CRISPRi/a screens in human iPSC-cardiomyocytes identify glycolytic activation as a druggable target for doxorubicin-induced cardiotoxicity

Chun Liu¹, Mengcheng Shen², Yanxia Liu³, Amit Manhas², Shane Rui Zhao², Mao Zhang², Nadjet Belbachir², Lu Ren², Joe Z Zhang², Arianne Caudal², Masataka Nishiga², Dilip Thomas², Angela Zhang⁴, Huaxiao Yang⁵, Yang Zhou², Mohamed Ameen², Nazish Sayed⁶, June-Wha Rhee⁷, Lei S Qi⁸, Joseph C Wu⁹

Affiliations

¹ Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA; Department of Physiology and Cancer Center, Milwaukee, WI, USA; Department of Medicine and Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, USA. Electronic address: chunliu@mcw.edu.
² Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA, USA; Department of Medicine (Division of Cardiology), Stanford, CA, USA.
³ Department of Bioengineering, Stanford, CA, USA; Sarafan ChEM-H, Stanford University, Stanford, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
⁴ Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA; Greentstone Biosciences, Palo Alto, CA, USA.
⁵ Department of Biomedical Engineering, University of North Texas, Denton, TX, USA.
⁶ Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA; Department of Medicine (Division of Cardiology), Stanford, CA, USA; Department of Surgery, Division of Vascular Surgery, Stanford University, Stanford, CA, USA.
⁷ Department of Medicine, City of Hope Comprehensive Cancer Center, Duarte, CA, USA.
⁸ Department of Bioengineering, Stanford, CA, USA; Sarafan ChEM-H, Stanford University, Stanford, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA. Electronic address: slqi@stanford.edu.
⁹ Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA, USA; Department of Medicine (Division of Cardiology), Stanford, CA, USA. Electronic address: joewu@stanford.edu.

PMID: 39515331
PMCID: PMC11646563 (available on 2025-12-05)
DOI: 10.1016/j.stem.2024.10.007

CRISPRi/a screens in human iPSC-cardiomyocytes identify glycolytic activation as a druggable target for doxorubicin-induced cardiotoxicity

Chun Liu et al. Cell Stem Cell. 2024.

. 2024 Dec 5;31(12):1760-1776.e9.

doi: 10.1016/j.stem.2024.10.007. Epub 2024 Nov 7.

Authors

Affiliations

¹ Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA; Department of Physiology and Cancer Center, Milwaukee, WI, USA; Department of Medicine and Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, USA. Electronic address: chunliu@mcw.edu.
² Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA, USA; Department of Medicine (Division of Cardiology), Stanford, CA, USA.
³ Department of Bioengineering, Stanford, CA, USA; Sarafan ChEM-H, Stanford University, Stanford, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
⁴ Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA; Greentstone Biosciences, Palo Alto, CA, USA.
⁵ Department of Biomedical Engineering, University of North Texas, Denton, TX, USA.
⁶ Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA; Department of Medicine (Division of Cardiology), Stanford, CA, USA; Department of Surgery, Division of Vascular Surgery, Stanford University, Stanford, CA, USA.
⁷ Department of Medicine, City of Hope Comprehensive Cancer Center, Duarte, CA, USA.
⁸ Department of Bioengineering, Stanford, CA, USA; Sarafan ChEM-H, Stanford University, Stanford, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA. Electronic address: slqi@stanford.edu.
⁹ Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA, USA; Department of Medicine (Division of Cardiology), Stanford, CA, USA. Electronic address: joewu@stanford.edu.

PMID: 39515331
PMCID: PMC11646563 (available on 2025-12-05)
DOI: 10.1016/j.stem.2024.10.007

Abstract

Doxorubicin is limited in its therapeutic utility due to its life-threatening cardiovascular side effects. Here, we present an integrated drug discovery pipeline combining human induced pluripotent stem cell (iPSC)-derived cardiomyocytes (iCMs), CRISPR interference and activation (CRISPRi/a) bidirectional pooled screens, and a small-molecule screening to identify therapeutic targets mitigating doxorubicin-induced cardiotoxicity (DIC) without compromising its oncological effects. The screens revealed several previously unreported candidate genes contributing to DIC, including carbonic anhydrase 12 (CA12). Genetic inhibition of CA12 protected iCMs against DIC by improving cell survival, sarcomere structural integrity, contractile function, and calcium handling. Indisulam, a CA12 antagonist, can effectively attenuate DIC in iCMs, engineered heart tissue, and animal models. Mechanistically, doxorubicin-induced CA12 potentiated a glycolytic activation in cardiomyocytes, contributing to DIC by interfering with cellular metabolism and functions. Collectively, our study provides a roadmap for future drug discovery efforts, potentially leading to more targeted therapies with minimal off-target toxicity.

Keywords: CRISPR screen; carbonic anhydrase; cardio-oncology; cardiomyoctye; doxorubicin; glycolysis; iPSC.

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Conflict of interest statement

Declaration of interests L.S.Q. is a founder and scientific advisory board member of Epic Bio, and a scientific advisory board member of Laboratory of Genomics Research and Kytopen Corp. J.C.W. is a co-founder and scientific advisory board member of Greenstone Biosciences.

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CRISPRi/a screens in human iPSC-cardiomyocytes identify glycolytic activation as a druggable target for doxorubicin-induced cardiotoxicity

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CRISPRi/a screens in human iPSC-cardiomyocytes identify glycolytic activation as a druggable target for doxorubicin-induced cardiotoxicity

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Abstract

Conflict of interest statement

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