Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Expressed barcodes enable clonal characterization of chemotherapeutic responses in chronic lymphocytic leukemia

Aziz Al’Khafaji, Catherine Gutierrez, Eric Brenner, Russell Durrett, Kaitlyn E. Johnson, Wandi Zhang, Shuqiang Li, Kenneth J. Livak, Donna Neuberg, Amy Brock, Catherine J. Wu
doi: https://doi.org/10.1101/761981
Aziz Al’Khafaji
1Institute of Cellular and Molecular Biology, University of Texas at Austin, TX, USA
2Biomedical Engineering, University of Texas at Austin, TX, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Catherine Gutierrez
3Harvard Medical School, Boston, MA, USA
4Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Eric Brenner
1Institute of Cellular and Molecular Biology, University of Texas at Austin, TX, USA
2Biomedical Engineering, University of Texas at Austin, TX, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Russell Durrett
1Institute of Cellular and Molecular Biology, University of Texas at Austin, TX, USA
2Biomedical Engineering, University of Texas at Austin, TX, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Kaitlyn E. Johnson
2Biomedical Engineering, University of Texas at Austin, TX, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Wandi Zhang
4Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Shuqiang Li
4Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
5Broad Institute of MIT and Harvard, Cambridge, MA, USA
6Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Kenneth J. Livak
4Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
6Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Donna Neuberg
7Department of Data Sciences, Dana Farber Cancer Institute, Boston, MA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Amy Brock
1Institute of Cellular and Molecular Biology, University of Texas at Austin, TX, USA
2Biomedical Engineering, University of Texas at Austin, TX, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: cwu@partners.org amy.brock@utexas.edu
Catherine J. Wu
3Harvard Medical School, Boston, MA, USA
4Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
5Broad Institute of MIT and Harvard, Cambridge, MA, USA
8Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: cwu@partners.org amy.brock@utexas.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

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.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted September 08, 2019.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Expressed barcodes enable clonal characterization of chemotherapeutic responses in chronic lymphocytic leukemia
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Expressed barcodes enable clonal characterization of chemotherapeutic responses in chronic lymphocytic leukemia
Aziz Al’Khafaji, Catherine Gutierrez, Eric Brenner, Russell Durrett, Kaitlyn E. Johnson, Wandi Zhang, Shuqiang Li, Kenneth J. Livak, Donna Neuberg, Amy Brock, Catherine J. Wu
bioRxiv 761981; doi: https://doi.org/10.1101/761981
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
Expressed barcodes enable clonal characterization of chemotherapeutic responses in chronic lymphocytic leukemia
Aziz Al’Khafaji, Catherine Gutierrez, Eric Brenner, Russell Durrett, Kaitlyn E. Johnson, Wandi Zhang, Shuqiang Li, Kenneth J. Livak, Donna Neuberg, Amy Brock, Catherine J. Wu
bioRxiv 761981; doi: https://doi.org/10.1101/761981

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Cancer Biology
Subject Areas
All Articles
  • Animal Behavior and Cognition (4382)
  • Biochemistry (9591)
  • Bioengineering (7090)
  • Bioinformatics (24857)
  • Biophysics (12600)
  • Cancer Biology (9956)
  • Cell Biology (14349)
  • Clinical Trials (138)
  • Developmental Biology (7948)
  • Ecology (12105)
  • Epidemiology (2067)
  • Evolutionary Biology (15988)
  • Genetics (10925)
  • Genomics (14738)
  • Immunology (9869)
  • Microbiology (23660)
  • Molecular Biology (9484)
  • Neuroscience (50860)
  • Paleontology (369)
  • Pathology (1539)
  • Pharmacology and Toxicology (2682)
  • Physiology (4013)
  • Plant Biology (8657)
  • Scientific Communication and Education (1508)
  • Synthetic Biology (2394)
  • Systems Biology (6433)
  • Zoology (1346)