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ccr-22-3209_supplementary_spreadsheet_s1_suppds1.xlsx (199.43 kB)

Supplementary Spreadsheet S1 from Multiomic Mapping of Acquired Chromosome 1 Copy-Number and Structural Variants to Identify Therapeutic Vulnerabilities in Multiple Myeloma

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posted on 2023-10-02, 07:21 authored by Eileen M. Boyle, Patrick Blaney, James H. Stoeckle, Yubao Wang, Hussein Ghamlouch, Dylan Gagler, Marc Braunstein, Louis Williams, Avital Tenenbaum, Ariel Siegel, Xiaoyi Chen, Gaurav Varma, Jason Avigan, Alexander Li, Monica Jinsi, David Kaminetzsky, Arnaldo Arbini, Lydia Montes, Jill Corre, Even H. Rustad, Ola Landgren, Francesco Maura, Brian A. Walker, Michael Bauer, Benedetto Bruno, Aristotelis Tsirigos, Faith E. Davies, Gareth J. Morgan

Bayes Factor output between genetic variables Correlation analysis between deletion region, gain regions, and other genetic events

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Leukemia and Lymphoma Society (LLS)

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ARTICLE ABSTRACT

Chromosome 1 (chr1) copy-number abnormalities (CNA) and structural variants (SV) are frequent in newly diagnosed multiple myeloma (NDMM) and are associated with a heterogeneous impact on outcomes, the drivers of which are largely unknown. A multiomic approach comprising CRISPR, gene mapping of CNAs and SVs, methylation, expression, and mutational analysis was used to document the extent of chr1 molecular variants and their impact on pathway utilization. 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 are associated 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. 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.

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