Genome-wide screens uncover KDM2B as a modifier of protein binding to heparan sulfate

Ryan J Weiss; Philipp N Spahn; Austin W T Chiang; Qing Liu; Jing Li; Kristina M Hamill; Sandra Rother; Thomas M Clausen; Marten A Hoeksema; Bryce M Timm; Kamil Godula; Christopher K Glass; Yitzhak Tor; Philip L S M Gordts; Nathan E Lewis; Jeffrey D Esko

doi:10.1038/s41589-021-00776-9

Genome-wide screens uncover KDM2B as a modifier of protein binding to heparan sulfate

Nat Chem Biol. 2021 Jun;17(6):684-692. doi: 10.1038/s41589-021-00776-9. Epub 2021 Apr 12.

Authors

Ryan J Weiss^#¹, Philipp N Spahn^#², Austin W T Chiang², Qing Liu¹, Jing Li¹, Kristina M Hamill³, Sandra Rother¹, Thomas M Clausen^{1

4}, Marten A Hoeksema¹, Bryce M Timm³, Kamil Godula^{3

5}, Christopher K Glass^{1

6}, Yitzhak Tor^{3

5}, Philip L S M Gordts^{5

6}, Nathan E Lewis^{7

8}, Jeffrey D Esko^{9

10}

Affiliations

¹ Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
² Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
³ Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA.
⁴ Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Disease, Copenhagen University Hospital, Copenhagen, Denmark.
⁵ Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA, USA.
⁶ Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
⁷ Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA, USA. [email protected].
⁸ Department of Pediatrics, The Novo Nordisk Foundation Center for Biosustainability and Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA. [email protected].
⁹ Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA. [email protected].
¹⁰ Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA, USA. [email protected].

^# Contributed equally.

Abstract

Heparan sulfate (HS) proteoglycans bind extracellular proteins that participate in cell signaling, attachment and endocytosis. These interactions depend on the arrangement of sulfated sugars in the HS chains generated by well-characterized biosynthetic enzymes; however, the regulation of these enzymes is largely unknown. We conducted genome-wide CRISPR-Cas9 screens with a small-molecule ligand that binds to HS. Screening of A375 melanoma cells uncovered additional genes and pathways impacting HS formation. The top hit was the epigenetic factor KDM2B, a histone demethylase. KDM2B inactivation suppressed multiple HS sulfotransferases and upregulated the sulfatase SULF1. These changes differentially affected the interaction of HS-binding proteins. KDM2B-deficient cells displayed decreased growth rates, which was rescued by SULF1 inactivation. In addition, KDM2B deficiency altered the expression of many extracellular matrix genes. Thus, KDM2B controls proliferation of A375 cells through the regulation of HS structure and serves as a master regulator of the extracellular matrix.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Algorithms
CRISPR-Cas Systems
Cell Line, Tumor
Cell Proliferation / drug effects
Drug Discovery
Extracellular Matrix / genetics
F-Box Proteins / antagonists & inhibitors*
Genome-Wide Association Study*
Heparitin Sulfate / metabolism*
High-Throughput Screening Assays
Humans
Jumonji Domain-Containing Histone Demethylases / antagonists & inhibitors*
Protein Binding / genetics
RNA-Seq
Sulfotransferases / antagonists & inhibitors

Substances

F-Box Proteins
Heparitin Sulfate
Jumonji Domain-Containing Histone Demethylases
KDM2A protein, human
SULF1 protein, human
Sulfotransferases

Abstract

Publication types

MeSH terms

Substances

Grants and funding