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Multiomic mapping of acquired chromosome 1 copy number and structural variants to identify therapeutic vulnerabilities in multiple myeloma

Boyle, Eileen M; Blaney, Patrick; Stoeckle, James H; Wang, Yubao; Ghamlouch, Hussein; Gagler, Dylan; Braunstein, Marc; Williams, Louis; Tenenbaum, Avital; Siegel, Ariel; Chen, Xiaoyi; Varma, Gaurav; Avigan, Jason; Li, Alexander; Jinsi, Monica; Kaminetzky, David; Arbini, Arnaldo; Montes, Lydia; Corre, Jill; Rustad, Even H; Landgren, Ola; Maura, Francesco; Walker, Brian A; Bauer, Michael; Bruno, Benedetto; Tsirigos, Aristotelis; Davies, Faith E; Morgan, Gareth J
PURPOSE/OBJECTIVE:Chromosome 1 (chr1) copy number abnormalities (CNAs) and structural variants (SV) are frequent in newly diagnosed multiple myeloma (NDMM) and associate with a heterogeneous impact on outcome the drivers of which are largely unknown. EXPERIMENTAL DESIGN/METHODS:A multiomic approach comprising CRISPR, gene mapping of CNA and SV, methylation, expression, and mutational analysis was used to document the extent of chr1 molecular variants and their impact on pathway utilisation. RESULTS:We identified two distinct groups of gain(1q): focal gains associated with limited gene expression changes and a neutral prognosis, and whole-arm gains, which associate with substantial gene expression changes, complex genetics and an adverse prognosis. CRISPR identified a number of dependencies on chr1 but only limited variants associated with acquired CNAs. We identified seven regions of deletion, nine of gain, three of chromothripsis (CT) and two of templated-insertion (TI), which contain a number of potential drivers. An additional mechanism involving hypomethylation of genes at 1q may contribute to the aberrant gene expression of a number of genes. Expression changes associated with whole-arm gains were substantial and gene set enrichment analysis identified metabolic processes, apoptotic resistance, signaling via the MAPK pathway, and upregulation of transcription factors as being key drivers of the adverse prognosis associated with these variants. CONCLUSIONS:Multiple layers of genetic complexity impact the phenotype associated with CNAs on chr1 to generate its associated clinical phenotype. Whole-arm gains of 1q are the critically important prognostic group that deregulate multiple pathways, which may offer therapeutic vulnerabilities.
PMID: 37449980
ISSN: 1557-3265
CID: 5537862

Hemoglobin Alpha Chain Variant Zara Associated With Familial Asymptomatic Hypoxemia [Case Report]

Pasquarella, Anthony; Miller, Erin; Wong, Edward C C; Ito, Masamichi; Braunstein, Marc J
Numerous hemoglobin (Hb) gene mutations have been identified, leading to a spectrum of phenotypes ranging from asymptomatic carrier states to complicated hemolytic anemias. We report a rare case of asymptomatic hypoxemia in a father and his teenage daughter both of whom were found to be carriers of Hb gene variant Zara. Workup for alternative cardiovascular causes of hypoxemia was unremarkable. Further sequencing of the alpha globin locus showed both individuals to be heterozygous for the Hb Zara c.274C>A (p.Leu92Ile) variant of unknown significance in the alpha2-globin gene. This is the first documented association of this Hb variant with familial asymptomatic hypoxemia, highlighting the importance of evaluating for hemoglobinopathies in patients with reduced oxygen saturation.
PMID: 36406831
ISSN: 1927-1220
CID: 5384012

Structural variants shape the genomic landscape and clinical outcome of multiple myeloma

Ashby, Cody; Boyle, Eileen M; Bauer, Michael A; Mikulasova, Aneta; Wardell, Christopher P; Williams, Louis; Siegel, Ariel; Blaney, Patrick; Braunstein, Marc; Kaminetsky, David; Keats, Jonathan; Maura, Francesco; Landgren, Ola; Walker, Brian A; Davies, Faith E; Morgan, Gareth J
Deciphering genomic architecture is key to identifying novel disease drivers and understanding the mechanisms underlying myeloma initiation and progression. In this work, using the CoMMpass dataset, we show that structural variants (SV) occur in a nonrandom fashion throughout the genome with an increased frequency in the t(4;14), RB1, or TP53 mutated cases and reduced frequency in t(11;14) cases. By mapping sites of chromosomal rearrangements to topologically associated domains and identifying significantly upregulated genes by RNAseq we identify both predicted and novel putative driver genes. These data highlight the heterogeneity of transcriptional dysregulation occurring as a consequence of both the canonical and novel structural variants. Further, it shows that the complex rearrangements chromoplexy, chromothripsis and templated insertions are common in MM with each variant having its own distinct frequency and impact on clinical outcome. Chromothripsis is associated with a significant independent negative impact on clinical outcome in newly diagnosed cases consistent with its use alongside other clinical and genetic risk factors to identify prognosis.
PMID: 35637217
ISSN: 2044-5385
CID: 5231522

Outcomes of Patients With Hematologic Malignancies Who Received Inpatient Palliative Care Consultation

Pasquarella, Anthony V; Islam, Shahidul; Ramdhanny, Angela; Gendy, Mina; Pinto, Priya; Braunstein, Marc J
PURPOSE:Palliative care (PC) plays an established role in improving outcomes in patients with solid tumors, yet these services are underutilized in hematologic malignancies (HMs). We reviewed records of hospitalized patients with active HM to determine associations between PC consultation and length of stay, intensive care unit stay, 30-day readmission, and 6-month mortality compared with those who were not seen by PC. METHODS:We reviewed all oncology admissions at our institution between 2013 and 2019 and included patients with HM actively on treatment, stratified by those seen by PC to controls not seen by PC. Groups were compared using Wilcoxon rank-sum, chi-square, and Fisher's exact tests on the basis of the type and distribution of data. Multiple logistic regression models with stepwise variable selection methods were used to find predictors of outcomes. RESULTS:< .001). These data were confirmed in multivariable models. CONCLUSION:In this retrospective study, more than two thirds of patients with HM did not receive PC consultation despite having similar comorbidities, suggesting that inpatient PC consultation is underutilized in patients with HM, despite the potential for decreased readmission rates.
PMID: 34986010
ISSN: 2688-1535
CID: 5284102

Chromothripsis as a pathogenic driver of multiple myeloma

Maura, Francesco; Boyle, Eileen M; Rustad, Even H; Ashby, Cody; Kaminetzky, David; Bruno, Benedetto; Braunstein, Marc; Bauer, Michael; Blaney, Patrick; Wang, Yubao; Ghamlouch, Hussein; Williams, Louis; Stoeckle, James; Davies, Faith E; Walker, Brian A; Maclachlan, Kylee; Diamond, Ben; Landgren, Ola; Morgan, Gareth J
Analysis of the genetic basis for multiple myeloma (MM) has informed many of our current concepts of the biology that underlies disease initiation and progression. Studying these events in further detail is predicted to deliver important insights into its pathogenesis, prognosis and treatment. Information from whole genome sequencing of structural variation is revealing the role of these events as drivers of MM. In particular, we discuss how the insights we have gained from studying chromothripsis suggest that it can be used to provide information on disease initiation and that, as a consequence, it can be used for the clinical classification of myeloma precursor diseases allowing for early intervention and prognostic determination. For newly diagnosed MM, the integration of information on the presence of chromothripsis has the potential to significantly enhance current risk prediction strategies and to better characterize patients with high-risk disease biology. In this article we summarize the genetic basis for MM and the role played by chromothripsis as a critical pathogenic factor active at early disease phases.
PMID: 33958284
ISSN: 1096-3634
CID: 4866742

Inflammation and infection in plasma cell disorders: how pathogens shape the fate of patients

Caro, Jessica; Braunstein, Marc; Williams, Louis; Bruno, Benedetto; Kaminetzky, David; Siegel, Ariel; Razzo, Beatrice; Alfandari, Serge; Morgan, Gareth J; Davies, Faith E; Boyle, Eileen M
The role of infection and chronic inflammation in plasma cell disorders (PCD) has been well-described. Despite not being a diagnostic criterion, infection is a common complication of most PCD and represents a significant cause of morbidity and mortality in this population. As immune-based therapeutic agents are being increasingly used in multiple myeloma, it is important to recognize their impact on the epidemiology of infections and to identify preventive measures to improve outcomes. This review outlines the multiple factors attributed to the high infectious risk in PCD (e.g. the underlying disease status, patient age and comorbidities, and myeloma-directed treatment), with the aim of highlighting future prophylactic and preventive strategies that could be implemented in the clinic. Beyond this, infection and pathogens as an entity are believed to also influence disease biology from initiation to response to treatment and progression through a complex interplay involving pathogen exposure, chronic inflammation, and immune response. This review will outline both the direct and indirect role played by oncogenic pathogens in PCD, highlight the requirement for large-scale studies to decipher the precise implication of the microbiome and direct pathogens in the natural history of myeloma and its precursor disease states, and understand how, in turn, pathogens shape plasma cell biology.
PMID: 35110727
ISSN: 1476-5551
CID: 5153682

Characterization of Second Primary Malignancies in Mucosa-Associated Lymphoid Tissue Lymphomas: A SEER Database Interrogation

Timilsina, Sunita; Damato, Aaron; Budhathoki, Nibash; Grossbard, Michael L; Braunstein, Marc
INTRODUCTION/BACKGROUND:Second primary malignancies (SPMs) are long-term complications in cancer survivors. Mucosa-associated lymphoid tissue (MALT) lymphomas are indolent extra-nodal marginal zone lymphomas, the majority of which typically have long-term survival. In this study, we investigated the incidence and pattern of SPMs in adult patients diagnosed with MALT lymphomas between January 2000 and December 2016. METHODS:Using the SEER-18 database and multiple primary standardized incidence ratio (MP-SIR) session of SEER stat software for statistical analysis, we assessed SPMs in MALT lymphomas. RESULTS:During this time, a total of 12,500 cases of MALT lymphomas were diagnosed, of which 1466 patients developed 1626 SPMs (O/E ratio: 1.48, 95% CI:1.41-1.55, P<.001). The median latency period for development of SPMs was 54 months (range 6-201 months). Secondary non-Hodgkin lymphomas, as defined by SEER as distinct from the primary lymphoma, was the most common SPM with 299 cases, followed by lung cancer (O/E ratio: 6.15, 95% CI:5.47-6.89, P<.0001). There were 898 SPMs that developed between 6- 59 months (O/E ratio: 1.47, 95% CI:1.37-1.57, P<.0001) and 728 after 60 months latency (O/E ratio: 1.5, 95% CI:1.39-1.61, P<.0001) after diagnosis of the primary MALT lymphomas. An increased incidence of both solid and hematologic cancers occurred in patients as early as 6 months after diagnosis of MALT lymphoma. CONCLUSION/CONCLUSIONS:These findings indicate that despite the indolent nature of most MALT lymphomas, there is an increased risk for SPMs warranting long-term follow up.
PMID: 34493476
ISSN: 2152-2669
CID: 5011962

Improving prognostic assignment in older adults with multiple myeloma using acquired genetic features, clonal hemopoiesis and telomere length

Boyle, Eileen M; Williams, Louis; Blaney, Patrick; Ashby, Cody; Bauer, Michael; Walker, Brian A; Ghamlouch, Hussein; Choi, Jinyoung; Perrial, Emeline; Wang, Yubao; Caro, Jessica; Stoeckle, James H; Arbini, Arnaldo; Kaminetzky, David; Braunstein, Marc; Bruno, Benedetto; Razzo, Beatrice; Diamond, Benjamin; Maclachlan, Kylee; Maura, Francesco; Landgren, Ola; Litke, Rachel; Fegan, Christopher D; Keats, Johnathan; Auclair, Daniel; Davies, Faith E; Morgan, Gareth J
PMID: 34148053
ISSN: 1476-5551
CID: 4918002

Racial disparities among patients with multiple myeloma enrolled in clinical trials [Meeting Abstract]

Nishat, N; Bari, T; Islam, S; Braunstein, M J
Background: Tremendous therapeutic progress has been made over the past decade in the field of multiple myeloma (MM). Although the incidence of MM is twice as high for black compared to white individuals, mortality rates remain higher for black patients (Marinac, et al. Blood Ca J 2020). In addition, black Americans are significantly less likely to participate in clinical trials in general (Hong, et al. Am J Prev Med 2021), leading to disproportionate enrollment in studies of novel agents. Various factors may account for these disparities, including access to clinical trials, clinician bias, and hesitancy to enroll in clinical trials among different patient populations. Furthermore, underrepresentation of racial groups within clinical trials impacts the generalizability of important findings from these studies. Here we characterized the racial representation of MM clinical trials.
Method(s): Randomized clinical trials focused on MM interventions published between 2012-2022 were included. We screened 431 publications during this period and characterized racial demographics as available in the literature. A twosided Cochran-Armitage Trend Test was used to assess if there was a linear trend in the percentage of black participants in clinical trials over time.
Result(s): Among 431 studies published over the past 10 years, 76 collected over past 5 years that included racial demographic details were included. Among the 38,830 participants, 87.5% were white, 4.8% were black, and 7.7% were other (reported as either Asian, mixed, or other). There was a significant trend toward increased enrollment comparing over time between 2018 to 2021 (2.1 to 7.0%, p < 0.001 for trend), however black individual remained largely underrepresented in all these studies.
Conclusion(s): While the number of black participating in randomized controlled trials involving MM patients over the past five years is significantly increasing, these studies included a disproportionate number of white participants, despite the incidence of MM being higher for black patients. Efforts are underway in the field to enhance enrollment of underrepresented populations, including a recent randomized study that included 19% black MM patients (Richardson, et al. New Eng J Med 2022). Our study was limited due to many trials not reporting details about racial demographics until relatively recently. Further investigations required to examine the reasons underlying racial disparities in MM trial recruitment and enrollment
ISSN: 1527-7755
CID: 5366892

A new decade: novel immunotherapies on the horizon for relapsed/refractory multiple myeloma

Braunstein, Marc; Weltz, Jonathan; Davies, Faith
INTRODUCTION/UNASSIGNED:: Survival in multiple myeloma (MM) has improved due to the ongoing revolution of therapeutic approaches. Nevertheless, many patients relapse, and additional novel approaches are required to prolong remissions and prevent disease progression. AREAS COVERED/UNASSIGNED:Considering the success of monoclonal antibodies (mAbs) against CD38 and SLAMF7 in relapsed/refractory MM (R/R MM), additional antigens expressed on malignant plasma cells are being investigated as treatment targets. Among these, many trials are focusing on B cell maturation antigen (BCMA), using either antibody-drug conjugates (ADCs), bispecific T cell engagers (TCE), or chimeric antigen receptor T cells (CAR-T). Other potential targets include the myeloma markers CD138, GPRC5D, FcRH5, the plasma cell differentiating factors APRIL, TACI and BAFF, and the immune checkpoint proteins CD47 and TIGIT. Additionally, novel immunomodulatory Cereblon E3 Ligase Modulators (CELMoDs) offer the potential to overcome resistance to conventional immunomodulatory agents. Based upon PubMed and abstract searches primarily from the past 4 years, here we review the data supporting novel immunotherapies for R/R MM. EXPERT OPINION/UNASSIGNED:: Overcoming disease resistance remains a challenge in R/R MM. Novel therapeutic approaches targeting MM antigens and/or enhancing immune cell function offer the potential to prolong survival and are actively being investigated in clinical trials.
PMID: 33769179
ISSN: 1747-4094
CID: 4823662