Integrated single cell analysis reveals co-evolution of malignant B cells and the tumor microenvironment in transformed follicular lymphoma

Clémentine Sarkozy; Shaocheng Wu; Katsuyoshi Takata; Tomohiro Aoki; Susana Ben Neriah; Katy Milne; Talia Goodyear; Celia Strong; Tashi Rastogi; Daniel Lai; Laurie Helen Sehn; Pedro Farinha; Brad H. Nelson; Andrew P. Weng; David W. Scott; Jeffrey W. Craig; Christian Steidl; Andrew J. L. Roth

doi:10.1101/2022.11.17.516951

BioinformaticsbioRxivNov 17, 2022

Preprint

Integrated single cell analysis reveals co-evolution of malignant B cells and the tumor microenvironment in transformed follicular lymphoma

Clémentine Sarkozy iD, Shaocheng Wu iD, Katsuyoshi Takata iD, Tomohiro Aoki iD, Susana Ben Neriah, Katy Milne iD, Talia Goodyear iD, Celia Strong iD, Tashi Rastogi, Daniel Lai iD, Laurie Helen Sehn iD, Pedro Farinha iD, Brad H. Nelson iD, Andrew P. Weng iD, David W. Scott iD, Jeffrey W. Craig iD, Christian Steidl iD, Andrew J. L. Roth iD

Abstract

Follicular lymphoma (FL) is the most common indolent form of non-Hodgkin lymphoma. Histological transformation of FL to a more aggressive form of lymphoma occurs with a linear incidence of 2-3% per year and is associated with poor outcome. Divergent clonal evolution and an altered tumour microenvironment (TME) have both been implicated in the transformation process. However, the phenotypic consequences of this evolution and its implication in reshaping the TME remain unknown. To address this knowledge gap we performed single cell whole genome (scWGS) and single cell whole transcriptome sequencing (scWTS) of paired pre/post transformation samples of 11 FL patients. We further performed scWTS analysis of additional 11 FL samples from patients that had not undergone transformation within 7 years. Our comprehensive single cell analysis revealed the evolutionary dynamics of transformation at unprecedented resolution. Computational integration of scWGS and scWTS allowed us to identify gene programs upregulated and positively selected during evolution. Furthermore, our scWTS analysis revealed a shifting TME landscape, with an exhausted CD8 T cell signature emerging during transformation. Using multi-color immunofluorescence we transferred these findings to a novel TME based biomarker of transformation, subsequently validated in 2 independent cohorts of pretreatment FL samples. Taken together, our results provide a comprehensive view of the combined genomic and phenotypic evolution of malignant cells during transformation, and the shifting cross-talk between malignant cells and the TME. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC="FIGDIR/small/516951v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@92abf7org.highwire.dtl.DTLVardef@157f2c2org.highwire.dtl.DTLVardef@102a879org.highwire.dtl.DTLVardef@182daec_HPS_FORMAT_FIGEXP M_FIG C_FIG

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