1
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Sharma P, Kim CY, Keys HR, Imada S, Joseph AB, Ferro L, Kunchok T, Anderson R, Sun Y, Yilmaz ÖH, Weng JK, Jain A. Genetically encoded fluorescent reporter for polyamines. Nat Commun 2025; 16:4921. [PMID: 40425580 PMCID: PMC12117157 DOI: 10.1038/s41467-025-60147-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2024] [Accepted: 05/16/2025] [Indexed: 05/29/2025] Open
Abstract
Polyamines are abundant and evolutionarily conserved metabolites that are essential for life. Dietary polyamine supplementation extends life-span and health-span. Dysregulation of polyamine homeostasis is linked to Parkinson's disease and cancer, driving interest in therapeutically targeting this pathway. However, measuring cellular polyamine levels, which vary across cell types and states, remains challenging. We introduce a genetically encoded polyamine reporter for real-time measurement of polyamine concentrations in single living cells. This reporter utilizes the polyamine-responsive ribosomal frameshift motif from the OAZ1 gene. We demonstrate broad applicability of this approach and reveal dynamic changes in polyamine levels in response to genetic and pharmacological perturbations. Using this reporter, we conduct a genome-wide CRISPR screen and uncover an unexpected link between mitochondrial respiration and polyamine import, which are both risk factors for Parkinson's disease. By offering a lens to examine polyamine biology, this reporter may advance our understanding of these ubiquitous metabolites and accelerate therapy development.
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Affiliation(s)
- Pushkal Sharma
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Colin Y Kim
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Heather R Keys
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Shinya Imada
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA
| | - Alex B Joseph
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Luke Ferro
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Tenzin Kunchok
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Rachel Anderson
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yulin Sun
- Institute for Plant-Human Interface, Northeastern University, Boston, MA, USA
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Department of Chemical Engineering, Northeastern University, Boston, MA, USA
| | - Ömer H Yilmaz
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Institute for Plant-Human Interface, Northeastern University, Boston, MA, USA
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Department of Chemical Engineering, Northeastern University, Boston, MA, USA
| | - Ankur Jain
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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2
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Wang Z, Yu H, Gu Z, Shi X, Ma J, Shao Q, Yao Y, Yao S, Xu Y, Gu Y, Dai J, Liu Q, Shi J, Qi R, Jin Y, Liu Y, Shen X, Huang W, Liu HJ, Jin M, Liu W, Brook M, Chen D. RNA-binding proteins DND1 and NANOS3 cooperatively suppress the entry of germ cell lineage. Nat Commun 2025; 16:4792. [PMID: 40410171 PMCID: PMC12102168 DOI: 10.1038/s41467-025-57490-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Accepted: 02/24/2025] [Indexed: 05/25/2025] Open
Abstract
Specification of primordial germ cells (PGCs) establishes germline development during early embryogenesis, yet the underlying mechanisms in humans remain largely unknown. Here, we reveal the functional roles of germline-specific RNA-binding protein (RBP) DND1 in human PGC (hPGC) specification. We discovered that DND1 forms a complex with another RBP, NANOS3, to restrict hPGC specification. Furthermore, by analyzing the mRNAs bound by DND1 and NANOS3, we found that DND1 facilitates the binding of NANOS3 to hPGC-like cells-related mRNAs. We identified SOX4 mRNAs as the key downstream factor for the DND1 and NANOS3 complex. Mechanistically, DND1 and NANOS3 function in processing bodies (P-bodies) to repress the translation of SOX4 mRNAs, with NANOS3 mediating the interaction between DND1 and the translational repressor 4E-T. Altogether, these findings identify the RBP complex formed by DND1 and NANOS3 functioning as a "braking system" to restrict the entry of germ cell fate in humans.
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Affiliation(s)
- Ziqi Wang
- Center for Reproductive Medicine of The Second Affiliated Hospital, Center for Regeneration and Cell Therapy of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang, China
| | - Honglin Yu
- Center for Reproductive Medicine of The Second Affiliated Hospital, Center for Regeneration and Cell Therapy of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang, China
- Edinburgh Medical School: Biomedical Sciences, College of Medicine and Veterinary Medicine, The University of Edinburgh, Edinburgh, UK
| | - Zhaoyu Gu
- Center for Reproductive Medicine of The Second Affiliated Hospital, Center for Regeneration and Cell Therapy of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang, China
| | - Xiaohui Shi
- Center for Reproductive Medicine of The Second Affiliated Hospital, Center for Regeneration and Cell Therapy of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang, China
| | - Jiayue Ma
- Center for Reproductive Medicine of The Second Affiliated Hospital, Center for Regeneration and Cell Therapy of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang, China
| | - Qizhe Shao
- Center for Reproductive Medicine of The Second Affiliated Hospital, Center for Regeneration and Cell Therapy of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang, China
| | - Yao Yao
- Center for Reproductive Medicine of The Second Affiliated Hospital, Center for Regeneration and Cell Therapy of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang, China
| | - Shuo Yao
- Center for Reproductive Medicine of The Second Affiliated Hospital, Center for Regeneration and Cell Therapy of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang, China
| | - Yan Xu
- Center for Reproductive Medicine of The Second Affiliated Hospital, Center for Regeneration and Cell Therapy of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang, China
| | - Yashi Gu
- Center for Reproductive Medicine of The Second Affiliated Hospital, Center for Regeneration and Cell Therapy of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang, China
- Edinburgh Medical School: Biomedical Sciences, College of Medicine and Veterinary Medicine, The University of Edinburgh, Edinburgh, UK
| | - Jiayue Dai
- Center for Reproductive Medicine of The Second Affiliated Hospital, Center for Regeneration and Cell Therapy of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang, China
- Edinburgh Medical School: Biomedical Sciences, College of Medicine and Veterinary Medicine, The University of Edinburgh, Edinburgh, UK
| | - Qi Liu
- Center for Reproductive Medicine of The Second Affiliated Hospital, Center for Regeneration and Cell Therapy of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang, China
| | - Jingyan Shi
- Center for Reproductive Medicine of The Second Affiliated Hospital, Center for Regeneration and Cell Therapy of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang, China
| | - Rujie Qi
- Center for Reproductive Medicine of The Second Affiliated Hospital, Center for Regeneration and Cell Therapy of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang, China
| | - Yue Jin
- Edinburgh Medical School: Biomedical Sciences, College of Medicine and Veterinary Medicine, The University of Edinburgh, Edinburgh, UK
- Center for Infection Immunity and Cancer, Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang, China
| | - Yuqian Liu
- Edinburgh Medical School: Biomedical Sciences, College of Medicine and Veterinary Medicine, The University of Edinburgh, Edinburgh, UK
- Center for Infection Immunity and Cancer, Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang, China
| | - Xinchen Shen
- Center for Reproductive Medicine of The Second Affiliated Hospital, Center for Regeneration and Cell Therapy of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang, China
| | - Wenwen Huang
- Center for Reproductive Medicine of The Second Affiliated Hospital, Center for Regeneration and Cell Therapy of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang, China
| | - Heng-Jia Liu
- Edinburgh Medical School: Biomedical Sciences, College of Medicine and Veterinary Medicine, The University of Edinburgh, Edinburgh, UK
- Center for Infection Immunity and Cancer, Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang, China
| | - Min Jin
- Center for Reproductive Medicine of The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Wanlu Liu
- Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Center of Biomedical Systems and Informatics of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), International Campus, Zhejiang University, Haining, Zhejiang, China
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, China
- Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Zhejiang University, Hangzhou, Zhejiang, China
| | - Matthew Brook
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, Scotland, UK.
| | - Di Chen
- Center for Reproductive Medicine of The Second Affiliated Hospital, Center for Regeneration and Cell Therapy of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang, China.
- Edinburgh Medical School: Biomedical Sciences, College of Medicine and Veterinary Medicine, The University of Edinburgh, Edinburgh, UK.
- State Key Laboratory of Biobased Transportation Fuel Technology, Haining, Zhejiang, China.
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
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3
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Teng H, Hang Q, Zheng C, Yan Y, Liu S, Zhao Y, Deng Y, Nie L, Wu W, Sheldon M, Yu Z, Shi W, Gao J, Meng C, Martinez C, Zhang J, Yao F, Sun Y, Zhao D, Gan B, Meng T, Ma L. In vivo CRISPR activation screen identifies acyl-CoA-binding protein as a driver of bone metastasis. Sci Transl Med 2025; 17:eado7225. [PMID: 40397713 DOI: 10.1126/scitranslmed.ado7225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 12/03/2024] [Accepted: 04/29/2025] [Indexed: 05/23/2025]
Abstract
One of the most common sites of cancer metastasis is to the bone. Bone metastasis is associated with substantial morbidity and mortality, and current therapeutic interventions remain largely palliative. Metastasizing tumor cells need to reprogram their metabolic states to adapt to the nutrient environment of distant organs; however, the role and translational relevance of lipid metabolism in bone metastasis remain unclear. Here, we used an in vivo CRISPR activation screening system coupled with positive selection to identify acyl-coenzyme A (CoA) binding protein (ACBP) as a bone metastasis driver. In nonmetastatic and weakly metastatic cancer cells, overexpression of wild-type ACBP, but not the acyl-CoA-binding deficient mutant, stimulated fatty acid oxidation (FAO) and bone metastasis. Conversely, knockout of ACBP in highly bone metastatic cancer cells abrogated metastatic bone colonization. Mechanistically, ACBP-mediated FAO increased ATP and NADPH production, reduced reactive oxygen species, and inhibited lipid peroxidation and ferroptosis. We found that ACBP expression correlated with metabolic signaling, bone metastatic ability, and poor clinical outcomes. In mouse models, pharmacological blockade of FAO or treatment with a ferroptosis inducer inhibited bone metastasis. Together, our findings reveal the role of lipid metabolism in tumor cells adapting and thriving in the bone and identify ACBP as a key regulator of this process. Agents that target FAO or induce ferroptosis represent a promising therapeutic approach for treating bone metastases.
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Affiliation(s)
- Hongqi Teng
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Qinglei Hang
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Caishang Zheng
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yuelong Yan
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shaomin Liu
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yang Zhao
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yalan Deng
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Litong Nie
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Weiche Wu
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Marisela Sheldon
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zachary Yu
- Department of Chemistry, Rice University, Houston, TX 77005, USA
| | - Wei Shi
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianxuan Gao
- Department of Orthopedics, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200080, China
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200080, China
| | - Chenling Meng
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Consuelo Martinez
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jie Zhang
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Fan Yao
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yutong Sun
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Di Zhao
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Boyi Gan
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Tong Meng
- Department of Orthopedics, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200080, China
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200080, China
| | - Li Ma
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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4
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Zolboot N, Xiao Y, Du JX, Ghanem MM, Choi SY, Junn MJ, Zampa F, Huang Z, MacRae IJ, Lippi G. MicroRNA mechanisms instructing Purkinje cell specification. Neuron 2025; 113:1629-1646.e15. [PMID: 40179877 DOI: 10.1016/j.neuron.2025.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Revised: 01/22/2025] [Accepted: 03/04/2025] [Indexed: 04/05/2025]
Abstract
MicroRNAs (miRNAs) are critical for brain development; however, if, when, and how miRNAs drive neuronal subtype specification remains poorly understood. To address this, we engineered technologies with vastly improved spatiotemporal resolution that allow the dissection of cell-type-specific miRNA-target networks. Fast and reversible miRNA loss of function showed that miRNAs are necessary for Purkinje cell (PC) differentiation, which previously appeared to be miRNA independent, and identified distinct critical miRNA windows for dendritogenesis and climbing fiber synaptogenesis, structural features defining PC identity. Using new mouse models that enable miRNA-target network mapping in rare cell types, we uncovered PC-specific post-transcriptional programs. Manipulation of these programs revealed that the PC-enriched miR-206 and targets Shank3, Prag1, En2, and Vash1, which are uniquely repressed in PCs, are critical regulators of PC-specific dendritogenesis and synaptogenesis, with miR-206 knockdown and target overexpression partially phenocopying miRNA loss of function. Our results suggest that gene expression regulation by miRNAs, beyond transcription, is critical for neuronal subtype specification.
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Affiliation(s)
- Norjin Zolboot
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yao Xiao
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jessica X Du
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Marwan M Ghanem
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Su Yeun Choi
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Miranda J Junn
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Federico Zampa
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Zeyi Huang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian J MacRae
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Giordano Lippi
- Department of Neuroscience, The Scripps Research Institute, La Jolla, CA 92037, USA.
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5
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Naara S, Cui Z, Izgutdina A, VanLandingham NK, Nazarenko A, Woerner LC, Hua Fu BX, Gilbert LA, Johnson DE, Grandis JR. Neddylation as a target in PIK3CA-mutated head and neck cancer. Biochem Biophys Res Commun 2025; 759:151703. [PMID: 40154000 PMCID: PMC12036330 DOI: 10.1016/j.bbrc.2025.151703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2025] [Revised: 03/22/2025] [Accepted: 03/24/2025] [Indexed: 04/01/2025]
Abstract
PIK3CA encodes the catalytic subunit of phosphoinositide 3-kinase (PI3K) enzyme and is the most commonly mutated oncogene in head and neck squamous cell carcinoma (HNSCC). This study aimed to identify potential therapeutic targets in HNSCC harboring mutant PIK3CA. We used CRISPR interference (CRISPRi)-based genome-wide screening methodology to reveal targetable genetic dependencies in PIK3CA-mutated HNSCC. Screening was conducted in an HPV-positive HNSCC cell line, UM-SCC-47, engineered to express the canonical E545K PIK3CA mutant. We identified 34 genes co-dependent on PIK3CA E545K mutation, including 5 genes in the neddylation pathway (NEDD8, NEDD8-MDP-1 and NAE1, USP8, UBA3). Validation experiments confirmed the essential role of NEDD8, NEDD8-MDP-1, and NAE1, indicating a novel regulatory mechanism in PIK3CA E545K-mutated HNSCC. Our findings suggest that PIK3CA mutation may serve as a predictive biomarker for neddylation inhibitor therapy in a subpopulation of HNSCC.
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Affiliation(s)
- Shorook Naara
- Department of Otolaryngology-Head and Neck Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Zhibin Cui
- Department of Otolaryngology-Head and Neck Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Adila Izgutdina
- Department of Otolaryngology-Head and Neck Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Nathan K VanLandingham
- Department of Otolaryngology-Head and Neck Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Andrew Nazarenko
- Department of Otolaryngology-Head and Neck Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Liam C Woerner
- Department of Otolaryngology-Head and Neck Surgery, University of California San Francisco, San Francisco, CA, USA
| | | | - Luke A Gilbert
- Arc Institute, 3181 Porter Drive, Palo Alto, CA, 94304, USA; University of California, San Francisco, Helen Diller Family Comprehensive Cancer Center, 13 CA, San Francisco, USA; Department of Urology, University of California San Francisco, San Francisco, CA, USA; Innovative Genomics Institute, University of California-Berkeley, Berkeley, CA, USA
| | - Daniel E Johnson
- Department of Otolaryngology-Head and Neck Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Jennifer R Grandis
- Department of Otolaryngology-Head and Neck Surgery, University of California San Francisco, San Francisco, CA, USA.
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6
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Gu S, Bodai Z, Anderson RA, So HYA, Cowan QT, Komor AC. Elucidating the genetic mechanisms governing cytosine base editing outcomes through CRISPRi screens. Nat Commun 2025; 16:4685. [PMID: 40394064 DOI: 10.1038/s41467-025-59948-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/09/2025] [Indexed: 05/22/2025] Open
Abstract
Cytosine base editors enable programmable and efficient genome editing using an intermediate featuring a U•G mismatch across from a DNA nick. This intermediate facilitates two major outcomes, C•G to T•A and C•G to G•C point mutations, and it is not currently well-understood which DNA repair factors are involved. Here, we couple reporters for cytosine base editing activity with knockdown of 2015 DNA processing genes to identify genes involved in these two outcomes. Our data suggest that mismatch repair factors facilitate C•G to T•A outcomes, while C•G to G•C outcomes are mediated by RFWD3, an E3 ubiquitin ligase. We also propose that XPF, a 3'-flap endonuclease, and LIG3, a DNA ligase, are involved in repairing the intermediate back to the original C•G base pair. Our results demonstrate that competition and collaboration among different DNA repair pathways shape cytosine base editing outcomes.
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Affiliation(s)
- Sifeng Gu
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA
| | - Zsolt Bodai
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA
| | - Rachel A Anderson
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA
| | - Hei Yu Annika So
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA
| | - Quinn T Cowan
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA.
- Moores UCSD Cancer Center, University of California, San Diego, CA, USA.
- Sanford Stem Cell Institute, University of California, San Diego, CA, USA.
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7
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Akers JF, LaScola M, Bothe A, Suh H, Jung C, Stolp ZD, Ghosh T, Yan LL, Wang Y, Macurak M, Devan A, McKinney MC, Grismer TS, Reyes AV, Ross EJ, Hu T, Xu SL, Ban N, Kostova KK. ZNF574 is a quality control factor for defective ribosome biogenesis intermediates. Mol Cell 2025; 85:2048-2060.e9. [PMID: 40328246 PMCID: PMC12101526 DOI: 10.1016/j.molcel.2025.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2024] [Revised: 03/08/2025] [Accepted: 04/15/2025] [Indexed: 05/08/2025]
Abstract
Eukaryotic ribosome assembly is an intricate process that involves four ribosomal RNAs, 80 ribosomal proteins, and over 200 biogenesis factors that participate in numerous interdependent steps. The complexity and essentiality of this process create opportunities for deleterious mutations to occur, accumulate, and impact downstream cellular processes. "Dead-end" ribosome intermediates that result from biogenesis errors are rapidly degraded, affirming the existence of quality control (QC) pathway(s) that monitor ribosome assembly. However, the factors that differentiate between on-path and dead-end intermediates are unknown. We engineered a system to perturb ribosome assembly in human cells and discovered that faulty ribosomes are degraded via the ubiquitin-proteasome system. We identified ZNF574 as a key component of a QC pathway, which we term the ribosome assembly surveillance pathway (RASP). In an animal model, loss of ZNF574 leads to developmental defects, emphasizing the importance of RASP in organismal health.
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Affiliation(s)
- Jared F Akers
- Carnegie Institution for Science, Department of Embryology, Baltimore, MD 21218, USA
| | - Michael LaScola
- Carnegie Institution for Science, Department of Embryology, Baltimore, MD 21218, USA
| | - Adrian Bothe
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Hanna Suh
- Carnegie Institution for Science, Department of Embryology, Baltimore, MD 21218, USA
| | - Carmen Jung
- Carnegie Institution for Science, Department of Embryology, Baltimore, MD 21218, USA
| | - Zachary D Stolp
- Carnegie Institution for Science, Department of Embryology, Baltimore, MD 21218, USA; Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Tanushree Ghosh
- Carnegie Institution for Science, Department of Embryology, Baltimore, MD 21218, USA; Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Liewei L Yan
- Carnegie Institution for Science, Department of Embryology, Baltimore, MD 21218, USA; Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Yuming Wang
- Carnegie Institution for Science, Department of Embryology, Baltimore, MD 21218, USA
| | - Michelle Macurak
- Carnegie Institution for Science, Department of Embryology, Baltimore, MD 21218, USA
| | - Amisha Devan
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Mary C McKinney
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Tarabryn S Grismer
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA 94305, USA
| | - Andres V Reyes
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA 94305, USA
| | - Eric J Ross
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Tianyi Hu
- Carnegie Institution for Science, Department of Embryology, Baltimore, MD 21218, USA
| | - Shou-Ling Xu
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA 94305, USA
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Kamena K Kostova
- Carnegie Institution for Science, Department of Embryology, Baltimore, MD 21218, USA; Stowers Institute for Medical Research, Kansas City, MO 64110, USA.
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8
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Fu H, Itoh Y, Sawaguchi T, Otake S, Omata C, Saitoh M, Miyazawa K. Identification of a Distal Enhancer That Regulates TGF-β-Induced SNAI1 Expression. Cancer Sci 2025. [PMID: 40364580 DOI: 10.1111/cas.70091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2024] [Revised: 04/14/2025] [Accepted: 04/23/2025] [Indexed: 05/15/2025] Open
Abstract
Snail is a zinc finger transcription factor encoded by the SNAI1 gene and triggers a cellular process termed epithelial-mesenchymal transition (EMT) upon its increased expression and/or functional activation. Snail expression and activity are regulated by various extracellular stimuli, including cytokines and environmental factors. Transforming growth factor-β (TGF-β) is a Snail inducer that functions via Smad3-mediated transcriptional activation. In the present study, we identified a distal enhancer that modulates TGF-β-induced SNAI1 expression. ChIP-seq and Hi-C analyses showed that the enhancer is located 46 kb downstream of the SNAI1 gene; in TGF-β-stimulated cells, it associates with Smad3 and interacts with the SNAI1 proximal promoter. Inhibiting the activity of the enhancer using CRISPRi attenuated TGF-β-induced SNAI1 expression, stress fiber formation, and cell motility enhancement, suggesting that the enhancer mediates TGF-β-induced EMT. The enhancer contains a Smad-binding CAGA motif and an activator protein-1 (AP-1) binding motif that function in transcriptional activation. Ras-responsive element binding protein 1 (RREB1), a transcription factor required for TGF-β-induced Snail expression, regulated the basal activity of the enhancer but not its inducibility by TGF-β. In contrast to the enhancer, the association of Smad3 with the proximal promoter was not evident. These findings suggest that the proximal promoter and the distal enhancer respond to distinct signaling cues, integrate them, and cooperatively function to drive SNAI1 expression.
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Affiliation(s)
- Hao Fu
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Chuo, Japan
| | - Yuka Itoh
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Chuo, Japan
| | - Tomoe Sawaguchi
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Chuo, Japan
- Research Training Program for Undergraduates, Graduate School of Medicine, University of Yamanashi, Chuo, Japan
| | - Shigeo Otake
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Chuo, Japan
| | - Chiho Omata
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Chuo, Japan
| | - Masao Saitoh
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Chuo, Japan
- Center for Medical Education and Sciences, Graduate School of Medicine, University of Yamanashi, Chuo, Japan
| | - Keiji Miyazawa
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Chuo, Japan
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9
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Zhang T, Zhang Y, Wang X, Hu H, Lin CG, Xu Y, Zheng H. Genome-wide CRISPR activation screen identifies ARL11 as a sensitivity determinant of PARP inhibitor therapy. Cancer Gene Ther 2025; 32:521-537. [PMID: 40123001 DOI: 10.1038/s41417-025-00893-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Revised: 02/16/2025] [Accepted: 03/13/2025] [Indexed: 03/25/2025]
Abstract
Resistance to poly-(ADP)-ribose polymerase inhibitors (PARPi) remains a significant challenge in clinical practice, leading to treatment failure in many patients. It is crucial to better understand the molecular mechanisms that underlie PARPi resistance. In this study, utilizing a genome-wide CRISPR activation screen with olaparib, we identified ARL11 as a potential modulator of PARPi treatment response in BRCA-wild-type MDA-MB-231 cells. Mechanistically, ARL11 interacts with STING to enhance innate immunity and forms positive feedback with type I interferon (IFN) induction, which induces ARL11 up-regulation and contributes to resistance to PARPi therapy. Additionally, we observed that ARL11 interacts with the RUVBL1 and RUVBL2 (RUVBL1/2) complex, the key DNA double-strand repair proteins, facilitating DNA homologous recombination (HR) repair and significantly reducing PARPi-induced DNA double-strand damages. Clinical sample analysis reveals that the expression levels of ARL11 and RUVBL1/2 are significantly elevated in breast cancer patients compared to healthy controls. Collectively, our findings suggested that ARL11 and RUVBL1/2 may be promising therapeutic targets to sensitize breast cancer cells to PARPi therapy.
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Affiliation(s)
- Tengjiang Zhang
- State Key Laboratory of Molecular Oncology and Center for Cancer Biology, School of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Yuan Zhang
- State Key Laboratory of Molecular Oncology and Center for Cancer Biology, School of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Xuxiang Wang
- State Key Laboratory of Molecular Oncology and Center for Cancer Biology, School of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Haitian Hu
- State Key Laboratory of Molecular Oncology and Center for Cancer Biology, School of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Christopher G Lin
- State Key Laboratory of Molecular Oncology and Center for Cancer Biology, School of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Yaru Xu
- State Key Laboratory of Molecular Oncology and Center for Cancer Biology, School of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Hanqiu Zheng
- State Key Laboratory of Molecular Oncology and Center for Cancer Biology, School of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China.
- SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, Shanxi Medical University, Taiyuan, Shanxi Province, China.
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10
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Kim Y, Oh J, Kim JR, Lee D, Kim JY. CRISPRi screening identifies PIKfyve as a co-therapeutic target for obinutuzumab. Clin Transl Med 2025; 15:e70333. [PMID: 40342289 PMCID: PMC12059204 DOI: 10.1002/ctm2.70333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2025] [Revised: 04/22/2025] [Accepted: 04/28/2025] [Indexed: 05/11/2025] Open
Affiliation(s)
- Yerim Kim
- Department of Pharmacology and Brain Korea 21 PLUS Project for Medical ScienceYonsei University College of MedicineSeoulRepublic of Korea
| | - Jinkyung Oh
- Department of Pharmacology and Brain Korea 21 PLUS Project for Medical ScienceYonsei University College of MedicineSeoulRepublic of Korea
| | - Jeong Ryeol Kim
- Department of Pharmacology and Brain Korea 21 PLUS Project for Medical ScienceYonsei University College of MedicineSeoulRepublic of Korea
| | - Donghyuk Lee
- Department of Pharmacology and Brain Korea 21 PLUS Project for Medical ScienceYonsei University College of MedicineSeoulRepublic of Korea
- Woo Choo Lee Institute for Precision Drug DevelopmentSeoulRepublic of Korea
| | - Joo Young Kim
- Department of Pharmacology and Brain Korea 21 PLUS Project for Medical ScienceYonsei University College of MedicineSeoulRepublic of Korea
- Woo Choo Lee Institute for Precision Drug DevelopmentSeoulRepublic of Korea
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11
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Zorab JM, Li H, Awasthi R, Schinasi A, Cho Y, O'Loughlin T, Wu X. Serotonin and neurotensin inputs in the vCA1 dictate opposing social valence. Nature 2025:10.1038/s41586-025-08809-2. [PMID: 40307550 DOI: 10.1038/s41586-025-08809-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 02/19/2025] [Indexed: 05/02/2025]
Abstract
The ability to evaluate valence of a social agent based on social experience is essential for an animal's survival in its social group1. Although hippocampal circuits have been implicated in distinguishing novel and familiar conspecifics2-7, it remains unclear how social valence is constructed on the basis of social history and what mechanisms underlie the heightened valence versatility in dynamic relationships. Here we demonstrate that the ventral (v)CA1 integrates serotonin (5-HT) inputs from the dorsal raphe and neurotensin inputs from the paraventricular nucleus of the thalamus (PVT) to determine positive or negative valence of conspecific representations. Specifically, during an appetitive social interaction 5-HT is released into the vCA1 and disinhibits pyramidal neurons through 5-HT1B receptors, whereas neurotensin is released during an aversive social interaction and potentiates vCA1 neurons directly through NTR1s. Optogenetic silencing of dorsal raphe 5-HT and PVT neurotensin inputs into the vCA1 impairs positive and negative social valence, respectively, and excitation flexibly switches valence assignment. These results show how aversive and rewarding social experiences are linked to conspecific identity through converging dorsal raphe 5-HT and PVT neurotensin signals in the vCA1 that instruct opposing valence, and represent a synaptic switch for flexible social valence computation.
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Affiliation(s)
- Julia M Zorab
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Huanhuan Li
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Richa Awasthi
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anna Schinasi
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yoonjeong Cho
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas O'Loughlin
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xiaoting Wu
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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12
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Lee JS, Dan T, Zhang H, Cheng Y, Rehfeld F, Brugarolas J, Mendell JT. An ultraconserved snoRNA-like element in long noncoding RNA CRNDE promotes ribosome biogenesis and cell proliferation. Mol Cell 2025; 85:1543-1560.e10. [PMID: 40185099 PMCID: PMC12009208 DOI: 10.1016/j.molcel.2025.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 01/02/2025] [Accepted: 03/05/2025] [Indexed: 04/07/2025]
Abstract
Cancer cells frequently upregulate ribosome production to support tumorigenesis. While small nucleolar RNAs (snoRNAs) are critical for ribosome biogenesis, the roles of other classes of noncoding RNAs in this process remain largely unknown. Here, we performed CRISPR interference (CRISPRi) screens to identify essential long noncoding RNAs (lncRNAs) in renal cell carcinoma (RCC) cells. This revealed that an alternatively spliced isoform of lncRNA colorectal neoplasia differentially expressed (CRNDE) containing an ultraconserved element (UCE), referred to as CRNDEUCE, is required for RCC cell proliferation. CRNDEUCE localizes to the nucleolus and promotes 60S ribosomal subunit biogenesis. The UCE of CRNDE functions as an unprocessed C/D box snoRNA that directly interacts with ribosomal RNA precursors. This facilitates delivery of eukaryotic initiation factor 6 (eIF6), a key 60S biogenesis factor, which binds to CRNDEUCE through a sequence element adjacent to the UCE. These findings highlight the functional versatility of snoRNA sequences and expand the known mechanisms through which noncoding RNAs orchestrate ribosome biogenesis.
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MESH Headings
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- Humans
- Cell Proliferation/genetics
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- Ribosomes/metabolism
- Ribosomes/genetics
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/pathology
- Carcinoma, Renal Cell/metabolism
- Kidney Neoplasms/genetics
- Kidney Neoplasms/pathology
- Kidney Neoplasms/metabolism
- Cell Line, Tumor
- Gene Expression Regulation, Neoplastic
- Cell Nucleolus/metabolism
- Cell Nucleolus/genetics
- Alternative Splicing
- HEK293 Cells
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- Conserved Sequence
- CRISPR-Cas Systems
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Affiliation(s)
- Jong-Sun Lee
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tu Dan
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - He Zhang
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yujing Cheng
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Frederick Rehfeld
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - James Brugarolas
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Joshua T Mendell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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13
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Chen B, Lyssiotis CA, Shah YM. Mitochondria-organelle crosstalk in establishing compartmentalized metabolic homeostasis. Mol Cell 2025; 85:1487-1508. [PMID: 40250411 DOI: 10.1016/j.molcel.2025.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2024] [Revised: 02/21/2025] [Accepted: 03/04/2025] [Indexed: 04/20/2025]
Abstract
Mitochondria serve as central hubs in cellular metabolism by sensing, integrating, and responding to metabolic demands. This integrative function is achieved through inter-organellar communication, involving the exchange of metabolites, lipids, and signaling molecules. The functional diversity of metabolite exchange and pathway interactions is enabled by compartmentalization within organelle membranes. Membrane contact sites (MCSs) are critical for facilitating mitochondria-organelle communication, creating specialized microdomains that enhance the efficiency of metabolite and lipid exchange. MCS dynamics, regulated by tethering proteins, adapt to changing cellular conditions. Dysregulation of mitochondrial-organelle interactions at MCSs is increasingly recognized as a contributing factor in the pathogenesis of multiple diseases. Emerging technologies, such as advanced microscopy, biosensors, chemical-biology tools, and functional genomics, are revolutionizing our understanding of inter-organellar communication. These approaches provide novel insights into the role of these interactions in both normal cellular physiology and disease states. This review will highlight the roles of metabolite transporters, lipid-transfer proteins, and mitochondria-organelle interfaces in the coordination of metabolism and transport.
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Affiliation(s)
- Brandon Chen
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Costas A Lyssiotis
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Division of Gastroenterology and Hepatology, Michigan Medicine at the University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.
| | - Yatrik M Shah
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Division of Gastroenterology and Hepatology, Michigan Medicine at the University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.
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14
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Berlind JE, Lai JD, Lie C, Vicente J, Lam K, Guo S, Chang J, Yu V, Ichida JK. KCTD20 suppression mitigates excitotoxicity in tauopathy patient organoids. Neuron 2025; 113:1169-1189.e7. [PMID: 40049159 PMCID: PMC12005969 DOI: 10.1016/j.neuron.2025.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 12/13/2024] [Accepted: 02/04/2025] [Indexed: 04/19/2025]
Abstract
Excitotoxicity is a major pathologic mechanism in patients with tauopathy and other neurodegenerative diseases. However, the key neurotoxic drivers and the most effective strategies for mitigating these degenerative processes are unclear. Here, we show that glutamate treatment of induced pluripotent stem cell (iPSC)-derived cerebral organoids induces tau oligomerization and neurodegeneration and that these phenotypes are enhanced in organoids derived from tauopathy patients. Using a genome-wide CRISPR interference (CRISPRi) screen, we find that the suppression of KCTD20 potently ameliorates tau pathology and neurodegeneration in glutamate-treated organoids and mice, as well as in transgenic mice overexpressing mutant human tau. KCTD20 suppression reduces oligomeric tau and improves neuron survival by activating lysosomal exocytosis, which clears pathological tau. Our results show that glutamate signaling can induce neuronal tau pathology and identify KCTD20 suppression and lysosomal exocytosis as effective strategies for clearing neurotoxic tau species.
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Affiliation(s)
- Joshua E Berlind
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC, Los Angeles, CA, USA
| | - Jesse D Lai
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC, Los Angeles, CA, USA; Department of Neuroscience, Amgen Inc., Cambridge, MA, USA; Neurological & Rare Diseases, Dewpoint Therapeutics, Boston, MA, USA.
| | - Cecilia Lie
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC, Los Angeles, CA, USA
| | - Jokabeth Vicente
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC, Los Angeles, CA, USA
| | - Kelsey Lam
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC, Los Angeles, CA, USA
| | - Sheron Guo
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC, Los Angeles, CA, USA
| | - Jonathan Chang
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC, Los Angeles, CA, USA
| | - Violeta Yu
- Neurological & Rare Diseases, Dewpoint Therapeutics, Boston, MA, USA
| | - Justin K Ichida
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC, Los Angeles, CA, USA; Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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15
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Zhang Z, Fu X, Wright N, Wang W, Ye Y, Asbury J, Li Y, Zhu C, Wu R, Wang S, Sun S. PTPσ-mediated PI3P regulation modulates neurodegeneration in C9ORF72-ALS/FTD. Neuron 2025; 113:1190-1205.e9. [PMID: 40073860 PMCID: PMC12005967 DOI: 10.1016/j.neuron.2025.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 12/09/2024] [Accepted: 02/06/2025] [Indexed: 03/14/2025]
Abstract
The most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) is the repeat expansion in C9ORF72. Dipeptide repeat (DPR) proteins translated from both sense and antisense repeats, especially arginine-rich DPRs (R-DPRs), contribute to neurodegeneration. Through CRISPR interference (CRISPRi) screening in human-derived neurons, we identified receptor-type tyrosine-protein phosphatase S (PTPσ) as a strong modifier of poly-GR-mediated toxicity. We showed that reducing PTPσ promotes the survival of both poly-GR- and poly-PR-expressing neurons by elevating phosphatidylinositol 3-phosphate (PI3P), accompanied by restored early endosomes and lysosomes. Remarkably, PTPσ knockdown or inhibition substantially rescues the PI3P-endolysosomal defects and improves the survival of C9ORF72-ALS/FTD patient-derived neurons. Furthermore, the PTPσ inhibitor diminishes GR toxicity and rescues pathological and behavioral phenotypes in mice. Overall, these findings emphasize the critical role of PI3P-mediated endolysosomal deficits induced by R-DPRs in disease pathogenesis and reveal the therapeutic potential of targeting PTPσ in C9ORF72-ALS/FTD.
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Affiliation(s)
- Zhe Zhang
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Xiujuan Fu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Noelle Wright
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Cellular and Molecular Physiology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Weiren Wang
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Biotechology Master Program, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Yingzhi Ye
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Cellular and Molecular Physiology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Julie Asbury
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Notre Dame of Maryland University, Baltimore, MD 21210, USA
| | - Yini Li
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Chengzhang Zhu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rong Wu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shaopeng Wang
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shuying Sun
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Solomon H. Snyder Department of Neuroscience and Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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16
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Okubo C, Nakamura M, Sato M, Shichino Y, Mito M, Takashima Y, Iwasaki S, Takahashi K. EIF3D safeguards the homeostasis of key signaling pathways in human primed pluripotency. SCIENCE ADVANCES 2025; 11:eadq5484. [PMID: 40203091 PMCID: PMC11980838 DOI: 10.1126/sciadv.adq5484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Accepted: 03/04/2025] [Indexed: 04/11/2025]
Abstract
Although pluripotent stem cell (PSC) properties, such as differentiation and infinite proliferation, have been well documented within the frameworks of transcription factor networks, epigenomes, and signal transduction, they remain unclear and fragmented. Directing attention toward translational regulation as a bridge between these events can yield additional insights into previously unexplained mechanisms. Our functional CRISPR interference screen-based approach revealed that EIF3D, a translation initiation factor, is crucial for maintaining primed pluripotency. Loss of EIF3D disrupted the balance of pluripotency-associated signaling pathways, thereby compromising primed pluripotency. Moreover, EIF3D ensured robust proliferation by controlling the translation of various p53 regulators, which maintain low p53 activity in the undifferentiated state. In this way, EIF3D-mediated translation contributes to tuning the homeostasis of the primed pluripotency networks, ensuring the maintenance of an undifferentiated state with high proliferative potential. This study provides further insights into the translation network in maintaining pluripotency.
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Affiliation(s)
- Chikako Okubo
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Michiko Nakamura
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Masae Sato
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Saitama, 351-0198, Japan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Saitama, 351-0198, Japan
| | - Yasuhiro Takashima
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Saitama, 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan
| | - Kazutoshi Takahashi
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
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17
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Minakaki G, Safren N, Bustos BI, Lubbe SJ, Mencacci NE, Krainc D. Commander complex regulates lysosomal function and is implicated in Parkinson's disease risk. Science 2025; 388:204-211. [PMID: 40209002 DOI: 10.1126/science.adq6650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 12/02/2024] [Accepted: 02/12/2025] [Indexed: 04/12/2025]
Abstract
Variants in GBA1 resulting in decreased lysosomal glucocerebrosidase (GCase) activity are a common risk factor for Parkinson's disease (PD) and dementia with Lewy bodies (DLB). Incomplete penetrance of GBA1 variants suggests that additional genes contribute to PD and DLB manifestation. By using a pooled genome-wide CRISPR interference screen, we identified copper metabolism MURR1 domain-containing 3 (COMMD3) protein, a component of the COMMD/coiled-coil domain-containing protein 22 (CCDC22)/CCDC93 (CCC) and Commander complexes, as a modifier of GCase and lysosomal activity. Loss of COMMD3 increased the release of lysosomal proteins through extracellular vesicles, leading to their impaired delivery to endolysosomes and consequent lysosomal dysfunction. Rare variants in the Commander gene family were associated with increased PD risk. Thus, COMMD genes and related complexes regulate lysosomal homeostasis and may represent modifiers in PD and other neurodegenerative diseases associated with lysosomal dysfunction.
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Affiliation(s)
- Georgia Minakaki
- Davee Department of Neurology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Nathaniel Safren
- Davee Department of Neurology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Bernabe I Bustos
- Davee Department of Neurology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Steven J Lubbe
- Davee Department of Neurology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Niccolò E Mencacci
- Davee Department of Neurology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Dimitri Krainc
- Davee Department of Neurology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
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18
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Saini A, Hopkins LS, Serna VA, McCullen MVD, Selner NG, Bhattarai B, Fachi JL, Glynn R, Hayer KE, Bassing CH, Colonna M, Oltz EM. Cell type-specific enhancers regulate IL-22 expression in innate and adaptive lymphoid cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.04.02.646834. [PMID: 40291691 PMCID: PMC12026504 DOI: 10.1101/2025.04.02.646834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2025]
Abstract
IL-22, a signature cytokine of type 3 lymphoid cells, mediates epithelial homeostasis and protective pathogen responses in barrier tissues, while its deregulated expression drives chronic inflammation associated with colitis and psoriasis. Despite its therapeutic value, little is known about regulatory elements for IL-22 expression. We identify two conserved enhancers, E22-1 and E22-2, which differentially regulate Il22 in type 3 lymphoid subsets. These enhancers are required for steady-state expression of gut antimicrobial peptides, protection from C. rodentium infection, and development of IL-22-mediated psoriasis. E22-1 resembles many known enhancers, functioning in both Th-ILC counterparts. However, E22-2 is only required for IL-22 expression in ILC3s. Its ILC3 restriction relies on multiple Runx3 sites, combined with the lack of a functional RORγt motif, which is present in E22-1. Thus, although responding to similar stimuli, type 3 lymphoid cells use distinct cis-elements for IL-22 expression, with E22-2 likely serving as a homeostatic enhancer in barrier tissues.
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19
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Teter OM, McQuade A, Hagan V, Liang W, Dräger NM, Sattler SM, Holmes BB, Castillo VC, Papakis V, Leng K, Boggess S, Nowakowski TJ, Wells J, Kampmann M. CRISPRi-based screen of autism spectrum disorder risk genes in microglia uncovers roles of ADNP in microglia endocytosis and synaptic pruning. Mol Psychiatry 2025:10.1038/s41380-025-02997-z. [PMID: 40188316 DOI: 10.1038/s41380-025-02997-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 03/06/2025] [Accepted: 03/26/2025] [Indexed: 04/07/2025]
Abstract
Autism Spectrum Disorders (ASD) are a set of neurodevelopmental disorders with complex biology. The identification of ASD risk genes from exome-wide association studies and de novo variation analyses has enabled mechanistic investigations into how ASD-risk genes alter development. Most functional genomics studies have focused on the role of these genes in neurons and neural progenitor cells. However, roles for ASD risk genes in other cell types are largely uncharacterized. There is evidence from postmortem tissue that microglia, the resident immune cells of the brain, appear activated in ASD. Here, we used CRISPRi-based functional genomics to systematically assess the impact of ASD risk gene knockdown on microglia activation and phagocytosis. We developed an iPSC-derived microglia-neuron coculture system and high-throughput flow cytometry readout for synaptic pruning to enable parallel CRISPRi-based screening of phagocytosis of beads, synaptosomes, and synaptic pruning. Our screen identified ADNP, a high-confidence ASD risk genes, as a modifier of microglial synaptic pruning. We found that microglia with ADNP loss have altered endocytic trafficking, remodeled proteomes, and increased motility in coculture.
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Affiliation(s)
- Olivia M Teter
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA, USA
| | - Amanda McQuade
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Venus Hagan
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Weiwei Liang
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Nina M Dräger
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Sydney M Sattler
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Brandon B Holmes
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Vincent Cele Castillo
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Vasileios Papakis
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
- Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Kun Leng
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
| | - Steven Boggess
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Tomasz J Nowakowski
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, 94158, USA
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, 94158, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94158, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - James Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA.
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
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20
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Liu M, Yue Y, Chen X, Xian K, Dong C, Shi M, Xiong H, Tian K, Li Y, Zhang QC, He A. Genome-coverage single-cell histone modifications for embryo lineage tracing. Nature 2025; 640:828-839. [PMID: 40011786 PMCID: PMC12003199 DOI: 10.1038/s41586-025-08656-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 01/16/2025] [Indexed: 02/28/2025]
Abstract
Substantial epigenetic resetting during early embryo development from fertilization to blastocyst formation ensures zygotic genome activation and leads to progressive cellular heterogeneities1-3. Mapping single-cell epigenomic profiles of core histone modifications that cover each individual cell is a fundamental goal in developmental biology. Here we develop target chromatin indexing and tagmentation (TACIT), a method that enabled genome-coverage single-cell profiling of seven histone modifications across mouse early embryos. We integrated these single-cell histone modifications with single-cell RNA sequencing data to chart a single-cell resolution epigenetic landscape. Multimodal chromatin-state annotations showed that the onset of zygotic genome activation at the early two-cell stage already primes heterogeneities in totipotency. We used machine learning to identify totipotency gene regulatory networks, including stage-specific transposable elements and putative transcription factors. CRISPR activation of a combination of these identified transcription factors induced totipotency activation in mouse embryonic stem cells. Together with single-cell co-profiles of multiple histone modifications, we developed a model that predicts the earliest cell branching towards the inner cell mass and the trophectoderm in latent multimodal space and identifies regulatory elements and previously unknown lineage-specifying transcription factors. Our work provides insights into single-cell epigenetic reprogramming, multimodal regulation of cellular lineages and cell-fate priming during mouse pre-implantation development.
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Affiliation(s)
- Min Liu
- Institute of Molecular Medicine and National Biomedical Imaging Center, College of Future Technology, Peking-Tsinghua Center for Life Sciences and State Key Laboratory of Gene Function and Modulation Research, Peking University, Beijing, China
| | - Yanzhu Yue
- Department of Cell Fate and Diseases, Jilin Provincial Key Laboratory of Women's Reproductive Health, Jilin Provincial Clinical Research Center for Birth Defect and Rare Disease, The First Hospital of Jilin University, Changchun, China
| | - Xubin Chen
- Institute of Molecular Medicine and National Biomedical Imaging Center, College of Future Technology, Peking-Tsinghua Center for Life Sciences and State Key Laboratory of Gene Function and Modulation Research, Peking University, Beijing, China
| | - Kexin Xian
- Institute of Molecular Medicine and National Biomedical Imaging Center, College of Future Technology, Peking-Tsinghua Center for Life Sciences and State Key Laboratory of Gene Function and Modulation Research, Peking University, Beijing, China
| | - Chao Dong
- Institute of Molecular Medicine and National Biomedical Imaging Center, College of Future Technology, Peking-Tsinghua Center for Life Sciences and State Key Laboratory of Gene Function and Modulation Research, Peking University, Beijing, China
| | - Ming Shi
- Institute of Molecular Medicine and National Biomedical Imaging Center, College of Future Technology, Peking-Tsinghua Center for Life Sciences and State Key Laboratory of Gene Function and Modulation Research, Peking University, Beijing, China
| | - Haiqing Xiong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Kang Tian
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Yuzhe Li
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Aibin He
- Institute of Molecular Medicine and National Biomedical Imaging Center, College of Future Technology, Peking-Tsinghua Center for Life Sciences and State Key Laboratory of Gene Function and Modulation Research, Peking University, Beijing, China.
- Key Laboratory of Carcinogenesis and Translational Research of Ministry of Education of China, Peking University Cancer Hospital and Institute, Peking University, Beijing, China.
- Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies, Chengdu, China.
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21
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Cui X, Yang H, Cai C, Beaman C, Yang X, Liu H, Ren X, Amador Z, Jones IR, Keough KC, Zhang M, Fair T, Abnousi A, Mishra S, Ye Z, Hu M, Pollen AA, Pollard KS, Shen Y. Comparative characterization of human accelerated regions in neurons. Nature 2025; 640:991-999. [PMID: 40011774 DOI: 10.1038/s41586-025-08622-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 01/10/2025] [Indexed: 02/28/2025]
Abstract
Human accelerated regions (HARs) are conserved genomic loci that have experienced rapid nucleotide substitutions following the divergence from chimpanzees1,2. HARs are enriched in candidate regulatory regions near neurodevelopmental genes, suggesting their roles in gene regulation3. However, their target genes and functional contributions to human brain development remain largely uncharacterized. Here we elucidate the cis-regulatory functions of HARs in human and chimpanzee induced pluripotent stem (iPS) cell-induced excitatory neurons. Using genomic4 and chromatin looping information, we prioritized 20 HARs and their chimpanzee orthologues for functional characterization via single-cell CRISPR interference, and demonstrated their species-specific gene regulatory functions. Our findings reveal diverse functional outcomes of HAR-mediated cis-regulation in human neurons, including attenuated NPAS3 expression by altering the binding affinities of multiple transcription factors in HAR202 and maintaining iPS cell pluripotency and neuronal differentiation capacities through the upregulation of PUM2 by 2xHAR.319. Finally, we used prime editing to demonstrate differential enhancer activity caused by several HAR26;2xHAR.178 variants. In particular, we link one variant in HAR26;2xHAR.178 to elevated SOCS2 expression and increased neurite outgrowth in human neurons. Thus, our study sheds new light on the endogenous gene regulatory functions of HARs and their potential contribution to human brain evolution.
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Affiliation(s)
- Xiekui Cui
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Han Yang
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Charles Cai
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Cooper Beaman
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Xiaoyu Yang
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Hongjiang Liu
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Xingjie Ren
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Zachary Amador
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Ian R Jones
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Kathleen C Keough
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Meng Zhang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
| | - Tyler Fair
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, Univeristy of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Armen Abnousi
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Shreya Mishra
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Zhen Ye
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Alex A Pollen
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, Univeristy of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Katherine S Pollard
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics and Bakar Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Yin Shen
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
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22
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Fielden J, Siegner SM, Gallagher DN, Schröder MS, Dello Stritto MR, Lam S, Kobel L, Schlapansky MF, Jackson SP, Cejka P, Jost M, Corn JE. Comprehensive interrogation of synthetic lethality in the DNA damage response. Nature 2025; 640:1093-1102. [PMID: 40205037 PMCID: PMC12018271 DOI: 10.1038/s41586-025-08815-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 02/19/2025] [Indexed: 04/11/2025]
Abstract
The DNA damage response (DDR) is a multifaceted network of pathways that preserves genome stability1,2. Unravelling the complementary interplay between these pathways remains a challenge3,4. Here we used CRISPR interference (CRISPRi) screening to comprehensively map the genetic interactions required for survival during normal human cell homeostasis across all core DDR genes. We captured known interactions and discovered myriad new connections that are available online. We defined the molecular mechanism of two of the strongest interactions. First, we found that WDR48 works with USP1 to restrain PCNA degradation in FEN1/LIG1-deficient cells. Second, we found that SMARCAL1 and FANCM directly unwind TA-rich DNA cruciforms, preventing catastrophic chromosome breakage by the ERCC1-ERCC4 complex. Our data yield fundamental insights into genome maintenance, provide a springboard for mechanistic investigations into new connections between DDR factors and pinpoint synthetic vulnerabilities that could be exploited in cancer therapy.
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Affiliation(s)
- John Fielden
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
| | - Sebastian M Siegner
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
| | - Danielle N Gallagher
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
| | - Markus S Schröder
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
| | - Maria Rosaria Dello Stritto
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Simon Lam
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Lena Kobel
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
| | - Moritz F Schlapansky
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
| | - Stephen P Jackson
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Petr Cejka
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Marco Jost
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Jacob E Corn
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland.
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23
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Carter AC, Koreman GT, Petrocelli JE, Robb JE, Bushinsky EM, Trowbridge SK, Kingsley DM, Walsh CA, Song JHT, Greenberg ME. FOS binding sites are a hub for the evolution of activity-dependent gene regulatory programs in human neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.31.646366. [PMID: 40236085 PMCID: PMC11996375 DOI: 10.1101/2025.03.31.646366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]
Abstract
After birth, sensory inputs to neurons trigger the induction of activity-dependent genes (ADGs) that mediate many aspects of neuronal maturation and plasticity. To identify human-specific ADGs, we characterized these genes in human-chimpanzee tetraploid neurons. We identified 235 ADGs that are differentially expressed between human and chimpanzee neurons and found that their nearby regulatory sites are species-biased in their binding of the transcription factor FOS. An assessment of these sites revealed that many are enriched for single nucleotide variants that promote or eliminate FOS binding in human neurons. Disrupting the function of individual species-biased FOS-bound enhancers diminishes expression of nearby genes and affects the firing dynamics of human neurons. Our findings indicate that FOS-bound enhancers are frequent sites of evolution and that they regulate human-specific ADGs that may contribute to the unusually protracted and complex process of postnatal human brain development.
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24
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Rahimian E, Koochak M, Traikov S, Schroeder M, Brilloff S, Schäfer S, Kufrin V, Küchler S, Krüger A, Mirtschink P, Baretton G, Schröck E, Schewe DM, Ball CR, Bornhäuser M, Glimm H, Bill M, Wurm AA. A quiescence-like/TGF-β1-specific CRISPRi screen reveals drug uptake transporters as secondary targets of kinase inhibitors in AML. Drug Resist Updat 2025; 81:101242. [PMID: 40184725 DOI: 10.1016/j.drup.2025.101242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2024] [Revised: 02/26/2025] [Accepted: 03/23/2025] [Indexed: 04/07/2025]
Abstract
Relapse in acute myeloid leukemia (AML) is driven by resistant subclones that survive chemotherapy. It is assumed that these resilient leukemic cells can modify their proliferative behavior by entering a quiescent-like state, similar to healthy hematopoietic stem cells (HSCs). These dormant cells can evade the effects of cytostatic drugs that primarily target actively dividing cells. Although quiescence has been extensively studied in healthy hematopoiesis and various solid cancers, its role in AML has remained unexplored. In this study, we applied an HSC-derived quiescence-associated gene signature to an AML patient cohort and found it to be strongly correlated with poor prognosis and active TGF-β signaling. In vitro treatment with TGF-β1 induces a quiescence-like phenotype, resulting in a G0 shift and reduced sensitivity to cytarabine. To find potential therapeutic targets that prevent AML-associated quiescence and improve response to cytarabine, we conducted a comprehensive CRISPR interference (CRISPRi) screen combined with TGF-β1 stimulation. This approach identified TGFBR1 inhibitors, like vactosertib, as effective agents for preventing the G0 shift in AML cell models. However, pretreatment with vactosertib unexpectedly induced complete resistance to cytarabine. To elucidate the underlying mechanism, we performed a multi-faceted approach combining a second CRISPRi screen, liquid chromatography-tandem mass spectrometry (LC-MS/MS), and in silico analysis. Our findings revealed that TGFBR1 inhibitors unintentionally target the nucleoside transporter SLC29A1 (ENT1), leading to reduced intracellular cytarabine levels. Importantly, we found that this drug interaction is not unique to TGFBR1 inhibitors, but extends to other clinically significant kinase inhibitors, such as the FLT3 inhibitor midostaurin. These findings may have important implications for optimizing combination therapies in AML treatment.
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Affiliation(s)
- Elahe Rahimian
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany; Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Germany
| | - Masoud Koochak
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany; Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Germany
| | - Sofia Traikov
- Institute for Clinical Chemistry and Laboratory Medicine, TU Dresden, Dresden, Germany
| | - Michael Schroeder
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Silke Brilloff
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany; Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Germany
| | - Silvia Schäfer
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany; Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Germany
| | - Vida Kufrin
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany; Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Germany
| | - Sandra Küchler
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany; Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Germany
| | - Alexander Krüger
- Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases Dresden (NCT), NCT/UCC Dresden, a partnership between German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Germany
| | - Peter Mirtschink
- Institute for Clinical Chemistry and Laboratory Medicine, TU Dresden, Dresden, Germany
| | - Gustavo Baretton
- Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases Dresden (NCT), NCT/UCC Dresden, a partnership between German Cancer Research Center (DKFZ), Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Germany; Institute for Pathology, Faculty of Medicine Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Evelin Schröck
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at TUD Dresden University of Technology and Faculty of Medicine of TUD Dresden University of Technology, Dresden, Germany; ERN GENTURIS, Hereditary Cancer Syndrome Center Dresden, Germany; National Center for Tumor Diseases (NCT), NCT/UCC Dresden, a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Germany; German Cancer Consortium (DKTK), Dresden, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Denis M Schewe
- Department of Pediatric Hematology and Oncology, University Hospital Dresden, Dresden, Germany
| | - Claudia R Ball
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Germany; Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany; German Cancer Consortium (DKTK), partner site Dresden, Germany; TUD Dresden University of Technology, Faculty of Biology, Dresden, Germany
| | - Martin Bornhäuser
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany; Department of Internal Medicine I, University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
| | - Hanno Glimm
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Germany; Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany; German Cancer Consortium (DKTK), partner site Dresden, Germany; Translational Functional Cancer Genomics, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marius Bill
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany; Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Germany; German Cancer Consortium (DKTK), partner site Dresden, Germany; Department of Internal Medicine I, University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
| | - Alexander A Wurm
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany; Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC), a partnership between DKFZ, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Germany; Department of Pediatric Hematology and Oncology, University Hospital Dresden, Dresden, Germany; Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany; German Cancer Consortium (DKTK), partner site Dresden, Germany.
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25
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Kufrin V, Seiler A, Brilloff S, Rothfuß H, Küchler S, Schäfer S, Rahimian E, Baumgarten J, Ding L, Buchholz F, Ball CR, Bornhäuser M, Glimm H, Bill M, Wurm AA. The histone modifier KAT2A presents a selective target in a subset of well-differentiated microsatellite-stable colorectal cancers. Cell Death Differ 2025:10.1038/s41418-025-01479-7. [PMID: 40140561 DOI: 10.1038/s41418-025-01479-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 01/27/2025] [Accepted: 03/14/2025] [Indexed: 03/28/2025] Open
Abstract
Lysine acetyltransferase 2 A (KAT2A) plays a pivotal role in epigenetic gene regulation across various types of cancer. In colorectal cancer (CRC), increased KAT2A expression is associated with a more aggressive phenotype. Our study aims to elucidate the molecular underpinnings of KAT2A dependency in CRC and assess the consequences of KAT2A depletion. We conducted a comprehensive analysis by integrating CRISPR-Cas9 screening data with genomics, transcriptomics, and global acetylation patterns in CRC cell lines to pinpoint molecular markers indicative of KAT2A dependency. Additionally, we characterized the phenotypic effect of a CRISPR-interference-mediated KAT2A knockdown in CRC cell lines and patient-derived 3D spheroid cultures. Moreover, we assessed the effect of KAT2A depletion within a patient-derived xenograft mouse model in vivo. Our findings reveal that KAT2A dependency is closely associated with microsatellite stability, lower mutational burden, and increased molecular differentiation signatures in CRC, independent of the KAT2A expression levels. KAT2A-dependent CRC cells display higher gene expression levels and enriched H3K27ac marks at gene loci linked to enterocytic differentiation. Furthermore, loss of KAT2A leads to decreased cell growth and viability in vitro and in vivo, downregulation of proliferation- and stem cell-associated genes, and induction of differentiation markers. Altogether, our data show that a specific subset of CRCs with a more differentiated phenotype relies on KAT2A. For these CRC cases, KAT2A might represent a promising novel therapeutic target.
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Affiliation(s)
- Vida Kufrin
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the TUD Dresden University of Technology, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Annika Seiler
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the TUD Dresden University of Technology, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Silke Brilloff
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the TUD Dresden University of Technology, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Helen Rothfuß
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the TUD Dresden University of Technology, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Sandra Küchler
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the TUD Dresden University of Technology, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Silvia Schäfer
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the TUD Dresden University of Technology, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Elahe Rahimian
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the TUD Dresden University of Technology, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Jonas Baumgarten
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the TUD Dresden University of Technology, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Li Ding
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
| | - Frank Buchholz
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
| | - Claudia R Ball
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the TUD Dresden University of Technology, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- TUD Dresden University of Technology, Faculty of Biology, Dresden, Germany
| | - Martin Bornhäuser
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
| | - Hanno Glimm
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the TUD Dresden University of Technology, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- Translational Functional Cancer Genomics, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marius Bill
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the TUD Dresden University of Technology, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- Department of Internal Medicine I, University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
| | - Alexander A Wurm
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany.
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the TUD Dresden University of Technology, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany.
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany.
- German Cancer Consortium (DKTK), Dresden, Germany.
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26
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Kim YM, Akana RV, Sun C, Laveroni O, Jerby L. Redirecting cytotoxic lymphocytes to breast cancer tumors via metabolite-sensing receptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.21.644686. [PMID: 40196673 PMCID: PMC11974742 DOI: 10.1101/2025.03.21.644686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/09/2025]
Abstract
Insufficient infiltration of cytotoxic lymphocytes to solid tumors limits the efficacy of immunotherapies and cell therapies. Here, we report a programmable mechanism to mobilize Natural Killer (NK) and T cells to breast cancer tumors by engineering these cells to express orphan and metabolite-sensing G protein-coupled receptors (GPCRs). First, in vivo and in vitro CRISPR activation screens in NK-92 cells identified GPR183, GPR84, GPR34, GPR18, FPR3, and LPAR2 as top enhancers of both tumor infiltration and chemotaxis to breast cancer. These genes equip NK and T cells with the ability to sense and migrate to chemoattracting metabolites such as 7α,25-dihydroxycholesterol and other factors released from breast cancer. Based on Perturb-seq and functional investigations, GPR183 also enhances effector functions, such that engineering NK and CAR NK cells to express GPR183 enhances their ability to migrate to, infiltrate, and control breast cancer tumors. Our study uncovered metabolite-based tumor immune recruitment mechanisms, opening avenues for spatially targeted cell therapies.
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Affiliation(s)
- Young-Min Kim
- Department of Genetics, Stanford University School of Medicine; Stanford, CA, USA
| | - Reece V Akana
- Department of Genetics, Stanford University School of Medicine; Stanford, CA, USA
- Cancer Biology Program, Stanford University; Stanford, CA, USA
| | - Chang Sun
- Department of Genetics, Stanford University School of Medicine; Stanford, CA, USA
| | - Olivia Laveroni
- Department of Genetics, Stanford University School of Medicine; Stanford, CA, USA
| | - Livnat Jerby
- Department of Genetics, Stanford University School of Medicine; Stanford, CA, USA
- Cancer Biology Program, Stanford University; Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine; Stanford, CA, USA
- Chan Zuckerberg Biohub; San Francisco, CA, USA
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27
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Villegas NK, Gaudreault YR, Keller A, Kearns P, Stapleton JA, Plesa C. Optimizing in vitro Transcribed CRISPR-Cas9 Single-Guide RNA Libraries for Improved Uniformity and Affordability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.24.644170. [PMID: 40196484 PMCID: PMC11974757 DOI: 10.1101/2025.03.24.644170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/09/2025]
Abstract
We describe a scalable and cost-effective sgRNA synthesis workflow that reduces costs by over 70% through the use of large pools of microarray-derived oligos encoding unique sgRNA spacers. These subpool oligos are assembled into full-length dsDNA templates via Golden Gate Assembly before in vitro transcription with T7 RNA polymerase. RNA-seq analysis reveals severe biases in spacer representation, with some spacers being highly overrepresented while others are completely absent. Consistent with previous studies, we identify guanine-rich sequences within the first four nucleotides of the spacer, immediately downstream of the T7 promoter, as the primary driver of this bias. To address this issue, we introduced a guanine tetramer upstream of all spacers, which reduced bias by an average of 19% in sgRNA libraries containing 389 spacers. However, this modification also increased the presence of high-molecular-weight RNA species after transcription. We also tested two alternative bias-reduction strategies: compartmentalizing spacers within emulsions and optimizing DNA input and reaction volumes. Both methods independently reduced bias in 2,626-plex sgRNA libraries, though to a lesser extent than the guanine tetramer approach. These advancements enhance both the affordability and uniformity of sgRNA libraries, with broad implications for improving CRISPR-Cas9 screens and optimizing guide RNA design for other CRISPR and nuclease systems.
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Affiliation(s)
- Natanya K. Villegas
- Department of Bioengineering, Phil and Penny Knight Campus for Accelerating Scientific Impact, University of Oregon, 1505 Franklin Blvd., Eugene, OR 97403, USA
- Institute of Molecular Biology, University of Oregon 1229 University of Oregon, 1318 Franklin Blvd., Room 273, Onyx Bridge, Eugene, OR 97403, USA
- Biology Department, University of Oregon 1210 University of Oregon, 77 Klamath Hall, Eugene, OR 97403, USA
| | - Yukiko R. Gaudreault
- Department of Bioengineering, Phil and Penny Knight Campus for Accelerating Scientific Impact, University of Oregon, 1505 Franklin Blvd., Eugene, OR 97403, USA
| | - Abigail Keller
- Department of Bioengineering, Phil and Penny Knight Campus for Accelerating Scientific Impact, University of Oregon, 1505 Franklin Blvd., Eugene, OR 97403, USA
| | - Phillip Kearns
- Department of Bioengineering, Phil and Penny Knight Campus for Accelerating Scientific Impact, University of Oregon, 1505 Franklin Blvd., Eugene, OR 97403, USA
| | - James A. Stapleton
- Department of Bioengineering, Phil and Penny Knight Campus for Accelerating Scientific Impact, University of Oregon, 1505 Franklin Blvd., Eugene, OR 97403, USA
| | - Calin Plesa
- Department of Bioengineering, Phil and Penny Knight Campus for Accelerating Scientific Impact, University of Oregon, 1505 Franklin Blvd., Eugene, OR 97403, USA
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28
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Chia BS, Seah YFS, Wang B, Shen K, Srivastava D, Chew WL. Engineering a New Generation of Gene Editors: Integrating Synthetic Biology and AI Innovations. ACS Synth Biol 2025; 14:636-647. [PMID: 39999982 PMCID: PMC11934138 DOI: 10.1021/acssynbio.4c00686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2024] [Revised: 01/06/2025] [Accepted: 01/16/2025] [Indexed: 02/27/2025]
Abstract
CRISPR-Cas technology has revolutionized biology by enabling precise DNA and RNA edits with ease. However, significant challenges remain for translating this technology into clinical applications. Traditional protein engineering methods, such as rational design, mutagenesis screens, and directed evolution, have been used to address issues like low efficacy, specificity, and high immunogenicity. These methods are labor-intensive, time-consuming, and resource-intensive and often require detailed structural knowledge. Recently, computational strategies have emerged as powerful solutions to these limitations. Using artificial intelligence (AI) and machine learning (ML), the discovery and design of novel gene-editing enzymes can be streamlined. AI/ML models predict activity, specificity, and immunogenicity while also enhancing mutagenesis screens and directed evolution. These approaches not only accelerate rational design but also create new opportunities for developing safer and more efficient genome-editing tools, which could eventually be translated into the clinic.
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Affiliation(s)
- Bing Shao Chia
- Genome
Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore 138672, Singapore
| | - Yu Fen Samantha Seah
- Genome
Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore 138672, Singapore
| | - Bolun Wang
- Genome
Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore 138672, Singapore
| | - Kimberle Shen
- Genome
Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore 138672, Singapore
| | - Diya Srivastava
- Genome
Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore 138672, Singapore
| | - Wei Leong Chew
- Genome
Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore 138672, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
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29
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Saxena T, Quan A, Chan E, Kozlova N, Matai L, Lee JD, Rupaimoole R, Beca F, Muranen T, Slack FJ. EGFR-induced lncRNA TRIDENT promotes drug resistance in non-small cell lung cancer via phospho-TRIM28-mediated DNA damage repair. Proc Natl Acad Sci U S A 2025; 122:e2415389122. [PMID: 40030013 PMCID: PMC11912419 DOI: 10.1073/pnas.2415389122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Accepted: 01/06/2025] [Indexed: 03/19/2025] Open
Abstract
Long noncoding RNAs (lncRNAs) play numerous roles in cellular biology and alterations in lncRNA expression profiles have been implicated in a variety of cancers. Here, we identify and characterize a lncRNA, TRIM28 Interacting DNA damage repair Enhancing Noncoding Transcript (TRIDENT), whose expression is induced upon epithelial growth factor receptor (EGFR) activation, and which exerts pro-oncogenic functions in EGFR-driven non-small cell lung cancer. Knocking down TRIDENT leads to decreased tumor-cell proliferation in both in vitro and in vivo model systems and induces sensitization to chemotherapeutic drugs. Using ChIRP-MS analysis we identified TRIM28 as a protein interactor of TRIDENT. TRIDENT promotes phosphorylation of TRIM28 and knocking down TRIDENT leads to accumulation of DNA damage in cancer cells via decreased TRIM28 phosphorylation. Altogether, our results reveal a molecular pathway in which TRIDENT regulates TRIM28 phosphorylation to promote tumor cell growth and drug resistance. Our findings suggest that TRIDENT can be developed as a biomarker or therapeutic target for EGFR mutant non-small cell lung cancer.
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Affiliation(s)
- Tanvi Saxena
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02215
| | - Anan Quan
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02215
| | - Erica Chan
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02215
| | - Nina Kozlova
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02215
| | - Latika Matai
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02215
| | - Jonathan D. Lee
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02215
| | - Rajesha Rupaimoole
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02215
| | - Francisco Beca
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02215
| | - Taru Muranen
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02215
| | - Frank J. Slack
- Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02215
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30
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Li X, Zhang W, Fang Y, Sun T, Chen J, Tian R. Large-scale CRISPRi screens link metabolic stress to glioblastoma chemoresistance. J Transl Med 2025; 23:289. [PMID: 40050992 PMCID: PMC11887098 DOI: 10.1186/s12967-025-06261-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2024] [Accepted: 02/14/2025] [Indexed: 03/09/2025] Open
Abstract
BACKGROUND Glioblastoma (GBM) patients frequently develop resistance to temozolomide (TMZ), the standard chemotherapy. While targeting cancer metabolism shows promise, the relationship between metabolic perturbation and drug resistance remains poorly understood. METHODS We performed high-throughput CRISPR interference screens in GBM cells to identify genes modulating TMZ sensitivity. Findings were validated using multiple GBM cell lines, patient-derived glioma stem cells, and clinical data. Molecular mechanisms were investigated through transcriptome analysis, metabolic profiling, and functional assays. RESULTS We identified phosphoglycerate kinase 1 (PGK1) as a key determinant of TMZ sensitivity. Paradoxically, while PGK1 inhibition suppressed tumor growth, it enhanced TMZ resistance by inducing metabolic stress. This activated AMPK and HIF-1α pathways, leading to enhanced DNA damage repair through 53BP1. PGK1 expression levels correlated with TMZ sensitivity across multiple GBM models and patient samples. CONCLUSIONS Our study reveals an unexpected link between metabolic stress and chemoresistance, demonstrating how metabolic adaptation can promote therapeutic resistance. These findings caution against single-agent metabolic targeting and suggest PGK1 as a potential biomarker for TMZ response in GBM.
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Affiliation(s)
- Xing Li
- School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, Guangdong Province, China
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, 518055, Guangdong Province, China
| | - Wansong Zhang
- School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, Guangdong Province, China
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, 518055, Guangdong Province, China
| | - Yitong Fang
- School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, Guangdong Province, China
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, 518055, Guangdong Province, China
| | - Tianhu Sun
- School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, Guangdong Province, China
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, 518055, Guangdong Province, China
| | - Jian Chen
- Research Unit of Medical Neurobiology, Chinese Institute for Brain Research, Beijing, Chinese Academy of Medical Sciences, Beijing, China
| | - Ruilin Tian
- School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, Guangdong Province, China.
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, 518055, Guangdong Province, China.
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31
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Pattali RK, Ornelas IJ, Nguyen CD, Xu D, Divekar NS, Nuñez NK. CRISPRoff epigenome editing for programmable gene silencing in human cell lines and primary T cells. Methods Enzymol 2025; 712:517-551. [PMID: 40121086 PMCID: PMC12052198 DOI: 10.1016/bs.mie.2025.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2025]
Abstract
The advent of CRISPR-based technologies has enabled the rapid advancement of programmable gene manipulation in cells, tissues, and whole organisms. An emerging platform for targeted gene perturbation is epigenetic editing, the direct editing of chemical modifications on DNA and histones that ultimately results in repression or activation of the targeted gene. In contrast to CRISPR nucleases, epigenetic editors modulate gene expression without inducing DNA breaks or altering the genomic sequence of host cells. Recently, we developed the CRISPRoff epigenetic editing technology that simultaneously establishes DNA methylation and repressive histone modifications at targeted gene promoters. Transient expression of CRISPRoff and the accompanying single guide RNAs in mammalian cells results in transcriptional repression of targeted genes that is memorized heritably by cells through cell division and differentiation. Here, we describe our protocol for the delivery of CRISPRoff through plasmid DNA transfection, as well as the delivery of CRISPRoff mRNA, into transformed human cell lines and primary immune cells. We also provide guidance on evaluating target gene silencing and highlight key considerations when utilizing CRISPRoff for gene perturbations. Our protocols are broadly applicable to other CRISPR-based epigenetic editing technologies, as programmable genome manipulation tools continue to evolve rapidly.
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Affiliation(s)
- Rithu K Pattali
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Izaiah J Ornelas
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Carolyn D Nguyen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Da Xu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Nikita S Divekar
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
| | - NunezJames K Nuñez
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States; Chan Zuckerberg Biohub San Francisco, San Francisco, CA, United States.
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32
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Li E, Benitez C, Boggess SC, Koontz M, Rose IVL, Martinez D, Dräger N, Teter OM, Samelson AJ, Pierce N, Ullian EM, Kampmann M. CRISPRi-based screens in iAssembloids to elucidate neuron-glia interactions. Neuron 2025; 113:701-718.e8. [PMID: 39814010 PMCID: PMC11886924 DOI: 10.1016/j.neuron.2024.12.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 11/25/2024] [Accepted: 12/17/2024] [Indexed: 01/18/2025]
Abstract
The complexity of the human brain makes it challenging to understand the molecular mechanisms underlying brain function. Genome-wide association studies have uncovered variants associated with neurological phenotypes. Single-cell transcriptomics have provided descriptions of changes brain cells undergo during disease. However, these approaches do not establish molecular mechanism. To facilitate the scalable interrogation of causal molecular mechanisms in brain cell types, we developed a 3D co-culture system of induced pluripotent stem cell (iPSC)-derived neurons and glia, termed iAssembloids. Using iAssembloids, we ask how glial and neuronal cells interact to control neuronal death and survival. Our CRISPRi-based screens identified that GSK3β inhibits the protective NRF2-mediated oxidative stress response elicited by high neuronal activity. We then investigate the role of APOE-ε4, a risk variant for Alzheimer's disease, on neuronal survival. We find that APOE-ε4-expressing astrocytes may promote neuronal hyperactivity as compared with APOE-ε3-expressing astrocytes. This platform allows for the unbiased identification of mechanisms of neuron-glia cell interactions.
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Affiliation(s)
- Emmy Li
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Camila Benitez
- TETRAD Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Steven C Boggess
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Mark Koontz
- Department of Ophthalmology, School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Indigo V L Rose
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA; Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Delsy Martinez
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Nina Dräger
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Olivia M Teter
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA; UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA, USA
| | - Avi J Samelson
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Na'im Pierce
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA; FirstGen Internship, Emerson Collective, Palo Alto, CA, USA; University of California, Berkeley, Berkeley, CA, USA
| | - Erik M Ullian
- Department of Ophthalmology, School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
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33
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Edington AR, Connor OM, Love AC, Marlar-Pavey M, Friedman JR. Functionally conserved inner mitochondrial membrane proteins CCDC51 and Mdm33 demarcate a subset of fission events. J Cell Biol 2025; 224:e202403140. [PMID: 39718510 PMCID: PMC11668171 DOI: 10.1083/jcb.202403140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 10/11/2024] [Accepted: 11/20/2024] [Indexed: 12/25/2024] Open
Abstract
While extensive work has examined the mechanisms of mitochondrial fission, it remains unclear whether internal mitochondrial proteins in metazoans play a direct role in the process. Previously, the yeast inner membrane protein Mdm33 was shown to be required for normal mitochondrial morphology and has been hypothesized to be involved in mitochondrial fission. However, it is unknown whether Mdm33 plays a direct role, and it is not thought to have a mammalian homolog. Here, we use a bioinformatic approach to identify a structural ortholog of Mdm33 in humans, CCDC51 (also called MITOK), whose depletion phenocopies loss of Mdm33. We find that knockdown of CCDC51 also leads to reduced rates of mitochondrial fission. Further, we spatially and temporally resolve Mdm33 and CCDC51 to a subset of mitochondrial fission events. Finally, we show that CCDC51 overexpression promotes its spatial association with Drp1 and induces mitochondrial fragmentation, suggesting it is a positive effector of mitochondrial fission. Together, our data reveal that Mdm33 and CCDC51 are functionally conserved and suggest that internal mitochondrial proteins are directly involved in at least a subset of mitochondrial fission events in human cells.
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Affiliation(s)
- Alia R. Edington
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Olivia M. Connor
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Abigail C. Love
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Madeleine Marlar-Pavey
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jonathan R. Friedman
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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Chesner LN, Polesso F, Graff JN, Hawley JE, Smith AK, Lundberg A, Das R, Shenoy T, Sjöström M, Zhao F, Hu YM, Linder S, Chen WS, Hawkins RM, Shrestha R, Zhu X, Foye A, Li H, Kim LM, Bhalla M, O’loughlin T, Kuzuoglu-Ozturk D, Hua JT, Badura ML, Wilkinson S, Trostel SY, Bergman AM, Ruggero D, Drake CG, Sowalsky AG, Fong L, Cooperberg MR, Zwart W, Guan X, Ashworth A, Xia Z, Quigley DA, Gilbert LA, Feng FY, Moran AE. Androgen Receptor Inhibition Increases MHC Class I Expression and Improves Immune Response in Prostate Cancer. Cancer Discov 2025; 15:481-494. [PMID: 39652470 PMCID: PMC11873725 DOI: 10.1158/2159-8290.cd-24-0559] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 09/10/2024] [Accepted: 12/03/2024] [Indexed: 03/04/2025]
Abstract
SIGNIFICANCE Immunotherapy options for immune cold tumors, like prostate cancer, are limited. We show that AR downregulates MHCI expression/antigen presentation and that AR inhibition improves T-cell responses and tumor control. This suggests that treatments combining AR inhibitors and checkpoint blockade may improve tumor immune surveillance and antitumor immunity in patients.
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Affiliation(s)
- Lisa N. Chesner
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California
| | - Fanny Polesso
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, Oregon
| | - Julie N. Graff
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
- VA Portland Health Care System, Portland, Oregon
| | - Jessica E. Hawley
- Department of Medicine, University of Washington, Seattle, Washington
- Clinical Research Division, Fred Hutch Cancer Center, Seattle, Washington
| | - Alexis K. Smith
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California
| | - Arian Lundberg
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California
- Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Rajdeep Das
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California
| | - Tanushree Shenoy
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Divsion of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Martin Sjöström
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California
| | - Faming Zhao
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon
| | - Ya-Mei Hu
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon
| | - Simon Linder
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - William S. Chen
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California
| | - Reed M. Hawkins
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, Oregon
| | - Raunak Shrestha
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California
| | - Xiaolin Zhu
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Divsion of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Divsion of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Haolong Li
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California
| | - Lisa M. Kim
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California
| | - Megha Bhalla
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California
| | - Thomas O’loughlin
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Urology, University of California San Francisco, San Francisco, California
| | - Duygu Kuzuoglu-Ozturk
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Urology, University of California San Francisco, San Francisco, California
| | - Junjie T. Hua
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California
| | - Michelle L. Badura
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California
| | - Scott Wilkinson
- Genitourinary Malignancies Branch, National Cancer Institute, Bethesda, Maryland
| | - Shana Y. Trostel
- Genitourinary Malignancies Branch, National Cancer Institute, Bethesda, Maryland
| | - Andries M. Bergman
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Davide Ruggero
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Urology, University of California San Francisco, San Francisco, California
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California
| | - Charles G. Drake
- Department of Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York
- Department of Urology, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York
| | - Adam G. Sowalsky
- Genitourinary Malignancies Branch, National Cancer Institute, Bethesda, Maryland
| | - Lawrence Fong
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Medicine, University of Washington, Seattle, Washington
- Clinical Research Division, Fred Hutch Cancer Center, Seattle, Washington
- Divsion of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Matthew R. Cooperberg
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Urology, University of California San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Xiangnan Guan
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Divsion of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Zheng Xia
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon
- Center for Biomedical Data Science, Oregon Health & Science University, Portland, Oregon
| | - David A. Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Urology, University of California San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - Luke A. Gilbert
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Urology, University of California San Francisco, San Francisco, California
| | - Felix Y. Feng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California
- Divsion of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California
- Department of Urology, University of California San Francisco, San Francisco, California
| | - Amy E. Moran
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, Oregon
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
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35
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Kovalski JR, Sarioglu G, Subramanyam V, Hernandez G, Rademaker G, Oses-Prieto JA, Slota M, Mohan N, Yiakis K, Liu I, Wen KW, Kim GE, Miglani S, Burlingame AL, Goodarzi H, Perera RM, Ruggero D. Functional screen identifies RBM42 as a mediator of oncogenic mRNA translation specificity. Nat Cell Biol 2025; 27:518-529. [PMID: 39905246 DOI: 10.1038/s41556-024-01604-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 12/20/2024] [Indexed: 02/06/2025]
Abstract
Oncogenic protein dosage is tightly regulated to enable cancer formation but how this is regulated by translational control remains unknown. The Myc oncogene is a paradigm of an exquisitely regulated oncogene and a driver of pancreatic ductal adenocarcinoma (PDAC). Here we use a CRISPR interference screen in PDAC cells to identify activators of selective MYC translation. The top hit, the RNA-binding protein RBM42, is highly expressed in PDAC and predicts poor survival. We show that RBM42 binds and selectively regulates the translation of MYC and a precise suite of pro-oncogenic transcripts, including JUN and EGFR. Mechanistically, we find that RBM42 binds and remodels the MYC 5' untranslated region structure, facilitating the formation of the translation pre-initiation complex. Importantly, RBM42 is necessary for PDAC tumorigenesis in a Myc-dependent manner in vivo. This work transforms the understanding of the translational code in cancer and illuminates therapeutic openings to target the expression of oncogenes.
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Affiliation(s)
- Joanna R Kovalski
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Goksu Sarioglu
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Vishvak Subramanyam
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Grace Hernandez
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Gilles Rademaker
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Juan A Oses-Prieto
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Macey Slota
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Nimmy Mohan
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Kaylee Yiakis
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Isabelle Liu
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Kwun Wah Wen
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Grace E Kim
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Sohit Miglani
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Hani Goodarzi
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Arc Institute, Palo Alto, CA, USA
| | - Rushika M Perera
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Davide Ruggero
- Department of Urology, University of California San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.
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36
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Pacalin NM, Steinhart Z, Shi Q, Belk JA, Dorovskyi D, Kraft K, Parker KR, Shy BR, Marson A, Chang HY. Bidirectional epigenetic editing reveals hierarchies in gene regulation. Nat Biotechnol 2025; 43:355-368. [PMID: 38760566 PMCID: PMC11569274 DOI: 10.1038/s41587-024-02213-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/19/2024] [Indexed: 05/19/2024]
Abstract
CRISPR perturbation methods are limited in their ability to study non-coding elements and genetic interactions. In this study, we developed a system for bidirectional epigenetic editing, called CRISPRai, in which we apply activating (CRISPRa) and repressive (CRISPRi) perturbations to two loci simultaneously in the same cell. We developed CRISPRai Perturb-seq by coupling dual perturbation gRNA detection with single-cell RNA sequencing, enabling study of pooled perturbations in a mixed single-cell population. We applied this platform to study the genetic interaction between two hematopoietic lineage transcription factors, SPI1 and GATA1, and discovered novel characteristics of their co-regulation on downstream target genes, including differences in SPI1 and GATA1 occupancy at genes that are regulated through different modes. We also studied the regulatory landscape of IL2 (interleukin-2) in Jurkat T cells, primary T cells and chimeric antigen receptor (CAR) T cells and elucidated mechanisms of enhancer-mediated IL2 gene regulation. CRISPRai facilitates investigation of context-specific genetic interactions, provides new insights into gene regulation and will enable exploration of non-coding disease-associated variants.
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Affiliation(s)
- Naomi M Pacalin
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Zachary Steinhart
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Quanming Shi
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Julia A Belk
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Dmytro Dorovskyi
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Katerina Kraft
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Kevin R Parker
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
- Cartography Biosciences, Inc., South San Francisco, CA, USA
| | - Brian R Shy
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
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37
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Novy B, Dagunts A, Weishaar T, Holland EE, Adoff H, Hutchinson E, De Maria M, Kampmann M, Tsvetanova NG, Lobingier BT. An engineered trafficking biosensor reveals a role for DNAJC13 in DOR downregulation. Nat Chem Biol 2025; 21:360-370. [PMID: 39223388 PMCID: PMC11867885 DOI: 10.1038/s41589-024-01705-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 07/17/2024] [Indexed: 09/04/2024]
Abstract
Trafficking of G protein-coupled receptors (GPCRs) through the endosomal-lysosomal pathway is critical to homeostatic regulation of GPCRs following activation with agonist. Identifying the genes involved in GPCR trafficking is challenging due to the complexity of sorting operations and the large number of cellular proteins involved in the process. Here, we developed a high-sensitivity biosensor for GPCR expression and agonist-induced trafficking to the lysosome by leveraging the ability of the engineered peroxidase APEX2 to activate the fluorogenic substrate Amplex UltraRed (AUR). We used the GPCR-APEX2/AUR assay to perform a genome-wide CRISPR interference screen focused on identifying genes regulating expression and trafficking of the δ-opioid receptor (DOR). We identified 492 genes consisting of both known and new regulators of DOR function. We demonstrate that one new regulator, DNAJC13, controls trafficking of multiple GPCRs, including DOR, through the endosomal-lysosomal pathway by regulating the composition of the endosomal proteome and endosomal homeostasis.
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Affiliation(s)
- Brandon Novy
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, USA
| | - Aleksandra Dagunts
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, USA
| | - Tatum Weishaar
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, USA
| | - Emily E Holland
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, USA
| | - Hayden Adoff
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, USA
| | - Emily Hutchinson
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, USA
| | - Monica De Maria
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, USA
| | - Martin Kampmann
- Department of Biochemistry and Biophysics and Institute for Neurodegenerative Disease, University of California, San Francisco, San Francisco, CA, USA
| | | | - Braden T Lobingier
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, USA.
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38
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Hsiung CCS, Wilson CM, Sambold NA, Dai R, Chen Q, Teyssier N, Misiukiewicz S, Arab A, O'Loughlin T, Cofsky JC, Shi J, Gilbert LA. Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations. Nat Biotechnol 2025; 43:369-383. [PMID: 38760567 PMCID: PMC11919711 DOI: 10.1038/s41587-024-02224-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/28/2024] [Indexed: 05/19/2024]
Abstract
Multiplexed genetic perturbations are critical for testing functional interactions among coding or non-coding genetic elements. Compared to double-stranded DNA cutting, repressive chromatin formation using CRISPR interference (CRISPRi) avoids genotoxicity and is more effective for perturbing non-coding regulatory elements in pooled assays. However, current CRISPRi pooled screening approaches are limited to targeting one to three genomic sites per cell. We engineer an Acidaminococcus Cas12a (AsCas12a) variant, multiplexed transcriptional interference AsCas12a (multiAsCas12a), that incorporates R1226A, a mutation that stabilizes the ribonucleoprotein-DNA complex via DNA nicking. The multiAsCas12a-KRAB fusion improves CRISPRi activity over DNase-dead AsCas12a-KRAB fusions, often rescuing the activities of lentivirally delivered CRISPR RNAs (crRNA) that are inactive when used with the latter. multiAsCas12a-KRAB supports CRISPRi using 6-plex crRNA arrays in high-throughput pooled screens. Using multiAsCas12a-KRAB, we discover enhancer elements and dissect the combinatorial function of cis-regulatory elements in human cells. These results instantiate a group testing framework for efficiently surveying numerous combinations of chromatin perturbations for biological discovery and engineering.
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Affiliation(s)
- C C-S Hsiung
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Arc Institute, Palo Alto, CA, USA
| | - C M Wilson
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Arc Institute, Palo Alto, CA, USA
- Tetrad Graduate Program, University of California, San Francisco, CA, USA
| | | | - R Dai
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Arc Institute, Palo Alto, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Q Chen
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - N Teyssier
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - S Misiukiewicz
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - A Arab
- Arc Institute, Palo Alto, CA, USA
| | - T O'Loughlin
- Department of Urology, University of California, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - J C Cofsky
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - J Shi
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - L A Gilbert
- Department of Urology, University of California, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Arc Institute, Palo Alto, CA, USA.
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Schmidt H, Zhang M, Chakarov D, Bansal V, Mourelatos H, Sánchez-Rivera FJ, Lowe SW, Ventura A, Leslie CS, Pritykin Y. Genome-wide CRISPR guide RNA design and specificity analysis with GuideScan2. Genome Biol 2025; 26:41. [PMID: 40011959 PMCID: PMC11863968 DOI: 10.1186/s13059-025-03488-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 01/28/2025] [Indexed: 02/28/2025] Open
Abstract
We present GuideScan2 for memory-efficient, parallelizable construction of high-specificity CRISPR guide RNA (gRNA) databases and user-friendly design and analysis of individual gRNAs and gRNA libraries for targeting coding and non-coding regions in custom genomes. GuideScan2 analysis identifies widespread confounding effects of low-specificity gRNAs in published CRISPR screens and enables construction of a gRNA library that reduces off-target effects in a gene essentiality screen. GuideScan2 also enables the design and experimental validation of allele-specific gRNAs in a hybrid mouse genome. GuideScan2 will facilitate CRISPR experiments across a wide range of applications.
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Affiliation(s)
- Henri Schmidt
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Minsi Zhang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dimitar Chakarov
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Vineet Bansal
- Center for Statistics and Machine Learning, Princeton University, Princeton, NJ, USA
| | - Haralambos Mourelatos
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell/Rockefeller/Memorial Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Francisco J Sánchez-Rivera
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Present address: David H. Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Scott W Lowe
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrea Ventura
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Christina S Leslie
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Yuri Pritykin
- Department of Computer Science, Princeton University, Princeton, NJ, USA.
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
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40
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Kirk RW, Sun L, Xiao R, Clark EA, Nelson S. Multiplexed CRISPRi Reveals a Transcriptional Switch Between KLF Activators and Repressors in the Maturing Neocortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.07.636951. [PMID: 39975013 PMCID: PMC11839100 DOI: 10.1101/2025.02.07.636951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
A critical phase of mammalian brain development takes place after birth. Neurons of the mouse neocortex undergo dramatic changes in their morphology, physiology, and synaptic connections during the first postnatal month, while properties of immature neurons, such as the capacity for robust axon outgrowth, are lost. The genetic and epigenetic programs controlling prenatal development are well studied, but our understanding of the transcriptional mechanisms that regulate postnatal neuronal maturation is comparatively lacking. By integrating chromatin accessibility and gene expression data from two subtypes of neocortical pyramidal neurons in the neonatal and maturing brain, we predicted a role for the Krüppel-Like Factor (KLF) family of Transcription Factors in the developmental regulation of neonatally expressed genes. Using a multiplexed CRISPR Interference (CRISPRi) knockdown strategy, we found that a shift in expression from KLF activators (Klf6, Klf7) to repressors (Klf9, Klf13) during early postnatal development functions as a transcriptional 'switch' to first activate, then repress a set of shared targets with cytoskeletal functions including Tubb2b and Dpysl3. We demonstrate that this switch is buffered by redundancy between KLF paralogs, which our multiplexed CRISPRi strategy is equipped to overcome and study. Our results indicate that competition between activators and repressors within the KLF family regulates a conserved component of the postnatal maturation program that may underlie the loss of intrinsic axon growth in maturing neurons. This could facilitate the transition from axon growth to synaptic refinement required to stabilize mature circuits.
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Affiliation(s)
- Ryan W Kirk
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Liwei Sun
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Ruixuan Xiao
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Erin A Clark
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Sacha Nelson
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
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41
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Zheng X, Thompson PC, White CM, Jin X. Massively parallel in vivo Perturb-seq screening. Nat Protoc 2025:10.1038/s41596-024-01119-3. [PMID: 39939709 DOI: 10.1038/s41596-024-01119-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2024] [Accepted: 11/25/2024] [Indexed: 02/14/2025]
Abstract
Advances in genomics have identified thousands of risk genes impacting human health and diseases, but the functions of these genes and their mechanistic contribution to disease are often unclear. Moving beyond identification to actionable biological pathways requires dissecting risk gene function and cell type-specific action in intact tissues. This gap can in part be addressed by in vivo Perturb-seq, a method that combines state-of-the-art gene editing tools for programmable perturbation of genes with high-content, high-resolution single-cell genomic assays as phenotypic readouts. Here we describe a detailed protocol to perform massively parallel in vivo Perturb-seq using several versatile adeno-associated virus (AAV) vectors and provide guidance for conducting successful downstream analyses. Expertise in mouse work, AAV production and single-cell genomics is required. We discuss key parameters for designing in vivo Perturb-seq experiments across diverse biological questions and contexts. We further detail the step-by-step procedure, from designing a perturbation library to producing and administering AAV, highlighting where quality control checks can offer critical go-no-go points for this time- and cost-expensive method. Finally, we discuss data analysis options and available software. In vivo Perturb-seq has the potential to greatly accelerate functional genomics studies in mammalian systems, and this protocol will help others adopt it to answer a broad array of biological questions. From guide RNA design to tissue collection and data collection, this protocol is expected to take 9-15 weeks to complete, followed by data analysis.
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Affiliation(s)
- Xinhe Zheng
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
| | - Patrick C Thompson
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
| | - Cassandra M White
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
| | - Xin Jin
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA.
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42
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Rohm D, Black JB, McCutcheon SR, Barrera A, Berry SS, Morone DJ, Nuttle X, de Esch CE, Tai DJC, Talkowski ME, Iglesias N, Gersbach CA. Activation of the imprinted Prader-Willi syndrome locus by CRISPR-based epigenome editing. CELL GENOMICS 2025; 5:100770. [PMID: 39947136 PMCID: PMC11872474 DOI: 10.1016/j.xgen.2025.100770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 10/01/2024] [Accepted: 01/17/2025] [Indexed: 02/19/2025]
Abstract
Epigenome editing with DNA-targeting technologies such as CRISPR-dCas9 can be used to dissect gene regulatory mechanisms and potentially treat associated disorders. For example, Prader-Willi syndrome (PWS) results from loss of paternally expressed imprinted genes on chromosome 15q11.2-q13.3, although the maternal allele is intact but epigenetically silenced. Using CRISPR repression and activation screens in human induced pluripotent stem cells (iPSCs), we identified genomic elements that control the expression of the PWS gene SNRPN from the paternal and maternal chromosomes. We showed that either targeted transcriptional activation or DNA demethylation can activate the silenced maternal SNRPN and downstream PWS transcripts. However, these two approaches function at unique regions, preferentially activating different transcript variants and involving distinct epigenetic reprogramming mechanisms. Remarkably, transient expression of the targeted demethylase leads to stable, long-term maternal SNRPN expression in PWS iPSCs. This work uncovers targeted epigenetic manipulations to reprogram a disease-associated imprinted locus and suggests possible therapeutic interventions.
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Affiliation(s)
- Dahlia Rohm
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Joshua B Black
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Sean R McCutcheon
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Alejandro Barrera
- Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27708, USA
| | - Shanté S Berry
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Daniel J Morone
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Xander Nuttle
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Celine E de Esch
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Derek J C Tai
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael E Talkowski
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nahid Iglesias
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA.
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43
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Boggess SC, Gandhi V, Tsai MC, Marzette E, Teyssier N, Chou JYY, Hu X, Cramer A, Yadanar L, Shroff K, Jeong CG, Eidenschenk C, Hanson JE, Tian R, Kampmann M. A Massively Parallel CRISPR-Based Screening Platform for Modifiers of Neuronal Activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.02.28.582546. [PMID: 39990495 PMCID: PMC11844385 DOI: 10.1101/2024.02.28.582546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2025]
Abstract
Understanding the complex interplay between gene expression and neuronal activity is crucial for unraveling the molecular mechanisms underlying cognitive function and neurological disorders. Here, we developed pooled screens for neuronal activity, using CRISPR interference (CRISPRi) and the fluorescent calcium integrator CaMPARI2. Using this screening method, we evaluated 1343 genes for their effect on excitability in human iPSC-derived neurons, revealing potential links to neurodegenerative and neurodevelopmental disorders. These genes include known regulators of neuronal excitability, such as TARPs and ion channels, as well as genes associated with autism spectrum disorder and Alzheimer's disease not previously described to affect neuronal excitability. This CRISPRi-based screening platform offers a versatile tool to uncover molecular mechanisms controlling neuronal activity in health and disease.
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44
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Abbasi AF, Asim MN, Dengel A. Transitioning from wet lab to artificial intelligence: a systematic review of AI predictors in CRISPR. J Transl Med 2025; 23:153. [PMID: 39905452 PMCID: PMC11796103 DOI: 10.1186/s12967-024-06013-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2024] [Accepted: 12/18/2024] [Indexed: 02/06/2025] Open
Abstract
The revolutionary CRISPR-Cas9 system leverages a programmable guide RNA (gRNA) and Cas9 proteins to precisely cleave problematic regions within DNA sequences. This groundbreaking technology holds immense potential for the development of targeted therapies for a wide range of diseases, including cancers, genetic disorders, and hereditary diseases. CRISPR-Cas9 based genome editing is a multi-step process such as designing a precise gRNA, selecting the appropriate Cas protein, and thoroughly evaluating both on-target and off-target activity of the Cas9-gRNA complex. To ensure the accuracy and effectiveness of CRISPR-Cas9 system, after the targeted DNA cleavage, the process requires careful analysis of the resultant outcomes such as indels and deletions. Following the success of artificial intelligence (AI) in various fields, researchers are now leveraging AI algorithms to catalyze and optimize the multi-step process of CRISPR-Cas9 system. To achieve this goal AI-driven applications are being integrated into each step, but existing AI predictors have limited performance and many steps still rely on expensive and time-consuming wet-lab experiments. The primary reason behind low performance of AI predictors is the gap between CRISPR and AI fields. Effective integration of AI into multi-step CRISPR-Cas9 system demands comprehensive knowledge of both domains. This paper bridges the knowledge gap between AI and CRISPR-Cas9 research. It offers a unique platform for AI researchers to grasp deep understanding of the biological foundations behind each step in the CRISPR-Cas9 multi-step process. Furthermore, it provides details of 80 available CRISPR-Cas9 system-related datasets that can be utilized to develop AI-driven applications. Within the landscape of AI predictors in CRISPR-Cas9 multi-step process, it provides insights of representation learning methods, machine and deep learning methods trends, and performance values of existing 50 predictive pipelines. In the context of representation learning methods and classifiers/regressors, a thorough analysis of existing predictive pipelines is utilized for recommendations to develop more robust and precise predictive pipelines.
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Affiliation(s)
- Ahtisham Fazeel Abbasi
- Smart Data and Knowledge Services, German Research Center for Artificial Intelligence, 67663, Kaiserslautern, Germany.
- Department of Computer Science, Rhineland-Palatinate Technical University Kaiserslautern-Landau, 67663, Kaiserslautern, Germany.
| | - Muhammad Nabeel Asim
- Department of Computer Science, Rhineland-Palatinate Technical University Kaiserslautern-Landau, 67663, Kaiserslautern, Germany
| | - Andreas Dengel
- Smart Data and Knowledge Services, German Research Center for Artificial Intelligence, 67663, Kaiserslautern, Germany
- Department of Computer Science, Rhineland-Palatinate Technical University Kaiserslautern-Landau, 67663, Kaiserslautern, Germany
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45
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Muhar MF, Farnung J, Cernakova M, Hofmann R, Henneberg LT, Pfleiderer MM, Denoth-Lippuner A, Kalčic F, Nievergelt AS, Peters Al-Bayati M, Sidiropoulos ND, Beier V, Mann M, Jessberger S, Jinek M, Schulman BA, Bode JW, Corn JE. C-terminal amides mark proteins for degradation via SCF-FBXO31. Nature 2025; 638:519-527. [PMID: 39880951 PMCID: PMC11821526 DOI: 10.1038/s41586-024-08475-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 12/02/2024] [Indexed: 01/31/2025]
Abstract
During normal cellular homeostasis, unfolded and mislocalized proteins are recognized and removed, preventing the build-up of toxic byproducts1. When protein homeostasis is perturbed during ageing, neurodegeneration or cellular stress, proteins can accumulate several forms of chemical damage through reactive metabolites2,3. Such modifications have been proposed to trigger the selective removal of chemically marked proteins3-6; however, identifying modifications that are sufficient to induce protein degradation has remained challenging. Here, using a semi-synthetic chemical biology approach coupled to cellular assays, we found that C-terminal amide-bearing proteins (CTAPs) are rapidly cleared from human cells. A CRISPR screen identified FBXO31 as a reader of C-terminal amides. FBXO31 is a substrate receptor for the SKP1-CUL1-F-box protein (SCF) ubiquitin ligase SCF-FBXO31, which ubiquitylates CTAPs for subsequent proteasomal degradation. A conserved binding pocket enables FBXO31 to bind to almost any C-terminal peptide bearing an amide while retaining exquisite selectivity over non-modified clients. This mechanism facilitates binding and turnover of endogenous CTAPs that are formed after oxidative stress. A dominant human mutation found in neurodevelopmental disorders reverses CTAP recognition, such that non-amidated neosubstrates are now degraded and FBXO31 becomes markedly toxic. We propose that CTAPs may represent the vanguard of a largely unexplored class of modified amino acid degrons that could provide a general strategy for selective yet broad surveillance of chemically damaged proteins.
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Affiliation(s)
- Matthias F Muhar
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
| | - Jakob Farnung
- Laboratory for Organic Chemistry, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Martina Cernakova
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
| | - Raphael Hofmann
- Laboratory for Organic Chemistry, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
| | - Lukas T Henneberg
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | - Annina Denoth-Lippuner
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, Zurich, Switzerland
| | - Filip Kalčic
- Laboratory for Organic Chemistry, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
| | - Ajse S Nievergelt
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Marwa Peters Al-Bayati
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
| | - Nikolaos D Sidiropoulos
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
| | - Viola Beier
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sebastian Jessberger
- Laboratory of Neural Plasticity, Faculties of Medicine and Science, Brain Research Institute, University of Zurich, Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jeffrey W Bode
- Laboratory for Organic Chemistry, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland.
| | - Jacob E Corn
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland.
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46
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Pena IA, Shi JS, Chang SM, Yang J, Block S, Adelmann CH, Keys HR, Ge P, Bathla S, Witham IH, Sienski G, Nairn AC, Sabatini DM, Lewis CA, Kory N, Vander Heiden MG, Heiman M. SLC25A38 is required for mitochondrial pyridoxal 5'-phosphate (PLP) accumulation. Nat Commun 2025; 16:978. [PMID: 39856062 PMCID: PMC11760969 DOI: 10.1038/s41467-025-56130-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Accepted: 01/08/2025] [Indexed: 01/30/2025] Open
Abstract
Many essential proteins require pyridoxal 5'-phosphate, the active form of vitamin B6, as a cofactor for their activity. These include enzymes important for amino acid metabolism, one-carbon metabolism, polyamine synthesis, erythropoiesis, and neurotransmitter metabolism. A third of all mammalian pyridoxal 5'-phosphate-dependent enzymes are localized in the mitochondria; however, the molecular machinery involved in the regulation of mitochondrial pyridoxal 5'-phosphate levels in mammals remains unknown. In this study, we used a genome-wide CRISPR interference screen in erythroleukemia cells and organellar metabolomics to identify the mitochondrial inner membrane protein SLC25A38 as a regulator of mitochondrial pyridoxal 5'-phosphate. Loss of SLC25A38 causes depletion of mitochondrial, but not cellular, pyridoxal 5'-phosphate, and impairs cellular proliferation under both physiological and low vitamin B6 conditions. Metabolic changes associated with SLC25A38 loss suggest impaired mitochondrial pyridoxal 5'-phosphate-dependent enzymatic reactions, including serine to glycine conversion catalyzed by serine hydroxymethyltransferase-2 as well as ornithine aminotransferase. The proliferation defect of SLC25A38-null K562 cells in physiological and low vitamin B6 media can be explained by the loss of serine hydroxymethyltransferase-2-dependent production of one-carbon units and downstream de novo nucleotide synthesis. Our work points to a role for SLC25A38 in mitochondrial pyridoxal 5'-phosphate accumulation and provides insights into the pathology of congenital sideroblastic anemia.
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Affiliation(s)
- Izabella A Pena
- The Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA.
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA.
- Children's Hospital of Eastern Ontario (CHEO) Research Institute, Ottawa, ON, Canada.
| | - Jeffrey S Shi
- The Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Biology, MIT, Cambridge, MA, USA
| | - Sarah M Chang
- Department of Biology, MIT, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Harvard-MIT MD/PhD Program, Boston, MA, USA
| | - Jason Yang
- Department of Biology, MIT, Cambridge, MA, USA
| | - Samuel Block
- Department of Biology, MIT, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
| | - Charles H Adelmann
- Department of Biology, MIT, Cambridge, MA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Dermatology, Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Heather R Keys
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Preston Ge
- The Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Harvard-MIT MD/PhD Program, Boston, MA, USA
| | - Shveta Bathla
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - Isabella H Witham
- The Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | | | - Angus C Nairn
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
| | - David M Sabatini
- Institute of Organic Chemistry and Biochemistry, IOCB, Prague, Czechia
| | - Caroline A Lewis
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- UMass Chan Medical School, Program in Molecular Medicine, Worcester, MA, USA
| | - Nora Kory
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew G Vander Heiden
- Department of Biology, MIT, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Myriam Heiman
- The Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA.
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA.
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47
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Fu BXH, Xu A, Li H, Johnson DE, Grandis JR, Gilbert LA. Loss of Fanconi anemia proteins causes a reliance on lysosomal exocytosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.23.634631. [PMID: 39896609 PMCID: PMC11785144 DOI: 10.1101/2025.01.23.634631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2025]
Abstract
Mutations in the FA pathway lead to a rare genetic disease that increases risk of bone marrow failure, acute myeloid leukemia, and solid tumors. FA patients have a 500 to 800-fold increase in head and neck squamous cell carcinoma compared to the general population and the treatment for these malignancies are ineffective and limited due to the deficiency in DNA damage repair. Using unbiased CRISPR-interference screening, we found the loss of FA function renders cells dependent on key exocytosis genes such as SNAP23. Further investigation revealed that loss of FA pathway function induced deficiencies in lysosomal health, dysregulation of autophagy and increased lysosomal exocytosis. The compromised cellular state caused by the loss of FA genes is accompanied with decreased lysosome abundance and increased lysosomal membrane permeabilization in cells. We found these signatures in vitro across multiple cell types and cell lines and in clinically relevant FA patient cancers. Our findings are the first to connect the FA pathway to lysosomal exocytosis and thus expands our understanding of FA as a disease and of induced dependencies in FA mutant cancers.
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48
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Sivakumar S, Wang Y, Goetsch SC, Pandit V, Wang L, Zhao H, Sundarrajan A, Armendariz D, Takeuchi C, Nzima M, Chen WC, Dederich AE, El Hayek L, Gao T, Ghazawi R, Gogate A, Kaur K, Kim HB, McCoy MK, Niederstrasser H, Oura S, Pinzon-Arteaga CA, Sanghvi M, Schmitz DA, Yu L, Zhang Y, Zhou Q, Kraus WL, Xu L, Wu J, Posner BA, Chahrour MH, Hon GC, Munshi NV. Benchmarking and optimizing Perturb-seq in differentiating human pluripotent stem cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.21.633969. [PMID: 39896670 PMCID: PMC11785042 DOI: 10.1101/2025.01.21.633969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/04/2025]
Abstract
Perturb-seq is a powerful approach to systematically assess how genes and enhancers impact the molecular and cellular pathways of development and disease. However, technical challenges have limited its application in stem cell-based systems. Here, we benchmarked Perturb-seq across multiple CRISPRi modalities, on diverse genomic targets, in multiple human pluripotent stem cells, during directed differentiation to multiple lineages, and across multiple sgRNA delivery systems. To ensure cost-effective production of large-scale Perturb-seq datasets as part of the Impact of Genomic Variants on Function (IGVF) consortium, our optimized protocol dynamically assesses experiment quality across the weeks-long procedure. Our analysis of 1,996,260 sequenced cells across benchmarking datasets reveals shared regulatory networks linking disease-associated enhancers and genes with downstream targets during cardiomyocyte differentiation. This study establishes open tools and resources for interrogating genome function during stem cell differentiation.
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Affiliation(s)
- Sushama Sivakumar
- Department of Internal Medicine, Division of Cardiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yihan Wang
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sean C Goetsch
- Department of Internal Medicine, Division of Cardiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Vrushali Pandit
- Department of Internal Medicine, Division of Cardiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lei Wang
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Huan Zhao
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Anjana Sundarrajan
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Daniel Armendariz
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chikara Takeuchi
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Mpathi Nzima
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Wei-Chen Chen
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ashley E Dederich
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lauretta El Hayek
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Taosha Gao
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Renad Ghazawi
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ashlesha Gogate
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kiran Kaur
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hyung Bum Kim
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Melissa K McCoy
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Seiya Oura
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Carolos A Pinzon-Arteaga
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Menaka Sanghvi
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Daniel A Schmitz
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Leqian Yu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yanfeng Zhang
- Quantitative Biomedical Research Center, Peter O’Donnell Jr School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Qinbo Zhou
- Quantitative Biomedical Research Center, Peter O’Donnell Jr School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - W. Lee Kraus
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lin Xu
- Quantitative Biomedical Research Center, Peter O’Donnell Jr School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pediatrics, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bruce A Posner
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Maria H Chahrour
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Peter O’Donnell Jr Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Gary C Hon
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Lyda Hill Department of Bioinformatics, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nikhil V Munshi
- Department of Internal Medicine, Division of Cardiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
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49
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Arvidsson E, Lobo DD, Sabarese E, Duarte F, Nobre RJ, Quintino L, Lundberg C. A systematic screening assay identifies efficient small guide RNAs for CRISPR activation. Front Bioeng Biotechnol 2025; 13:1336313. [PMID: 39917018 PMCID: PMC11799263 DOI: 10.3389/fbioe.2025.1336313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/06/2025] [Indexed: 02/09/2025] Open
Abstract
CRISPR-mediated gene activation (CRISPRa) encompasses a growing field of biotechnological approaches with exciting implications for gene therapy. However, there is a lack of experimental validation tools for selecting efficient sgRNAs for downstream applications. Here, we present a screening assay capable of identifying efficient single- and double sgRNAs through fluorescence quantification in vitro. In addition, we provide a tailored Golden Gate cloning workflow for streamlined incorporation of selected sgRNA candidates into lentiviral (LVs) or adeno-associated viral vectors (AAVs). The overall workflow was validated using therapeutically relevant genes for neurodegenerative diseases, including Tfeb, Adam17, and Sirt1. The most efficient sgRNAs also demonstrated activation of endogenous gene expression at mRNA level. Correlation analysis of gene activation relative to sgRNA binding site distance to transcription start-site or nearby transcription factor binding sites failed to detect common characteristics influencing gene activation in the selected promoter regions. This data demonstrates the potential of the screening assay to identify functionally efficient sgRNA candidates across multiple genes along with streamlined cloning of viral vectors and may assist in accelerating future developments of CRISPRa-focused applications.
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Affiliation(s)
- Elin Arvidsson
- CNS Gene Therapy, Department of Experimental Medical Sciences, Lund University, Lund, Sweden
| | - Diana Duarte Lobo
- CNC - Center for Neuroscience and Cell Biology of Coimbra, University of Coimbra, Coimbra, Portugal
- Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Ermelinda Sabarese
- CNS Gene Therapy, Department of Experimental Medical Sciences, Lund University, Lund, Sweden
| | - Fabio Duarte
- CNS Gene Therapy, Department of Experimental Medical Sciences, Lund University, Lund, Sweden
| | - Rui Jorge Nobre
- CNC - Center for Neuroscience and Cell Biology of Coimbra, University of Coimbra, Coimbra, Portugal
- Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
- ViraVector – Viral Vector for Gene Transfer Core Facility, University of Coimbra, Coimbra, Portugal
| | - Luis Quintino
- CNS Gene Therapy, Department of Experimental Medical Sciences, Lund University, Lund, Sweden
| | - Cecilia Lundberg
- CNS Gene Therapy, Department of Experimental Medical Sciences, Lund University, Lund, Sweden
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50
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Rengarajan S, Derks J, Bellott DW, Slavov N, Page DC. Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicases DDX3X and DDX3Y. Genome Res 2025; 35:20-30. [PMID: 39794123 PMCID: PMC11789639 DOI: 10.1101/gr.279707.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Accepted: 11/26/2024] [Indexed: 01/13/2025]
Abstract
The Y-linked gene DDX3Y and its X-linked homolog DDX3X survived the evolution of the human sex chromosomes from ordinary autosomes. DDX3X encodes a multifunctional RNA helicase, with mutations causing developmental disorders and cancers. We find that, among X-linked genes with surviving Y homologs, DDX3X is extraordinarily dosage sensitive. Studying cells of individuals with sex chromosome aneuploidy, we observe that when the number of Y Chromosomes increases, DDX3X transcript levels fall; conversely, when the number of X Chromosomes increases, DDX3Y transcript levels fall. In 46,XY cells, CRISPRi knockdown of either DDX3X or DDX3Y causes transcript levels of the homologous gene to rise. In 46,XX cells, chemical inhibition of DDX3X protein activity elicits an increase in DDX3X transcript levels. Thus, perturbation of either DDX3X or DDX3Y expression is buffered: by negative cross-regulation of DDX3X and DDX3Y in 46,XY cells and by negative auto-regulation of DDX3X in 46,XX cells. DDX3X-DDX3Y cross-regulation is mediated through mRNA destabilization-as shown by metabolic labeling of newly transcribed RNA-and buffers total levels of DDX3X and DDX3Y protein in human cells. We infer that post-transcriptional auto-regulation of the ancestral (autosomal) DDX3X gene transmuted into auto- and cross-regulation of DDX3X and DDX3Y as these sex-linked genes evolved from ordinary alleles of their autosomal precursor.
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Affiliation(s)
- Shruthi Rengarajan
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jason Derks
- Departments of Bioengineering, Biology, Chemistry, and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, Massachusetts 02115, USA
| | | | - Nikolai Slavov
- Departments of Bioengineering, Biology, Chemistry, and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, Massachusetts 02115, USA
| | - David C Page
- Whitehead Institute, Cambridge, Massachusetts 02142, USA;
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
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