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Tang X, Xue D, Zhang T, Nilsson-Payant BE, Carrau L, Duan X, Gordillo M, Tan AY, Qiu Y, Xiang J, Schwartz RE, tenOever BR, Evans T, Chen S. A multi-organoid platform identifies CIART as a key factor for SARS-CoV-2 infection. Nat Cell Biol 2023; 25:381-389. [PMID: 36918693 PMCID: PMC10014579 DOI: 10.1038/s41556-023-01095-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 01/25/2023] [Indexed: 03/16/2023]
Abstract
COVID-19 is a systemic disease involving multiple organs. We previously established a platform to derive organoids and cells from human pluripotent stem cells to model SARS-CoV-2 infection and perform drug screens1,2. This provided insight into cellular tropism and the host response, yet the molecular mechanisms regulating SARS-CoV-2 infection remain poorly defined. Here we systematically examined changes in transcript profiles caused by SARS-CoV-2 infection at different multiplicities of infection for lung airway organoids, lung alveolar organoids and cardiomyocytes, and identified several genes that are generally implicated in controlling SARS-CoV-2 infection, including CIART, the circadian-associated repressor of transcription. Lung airway organoids, lung alveolar organoids and cardiomyocytes derived from isogenic CIART-/- human pluripotent stem cells were significantly resistant to SARS-CoV-2 infection, independently of viral entry. Single-cell RNA-sequencing analysis further validated the decreased levels of SARS-CoV-2 infection in ciliated-like cells of lung airway organoids. CUT&RUN, ATAC-seq and RNA-sequencing analyses showed that CIART controls SARS-CoV-2 infection at least in part through the regulation of NR4A1, a gene also identified from the multi-organoid analysis. Finally, transcriptional profiling and pharmacological inhibition led to the discovery that the Retinoid X Receptor pathway regulates SARS-CoV-2 infection downstream of CIART and NR4A1. The multi-organoid platform identified the role of circadian-clock regulation in SARS-CoV-2 infection, which provides potential therapeutic targets for protection against COVID-19 across organ systems.
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Affiliation(s)
- Xuming Tang
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA
- Center for Genomic Health, Weill Cornell Medicine, New York, NY, USA
| | - Dongxiang Xue
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA
- Center for Genomic Health, Weill Cornell Medicine, New York, NY, USA
| | - Tuo Zhang
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Benjamin E Nilsson-Payant
- Department of Microbiology, New York University, New York, NY, USA
- TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Lucia Carrau
- Department of Microbiology, New York University, New York, NY, USA
| | - Xiaohua Duan
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA
- Center for Genomic Health, Weill Cornell Medicine, New York, NY, USA
| | - Miriam Gordillo
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA
- Center for Genomic Health, Weill Cornell Medicine, New York, NY, USA
| | - Adrian Y Tan
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Yunping Qiu
- Stable Isotope and Metabolomics Core Facility, The Einstein-Mount Sinai Diabetes Research Center, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Jenny Xiang
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Robert E Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | | | - Todd Evans
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA
- Center for Genomic Health, Weill Cornell Medicine, New York, NY, USA
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA.
- Center for Genomic Health, Weill Cornell Medicine, New York, NY, USA.
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Tang R, Shuldiner EG, Kelly M, Murray CW, Hebert JD, Andrejka L, Tsai MK, Hughes NW, Parker MI, Cai H, Li YC, Wahl GM, Dunbrack RL, Jackson PK, Petrov DA, Winslow MM. Multiplexed screens identify RAS paralogues HRAS and NRAS as suppressors of KRAS-driven lung cancer growth. Nat Cell Biol 2023; 25:159-169. [PMID: 36635501 PMCID: PMC10521195 DOI: 10.1038/s41556-022-01049-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/09/2022] [Indexed: 01/13/2023]
Abstract
Oncogenic KRAS mutations occur in approximately 30% of lung adenocarcinoma. Despite several decades of effort, oncogenic KRAS-driven lung cancer remains difficult to treat, and our understanding of the regulators of RAS signalling is incomplete. Here to uncover the impact of diverse KRAS-interacting proteins on lung cancer growth, we combined multiplexed somatic CRISPR/Cas9-based genome editing in genetically engineered mouse models with tumour barcoding and high-throughput barcode sequencing. Through a series of CRISPR/Cas9 screens in autochthonous lung cancer models, we show that HRAS and NRAS are suppressors of KRASG12D-driven tumour growth in vivo and confirm these effects in oncogenic KRAS-driven human lung cancer cell lines. Mechanistically, RAS paralogues interact with oncogenic KRAS, suppress KRAS-KRAS interactions, and reduce downstream ERK signalling. Furthermore, HRAS and NRAS mutations identified in oncogenic KRAS-driven human tumours partially abolished this effect. By comparing the tumour-suppressive effects of HRAS and NRAS in oncogenic KRAS- and oncogenic BRAF-driven lung cancer models, we confirm that RAS paralogues are specific suppressors of KRAS-driven lung cancer in vivo. Our study outlines a technological avenue to uncover positive and negative regulators of oncogenic KRAS-driven cancer in a multiplexed manner in vivo and highlights the role RAS paralogue imbalance in oncogenic KRAS-driven lung cancer.
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Affiliation(s)
- Rui Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Marcus Kelly
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
- Baxter Laboratories, Stanford University School of Medicine, Stanford, CA, USA
| | - Christopher W Murray
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Jess D Hebert
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Laura Andrejka
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Min K Tsai
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicholas W Hughes
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Mitchell I Parker
- Molecular Therapeutics Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA
- Molecular and Cell Biology and Genetics Program, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Hongchen Cai
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Yao-Cheng Li
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Geoffrey M Wahl
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Roland L Dunbrack
- Molecular Therapeutics Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Peter K Jackson
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
- Baxter Laboratories, Stanford University School of Medicine, Stanford, CA, USA
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, CA, USA
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
- The Chan Zuckerberg BioHub, San Francisco, CA, USA
| | - Monte M Winslow
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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3
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Xia Y, Wang X, Liu Y, Shapiro E, Lepor H, Tang MS, Sun TT, Wu XR. PKM2 Is Essential for Bladder Cancer Growth and Maintenance. Cancer Res 2022; 82:571-585. [PMID: 34903602 PMCID: PMC8857058 DOI: 10.1158/0008-5472.can-21-0403] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 08/30/2021] [Accepted: 12/02/2021] [Indexed: 11/16/2022]
Abstract
Pyruvate kinase M2 (PKM2) has been shown to promote tumorigenesis by facilitating the Warburg effect and enhancing the activities of oncoproteins. However, this paradigm has recently been challenged by studies in which the absence of PKM2 failed to inhibit and instead accelerated tumorigenesis in mouse models. These results seem inconsistent with the fact that most human tumors overexpress PKM2. To further elucidate the role of PKM2 in tumorigenesis, we investigated the effect of PKM2 knockout in oncogenic HRAS-driven urothelial carcinoma. While PKM2 ablation in mouse urothelial cells did not affect tumor initiation, it impaired the growth and maintenance of HRAS-driven tumors. Chemical inhibition of PKM2 recapitulated these effects. Both conditions substantially reduced complex formation of PKM2 with STAT3, their nuclear translocation, and HIF1α- and VEGF-related angiogenesis. The reduction in nuclear STAT3 in the absence of PKM2 also correlated with decreased autophagy and increased apoptosis. Time-controlled, inducible PKM2 overexpression in simple urothelial hyperplasia did not trigger tumorigenesis, while overexpression of PKM2, but not PKM1, in nodular urothelial hyperplasia with angiogenesis strongly accelerated tumorigenesis. Finally, in human patients, PKM2 was overexpressed in low-grade nonmuscle-invasive and high-grade muscle-invasive bladder cancer. Based on these data, PKM2 is not required for tumor initiation but is essential for tumor growth and maintenance by enhancing angiogenesis and metabolic addiction. The PKM2-STAT3-HIF1α/VEGF signaling axis may play a critical role in bladder cancer and may serve as an actionable therapeutic target. SIGNIFICANCE Genetic manipulation and pharmacologic inhibition of PKM2 in mouse urothelial lesions highlight its essential role in promoting angiogenesis and metabolic addiction, events indispensable for tumor growth and maintenance.
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MESH Headings
- Active Transport, Cell Nucleus/genetics
- Animals
- Apoptosis/genetics
- Autophagy/genetics
- Carcinogenesis/genetics
- Carcinoma, Transitional Cell/blood supply
- Carcinoma, Transitional Cell/genetics
- Carcinoma, Transitional Cell/metabolism
- Cell Line, Tumor
- Cell Proliferation/genetics
- Gene Expression Regulation, Neoplastic
- Humans
- Hypoxia-Inducible Factor 1, alpha Subunit/genetics
- Hypoxia-Inducible Factor 1, alpha Subunit/metabolism
- Male
- Mice, Knockout
- Mice, Transgenic
- Neovascularization, Pathologic/genetics
- Neovascularization, Pathologic/metabolism
- Proto-Oncogene Proteins p21(ras)/genetics
- Proto-Oncogene Proteins p21(ras)/metabolism
- Pyruvate Kinase/genetics
- Pyruvate Kinase/metabolism
- STAT3 Transcription Factor/genetics
- STAT3 Transcription Factor/metabolism
- Urinary Bladder Neoplasms/genetics
- Urinary Bladder Neoplasms/metabolism
- Urinary Bladder Neoplasms/pathology
- Vascular Endothelial Growth Factor A/genetics
- Vascular Endothelial Growth Factor A/metabolism
- Mice
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Affiliation(s)
- Yong Xia
- Department of Urology, New York University School of Medicine, New York, NY 10016
| | - Xing Wang
- Department of Urology, New York University School of Medicine, New York, NY 10016
- Veterans Affairs New York Harbor Healthcare System, Manhattan Campus, New York, NY 10010
| | - Yan Liu
- Department of Urology, New York University School of Medicine, New York, NY 10016
- Veterans Affairs New York Harbor Healthcare System, Manhattan Campus, New York, NY 10010
| | - Ellen Shapiro
- Department of Urology, New York University School of Medicine, New York, NY 10016
| | - Herbert Lepor
- Department of Urology, New York University School of Medicine, New York, NY 10016
| | - Moon-shong Tang
- Department of Environmental Medicine, New York University School of Medicine, New York, NY 10016
| | - Tung-Tien Sun
- Department of Urology, New York University School of Medicine, New York, NY 10016
- Department of Cell Biology, New York University School of Medicine, New York, NY 10016
| | - Xue-Ru Wu
- Department of Urology, New York University School of Medicine, New York, NY 10016
- Department of Pathology, New York University School of Medicine, New York, NY 10016
- Veterans Affairs New York Harbor Healthcare System, Manhattan Campus, New York, NY 10010
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Abstract
The three RAS genes - HRAS, NRAS and KRAS - are collectively mutated in one-third of human cancers, where they act as prototypic oncogenes. Interestingly, there are rather distinct patterns to RAS mutations; the isoform mutated as well as the position and type of substitution vary between different cancers. As RAS genes are among the earliest, if not the first, genes mutated in a variety of cancers, understanding how these mutation patterns arise could inform on not only how cancer begins but also the factors influencing this event, which has implications for cancer prevention. To this end, we suggest that there is a narrow window or 'sweet spot' by which oncogenic RAS signalling can promote tumour initiation in normal cells. As a consequence, RAS mutation patterns in each normal cell are a product of the specific RAS isoform mutated, as well as the position of the mutation and type of substitution to achieve an ideal level of signalling.
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Affiliation(s)
- Siqi Li
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
| | - Allan Balmain
- Helen Diller Family Comprehensive Cancer Center and Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Christopher M Counter
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA.
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