Study Characterizes Spectrum of Somatic Mutations in Chronic Lymphocytic Leukemia

Researchers using massively parallel sequencing to characterize the spectrum of somatic mutations in chronic lymphocytic leukemia identified nine genes that are mutated at significant frequencies in the disease.

Of these nine "driver" genes, which were identified from DNA samples from normal tissues and tumors in 91 patients with chronic lymphocytic leukemia, four have previously established roles in the disease (TP53, ATM, MYD88, and NOTCH1), and five do not (SF3B1, ZMYM3, MAPK1, FBXW7, and DDX3X), Dr. Lili Wang of the Dana-Farber Cancer Institute, Boston, and her colleagues reported online in the Dec. 12 issue of the New England Journal of Medicine. The findings were reported simultaneously at the annual meeting of the American Society of Hematology.

"Strikingly, the second most frequently mutated gene in our cohort was splicing factor 3b, subunit 1 (SF3B1), with missense mutations occurring in 14 of 91 patients (15%). SF3B1 is a component of the SF3B complex, which is associated with the U2 small nuclear ribonucleoprotein (snRNP), at the catalytic center of the spliceosome," the investigators said (N. Engl. J. Med. 2011 Dec. 12 [doi:10.1056/NEJMoa1109016]).

The nine driver genes identified in this study appear in five core signaling pathways, and the genes each play different, though well-established roles in these pathways, such as DNA repair and cell-cycle control, Notch signaling, inflammatory pathways, and RNA splicing (in which SF3B1, in particular, was implicated). Furthermore, each driver mutation was found to be associated with different key abnormalities; for example, the findings indicate there may be an interaction between del(11q), which is associated with aggressive disease, and SF3B1 mutation in the pathogenesis of a clinical subgroup of chronic lymphocytic leukemia.

Overall, the investigators concluded that:

• Chronic lymphocytic leukemia has a lower rate of somatic mutation than most solid tumors.

• The rate of nonsynonymous mutation was not strongly affected by therapy.

• In addition to the expected mutations in cell-cycle and DNA-repair pathways, genetic alterations in Notch signaling, inflammatory pathways, and RNA splicing and processing also exist.

• Driver mutations showed striking associations with standard prognostic markers.

The latter suggests that "particular combinations of genetic alterations may act in concert to drive cancer," the investigators said.

The findings regarding the core spliceosome component SF3B1, which they described as a "major surprise," led to further analyses that suggested that SF3B1 mutations lead to "mistakes in the splicing of ... transcripts that affect the pathogenesis of chronic lymphocytic leukemia," they said, adding that ongoing studies will evaluate how mutations in SF3B1 alter its function in the processing of critical messenger RNAs.

The study, and in particular the findings regarding SF3B1 mutations, illustrate how identification of coding mutations in chronic lymphocytic leukemia can lead to the development of mechanistic hypotheses, novel prognostic markers, and potential therapeutic targets, Dr. Wang and her associates said.

They also noted the information provides a starting point for determining "which genes within chromosomal deletions and amplifications are essential, how each mutation alters cellular networks and phenotypes, which combinations of mutations are critical in the development of cancer, and how genetic events in the host may affect the importance of specific mutations and their combinations."

In an accompanying editorial, Dr. Benjamin Ebert and Olivier A. Bernard, Ph.D., commented that the study finding regarding mutations in genes involved in RNA splicing, although highly unexpected, converge remarkably with recent published findings from studies of myelodysplastic syndromes (N. Engl. J. Med. 2011;35:1384-95; Nature 2011;478:64-9).

SF3B1 mutations were found in 20% of patients with myelodysplastic syndromes, and in 65% of patients with refractory anemia and ring sideroblasts in one study (N. Engl. J. Med. 2011;35:1384-95).

"Moreover, mutations have been reported in multiple components of the spliceosome in 45%-85% of patients with myelodysplastic syndrome. SF3B1 mutations also occur in 1%-5% of samples from a wide range of tumor types, which indicates that mutations in RNA splicing factors are a widespread cause of oncogenic transformation," they added.

These and other findings, taken together, raise the "provocative possibility" that SF3B1 mutations may sometimes occur first in hematopoietic stem cells, with "additional mutations then being acquired in either the lymphoid or the myeloid lineages and causing chronic lymphocytic leukemia or myelodysplastic syndromes, respectively," Dr. Ebert of Brigham and Women’s Hospital, Boston, and Dr. Bernard, who is with INSERM at Institut Gustave Roussy, Villejuif, France, wrote (N. Engl. J. Med. 2011 Dec. 12 [doi:10.1056/NEJMe1111584]).

The findings have implications for determining prognosis, and for identifying targets for treatment. For example, the identification of mutations in genes encoding the RNA splicing machinery raises the possibility that spliceosome could be a therapeutic target, they said.

This study was supported by grants from the National Institutes of Health, the National Cancer Institute, the Melton and Rosenbach Funds, the Blavatnik Family Foundation, the Howard Hughes Medical Institute (via an Early Career Physician-Scientist Award), and the Damon Runyon Cancer Research Foundation. Dr. Wang said she had no relevant financial disclosures. Some of the coauthors said they were consultants to numerous pharmaceutical companies or owned stock in pharmaceutical companies. Other than employment by INSERM on the part of Dr. Bernard, neither he nor Dr. Ebert had any relevant financial disclosures to report.

Researchers using massively parallel sequencing to characterize the spectrum of somatic mutations in chronic lymphocytic leukemia identified nine genes that are mutated at significant frequencies in the disease.

Of these nine "driver" genes, which were identified from DNA samples from normal tissues and tumors in 91 patients with chronic lymphocytic leukemia, four have previously established roles in the disease (TP53, ATM, MYD88, and NOTCH1), and five do not (SF3B1, ZMYM3, MAPK1, FBXW7, and DDX3X), Dr. Lili Wang of the Dana-Farber Cancer Institute, Boston, and her colleagues reported online in the Dec. 12 issue of the New England Journal of Medicine. The findings were reported simultaneously at the annual meeting of the American Society of Hematology.

"Strikingly, the second most frequently mutated gene in our cohort was splicing factor 3b, subunit 1 (SF3B1), with missense mutations occurring in 14 of 91 patients (15%). SF3B1 is a component of the SF3B complex, which is associated with the U2 small nuclear ribonucleoprotein (snRNP), at the catalytic center of the spliceosome," the investigators said (N. Engl. J. Med. 2011 Dec. 12 [doi:10.1056/NEJMoa1109016]).

The nine driver genes identified in this study appear in five core signaling pathways, and the genes each play different, though well-established roles in these pathways, such as DNA repair and cell-cycle control, Notch signaling, inflammatory pathways, and RNA splicing (in which SF3B1, in particular, was implicated). Furthermore, each driver mutation was found to be associated with different key abnormalities; for example, the findings indicate there may be an interaction between del(11q), which is associated with aggressive disease, and SF3B1 mutation in the pathogenesis of a clinical subgroup of chronic lymphocytic leukemia.

Overall, the investigators concluded that:

• Chronic lymphocytic leukemia has a lower rate of somatic mutation than most solid tumors.

• The rate of nonsynonymous mutation was not strongly affected by therapy.

• In addition to the expected mutations in cell-cycle and DNA-repair pathways, genetic alterations in Notch signaling, inflammatory pathways, and RNA splicing and processing also exist.

• Driver mutations showed striking associations with standard prognostic markers.

The latter suggests that "particular combinations of genetic alterations may act in concert to drive cancer," the investigators said.

The findings regarding the core spliceosome component SF3B1, which they described as a "major surprise," led to further analyses that suggested that SF3B1 mutations lead to "mistakes in the splicing of ... transcripts that affect the pathogenesis of chronic lymphocytic leukemia," they said, adding that ongoing studies will evaluate how mutations in SF3B1 alter its function in the processing of critical messenger RNAs.

The study, and in particular the findings regarding SF3B1 mutations, illustrate how identification of coding mutations in chronic lymphocytic leukemia can lead to the development of mechanistic hypotheses, novel prognostic markers, and potential therapeutic targets, Dr. Wang and her associates said.

They also noted the information provides a starting point for determining "which genes within chromosomal deletions and amplifications are essential, how each mutation alters cellular networks and phenotypes, which combinations of mutations are critical in the development of cancer, and how genetic events in the host may affect the importance of specific mutations and their combinations."

In an accompanying editorial, Dr. Benjamin Ebert and Olivier A. Bernard, Ph.D., commented that the study finding regarding mutations in genes involved in RNA splicing, although highly unexpected, converge remarkably with recent published findings from studies of myelodysplastic syndromes (N. Engl. J. Med. 2011;35:1384-95; Nature 2011;478:64-9).

SF3B1 mutations were found in 20% of patients with myelodysplastic syndromes, and in 65% of patients with refractory anemia and ring sideroblasts in one study (N. Engl. J. Med. 2011;35:1384-95).

"Moreover, mutations have been reported in multiple components of the spliceosome in 45%-85% of patients with myelodysplastic syndrome. SF3B1 mutations also occur in 1%-5% of samples from a wide range of tumor types, which indicates that mutations in RNA splicing factors are a widespread cause of oncogenic transformation," they added.

These and other findings, taken together, raise the "provocative possibility" that SF3B1 mutations may sometimes occur first in hematopoietic stem cells, with "additional mutations then being acquired in either the lymphoid or the myeloid lineages and causing chronic lymphocytic leukemia or myelodysplastic syndromes, respectively," Dr. Ebert of Brigham and Women’s Hospital, Boston, and Dr. Bernard, who is with INSERM at Institut Gustave Roussy, Villejuif, France, wrote (N. Engl. J. Med. 2011 Dec. 12 [doi:10.1056/NEJMe1111584]).

The findings have implications for determining prognosis, and for identifying targets for treatment. For example, the identification of mutations in genes encoding the RNA splicing machinery raises the possibility that spliceosome could be a therapeutic target, they said.

This study was supported by grants from the National Institutes of Health, the National Cancer Institute, the Melton and Rosenbach Funds, the Blavatnik Family Foundation, the Howard Hughes Medical Institute (via an Early Career Physician-Scientist Award), and the Damon Runyon Cancer Research Foundation. Dr. Wang said she had no relevant financial disclosures. Some of the coauthors said they were consultants to numerous pharmaceutical companies or owned stock in pharmaceutical companies. Other than employment by INSERM on the part of Dr. Bernard, neither he nor Dr. Ebert had any relevant financial disclosures to report.

Researchers using massively parallel sequencing to characterize the spectrum of somatic mutations in chronic lymphocytic leukemia identified nine genes that are mutated at significant frequencies in the disease.

Of these nine "driver" genes, which were identified from DNA samples from normal tissues and tumors in 91 patients with chronic lymphocytic leukemia, four have previously established roles in the disease (TP53, ATM, MYD88, and NOTCH1), and five do not (SF3B1, ZMYM3, MAPK1, FBXW7, and DDX3X), Dr. Lili Wang of the Dana-Farber Cancer Institute, Boston, and her colleagues reported online in the Dec. 12 issue of the New England Journal of Medicine. The findings were reported simultaneously at the annual meeting of the American Society of Hematology.

"Strikingly, the second most frequently mutated gene in our cohort was splicing factor 3b, subunit 1 (SF3B1), with missense mutations occurring in 14 of 91 patients (15%). SF3B1 is a component of the SF3B complex, which is associated with the U2 small nuclear ribonucleoprotein (snRNP), at the catalytic center of the spliceosome," the investigators said (N. Engl. J. Med. 2011 Dec. 12 [doi:10.1056/NEJMoa1109016]).

The nine driver genes identified in this study appear in five core signaling pathways, and the genes each play different, though well-established roles in these pathways, such as DNA repair and cell-cycle control, Notch signaling, inflammatory pathways, and RNA splicing (in which SF3B1, in particular, was implicated). Furthermore, each driver mutation was found to be associated with different key abnormalities; for example, the findings indicate there may be an interaction between del(11q), which is associated with aggressive disease, and SF3B1 mutation in the pathogenesis of a clinical subgroup of chronic lymphocytic leukemia.

Overall, the investigators concluded that:

• Chronic lymphocytic leukemia has a lower rate of somatic mutation than most solid tumors.

• The rate of nonsynonymous mutation was not strongly affected by therapy.

• In addition to the expected mutations in cell-cycle and DNA-repair pathways, genetic alterations in Notch signaling, inflammatory pathways, and RNA splicing and processing also exist.

• Driver mutations showed striking associations with standard prognostic markers.

The latter suggests that "particular combinations of genetic alterations may act in concert to drive cancer," the investigators said.

The findings regarding the core spliceosome component SF3B1, which they described as a "major surprise," led to further analyses that suggested that SF3B1 mutations lead to "mistakes in the splicing of ... transcripts that affect the pathogenesis of chronic lymphocytic leukemia," they said, adding that ongoing studies will evaluate how mutations in SF3B1 alter its function in the processing of critical messenger RNAs.

The study, and in particular the findings regarding SF3B1 mutations, illustrate how identification of coding mutations in chronic lymphocytic leukemia can lead to the development of mechanistic hypotheses, novel prognostic markers, and potential therapeutic targets, Dr. Wang and her associates said.

They also noted the information provides a starting point for determining "which genes within chromosomal deletions and amplifications are essential, how each mutation alters cellular networks and phenotypes, which combinations of mutations are critical in the development of cancer, and how genetic events in the host may affect the importance of specific mutations and their combinations."

In an accompanying editorial, Dr. Benjamin Ebert and Olivier A. Bernard, Ph.D., commented that the study finding regarding mutations in genes involved in RNA splicing, although highly unexpected, converge remarkably with recent published findings from studies of myelodysplastic syndromes (N. Engl. J. Med. 2011;35:1384-95; Nature 2011;478:64-9).

SF3B1 mutations were found in 20% of patients with myelodysplastic syndromes, and in 65% of patients with refractory anemia and ring sideroblasts in one study (N. Engl. J. Med. 2011;35:1384-95).

"Moreover, mutations have been reported in multiple components of the spliceosome in 45%-85% of patients with myelodysplastic syndrome. SF3B1 mutations also occur in 1%-5% of samples from a wide range of tumor types, which indicates that mutations in RNA splicing factors are a widespread cause of oncogenic transformation," they added.

These and other findings, taken together, raise the "provocative possibility" that SF3B1 mutations may sometimes occur first in hematopoietic stem cells, with "additional mutations then being acquired in either the lymphoid or the myeloid lineages and causing chronic lymphocytic leukemia or myelodysplastic syndromes, respectively," Dr. Ebert of Brigham and Women’s Hospital, Boston, and Dr. Bernard, who is with INSERM at Institut Gustave Roussy, Villejuif, France, wrote (N. Engl. J. Med. 2011 Dec. 12 [doi:10.1056/NEJMe1111584]).

The findings have implications for determining prognosis, and for identifying targets for treatment. For example, the identification of mutations in genes encoding the RNA splicing machinery raises the possibility that spliceosome could be a therapeutic target, they said.

This study was supported by grants from the National Institutes of Health, the National Cancer Institute, the Melton and Rosenbach Funds, the Blavatnik Family Foundation, the Howard Hughes Medical Institute (via an Early Career Physician-Scientist Award), and the Damon Runyon Cancer Research Foundation. Dr. Wang said she had no relevant financial disclosures. Some of the coauthors said they were consultants to numerous pharmaceutical companies or owned stock in pharmaceutical companies. Other than employment by INSERM on the part of Dr. Bernard, neither he nor Dr. Ebert had any relevant financial disclosures to report.