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Ozturk K, Dow M, Carlin DE, Bejar R, Carter H. The Emerging Potential for Network Analysis to Inform Precision Cancer Medicine. J Mol Biol 2018; 430:2875-2899. [PMID: 29908887 PMCID: PMC6097914 DOI: 10.1016/j.jmb.2018.06.016] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/30/2018] [Accepted: 06/06/2018] [Indexed: 12/19/2022]
Abstract
Precision cancer medicine promises to tailor clinical decisions to patients using genomic information. Indeed, successes of drugs targeting genetic alterations in tumors, such as imatinib that targets BCR-ABL in chronic myelogenous leukemia, have demonstrated the power of this approach. However, biological systems are complex, and patients may differ not only by the specific genetic alterations in their tumor, but also by more subtle interactions among such alterations. Systems biology and more specifically, network analysis, provides a framework for advancing precision medicine beyond clinical actionability of individual mutations. Here we discuss applications of network analysis to study tumor biology, early methods for N-of-1 tumor genome analysis, and the path for such tools to the clinic.
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Wang HY, Dell'Aquila ML, Dvanajscak Z, Bejar R, Broome HE, Hsi E, Murray SS, Thorson JA. JAK2 double minutes with resultant simultaneous amplification of JAK2 and CD274 in a therapy-related myelodysplastic syndrome evolving into an acute myeloid leukaemia. Br J Haematol 2018; 185:566-570. [PMID: 30132795 DOI: 10.1111/bjh.15538] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
Purpose of Review Clonal hematopoiesis of indeterminate potential (CHIP) is a common, age-associated condition characterized by the acquisition of somatic mutations. This concise review explores our current understanding of the mechanisms that influence the development of clonality with aging and its potential malignant and non-malignant clinical implications. Recent Findings Aging of the hematopoietic system results in phenotypic changes that favor clonal dominance. Cell-extrinsic factors provide additional selective pressures that further shape clonal architecture. Even so, small clones with candidate driver mutations appear to be ubiquitous with age and largely benign in the absence of strong selective pressures. Benign clonal expansion may compensate for the loss of regenerative HSC capacity as we age. Summary CHIP is a marker of aging that reflects the biologic interplay between HSC aging and cell-extrinsic factors. The clinical significance of CHIP is highly variable and dependent on clinical context. Distinguishing the causal relationships and confounding factors that regulate clonal behavior will be essential to define the mechanistic role of CHIP in aging and potentially mitigate its clinical consequences.
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Haider M, Duncavage EJ, Afaneh KF, Bejar R, List AF. New Insight Into the Biology, Risk Stratification, and Targeted Treatment of Myelodysplastic Syndromes. Am Soc Clin Oncol Educ Book 2017; 37:480-494. [PMID: 28561687 DOI: 10.1200/edbk_175397] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In myelodysplastic syndromes (MDS), somatic mutations occur in five major categories: RNA splicing, DNA methylation, activated cell signaling, myeloid transcription factors, and chromatin modifiers. Although many MDS cases harbor more than one somatic mutation, in general, there is mutual exclusivity of mutated genes within a class. In addition to the prognostic significance of individual somatic mutations, more somatic mutations in MDS have been associated with poor prognosis. Prognostic assessment remains a critical component of the personalization of care for patient with MDS because treatment is highly risk adapted. Multiple methods for risk stratification are available with the revised International Prognostic Scoring System (IPSS-R), currently considered the gold standard. Increasing access to myeloid gene panels and greater evidence for the diagnostic and predictive value of somatic mutations will soon make sequencing part of the standard evaluation of patients with MDS. In the absence of formal guidelines for their prognostic use, well-validated mutations can still refine estimates of risk made with the IPSS-R. Not only are somatic gene mutations advantageous in understanding the biology of MDS and prognosis, they also offer potential as biomarkers and targets for the treatment of patients with MDS. Examples include deletion 5q, spliceosome complex gene mutations, and TP53 mutations.
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Sallman DA, Tanaka TN, List A, Bejar R. SOHO State of the Art Update and Next Questions: Biology and Treatment of Myelodysplastic Syndromes. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2017; 17:613-620. [PMID: 29025689 DOI: 10.1016/j.clml.2017.09.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 09/19/2017] [Indexed: 11/17/2022]
Abstract
Myelodysplastic syndromes (MDS) are a heterogeneous group of myeloid neoplasms characterized by clonal hematopoiesis leading to bone marrow dysplasia and cytopenias. Recently, significant advancements have been made in understanding the pathogenic mechanisms of this disease. In particular, how a wide array of somatic mutations can induce a common clinical phenotype has been investigated. Specifically, activation of innate immune signaling (i.e. myeloid derived suppressor cells) and the NLRP3 inflammasome in hematopoietic stem/progenitor cells play a central role in the biology of MDS, leading to pyroptotic cell death and clonal expansion. Additionally, deciphering the molecular drivers of MDS using next-generation sequencing has rapidly expanded our understanding of MDS with profound implications for prognosis, treatment decisions, and future clinical investigations. Together, unraveling of the role of innate immunity/pyroptosis in the clinical phenotype of MDS patients and comprehensive molecular characterization has identified novel therapeutic strategies that offer significant promise.
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Spira A, Yurgelun MB, Alexandrov L, Rao A, Bejar R, Polyak K, Giannakis M, Shilatifard A, Finn OJ, Dhodapkar M, Kay NE, Braggio E, Vilar E, Mazzilli SA, Rebbeck TR, Garber JE, Velculescu VE, Disis ML, Wallace DC, Lippman SM. Precancer Atlas to Drive Precision Prevention Trials. Cancer Res 2017; 77:1510-1541. [PMID: 28373404 DOI: 10.1158/0008-5472.can-16-2346] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 01/20/2017] [Accepted: 01/20/2017] [Indexed: 02/07/2023]
Abstract
Cancer development is a complex process driven by inherited and acquired molecular and cellular alterations. Prevention is the holy grail of cancer elimination, but making this a reality will take a fundamental rethinking and deep understanding of premalignant biology. In this Perspective, we propose a national concerted effort to create a Precancer Atlas (PCA), integrating multi-omics and immunity - basic tenets of the neoplastic process. The biology of neoplasia caused by germline mutations has led to paradigm-changing precision prevention efforts, including: tumor testing for mismatch repair (MMR) deficiency in Lynch syndrome establishing a new paradigm, combinatorial chemoprevention efficacy in familial adenomatous polyposis (FAP), signal of benefit from imaging-based early detection research in high-germline risk for pancreatic neoplasia, elucidating early ontogeny in BRCA1-mutation carriers leading to an international breast cancer prevention trial, and insights into the intricate germline-somatic-immunity interaction landscape. Emerging genetic and pharmacologic (metformin) disruption of mitochondrial (mt) respiration increased autophagy to prevent cancer in a Li-Fraumeni mouse model (biology reproduced in clinical pilot) and revealed profound influences of subtle changes in mt DNA background variation on obesity, aging, and cancer risk. The elaborate communication between the immune system and neoplasia includes an increasingly complex cellular microenvironment and dynamic interactions between host genetics, environmental factors, and microbes in shaping the immune response. Cancer vaccines are in early murine and clinical precancer studies, building on the recent successes of immunotherapy and HPV vaccine immune prevention. Molecular monitoring in Barrett's esophagus to avoid overdiagnosis/treatment highlights an important PCA theme. Next generation sequencing (NGS) discovered age-related clonal hematopoiesis of indeterminate potential (CHIP). Ultra-deep NGS reports over the past year have redefined the premalignant landscape remarkably identifying tiny clones in the blood of up to 95% of women in their 50s, suggesting that potentially premalignant clones are ubiquitous. Similar data from eyelid skin and peritoneal and uterine lavage fluid provide unprecedented opportunities to dissect the earliest phases of stem/progenitor clonal (and microenvironment) evolution/diversity with new single-cell and liquid biopsy technologies. Cancer mutational signatures reflect exogenous or endogenous processes imprinted over time in precursors. Accelerating the prevention of cancer will require a large-scale, longitudinal effort, leveraging diverse disciplines (from genetics, biochemistry, and immunology to mathematics, computational biology, and engineering), initiatives, technologies, and models in developing an integrated multi-omics and immunity PCA - an immense national resource to interrogate, target, and intercept events that drive oncogenesis. Cancer Res; 77(7); 1510-41. ©2017 AACR.
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Bejar R. Splicing Factor Mutations in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 907:215-28. [PMID: 27256388 DOI: 10.1007/978-3-319-29073-7_9] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Many cancers demonstrate aberrant splicing patterns that contribute to their development and progression. Recently, recurrent somatic mutations of genes encoding core subunits of the spliceosome have been identified in several different cancer types. These mutations are most common in hematologic malignancies like the myelodysplastic syndromes (MDS), acute myeloid leukemia, and chronic lymphocytic leukemia, but also in occur in several solid tumors at lower frequency. The most frequent mutations occur in SF3B1, U2AF1, SRSF2, and ZRSR2 and are largely exclusive of each other. Mutations in SF3B1, U2AF1, and SRSF2 acquire heterozygous missense mutations in specific codons, resembling oncogenes. ZRSR2 mutations include clear loss-of-function variants, a pattern more common to tumor suppressor genes. These splicing factors are associated with distinct clinical phenotypes and patterns of mutation in different malignancies. Mutations have both diagnostic and prognostic relevance. Splicing factor mutations appear to affect only a minority of transcripts which show little overlap by mutation type. How differences in splicing caused by somatic mutations of spliceosome subunits lead to oncogenesis is not clear and may involve different targets in each disease type. However, cells with mutated splicing machinery may be particularly vulnerable to further disruption of the spliceosome suggesting a novel strategy for the targeted therapy of cancers.
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Galanina N, Goodman A, Tran L, Bejar R, Choi MY, Kurzrock R. Next generation sequencing to reveal potentially actionable alterations in the majority of patients with hematologic malignancies. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.e23133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e23133 Background: Next generation sequencing (NGS) permits identification of genomic alterations that inform disease classification and prognosis and may also guide therapy selection. Methods: Using NGS (406 genes), we analyzed the clinical characteristics, genomic alterations, and potential actionability of 235 patients (pts) with diverse hematologic malignancies. Results: A total of 227 pts (96.5%) (59% men; median age 59 yrs) had adequate tissue for analysis. Most common diagnoses included myelodysplastic syndrome (22.9%), chronic lymphocytic leukemia (17.2%), non-Hodgkin lymphoma (13.2%), myeloproliferative neoplasm (9.2%), acute myeloid (11%) / lymphoid (8.8%) leukemia and multiple myeloma (7.5%). The majority of pts (N = 197/227 (86.8%)) harbored ≥1 genomic alteration(s); 164 pts (72%) had ≥1 potentially actionable alteration(s) targetable by an existing FDA-approved drug (mostly off label) or an investigational agent. A total of 551 distinct alteration s were seen with the most common involving TP53 (9.3%), TET2 (4.2%), DNMT3A (3.3%), ASXL1 (2.5%), MLL (2.5%), KRAS (2.2%). The vast majority of pts had unique molecular profile. Conclusions: About 96.5% of pts with hematologic malignancies have adequate tissue for NGS. Most pts had unique molecular signatures, and 72% had alterations that may be pharmacologically tractable. [Table: see text]
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Drusbosky L, Medina C, Martuscello R, Hawkins KE, Chang M, Lamba JK, Vali S, Kumar A, Singh NK, Abbasi T, Sekeres MA, Mallo M, Sole F, Bejar R, Cogle CR. Computational drug treatment simulations on projections of dysregulated protein networks derived from the myelodysplastic mutanome match clinical response in patients. Leuk Res 2017; 52:1-7. [DOI: 10.1016/j.leukres.2016.11.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 11/02/2016] [Accepted: 11/04/2016] [Indexed: 01/19/2023]
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Greenberg PL, Stone RM, Al-Kali A, Barta SK, Bejar R, Bennett JM, Carraway H, De Castro CM, Deeg HJ, DeZern AE, Fathi AT, Frankfurt O, Gaensler K, Garcia-Manero G, Griffiths EA, Head D, Horsfall R, Johnson RA, Juckett M, Klimek VM, Komrokji R, Kujawski LA, Maness LJ, O'Donnell MR, Pollyea DA, Shami PJ, Stein BL, Walker AR, Westervelt P, Zeidan A, Shead DA, Smith C. Myelodysplastic Syndromes, Version 2.2017, NCCN Clinical Practice Guidelines in Oncology. J Natl Compr Canc Netw 2016; 15:60-87. [DOI: 10.6004/jnccn.2017.0007] [Citation(s) in RCA: 214] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Bejar R, Greenberg PL. The Impact of Somatic and Germline Mutations in Myelodysplastic Syndromes and Related Disorders. J Natl Compr Canc Netw 2016; 15:131-135. [DOI: 10.6004/jnccn.2017.0010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Qiu J, Zhou B, Thol F, Zhou Y, Chen L, Shao C, DeBoever C, Hou J, Li H, Chaturvedi A, Ganser A, Bejar R, Zhang DE, Fu XD, Heuser M. Distinct splicing signatures affect converged pathways in myelodysplastic syndrome patients carrying mutations in different splicing regulators. RNA (NEW YORK, N.Y.) 2016; 22:1535-1549. [PMID: 27492256 PMCID: PMC5029452 DOI: 10.1261/rna.056101.116] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 06/08/2016] [Indexed: 06/06/2023]
Abstract
Myelodysplastic syndromes (MDS) are heterogeneous myeloid disorders with prevalent mutations in several splicing factors, but the splicing programs linked to specific mutations or MDS in general remain to be systematically defined. We applied RASL-seq, a sensitive and cost-effective platform, to interrogate 5502 annotated splicing events in 169 samples from MDS patients or healthy individuals. We found that splicing signatures associated with normal hematopoietic lineages are largely related to cell signaling and differentiation programs, whereas MDS-linked signatures are primarily involved in cell cycle control and DNA damage responses. Despite the shared roles of affected splicing factors in the 3' splice site definition, mutations in U2AF1, SRSF2, and SF3B1 affect divergent splicing programs, and interestingly, the affected genes fall into converging cancer-related pathways. A risk score derived from 11 splicing events appears to be independently associated with an MDS prognosis and AML transformation, suggesting potential clinical relevance of altered splicing patterns in MDS.
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Steensma DP, Abedi M, Bejar R, Cogle CR, Foucar K, Garcia-Manero G, George TI, Grinblatt D, Komrokji R, Ma X, Maciejewski J, Pollyea DA, Savona MR, Scott B, Sekeres MA, Thompson MA, Swern AS, Nifenecker M, Sugrue MM, Erba H. Connect MDS/AML: design of the myelodysplastic syndromes and acute myeloid leukemia disease registry, a prospective observational cohort study. BMC Cancer 2016; 16:652. [PMID: 27538433 PMCID: PMC4991094 DOI: 10.1186/s12885-016-2710-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 08/11/2016] [Indexed: 12/18/2022] Open
Abstract
Background Myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) are myeloid neoplasms in which outgrowth of neoplastic clones disrupts normal hematopoiesis. Some patients with unexplained persistent cytopenias may not meet minimal diagnostic criteria for MDS but an alternate diagnosis is not apparent; the term idiopathic cytopenia of undetermined significance (ICUS) has been used to describe this state. MDS and AML occur primarily in older patients who are often treated outside the clinical trial setting. Consequently, our understanding of the patterns of diagnostic evaluation, management, and outcomes of these patients is limited. Furthermore, there are few natural history studies of ICUS. To better understand how patients who have MDS, ICUS, or AML are managed in the routine clinical setting, the Connect MDS/AML Disease Registry, a multicenter, prospective, observational cohort study of patients newly diagnosed with these conditions has been initiated. Methods/Design The Connect MDS/AML Disease Registry will capture diagnosis, risk assessment, treatment, and outcomes data for approximately 1500 newly diagnosed patients from approximately 150 community and academic sites in the United States in 4 cohorts: (1) lower-risk MDS (International Prognostic Scoring System [IPSS] low and intermediate-1 risk), with and without del(5q); (2) higher-risk MDS (IPSS intermediate-2 and high risk); (3) ICUS; and (4) AML in patients aged ≥ 55 years (excluding acute promyelocytic leukemia). Diagnosis will be confirmed by central review. Baseline patient characteristics, diagnostic patterns, treatment patterns, clinical outcomes, health economics outcomes, and patient-reported health-related quality of life will be entered into an electronic data capture system at enrollment and quarterly for 8 years. A tissue substudy to explore the relationship between karyotypes, molecular markers, and clinical outcomes will be conducted, and is optional for patients. Discussion The Connect MDS/AML Disease Registry will be the first prospective, observational, non-interventional study in the United States to collect clinical information, patient-reported outcomes, and tissue samples from patients with MDS, ICUS, or AML receiving multiple therapies. Results from this registry may provide new insights into the relationship between diagnostic practices, treatment regimens, and outcomes in patients with these diseases and identify areas for future investigation. Trial registration Connect MDS/AML Disease Registry (NCT01688011). Registered 14 September 2012. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2710-6) contains supplementary material, which is available to authorized users.
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Greenberg PL, Stone RM, Bejar R, Bennett JM, Bloomfield CD, Borate U, De Castro CM, Deeg HJ, DeZern AE, Fathi AT, Frankfurt O, Gaensler K, Garcia-Manero G, Griffiths EA, Head D, Klimek V, Komrokji R, Kujawski LA, Maness LJ, O'Donnell MR, Pollyea DA, Scott B, Shami PJ, Stein BL, Westervelt P, Wheeler B, Shead DA, Smith C. Myelodysplastic syndromes, version 2.2015. J Natl Compr Canc Netw 2015; 13:261-72. [PMID: 25736003 DOI: 10.6004/jnccn.2015.0038] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The NCCN Guidelines for Myelodysplastic Syndromes (MDS) comprise a heterogeneous group of myeloid disorders with a highly variable disease course that depends largely on risk factors. Risk evaluation is therefore a critical component of decision-making in the treatment of MDS. The development of newer treatments and the refinement of current treatment modalities are designed to improve patient outcomes and reduce side effects. These NCCN Guidelines Insights focus on the recent updates to the guidelines, which include the incorporation of a revised prognostic scoring system, addition of molecular abnormalities associated with MDS, and refinement of treatment options involving a discussion of cost of care.
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Song C, Castellanos-Rizaldos E, Bejar R, Ebert BL, Makrigiorgos GM. DMSO Increases Mutation Scanning Detection Sensitivity of High-Resolution Melting in Clinical Samples. Clin Chem 2015; 61:1354-62. [PMID: 26432802 DOI: 10.1373/clinchem.2015.245357] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/17/2015] [Indexed: 02/02/2023]
Abstract
BACKGROUND Mutation scanning provides the simplest, lowest-cost method for identifying DNA variations on single PCR amplicons, and it may be performed before sequencing to avoid screening of noninformative wild-type samples. High-resolution melting (HRM) is the most commonly used method for mutation scanning. With PCR-HRM, however, mutations less abundant than approximately 3%-10% that can still be clinically significant may often be missed. Therefore, enhancing HRM detection sensitivity is important for mutation scanning and its clinical application. METHODS We used serial dilution of cell lines containing the TP53 exon 8 mutation to demonstrate the improvement in detection sensitivity for conventional-PCR-HRM in the presence of DMSO. We also conducted coamplification at lower denaturation temperature (COLD)-PCR with an extra step for cross-hybridization, followed by preferential denaturation and amplification at optimized critical temperature (full-COLD-PCR), to further enrich low-level mutations before HRM with or without DMSO, and we used droplet-digital PCR to derive the optimal conditions for mutation enrichment. Both conventional PCR-HRM and full-COLD-PCR-HRM with and without DMSO were used for mutation scanning of TP53 exon 8 in cancer samples containing known mutations and myelodysplastic syndrome samples with unknown mutations. Mutations in other genes were also examined. RESULTS The detection sensitivity of PCR-HRM scanning increases 2- to 5-fold in the presence of DMSO, depending on mutation type and sequence context, and can typically detect mutation abundance of approximately 1%. When mutation enrichment is applied during amplification with full-COLD-PCR followed by HRM in the presence of DMSO, mutations with 0.2%-0.3% abundance in TP53 exon 8 can be detected. CONCLUSIONS DMSO improves HRM mutation scanning sensitivity with saturating dyes. When full-COLD-PCR is used, followed by DMSO-HRM, the overall improvement is about 20-fold compared with conventional PCR-HRM.
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Abstract
Diagnosing a myelodysplastic syndrome (MDS) can be challenging. Somatic mutations are common in MDS and might have diagnostic utility in patients with idiopathic cytopenias of undetermined significance (ICUS). However, using mutations to diagnose MDS is complicated by several issues: (1) no gene is mutated in most cases, (2) no mutated gene is highly specific for MDS, (3) clonal hematopoiesis is common in older individuals without disease, and (4) we lack outcome data for ICUS patients with clonal cytopenias of undetermined significance (CCUS). Despite these caveats, genetic sequencing can inform the diagnosis of MDS. CCUS patients more closely resemble patients with MDS than age matched controls with somatic mutations. Genetic testing can identify alternative diagnoses in cytopenic patients and help risk stratify those with proven MDS. While we cannot include somatic mutations in the diagnostic definition of MDS now, testing to recognize CCUS will help characterize outcomes in these diagnostically challenging patients.
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Abstract
Myelodysplastic syndromes are a collection of clonal hematopoietic disorders with a wide range of clinical manifestations and eventual outcomes. Accurate prediction of a patient's prognosis is useful to define the risk posed by the disease and which treatment options are most appropriate. Several models have been created to help predict the prognosis for patients with myelodysplastic syndromes. The International Prognostic Scoring System (IPSS) has been the standard tool used to risk stratify MDS patients since its publication in 1997. Other models have since been created to improve upon the IPSS, including the recent Revised International Prognostic Scoring System. Most models include the presence or severity of peripheral blood cytopenias, the proportion of bone marrow blasts, and specific karyotype abnormalities. Other factors including age, performance status, co-morbidities, transfusion dependence, and molecular biomarkers can further refine the prediction of prognosis in some models. Novel, disease specific biomarkers with prognostic value in myelodysplastic syndromes including cell surface markers, gene expression profiles, and high resolution copy number analyses have been proposed but not yet adopted clinically. Somatic abnormalities in recurrently mutated genes are the most informative prognostic biomarkers not currently considered by clinical risk models. Mutations in specific genes have independent prognostic significance and, unlike cytogenetic abnormalities, are present in the majority of myelodysplastic syndrome cases. However, mutational information can be complex and there are challenges to its clinical implementation. Despite these limitations, DNA sequencing can refine the prediction of prognosis for myelodysplastic syndrome patients and has become increasingly available in the clinic where it will help improve the care of patients with myelodysplastic syndromes.
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Steensma D, Abedi M, Bejar R, Cogle C, Foucar K, Garcia-Manero G, George T, Grinblatt D, Komrokji R, Maciejewski J, Pollyea D, Roboz G, Savona M, Scott B, Sekeres M, Thompson M, Sugrue M, Swern A, Nifenecker M, Erba H. 249 CONNECT MDS AND AML: THE MYELODYSPLASTIC SYNDROMES (MDS) AND ACUTE MYELOID LEUKEMIA (AML) DISEASE REGISTRY. Leuk Res 2015. [DOI: 10.1016/s0145-2126(15)30250-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Sankaran VG, Ulirsch JC, Tchaikovskii V, Ludwig LS, Wakabayashi A, Kadirvel S, Lindsley RC, Bejar R, Shi J, Lovitch SB, Bishop DF, Steensma DP. X-linked macrocytic dyserythropoietic anemia in females with an ALAS2 mutation. J Clin Invest 2015; 125:1665-9. [PMID: 25705881 DOI: 10.1172/jci78619] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 01/08/2015] [Indexed: 01/19/2023] Open
Abstract
Macrocytic anemia with abnormal erythropoiesis is a common feature of megaloblastic anemias, congenital dyserythropoietic anemias, and myelodysplastic syndromes. Here, we characterized a family with multiple female individuals who have macrocytic anemia. The proband was noted to have dyserythropoiesis and iron overload. After an extensive diagnostic evaluation that did not provide insight into the cause of the disease, whole-exome sequencing of multiple family members revealed the presence of a mutation in the X chromosomal gene ALAS2, which encodes 5'-aminolevulinate synthase 2, in the affected females. We determined that this mutation (Y365C) impairs binding of the essential cofactor pyridoxal 5'-phosphate to ALAS2, resulting in destabilization of the enzyme and consequent loss of function. X inactivation was not highly skewed in wbc from the affected individuals. In contrast, and consistent with the severity of the ALAS2 mutation, there was a complete skewing toward expression of the WT allele in mRNA from reticulocytes that could be recapitulated in primary erythroid cultures. Together, the results of the X inactivation and mRNA studies illustrate how this X-linked dominant mutation in ALAS2 can perturb normal erythropoiesis through cell-nonautonomous effects. Moreover, our findings highlight the value of whole-exome sequencing in diagnostically challenging cases for the identification of disease etiology and extension of the known phenotypic spectrum of disease.
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MESH Headings
- 5-Aminolevulinate Synthetase/genetics
- 5-Aminolevulinate Synthetase/metabolism
- Adult
- Anemia, Dyserythropoietic, Congenital/genetics
- Anemia, Macrocytic/genetics
- Cells, Cultured
- Erythropoiesis/genetics
- Exome/genetics
- Female
- Genes, Dominant
- Genes, X-Linked
- Genetic Diseases, X-Linked/blood
- Genetic Diseases, X-Linked/genetics
- Hemorrhage/etiology
- Humans
- Iron Overload/etiology
- Male
- Models, Molecular
- Molecular Sequence Data
- Mutation, Missense
- Point Mutation
- Pregnancy
- Pregnancy Complications, Hematologic/genetics
- Protein Binding
- Protein Conformation
- Puerperal Disorders/etiology
- Pyridoxal Phosphate/metabolism
- RNA, Messenger/genetics
- Reticulocytes/metabolism
- X Chromosome Inactivation
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Schneider RK, Ademà V, Heckl D, Järås M, Mallo M, Lord AM, Chu LP, McConkey ME, Kramann R, Mullally A, Bejar R, Solé F, Ebert BL. Role of casein kinase 1A1 in the biology and targeted therapy of del(5q) MDS. Cancer Cell 2014; 26:509-20. [PMID: 25242043 PMCID: PMC4199102 DOI: 10.1016/j.ccr.2014.08.001] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/09/2014] [Accepted: 08/01/2014] [Indexed: 01/16/2023]
Abstract
The casein kinase 1A1 gene (CSNK1A1) is a putative tumor suppressor gene located in the common deleted region for del(5q) myelodysplastic syndrome (MDS). We generated a murine model with conditional inactivation of Csnk1a1 and found that Csnk1a1 haploinsufficiency induces hematopoietic stem cell expansion and a competitive repopulation advantage, whereas homozygous deletion induces hematopoietic stem cell failure. Based on this finding, we found that heterozygous inactivation of Csnk1a1 sensitizes cells to a CSNK1 inhibitor relative to cells with two intact alleles. In addition, we identified recurrent somatic mutations in CSNK1A1 on the nondeleted allele of patients with del(5q) MDS. These studies demonstrate that CSNK1A1 plays a central role in the biology of del(5q) MDS and is a promising therapeutic target.
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Bejar R, Stevenson KE, Caughey B, Lindsley RC, Mar BG, Stojanov P, Getz G, Steensma DP, Ritz J, Soiffer R, Antin JH, Alyea E, Armand P, Ho V, Koreth J, Neuberg D, Cutler CS, Ebert BL. Somatic mutations predict poor outcome in patients with myelodysplastic syndrome after hematopoietic stem-cell transplantation. J Clin Oncol 2014; 32:2691-8. [PMID: 25092778 DOI: 10.1200/jco.2013.52.3381] [Citation(s) in RCA: 308] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
PURPOSE Recurrently mutated genes in myelodysplastic syndrome (MDS) are pathogenic drivers and powerfully associated with clinical phenotype and prognosis. Whether these types of mutations predict outcome after allogeneic hematopoietic stem-cell transplantation (HSCT) in patients with MDS is not known. PATIENTS AND METHODS We used massively parallel sequencing to examine tumor samples collected from 87 patients with MDS before HSCT for coding mutations in 40 recurrently mutated MDS genes. RESULTS Mutations were identified in 92% of patients, most frequently in the ASXL1 (29%), TP53 (21%), DNMT3A (18%), and RUNX1 (16%) genes. In univariable analyses, only TP53 mutations were associated with shorter overall (OS; hazard ratio [HR], 3.74; P < .001) and progression-free survival (HR, 3.97; P < .001). After adjustment for clinical variables associated with these end points, mutations in TP53 (HR, 2.30; P = .027), TET2 (HR, 2.40; P = .033), and DNMT3A (HR, 2.08; P = .049) were associated with decreased OS. In multivariable analysis including clinical variables, complex karyotype status, and candidate genes, mutations in TP53 (HR, 4.22; P ≤ .001) and TET2 (HR, 1.68; P = .037) were each independently associated with shorter OS. Nearly one half of patients (46%) carried a mutation in TP53, DNMT3A, or TET2 and accounted for 64% of deaths. Three-year OS in patients without these mutations was 59% (95% CI, 43% to 72%), versus 19% (95% CI, 9% to 33%) in patients with these mutations. CONCLUSION Mutations in TP53, TET2, or DNMT3A identify patients with MDS with shorter OS after HSCT.
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Steensma DP, Abedi M, Attar EC, Bejar R, Cogle CR, Garcia-Manero G, Grinblatt DL, Ma X, Maciejewski JP, Pollyea DA, Roboz GJ, Savona M, Scott BL, Sekeres MA, Thompson MA, Zernovak O, Sugrue MM, Swern AS, Nifenecker M, Erba HP. Connect MDS and AML: The myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) disease registry. J Clin Oncol 2014. [DOI: 10.1200/jco.2014.32.15_suppl.tps7126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Wei Y, Dimicoli S, Bueso-Ramos C, Chen R, Yang H, Neuberg D, Pierce S, Jia Y, Zheng H, Wang H, Wang X, Nguyen M, Wang SA, Ebert B, Bejar R, Levine R, Abdel-Wahab O, Kleppe M, Ganan-Gomez I, Kantarjian H, Garcia-Manero G. Toll-like receptor alterations in myelodysplastic syndrome. Leukemia 2013; 27:1832-40. [PMID: 23765228 DOI: 10.1038/leu.2013.180] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 05/28/2013] [Accepted: 06/03/2013] [Indexed: 02/03/2023]
Abstract
Recent studies have implicated the innate immunity system in the pathogenesis of myelodysplastic syndromes (MDS). Toll-like receptor (TLR) genes encode key innate immunity signal initiators. We recently identified multiple genes, known to be regulated by TLRs, to be overexpressed in MDS bone marrow (BM) CD34+ cells, and hypothesized that TLR signaling is abnormally activated in MDS. We analyzed a large cohort of MDS cases and identified TLR1, TLR2 and TLR6 to be significantly overexpressed in MDS BM CD34+ cells. Deep sequencing followed by Sanger resequencing of TLR1, TLR2, TLR4 and TLR6 genes uncovered a recurrent genetic variant, TLR2-F217S, in 11% of 149 patients. Functionally, TLR2-F217S results in enhanced activation of downstream signaling including NF-κB activity after TLR2 agonist treatment. In cultured primary BM CD34+ cells of normal donors, TLR2 agonists induced histone demethylase JMJD3 and interleukin-8 gene expression. Inhibition of TLR2 in BM CD34+ cells from patients with lower-risk MDS using short hairpin RNA resulted in increased erythroid colony formation. Finally, RNA expression levels of TLR2 and TLR6, as well as presence of TLR2-F217S, are associated with distinct prognosis and clinical characteristics. These findings indicate that TLR2-centered signaling is deregulated in MDS, and that its targeting may have potential therapeutic benefit in MDS.
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Bejar R, Murphy D, Stevenson K, Neuberg D, Shi Y, Cubrich C, Richardson K, Eastlake P, Garcia-Manero G, Kantarjian H, Ebert B, Makrigiorgos G. P-103 Occult NRAS mutations with very low allele burden have independent prognostic significance in lower-risk myelodysplastic syndromes. Leuk Res 2013. [DOI: 10.1016/s0145-2126(13)70151-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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