RT Journal Article
SR Electronic
T1 Expressed barcodes enable clonal characterization of chemotherapeutic responses in chronic lymphocytic leukemia
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 761981
DO 10.1101/761981
A1 Aziz Al’Khafaji
A1 Catherine Gutierrez
A1 Eric Brenner
A1 Russell Durrett
A1 Kaitlyn E. Johnson
A1 Wandi Zhang
A1 Shuqiang Li
A1 Kenneth J. Livak
A1 Donna Neuberg
A1 Amy Brock
A1 Catherine J. Wu
YR 2019
UL http://biorxiv.org/content/early/2019/09/08/761981.abstract
AB The remarkable evolutionary capacity of cancer is a major challenge to current therapeutic efforts. Fueling this evolution is its vast clonal heterogeneity and ability to adapt to diverse selective pressures. Although the genetic and transcriptional mechanisms underlying these responses have been independently evaluated, the ability to couple genetic alterations present within individual clones to their respective transcriptional or functional outputs has been lacking in the field. To this end, we developed a high-complexity expressed barcode library that integrates DNA barcoding with single-cell RNA sequencing through use of the CROP-seq sgRNA expression/capture system, and which is compatible with the COLBERT clonal isolation workflow for subsequent genomic and epigenomic characterization of specific clones of interest. We applied this approach to study chronic lymphocytic leukemia (CLL), a mature B cell malignancy notable for its genetic and transcriptomic heterogeneity and variable disease course. Here, we demonstrate the clonal composition and gene expression states of HG3, a CLL cell line harboring the common alteration del(13q), in response to front-line cytotoxic therapy of fludarabine and mafosfamide (an analog of the clinically used cyclophosphamide). Analysis of clonal abundance and clonally-resolved single-cell RNA sequencing revealed that only a small fraction of clones consistently survived therapy. These rare highly drug tolerant clones comprise 94% of the post-treatment population and share a stable, pre-existing gene expression state characterized by upregulation of CXCR4 and WNT signaling and a number of DNA damage and cell survival genes. Taken together, these data demonstrate at unprecedented resolution the diverse clonal characteristics and therapeutic responses of a heterogeneous cancer cell population. Further, this approach provides a template for the high-resolution study of thousands of clones and the respective gene expression states underlying their response to therapy.