Interface-guided phenotyping of coding variants in the transcription factor RUNX1.

CP: Genomics CP: Molecular biology Perturb-seq RNA-seq cancer coding variant interface protein-protein interaction single-cell transcription factor

Journal

Cell reports
ISSN: 2211-1247
Titre abrégé: Cell Rep
Pays: United States
ID NLM: 101573691

Informations de publication

Date de publication:
04 Jul 2024
Historique:
received: 08 12 2023
revised: 15 05 2024
accepted: 19 06 2024
medline: 5 7 2024
pubmed: 5 7 2024
entrez: 5 7 2024
Statut: aheadofprint

Résumé

Single-gene missense mutations remain challenging to interpret. Here, we deploy scalable functional screening by sequencing (SEUSS), a Perturb-seq method, to generate mutations at protein interfaces of RUNX1 and quantify their effect on activities of downstream cellular programs. We evaluate single-cell RNA profiles of 115 mutations in myelogenous leukemia cells and categorize them into three functionally distinct groups, wild-type (WT)-like, loss-of-function (LoF)-like, and hypomorphic, that we validate in orthogonal assays. LoF-like variants dominate the DNA-binding site and are recurrent in cancer; however, recurrence alone does not predict functional impact. Hypomorphic variants share characteristics with LoF-like but favor protein interactions, promoting gene expression indicative of nerve growth factor (NGF) response and cytokine recruitment of neutrophils. Accessible DNA near differentially expressed genes frequently contains RUNX1-binding motifs. Finally, we reclassify 16 variants of uncertain significance and train a classifier to predict 103 more. Our work demonstrates the potential of targeting protein interactions to better define the landscape of phenotypes reachable by missense mutations.

Identifiants

DOI: 10.1016/j.celrep.2024.114436 PMID: 38968069
pubmed: 38968069
pii: S2211-1247(24)00765-4
doi: 10.1016/j.celrep.2024.114436
pii:
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

114436

Informations de copyright

Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.

Déclaration de conflit d'intérêts

Declaration of interests P.M. is a scientific co-founder of Shape Therapeutics, Navega Therapeutics, Boundless Biosciences, and Engine Biosciences. The terms of these arrangements have been reviewed and approved by the University of California, San Diego in accordance with its conflict-of-interest policies.

Auteurs

Kivilcim Ozturk (K)

Division of Medical Genetics, Department of Medicine, University of California, San Diego, La Jolla, CA, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA.

Rebecca Panwala (R)

Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.

Jeanna Sheen (J)

School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.

Kyle Ford (K)

Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.

Nathan Jayne (N)

School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.

Andrew Portell (A)

Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.

Dong-Er Zhang (DE)

Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.

Stephan Hutter (S)

MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany.

Torsten Haferlach (T)

MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377 Munich, Germany.

Trey Ideker (T)

Division of Medical Genetics, Department of Medicine, University of California, San Diego, La Jolla, CA, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.

Prashant Mali (P)

Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA. Electronic address: pmali@ucsd.edu.

Hannah Carter (H)

Division of Medical Genetics, Department of Medicine, University of California, San Diego, La Jolla, CA, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA. Electronic address: hkcarter@health.ucsd.edu.

Classifications MeSH