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Ji J, Cui MK, Zou R, Wu MZ, Ge MX, Li J, Zhang ZR. An ATP13A1-assisted topogenesis pathway for folding multi-spanning membrane proteins. Mol Cell 2024; 84:1917-1931.e15. [PMID: 38723633 DOI: 10.1016/j.molcel.2024.04.010] [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: 06/27/2023] [Revised: 02/15/2024] [Accepted: 04/17/2024] [Indexed: 05/19/2024]
Abstract
Many multi-spanning membrane proteins contain poorly hydrophobic transmembrane domains (pTMDs) protected from phospholipid in mature structure. Nascent pTMDs are difficult for translocon to recognize and insert. How pTMDs are discerned and packed into mature, muti-spanning configuration remains unclear. Here, we report that pTMD elicits a post-translational topogenesis pathway for its recognition and integration. Using six-spanning protein adenosine triphosphate-binding cassette transporter G2 (ABCG2) and cultured human cells as models, we show that ABCG2's pTMD2 can pass through translocon into the endoplasmic reticulum (ER) lumen, yielding an intermediate with inserted yet mis-oriented downstream TMDs. After translation, the intermediate recruits P5A-ATPase ATP13A1, which facilitates TMD re-orientation, allowing further folding and the integration of the remaining lumen-exposed pTMD2. Depleting ATP13A1 or disrupting pTMD-characteristic residues arrests intermediates with mis-oriented and exposed TMDs. Our results explain how a "difficult" pTMD is co-translationally skipped for insertion and post-translationally buried into the final correct structure at the late folding stage to avoid excessive lipid exposure.
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Affiliation(s)
- Jia Ji
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China
| | - Meng-Ke Cui
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China
| | - Rong Zou
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China
| | - Ming-Zhi Wu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China
| | - Man-Xi Ge
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China
| | - Jiqiang Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China
| | - Zai-Rong Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100101, China.
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Gentili M, Carlson RJ, Liu B, Hellier Q, Andrews J, Qin Y, Blainey PC, Hacohen N. Classification and functional characterization of regulators of intracellular STING trafficking identified by genome-wide optical pooled screening. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.07.588166. [PMID: 38645119 PMCID: PMC11030420 DOI: 10.1101/2024.04.07.588166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
STING is an innate immune sensor that traffics across many cellular compartments to carry out its function of detecting cyclic di-nucleotides and triggering defense processes. Mutations in factors that regulate this process are often linked to STING-dependent human inflammatory disorders. To systematically identify factors involved in STING trafficking, we performed a genome-wide optical pooled screen and examined the impact of genetic perturbations on intracellular STING localization. Based on subcellular imaging of STING protein and trafficking markers in 45 million cells perturbed with sgRNAs, we defined 464 clusters of gene perturbations with similar cellular phenotypes. A higher-dimensional focused optical pooled screen on 262 perturbed genes which assayed 11 imaging channels identified 73 finer phenotypic clusters. In a cluster containing USE1, a protein that mediates Golgi to ER transport, we found a gene of unknown function, C19orf25. Consistent with the known role of USE1, loss of C19orf25 enhanced STING signaling. Other clusters contained subunits of the HOPS, GARP and RIC1-RGP1 complexes. We show that HOPS deficiency delayed STING degradation and consequently increased signaling. Similarly, GARP/RIC1-RGP1 loss increased STING signaling by delaying STING exit from the Golgi. Our findings demonstrate that genome-wide genotype-phenotype maps based on high-content cell imaging outperform other screening approaches, and provide a community resource for mining for factors that impact STING trafficking as well as other cellular processes observable in our dataset.
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3
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Carlson RJ, Patten JJ, Stefanakis G, Soong BY, Radhakrishnan A, Singh A, Thakur N, Amarasinghe GK, Hacohen N, Basler CF, Leung D, Uhler C, Davey RA, Blainey PC. Single-cell image-based genetic screens systematically identify regulators of Ebola virus subcellular infection dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.06.588168. [PMID: 38617272 PMCID: PMC11014611 DOI: 10.1101/2024.04.06.588168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Ebola virus (EBOV) is a high-consequence filovirus that gives rise to frequent epidemics with high case fatality rates and few therapeutic options. Here, we applied image-based screening of a genome-wide CRISPR library to systematically identify host cell regulators of Ebola virus infection in 39,085,093 million single cells. Measuring viral RNA and protein levels together with their localization in cells identified over 998 related host factors and provided detailed information about the role of each gene across the virus replication cycle. We trained a deep learning model on single-cell images to associate each host factor with predicted replication steps, and confirmed the predicted relationship for select host factors. Among the findings, we showed that the mitochondrial complex III subunit UQCRB is a post-entry regulator of Ebola virus RNA replication, and demonstrated that UQCRB inhibition with a small molecule reduced overall Ebola virus infection with an IC50 of 5 μM. Using a random forest model, we also identified perturbations that reduced infection by disrupting the equilibrium between viral RNA and protein. One such protein, STRAP, is a spliceosome-associated factor that was found to be closely associated with VP35, a viral protein required for RNA processing. Loss of STRAP expression resulted in a reduction in full-length viral genome production and subsequent production of non-infectious virus particles. Overall, the data produced in this genome-wide high-content single-cell screen and secondary screens in additional cell lines and related filoviruses (MARV and SUDV) revealed new insights about the role of host factors in virus replication and potential new targets for therapeutic intervention.
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Affiliation(s)
- Rebecca J Carlson
- Massachusetts Institute of Technology, Department of Health Sciences and Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - J J Patten
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - George Stefanakis
- Laboratory for Information & Decision Systems, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Brian Y Soong
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Adityanarayanan Radhakrishnan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard School of Engineering and Applied Sciences, Cambridge, MA, USA
| | - Avtar Singh
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Naveen Thakur
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gaya K Amarasinghe
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital, Cancer Center, Boston, MA, USA
| | - Christopher F Basler
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daisy Leung
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Caroline Uhler
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Laboratory for Information & Decision Systems, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Robert A Davey
- Department of Virology, Immunology, and Microbiology, Boston University School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Massachusetts Institute of Technology, Department of Biological Engineering, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
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Walton RT, Qin Y, Blainey PC. CROPseq-multi: a versatile solution for multiplexed perturbation and decoding in pooled CRISPR screens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.17.585235. [PMID: 38558968 PMCID: PMC10979941 DOI: 10.1101/2024.03.17.585235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Forward genetic screens seek to dissect complex biological systems by systematically perturbing genetic elements and observing the resulting phenotypes. While standard screening methodologies introduce individual perturbations, multiplexing perturbations improves the performance of single-target screens and enables combinatorial screens for the study of genetic interactions. Current tools for multiplexing perturbations are incompatible with pooled screening methodologies that require mRNA-embedded barcodes, including some microscopy and single cell sequencing approaches. Here, we report the development of CROPseq-multi, a CROPseq1-inspired lentiviral system to multiplex Streptococcus pyogenes (Sp) Cas9-based perturbations with mRNA-embedded barcodes. CROPseq-multi has equivalent per-guide activity to CROPseq and low lentiviral recombination frequencies. CROPseq-multi is compatible with enrichment screening methodologies and optical pooled screens, and is extensible to screens with single-cell sequencing readouts. For optical pooled screens, an optimized and multiplexed in situ detection protocol improves barcode detection efficiency 10-fold, enables detection of recombination events, and increases decoding efficiency 3-fold relative to CROPseq. CROPseq-multi is a widely applicable multiplexing solution for diverse SpCas9-based genetic screening approaches.
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Affiliation(s)
- Russell T. Walton
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Yue Qin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Eric and Wendy Schmidt Center, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paul C. Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
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Gu J, Iyer A, Wesley B, Taglialatela A, Leuzzi G, Hangai S, Decker A, Gu R, Klickstein N, Shuai Y, Jankovic K, Parker-Burns L, Jin Y, Zhang JY, Hong J, Niu S, Chou J, Landau DA, Azizi E, Chan EM, Ciccia A, Gaublomme JT. CRISPRmap: Sequencing-free optical pooled screens mapping multi-omic phenotypes in cells and tissue. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.26.572587. [PMID: 38234835 PMCID: PMC10793456 DOI: 10.1101/2023.12.26.572587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Pooled genetic screens are powerful tools to study gene function in a high-throughput manner. Typically, sequencing-based screens require cell lysis, which limits the examination of critical phenotypes such as cell morphology, protein subcellular localization, and cell-cell/tissue interactions. In contrast, emerging optical pooled screening methods enable the investigation of these spatial phenotypes in response to targeted CRISPR perturbations. In this study, we report a multi-omic optical pooled CRISPR screening method, which we have named CRISPRmap. Our method combines a novel in situ CRISPR guide identifying barcode readout approach with concurrent multiplexed immunofluorescence and in situ RNA detection. CRISPRmap barcodes are detected and read out through combinatorial hybridization of DNA oligos, enhancing barcode detection efficiency, while reducing both dependency on third party proprietary sequencing reagents and assay cost. Notably, we conducted a multi-omic base-editing screen in a breast cancer cell line on core DNA damage repair genes involved in the homologous recombination and Fanconi anemia pathways investigating how nucleotide variants in those genes influence DNA damage signaling and cell cycle regulation following treatment with ionizing radiation or DNA damaging agents commonly used for cancer therapy. Approximately a million cells were profiled with our multi-omic approach, providing a comprehensive phenotypic assessment of the functional consequences of the studied variants. CRISPRmap enabled us to pinpoint likely-pathogenic patient-derived mutations that were previously classified as variants of unknown clinical significance. Furthermore, our approach effectively distinguished barcodes of a pooled library in tumor tissue, and we coupled it with cell-type and molecular phenotyping by cyclic immunofluorescence. Multi-omic spatial analysis of how CRISPR-perturbed cells respond to various environmental cues in the tissue context offers the potential to significantly expand our understanding of tissue biology in both health and disease.
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Affiliation(s)
- Jiacheng Gu
- Department of Biological Sciences, Columbia University, NY, USA
| | - Abhishek Iyer
- Department of Biological Sciences, Columbia University, NY, USA
| | - Ben Wesley
- Department of Biological Sciences, Columbia University, NY, USA
| | - Angelo Taglialatela
- Department of Genetics and Development, Columbia University Irving Medical Center, NY, USA
| | - Giuseppe Leuzzi
- Department of Genetics and Development, Columbia University Irving Medical Center, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, NY, USA
- Institute for Cancer Genetics, Columbia University Irving Medical Center, NY, USA
| | - Sho Hangai
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, NY, USA
| | | | - Ruoyu Gu
- Department of Biological Sciences, Columbia University, NY, USA
| | | | - Yuanlong Shuai
- Department of Biological Sciences, Columbia University, NY, USA
| | - Kristina Jankovic
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, NY, USA
| | - Lucy Parker-Burns
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, NY, USA
| | - Yinuo Jin
- Department of Biomedical Engineering, Columbia University, NY, USA
| | - Jia Yi Zhang
- Department of Biomedical Engineering, Columbia University, NY, USA
| | - Justin Hong
- Department of Computer Science, Columbia University, NY, USA
| | - Steve Niu
- Weill Cornell Medicine, NY, USA
- Genentech Research and Early Development, CA, USA
| | - Jacqueline Chou
- Department of Biological Sciences, Columbia University, NY, USA
- Weill Cornell Medicine, NY, USA
| | - Dan A. Landau
- Weill Cornell Medicine, NY, USA
- New York Genome Center, NY, USA
| | - Elham Azizi
- Department of Biomedical Engineering, Columbia University, NY, USA
- Department of Computer Science, Columbia University, NY, USA
- Irving Institute for Cancer Dynamics, Columbia University, NY, USA
| | - Edmond M. Chan
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, NY, USA
- New York Genome Center, NY, USA
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, NY, USA
| | - Alberto Ciccia
- Department of Genetics and Development, Columbia University Irving Medical Center, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, NY, USA
- Institute for Cancer Genetics, Columbia University Irving Medical Center, NY, USA
| | - Jellert T. Gaublomme
- Department of Biological Sciences, Columbia University, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, NY, USA
- New York Genome Center, NY, USA
- Irving Institute for Cancer Dynamics, Columbia University, NY, USA
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6
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Gokhale NS, Somfleth K, Thompson MG, Sam RK, Marciniak DM, Chu LH, Park M, Dvorkin S, Oberst A, Horner SM, Ong SE, Gale M, Savan R. CELLULAR RNA INTERACTS WITH MAVS TO PROMOTE ANTIVIRAL SIGNALING. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.559083. [PMID: 37808873 PMCID: PMC10557580 DOI: 10.1101/2023.09.25.559083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Immune signaling needs to be well-regulated to promote clearance of pathogens, while preventing aberrant inflammation. Interferons (IFNs) and antiviral genes are activated by the detection of viral RNA by RIG-I-like receptors (RLRs). Signal transduction downstream of RLRs proceeds through a multi-protein complex organized around the central adaptor protein MAVS. Recent work has shown that protein complex function can be modulated by RNA molecules providing allosteric regulation or acting as molecular guides or scaffolds. Thus, we hypothesized that RNA plays a role in organizing MAVS signaling platforms. Here, we show that MAVS, through its central intrinsically disordered domain, directly interacts with the 3' untranslated regions of cellular mRNAs. Importantly, elimination of RNA by RNase treatment disrupts the MAVS signalosome, including newly identified regulators of RLR signaling, and inhibits phosphorylation of the transcription factor IRF3. This supports the hypothesis that RNA molecules scaffold proteins in the MAVS signalosome to induce IFNs. Together, this work uncovers a function for cellular RNA in promoting signaling through MAVS and highlights a generalizable principle of RNA regulatory control of cytoplasmic immune signaling complexes.
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Affiliation(s)
| | - Kim Somfleth
- Department of Immunology, University of Washington, Seattle, WA
| | | | - Russell K Sam
- Department of Immunology, University of Washington, Seattle, WA
| | | | - Lan H Chu
- Department of Immunology, University of Washington, Seattle, WA
| | - Moonhee Park
- Department of Integrative Immunobiology, Duke University, Durham, NC
| | - Steve Dvorkin
- Department of Immunology, University of Washington, Seattle, WA
| | - Andrew Oberst
- Department of Immunology, University of Washington, Seattle, WA
| | - Stacy M Horner
- Department of Integrative Immunobiology, Duke University, Durham, NC
- Department of Medicine, Duke University, Durham NC
| | - Shao-En Ong
- Department of Pharmacology, University of Washington, Seattle, WA
| | - Michael Gale
- Department of Immunology, University of Washington, Seattle, WA
| | - Ram Savan
- Department of Immunology, University of Washington, Seattle, WA
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Carlson RJ, Leiken MD, Guna A, Hacohen N, Blainey PC. A genome-wide optical pooled screen reveals regulators of cellular antiviral responses. Proc Natl Acad Sci U S A 2023; 120:e2210623120. [PMID: 37043539 PMCID: PMC10120039 DOI: 10.1073/pnas.2210623120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 02/06/2023] [Indexed: 04/13/2023] Open
Abstract
The infection of mammalian cells by viruses and innate immune responses to infection are spatiotemporally organized processes. Cytosolic RNA sensors trigger nuclear translocation of the transcription factor interferon regulatory factor 3 (IRF3) and consequent induction of host immune responses to RNA viruses. Previous genetic screens for factors involved in viral sensing did not resolve changes in the subcellular localization of host or viral proteins. Here, we increased the throughput of our optical pooled screening technology by over fourfold. This allowed us to carry out a genome-wide CRISPR knockout screen using high-resolution multiparameter imaging of cellular responses to Sendai virus infection coupled with in situ cDNA sequencing by synthesis (SBS) to identify 80,408 single guide RNAs (sgRNAs) in 10,366,390 cells-over an order of magnitude more genomic perturbations than demonstrated previously using an in situ SBS readout. By ranking perturbations using human-designed and deep learning image feature scores, we identified regulators of IRF3 translocation, Sendai virus localization, and peroxisomal biogenesis. Among the hits, we found that ATP13A1, an ER-localized P5A-type ATPase, is essential for viral sensing and is required for targeting of mitochondrial antiviral signaling protein (MAVS) to mitochondrial membranes where MAVS must be localized for effective signaling through retinoic acid-inducible gene I (RIG-I). The ability to carry out genome-wide pooled screens with complex high-resolution image-based phenotyping dramatically expands the scope of functional genomics approaches.
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Affiliation(s)
- Rebecca J. Carlson
- Department of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA02139
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
| | - Michael D. Leiken
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
| | | | - Nir Hacohen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA02114
| | - Paul C. Blainey
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02142
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA02139
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