, malignant peripheral nerve sheath tumor, and others.

A total of 52 patients were in the low P-OS group, including 24 treated with observation, and 28 with adjuvant chemotherapy. Respective numbers for the intermediate and high P-OS categories were 34/34, and 90/80.

The investigators found that for patients in the low P-OS group, adjuvant chemotherapy cut the risk of death by slightly more than half, with a hazard ratio of 0.46 (P = .033). In contrast, there were no significant differences in the risk of death for patients at either intermediate or high probability of 10 year OS (HR, 1.00 and 1.08, respectively; P values not significant).

Similarly, adjuvant chemotherapy cut the risk of disease progression by the same amount, with an HR of 0.46 (P = .021), whereas there was no additional benefit among patients at either intermediate or high probability of 10-year OS (HR 0.74 and 0.90; P values were not significant).

The absolute risk reduction for adjuvant chemotherapy was 21% (8-yr disease-free survival of 34% for adjuvant chemotherapy vs. 13% for observation), with a number needed to treated of 4.76.

The study was supported by the European Organization for Research and Treatment of Cancer. Dr. Pasquali reported having no conflicts of interest.
 

SOURCE: Pasquali S et al. ASCO 2018, Abstract 115118.
 

CHICAGO – Patients with high-risk soft-tissue sarcomas identified by patient data and a risk calculator had significantly better overall and disease-free survival when they were treated with adjuvant doxorubicin and ifosfamide, a retrospective analysis from a randomized clinical trial showed.

The findings suggest that future clinical trials for sarcoma therapies may need to focus on specific risk categories, investigators said.

Among 290 patients with soft tissues sarcomas (STS) of the trunk wall or extremities, adjuvant chemotherapy with doxorubicin, ifosfamide, mesna, and lenograstim more than halved the risk of death for patients determined by the nomogram to have a low probability of 10-year overall survival, reported Sandro Pasquali, MD, from the Fondazione IRCCS Istituto Nazionale dei Tumori in Milan, and his colleagues.

“These findings interpret conflicting results of randomized controlled trials on perioperative chemotherapy in STS showing that inclusion of low-risk tumors have diluted the effect of chemotherapy leading to negative results and small study effect in meta-analysis,” they wrote in a poster presented at the annual meeting of the American Society of Clinical Oncology.

The clinical trial in question, EORTC-STBSG 62931, results of which were published in 2012 in The Lancet Oncology, was technically a failure, because it did not show a significant benefit of adjuvant chemotherapy vs. observation in patients with STS.

To see whether adjuvant chemotherapy may have benefited select patients, the investigators calculated 10-year probabilities of overall survival (P-OS) for 290 patients with STS of the trunk wall or extremities out of the total trial cohort of 351 patients. The P-OS for each of three categories – low (51% or less), intermediate (52%-66%), and high (67% or greater) – was calculated using individual patient data and the freely available smartphone-based nomogram Sarculator (available in the Apple App Store and Google Play).

They calculated disease-free survival at the study median follow-up of 8 years.

The tumor histologies included malignant fibrous histiocytoma/undifferentiated pleomorphic sarcoma, liposarcoma, leiomyosarcoma, rhabdomyosarcoma, angiosarcoma, synovial sarcoma, malignant peripheral nerve sheath tumor, and others.

A total of 52 patients were in the low P-OS group, including 24 treated with observation, and 28 with adjuvant chemotherapy. Respective numbers for the intermediate and high P-OS categories were 34/34, and 90/80.

The investigators found that for patients in the low P-OS group, adjuvant chemotherapy cut the risk of death by slightly more than half, with a hazard ratio of 0.46 (P = .033). In contrast, there were no significant differences in the risk of death for patients at either intermediate or high probability of 10 year OS (HR, 1.00 and 1.08, respectively; P values not significant).

Similarly, adjuvant chemotherapy cut the risk of disease progression by the same amount, with an HR of 0.46 (P = .021), whereas there was no additional benefit among patients at either intermediate or high probability of 10-year OS (HR 0.74 and 0.90; P values were not significant).

The absolute risk reduction for adjuvant chemotherapy was 21% (8-yr disease-free survival of 34% for adjuvant chemotherapy vs. 13% for observation), with a number needed to treated of 4.76.

The study was supported by the European Organization for Research and Treatment of Cancer. Dr. Pasquali reported having no conflicts of interest.
 

SOURCE: Pasquali S et al. ASCO 2018, Abstract 115118.