scCNVseq Datasets Supporting Integrated Epigenetic and Transcriptional Single-Cell Analysis of t(11;14) Multiple Myeloma and Its BCL2 Dependency

The translocation t(11;14) occurs in 20% of multiple myeloma (MM) patients and results in the upregulation of CCND1. Nearly two-thirds of t(11;14) MM cells are BCL2 primed and highly responsive to the oral BCL2 inhibitor venetoclax. While it is evident that this unique sensitivity to venetoclax depends on the BH3-proapoptotic protein priming of BCL2, the biology underlying t(11;14) MM dependency on BCL2 is poorly defined. Importantly, the epigenetic regulation of t(11;14) transcriptomes and its impact on gene regulation and clinical response to venetoclax remains elusive. In this study, by integrating ATACseq and RNAseq at the single-cell level in primary MM samples, we have defined the epigenetic regulome and transcriptome associated with t(11;14) MM. A "B cell-like" epigenetic signature was enriched in t(11;14) MM, confirming its phylogeny link to B cell rather than plasma cell biology. Of note, a loss of a "B cell-like" epigenetic signature with a gain of canonical plasma cell transcription factors was observed at the time of resistance to venetoclax. In addition, MCL1 and BCL2L1 copy number gains and structural rearrangements were linked to venetoclax resistance in t(11;14) MM patients. To date, this is the first study in which both scATAC-seq and scRNA-seq analysis are integrated into primary MM cells to obtain a deeper resolution of the epigenetic regulome and transcriptome associated with t(11;14) MM biology and venetoclax resistance. Overall design: Single-cell DNA sequencing (scDNA-seq) Frozen cells were thawed at 37?°C, resuspended in RPMI 1640 medium (Gibco) and washed twice with cells being collected by centrifugation at 2000 rpm for 5?min. Viable CD138+ cells were counted and resuspended in a resuspension buffer at 1,000 cells per ul. Single-cell capture was then performed according to the manufacturer's protocol, using Single Cell Bead Kit (10x Genomics, PN-1000057) and Chromium Chip C (PN-1000022) and D (PN-1000042) with a target capture of 1,000 cells. Quality control and quantification were performed using a KAPA Library Quantification qPCR kit (Roche, Basel, Switzerland) on a BioRad qPCR instrument. DNA libraries were prepared using Single Cell DNA Library & Gel Bead Kit (10x Genomics, PN-1000040) and sequenced on an Illumina NextSeq 500 sequencer with a high-output v2.5 300 cycle sequencing kit as per the standard Illumina protocols. After sequencing, bcl data were converted to fastq data files using the Illumina BCL2FASTQ utility. Samples were processed with CellRanger DNA v1.0.0 and downstream analyses were performed as indicated below.