1
|
König LE, Rodriguez S, Hug C, Daneshvari S, Chung A, Bradshaw GA, Sahin A, Zhou G, Eisert RJ, Piccioni F, Das S, Kalocsay M, Sokolov A, Sorger P, Root DE, Albers MW. TYK2 as a novel therapeutic target in Alzheimer's Disease with TDP-43 inclusions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.595773. [PMID: 38895380 PMCID: PMC11185596 DOI: 10.1101/2024.06.04.595773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Neuroinflammation is a pathological feature of many neurodegenerative diseases, including Alzheimer's disease (AD)1,2 and amyotrophic lateral sclerosis (ALS)3, raising the possibility of common therapeutic targets. We previously established that cytoplasmic double-stranded RNA (cdsRNA) is spatially coincident with cytoplasmic pTDP-43 inclusions in neurons of patients with C9ORF72-mediated ALS4. CdsRNA triggers a type-I interferon (IFN-I)-based innate immune response in human neural cells, resulting in their death4. Here, we report that cdsRNA is also spatially coincident with pTDP-43 cytoplasmic inclusions in brain cells of patients with AD pathology and that type-I interferon response genes are significantly upregulated in brain regions affected by AD. We updated our machine-learning pipeline DRIAD-SP (Drug Repurposing In Alzheimer's Disease with Systems Pharmacology) to incorporate cryptic exon (CE) detection as a proxy of pTDP-43 inclusions and demonstrated that the FDA-approved JAK inhibitors baricitinib and ruxolitinib that block interferon signaling show a protective signal only in cortical brain regions expressing multiple CEs. Furthermore, the JAK family member TYK2 was a top hit in a CRISPR screen of cdsRNA-mediated death in differentiated human neural cells. The selective TYK2 inhibitor deucravacitinib, an FDA-approved drug for psoriasis, rescued toxicity elicited by cdsRNA. Finally, we identified CCL2, CXCL10, and IL-6 as candidate predictive biomarkers for cdsRNA-related neurodegenerative diseases. Together, we find parallel neuroinflammatory mechanisms between TDP-43 associated-AD and ALS and nominate TYK2 as a possible disease-modifying target of these incurable neurodegenerative diseases.
Collapse
Affiliation(s)
- Laura E. König
- Laboratory of Systems Pharmacology, Harvard Program in
Therapeutic Science, Harvard Medical School, Armenise 132, 200 Longwood Avenue,
Boston, MA 02115, USA
- Department of Neurology, Massachusetts General Hospital,
114 16 Street, Charlestown, MA 02129, USA
| | - Steve Rodriguez
- Laboratory of Systems Pharmacology, Harvard Program in
Therapeutic Science, Harvard Medical School, Armenise 132, 200 Longwood Avenue,
Boston, MA 02115, USA
- Department of Neurology, Massachusetts General Hospital,
114 16 Street, Charlestown, MA 02129, USA
| | - Clemens Hug
- Laboratory of Systems Pharmacology, Harvard Program in
Therapeutic Science, Harvard Medical School, Armenise 132, 200 Longwood Avenue,
Boston, MA 02115, USA
| | - Shayda Daneshvari
- Laboratory of Systems Pharmacology, Harvard Program in
Therapeutic Science, Harvard Medical School, Armenise 132, 200 Longwood Avenue,
Boston, MA 02115, USA
- Department of Neurology, Massachusetts General Hospital,
114 16 Street, Charlestown, MA 02129, USA
| | - Alexander Chung
- Laboratory of Systems Pharmacology, Harvard Program in
Therapeutic Science, Harvard Medical School, Armenise 132, 200 Longwood Avenue,
Boston, MA 02115, USA
- Department of Neurology, Massachusetts General Hospital,
114 16 Street, Charlestown, MA 02129, USA
| | - Gary A. Bradshaw
- Laboratory of Systems Pharmacology, Harvard Program in
Therapeutic Science, Harvard Medical School, Armenise 132, 200 Longwood Avenue,
Boston, MA 02115, USA
| | - Asli Sahin
- Department of Neurology, Massachusetts General Hospital,
114 16 Street, Charlestown, MA 02129, USA
| | - George Zhou
- Department of Neurology, Massachusetts General Hospital,
114 16 Street, Charlestown, MA 02129, USA
| | - Robyn J. Eisert
- Laboratory of Systems Pharmacology, Harvard Program in
Therapeutic Science, Harvard Medical School, Armenise 132, 200 Longwood Avenue,
Boston, MA 02115, USA
| | - Federica Piccioni
- Broad Institute of MIT and Harvard, 75 Ames Street,
Cambridge, MA 02142, USA
| | - Sudeshna Das
- Department of Neurology, Massachusetts General Hospital,
114 16 Street, Charlestown, MA 02129, USA
| | - Marian Kalocsay
- Laboratory of Systems Pharmacology, Harvard Program in
Therapeutic Science, Harvard Medical School, Armenise 132, 200 Longwood Avenue,
Boston, MA 02115, USA
| | - Artem Sokolov
- Laboratory of Systems Pharmacology, Harvard Program in
Therapeutic Science, Harvard Medical School, Armenise 132, 200 Longwood Avenue,
Boston, MA 02115, USA
| | - Peter Sorger
- Laboratory of Systems Pharmacology, Harvard Program in
Therapeutic Science, Harvard Medical School, Armenise 132, 200 Longwood Avenue,
Boston, MA 02115, USA
| | - David E. Root
- Broad Institute of MIT and Harvard, 75 Ames Street,
Cambridge, MA 02142, USA
| | - Mark W. Albers
- Laboratory of Systems Pharmacology, Harvard Program in
Therapeutic Science, Harvard Medical School, Armenise 132, 200 Longwood Avenue,
Boston, MA 02115, USA
- Department of Neurology, Massachusetts General Hospital,
114 16 Street, Charlestown, MA 02129, USA
| |
Collapse
|
2
|
Ast T, Itoh Y, Sadre S, McCoy JG, Namkoong G, Wengrod JC, Chicherin I, Joshi PR, Kamenski P, Suess DLM, Amunts A, Mootha VK. METTL17 is an Fe-S cluster checkpoint for mitochondrial translation. Mol Cell 2024; 84:359-374.e8. [PMID: 38199006 PMCID: PMC11046306 DOI: 10.1016/j.molcel.2023.12.016] [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: 11/02/2022] [Revised: 08/13/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024]
Abstract
Friedreich's ataxia (FA) is a debilitating, multisystemic disease caused by the depletion of frataxin (FXN), a mitochondrial iron-sulfur (Fe-S) cluster biogenesis factor. To understand the cellular pathogenesis of FA, we performed quantitative proteomics in FXN-deficient human cells. Nearly every annotated Fe-S cluster-containing protein was depleted, indicating that as a rule, cluster binding confers stability to Fe-S proteins. We also observed depletion of a small mitoribosomal assembly factor METTL17 and evidence of impaired mitochondrial translation. Using comparative sequence analysis, mutagenesis, biochemistry, and cryoelectron microscopy, we show that METTL17 binds to the mitoribosomal small subunit during late assembly and harbors a previously unrecognized [Fe4S4]2+ cluster required for its stability. METTL17 overexpression rescued the mitochondrial translation and bioenergetic defects, but not the cellular growth, of FXN-depleted cells. These findings suggest that METTL17 acts as an Fe-S cluster checkpoint, promoting translation of Fe-S cluster-rich oxidative phosphorylation (OXPHOS) proteins only when Fe-S cofactors are replete.
Collapse
Affiliation(s)
- Tslil Ast
- Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Yuzuru Itoh
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Shayan Sadre
- Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jason G McCoy
- Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Gil Namkoong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jordan C Wengrod
- Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Ivan Chicherin
- Department of Biology, M.V.Lomonosov Moscow State University, Moscow 119234, Russia
| | - Pallavi R Joshi
- Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Piotr Kamenski
- Department of Biology, M.V.Lomonosov Moscow State University, Moscow 119234, Russia
| | - Daniel L M Suess
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alexey Amunts
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Vamsi K Mootha
- Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
3
|
Hofman DA, Ruiz-Orera J, Yannuzzi I, Murugesan R, Brown A, Clauser KR, Condurat AL, van Dinter JT, Engels SAG, Goodale A, van der Lugt J, Abid T, Wang L, Zhou KN, Vogelzang J, Ligon KL, Phoenix TN, Roth JA, Root DE, Hubner N, Golub TR, Bandopadhayay P, van Heesch S, Prensner JR. Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma. Mol Cell 2024; 84:261-276.e18. [PMID: 38176414 PMCID: PMC10872554 DOI: 10.1016/j.molcel.2023.12.003] [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: 05/16/2023] [Revised: 08/30/2023] [Accepted: 12/01/2023] [Indexed: 01/06/2024]
Abstract
A hallmark of high-risk childhood medulloblastoma is the dysregulation of RNA translation. Currently, it is unknown whether medulloblastoma dysregulates the translation of putatively oncogenic non-canonical open reading frames (ORFs). To address this question, we performed ribosome profiling of 32 medulloblastoma tissues and cell lines and observed widespread non-canonical ORF translation. We then developed a stepwise approach using multiple CRISPR-Cas9 screens to elucidate non-canonical ORFs and putative microproteins implicated in medulloblastoma cell survival. We determined that multiple lncRNA-ORFs and upstream ORFs (uORFs) exhibited selective functionality independent of main coding sequences. A microprotein encoded by one of these ORFs, ASNSD1-uORF or ASDURF, was upregulated, associated with MYC-family oncogenes, and promoted medulloblastoma cell survival through engagement with the prefoldin-like chaperone complex. Our findings underscore the fundamental importance of non-canonical ORF translation in medulloblastoma and provide a rationale to include these ORFs in future studies seeking to define new cancer targets.
Collapse
Affiliation(s)
- Damon A Hofman
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Ian Yannuzzi
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Adam Brown
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Karl R Clauser
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexandra L Condurat
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jip T van Dinter
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Sem A G Engels
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Amy Goodale
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jasper van der Lugt
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Tanaz Abid
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Li Wang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kevin N Zhou
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jayne Vogelzang
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Keith L Ligon
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02215, USA; Department of Pathology, Boston Children's Hospital, Boston MA 02115, USA
| | - Timothy N Phoenix
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Jennifer A Roth
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; Charité-Universitätsmedizin, 10117 Berlin, Germany; German Centre for Cardiovascular Research, Partner Site Berlin, 13347 Berlin, Germany
| | - Todd R Golub
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Pratiti Bandopadhayay
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Sebastiaan van Heesch
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands.
| | - John R Prensner
- Department of Pediatrics, Division of Pediatric Hematology/Oncology and Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| |
Collapse
|
4
|
Abid T, Goodale AB, Kalani Z, Wyatt M, Gonzalez EM, Zhou KN, Qian K, Novikov D, Condurat AL, Bandopadhayay P, Piccioni F, Persky NS, Root DE. Genome-wide pooled CRISPR screening in neurospheres. Nat Protoc 2023:10.1038/s41596-023-00835-6. [PMID: 37286821 DOI: 10.1038/s41596-023-00835-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 03/20/2023] [Indexed: 06/09/2023]
Abstract
Spheroid culture systems have allowed in vitro propagation of cells unable to grow in canonical cell culturing conditions, and may capture cellular contexts that model tumor growth better than current model systems. The insights gleaned from genome-wide clustered regularly interspaced short palindromic repeat (CRISPR) screening of thousands of cancer cell lines grown in conventional culture conditions illustrate the value of such CRISPR pooled screens. It is clear that similar genome-wide CRISPR screens of three-dimensional spheroid cultures will be important for future biological discovery. Here, we present a protocol for genome-wide CRISPR screening of three-dimensional neurospheres. While many in-depth protocols and discussions have been published for more typical cell lines, few detailed protocols are currently available in the literature for genome-wide screening in spheroidal cell lines. For those who want to screen such cell lines, and particularly neurospheres, we provide a step-by-step description of assay development tests to be performed before screening, as well as for the screen itself. We highlight considerations of variables that make these screens distinct from, or similar to, typical nonspheroid cell lines throughout. Finally, we illustrate typical outcomes of neurosphere genome-wide screens, and how neurosphere screens typically produce slightly more heterogeneous signal distributions than more canonical cancer cell lines. Completion of this entire protocol will take 8-12 weeks from the initial assay development tests to deconvolution of the sequencing data.
Collapse
Affiliation(s)
- Tanaz Abid
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amy B Goodale
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zohra Kalani
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Meghan Wyatt
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Elizabeth M Gonzalez
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Kevin Ning Zhou
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Kenin Qian
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Dana Novikov
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Alexandra-Larisa Condurat
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Pratiti Bandopadhayay
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
| | - Federica Piccioni
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Merck Research Laboratories, Cambridge, MA, USA.
| | - Nicole S Persky
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Aera Therapeutics, Boston, MA, USA.
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| |
Collapse
|
5
|
Wells MF, Nemesh J, Ghosh S, Mitchell JM, Salick MR, Mello CJ, Meyer D, Pietilainen O, Piccioni F, Guss EJ, Raghunathan K, Tegtmeyer M, Hawes D, Neumann A, Worringer KA, Ho D, Kommineni S, Chan K, Peterson BK, Raymond JJ, Gold JT, Siekmann MT, Zuccaro E, Nehme R, Kaykas A, Eggan K, McCarroll SA. Natural variation in gene expression and viral susceptibility revealed by neural progenitor cell villages. Cell Stem Cell 2023; 30:312-332.e13. [PMID: 36796362 PMCID: PMC10581885 DOI: 10.1016/j.stem.2023.01.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/28/2022] [Accepted: 01/23/2023] [Indexed: 02/17/2023]
Abstract
Human genome variation contributes to diversity in neurodevelopmental outcomes and vulnerabilities; recognizing the underlying molecular and cellular mechanisms will require scalable approaches. Here, we describe a "cell village" experimental platform we used to analyze genetic, molecular, and phenotypic heterogeneity across neural progenitor cells from 44 human donors cultured in a shared in vitro environment using algorithms (Dropulation and Census-seq) to assign cells and phenotypes to individual donors. Through rapid induction of human stem cell-derived neural progenitor cells, measurements of natural genetic variation, and CRISPR-Cas9 genetic perturbations, we identified a common variant that regulates antiviral IFITM3 expression and explains most inter-individual variation in susceptibility to the Zika virus. We also detected expression QTLs corresponding to GWAS loci for brain traits and discovered novel disease-relevant regulators of progenitor proliferation and differentiation such as CACHD1. This approach provides scalable ways to elucidate the effects of genes and genetic variation on cellular phenotypes.
Collapse
Affiliation(s)
- Michael F Wells
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Department of Human Genetics, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - James Nemesh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sulagna Ghosh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jana M Mitchell
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Insitro, South San Francisco, CA 94080, USA
| | | | - Curtis J Mello
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel Meyer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Olli Pietilainen
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Federica Piccioni
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Ellen J Guss
- Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Kavya Raghunathan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Matthew Tegtmeyer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Derek Hawes
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Anna Neumann
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Kathleen A Worringer
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Daniel Ho
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Sravya Kommineni
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Karrie Chan
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Brant K Peterson
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Joseph J Raymond
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - John T Gold
- Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Department of Biology, Davidson College, Davidson, NC 28035, USA
| | - Marco T Siekmann
- Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Emanuela Zuccaro
- Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Ralda Nehme
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | | | - Kevin Eggan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
6
|
Systematic identification of biomarker-driven drug combinations to overcome resistance. Nat Chem Biol 2022; 18:615-624. [PMID: 35332332 DOI: 10.1038/s41589-022-00996-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 02/11/2022] [Indexed: 02/06/2023]
Abstract
The ability to understand and predict variable responses to therapeutic agents may improve outcomes in patients with cancer. We hypothesized that the basal gene-transcription state of cancer cell lines, coupled with cell viability profiles of small molecules, might be leveraged to nominate specific mechanisms of intrinsic resistance and to predict drug combinations that overcome resistance. We analyzed 564,424 sensitivity profiles to identify candidate gene-compound pairs, and validated nine such relationships. We determined the mechanism of a novel relationship, in which expression of the serine hydrolase enzymes monoacylglycerol lipase (MGLL) or carboxylesterase 1 (CES1) confers resistance to the histone lysine demethylase inhibitor GSK-J4 by direct enzymatic modification. Insensitive cell lines could be sensitized to GSK-J4 by inhibition or gene knockout. These analytical and mechanistic studies highlight the potential of integrating gene-expression features with small-molecule response to identify patient populations that are likely to benefit from treatment, to nominate rational candidates for combinations and to provide insights into mechanisms of action.
Collapse
|
7
|
Thompson EL, Pickett-Leonard M, Riddle MJ, Chen W, Albert FW, Tolar J. Genes and compounds that increase type VII collagen expression as potential treatments for dystrophic epidermolysis bullosa. Exp Dermatol 2022; 31:1065-1075. [PMID: 35243691 DOI: 10.1111/exd.14555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 02/07/2022] [Accepted: 02/27/2022] [Indexed: 11/28/2022]
Abstract
Dystrophic epidermolysis bullosa (DEB) is a skin-blistering disease caused by mutations in COL7A1, which encodes type VII collagen (C7). There is no cure for DEB, but previous work has shown potential therapeutic benefit of increased production of even partially functional C7. Genome-wide screens using CRISPR-Cas9 have enabled the identification of genes involved in cancer development, drug resistance, and other genetic diseases, suggesting that they could be used to identify drivers of C7 production. A keratinocyte C7 reporter cell line was created and used in a genome-wide CRISPR activation (CRISPRa) screen to identify genes and pathways that increase C7 expression. The CRISPRa screen results were used to develop a targeted drug screen to identify compounds that upregulate C7 expression. The C7_tdTomato cell line was validated as an effective reporter for detection of C7 upregulation. The CRISPRa screen identified DENND4B and TYROBP as top gene hits plus pathways related to calcium uptake and immune signaling in C7 regulation. The targeted drug screen identified several compounds that increase C7 expression in keratinocytes, of which kaempferol, a plant flavonoid, also significantly increased C7 mRNA and protein in DEB patient cells.
Collapse
Affiliation(s)
- Elizabeth L Thompson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Michael Pickett-Leonard
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Megan J Riddle
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Weili Chen
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Frank W Albert
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Jakub Tolar
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, 55455, USA.,Stem Cell Institute, University of Minnesota, MN, 55455, USA
| |
Collapse
|
8
|
Khadka P, Reitman ZJ, Lu S, Buchan G, Gionet G, Dubois F, Carvalho DM, Shih J, Zhang S, Greenwald NF, Zack T, Shapira O, Pelton K, Hartley R, Bear H, Georgis Y, Jarmale S, Melanson R, Bonanno K, Schoolcraft K, Miller PG, Condurat AL, Gonzalez EM, Qian K, Morin E, Langhnoja J, Lupien LE, Rendo V, Digiacomo J, Wang D, Zhou K, Kumbhani R, Guerra Garcia ME, Sinai CE, Becker S, Schneider R, Vogelzang J, Krug K, Goodale A, Abid T, Kalani Z, Piccioni F, Beroukhim R, Persky NS, Root DE, Carcaboso AM, Ebert BL, Fuller C, Babur O, Kieran MW, Jones C, Keshishian H, Ligon KL, Carr SA, Phoenix TN, Bandopadhayay P. PPM1D mutations are oncogenic drivers of de novo diffuse midline glioma formation. Nat Commun 2022; 13:604. [PMID: 35105861 PMCID: PMC8807747 DOI: 10.1038/s41467-022-28198-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/07/2022] [Indexed: 12/23/2022] Open
Abstract
The role of PPM1D mutations in de novo gliomagenesis has not been systematically explored. Here we analyze whole genome sequences of 170 pediatric high-grade gliomas and find that truncating mutations in PPM1D that increase the stability of its phosphatase are clonal driver events in 11% of Diffuse Midline Gliomas (DMGs) and are enriched in primary pontine tumors. Through the development of DMG mouse models, we show that PPM1D mutations potentiate gliomagenesis and that PPM1D phosphatase activity is required for in vivo oncogenesis. Finally, we apply integrative phosphoproteomic and functional genomics assays and find that oncogenic effects of PPM1D truncation converge on regulators of cell cycle, DNA damage response, and p53 pathways, revealing therapeutic vulnerabilities including MDM2 inhibition.
Collapse
Affiliation(s)
- Prasidda Khadka
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Harvard Biological and Biomedical Sciences PhD Program, Harvard University, Cambridge, MA, 02138, USA
| | - Zachary J Reitman
- Department of Radiation Oncology, Duke University, Durham, NC, 27710, USA
- Duke Cancer Institute, Duke University, Durham, NC, 27710, USA
- The Preston Robert Tisch Brain Tumor Center at Duke, Duke University, Durham, NC, 27710, USA
| | - Sophie Lu
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA
| | - Graham Buchan
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA
| | - Gabrielle Gionet
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA
| | - Frank Dubois
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Diana M Carvalho
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | - Juliann Shih
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Shu Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Noah F Greenwald
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, 02215, USA
| | - Travis Zack
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, 02215, USA
| | - Ofer Shapira
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, 02215, USA
| | - Kristine Pelton
- Department of Oncologic Pathology, Dana Farber Cancer Institute, Boston, MA, 02215, USA
| | - Rachel Hartley
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Heather Bear
- Research in Patient Services, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45267, USA
| | - Yohanna Georgis
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA
| | - Spandana Jarmale
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA
| | - Randy Melanson
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Kevin Bonanno
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Kathleen Schoolcraft
- Department of Oncologic Pathology, Dana Farber Cancer Institute, Boston, MA, 02215, USA
| | - Peter G Miller
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Alexandra L Condurat
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA
| | - Elizabeth M Gonzalez
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA
| | - Kenin Qian
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA
| | - Eric Morin
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA
| | - Jaldeep Langhnoja
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Leslie E Lupien
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA
| | - Veronica Rendo
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, 02215, USA
| | - Jeromy Digiacomo
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA
| | - Dayle Wang
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA
| | - Kevin Zhou
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA
| | - Rushil Kumbhani
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA
| | | | - Claire E Sinai
- Department of Oncologic Pathology, Dana Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sarah Becker
- Department of Oncologic Pathology, Dana Farber Cancer Institute, Boston, MA, 02215, USA
| | - Rachel Schneider
- Department of Oncologic Pathology, Dana Farber Cancer Institute, Boston, MA, 02215, USA
| | - Jayne Vogelzang
- Department of Oncologic Pathology, Dana Farber Cancer Institute, Boston, MA, 02215, USA
| | - Karsten Krug
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Amy Goodale
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Tanaz Abid
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Zohra Kalani
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | | | - Rameen Beroukhim
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Nicole S Persky
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Angel M Carcaboso
- Department of Pediatric Hematology and Oncology, Hospital Sant Joan de Deu, Institut de Recerca Sant Joan de Deu, Barcelona, 08950, Spain
| | - Benjamin L Ebert
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Christine Fuller
- Department of Pathology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45267, USA
| | - Ozgun Babur
- College of Science and Mathematics, University of Massachusetts Boston, Boston, MA, 02125, USA
| | - Mark W Kieran
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA
- Bristol Myers Squibb, Boston, Devens, MA, 01434, USA
| | - Chris Jones
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | | | - Keith L Ligon
- Department of Oncologic Pathology, Dana Farber Cancer Institute, Boston, MA, 02215, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Timothy N Phoenix
- Division of Pharmaceutical Sciences, James L. Winkle College of Pharmacy, University of Cincinnati, Cincinnati, OH, 45267, USA.
- Research in Patient Services, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45267, USA.
| | - Pratiti Bandopadhayay
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, 02215, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02215, USA.
| |
Collapse
|
9
|
Murawska GM, Vogel C, Jan M, Lu X, Schild M, Slabicki M, Zou C, Zhanybekova S, Manojkumar M, Petzold G, Kaiser P, Thomä N, Ebert B, Gillingham D. Repurposing the Damage Repair Protein Methyl Guanine Methyl Transferase as a Ligand Inducible Fusion Degron. ACS Chem Biol 2022; 17:24-31. [PMID: 34982531 DOI: 10.1021/acschembio.1c00771] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We successfully repurpose the DNA repair protein methylguanine methyltransferase (MGMT) as an inducible degron for protein fusions. MGMT is a suicide protein that removes alkyl groups from the O6 position of guanine (O6G) and is thereafter quickly degraded by the ubiquitin proteasome pathway (UPP). Starting with MGMT pseudosubstrates (benzylguanine and lomeguatrib), we first demonstrate that these lead to potent MGMT depletion while affecting little else in the proteome. We then show that fusion proteins of MGMT undergo rapid UPP-dependent degradation in response to pseudosubstrates. Mechanistic studies confirm the involvement of the UPP, while revealing that at least two E3 ligase classes can degrade MGMT depending on cell-line and expression type (native or ectopic). We also demonstrate the technique's versatility with two clinically relevant examples: degradation of KRASG12C and a chimeric antigen receptor.
Collapse
Affiliation(s)
- Gosia M. Murawska
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
| | - Caspar Vogel
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
| | - Max Jan
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Xinyan Lu
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
| | - Matthias Schild
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
| | - Mikolaj Slabicki
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Charles Zou
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Saule Zhanybekova
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
| | - Manisha Manojkumar
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Georg Petzold
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Peter Kaiser
- Department of Biological Chemistry, University of California, Irvine, California 92697, United States
| | - Nicolas Thomä
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Benjamin Ebert
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Dennis Gillingham
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
| |
Collapse
|
10
|
Seong BKA, Dharia NV, Lin S, Donovan KA, Chong S, Robichaud A, Conway A, Hamze A, Ross L, Alexe G, Adane B, Nabet B, Ferguson FM, Stolte B, Wang EJ, Sun J, Darzacq X, Piccioni F, Gray NS, Fischer ES, Stegmaier K. TRIM8 modulates the EWS/FLI oncoprotein to promote survival in Ewing sarcoma. Cancer Cell 2021; 39:1262-1278.e7. [PMID: 34329586 PMCID: PMC8443273 DOI: 10.1016/j.ccell.2021.07.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 02/24/2021] [Accepted: 07/01/2021] [Indexed: 12/26/2022]
Abstract
Fusion-transcription factors (fusion-TFs) represent a class of driver oncoproteins that are difficult to therapeutically target. Recently, protein degradation has emerged as a strategy to target these challenging oncoproteins. The mechanisms that regulate fusion-TF stability, however, are generally unknown. Using CRISPR-Cas9 screening, we discovered tripartite motif-containing 8 (TRIM8) as an E3 ubiquitin ligase that ubiquitinates and degrades EWS/FLI, a driver fusion-TF in Ewing sarcoma. Moreover, we identified TRIM8 as a selective dependency in Ewing sarcoma compared with >700 other cancer cell lines. Mechanistically, TRIM8 knockout led to an increase in EWS/FLI protein levels that was not tolerated. EWS/FLI acts as a neomorphic substrate for TRIM8, defining the selective nature of the dependency. Our results demonstrate that fusion-TF protein stability is tightly regulated and highlight fusion oncoprotein-specific regulators as selective therapeutic targets. This study provides a tractable strategy to therapeutically exploit oncogene overdose in Ewing sarcoma and potentially other fusion-TF-driven cancers.
Collapse
Affiliation(s)
- Bo Kyung A Seong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Neekesh V Dharia
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Shan Lin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Shasha Chong
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Amanda Robichaud
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amy Conway
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amanda Hamze
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Linda Ross
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gabriela Alexe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Biniam Adane
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Behnam Nabet
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Fleur M Ferguson
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Björn Stolte
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Dr.von Hauner Children's Hospital, Department of Pediatrics, University Hospital, LMU Munich, Munich, Germany
| | - Emily Jue Wang
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jialin Sun
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA; CIRM Center of Excellence, University of California, Berkeley, CA, USA
| | | | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
| |
Collapse
|
11
|
Hartin SN, Means JC, Alaimo JT, Younger ST. Expediting rare disease diagnosis: a call to bridge the gap between clinical and functional genomics. Mol Med 2020; 26:117. [PMID: 33238891 PMCID: PMC7691058 DOI: 10.1186/s10020-020-00244-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/18/2020] [Indexed: 11/10/2022] Open
Abstract
Approximately 400 million people throughout the world suffer from a rare disease. Although advances in whole exome and whole genome sequencing have greatly facilitated rare disease diagnosis, overall diagnostic rates remain below 50%. Furthermore, in cases where accurate diagnosis is achieved the process requires an average of 4.8 years. Reducing the time required for disease diagnosis is among the most critical needs of patients impacted by a rare disease. In this perspective we describe current challenges associated with rare disease diagnosis and discuss several cutting-edge functional genomic screening technologies that have the potential to rapidly accelerate the process of distinguishing pathogenic variants that lead to disease.
Collapse
Affiliation(s)
- Samantha N Hartin
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.,Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - John C Means
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.,Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Joseph T Alaimo
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.,Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.,Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, MO, 64110, USA.,Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Scott T Younger
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, 64108, USA. .,Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA. .,Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, MO, 64110, USA. .,Department of Pediatrics, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
| |
Collapse
|
12
|
Sulahian R, Kwon JJ, Walsh KH, Pailler E, Bosse TL, Thaker M, Almanza D, Dempster JM, Pan J, Piccioni F, Dumont N, Gonzalez A, Rennhack J, Nabet B, Bachman JA, Goodale A, Lee Y, Bagul M, Liao R, Navarro A, Yuan TL, Ng RWS, Raghavan S, Gray NS, Tsherniak A, Vazquez F, Root DE, Firestone AJ, Settleman J, Hahn WC, Aguirre AJ. Synthetic Lethal Interaction of SHOC2 Depletion with MEK Inhibition in RAS-Driven Cancers. Cell Rep 2020; 29:118-134.e8. [PMID: 31577942 DOI: 10.1016/j.celrep.2019.08.090] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 07/22/2019] [Accepted: 08/27/2019] [Indexed: 12/17/2022] Open
Abstract
The mitogen-activated protein kinase (MAPK) pathway is a critical effector of oncogenic RAS signaling, and MAPK pathway inhibition may be an effective combination treatment strategy. We performed genome-scale loss-of-function CRISPR-Cas9 screens in the presence of a MEK1/2 inhibitor (MEKi) in KRAS-mutant pancreatic and lung cancer cell lines and identified genes that cooperate with MEK inhibition. While we observed heterogeneity in genetic modifiers of MEKi sensitivity across cell lines, several recurrent classes of synthetic lethal vulnerabilities emerged at the pathway level. Multiple members of receptor tyrosine kinase (RTK)-RAS-MAPK pathways scored as sensitizers to MEKi. In particular, we demonstrate that knockout, suppression, or degradation of SHOC2, a positive regulator of MAPK signaling, specifically cooperated with MEK inhibition to impair proliferation in RAS-driven cancer cells. The depletion of SHOC2 disrupted survival pathways triggered by feedback RTK signaling in response to MEK inhibition. Thus, these findings nominate SHOC2 as a potential target for combination therapy.
Collapse
Affiliation(s)
- Rita Sulahian
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jason J Kwon
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Emma Pailler
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Timothy L Bosse
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Maneesha Thaker
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Diego Almanza
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Joshua Pan
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Nancy Dumont
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Jonathan Rennhack
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Behnam Nabet
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - John A Bachman
- Laboratory of Systems Pharmacology, Harvard Medical School, 200 Longwood Ave., Boston, MA 02115, USA
| | - Amy Goodale
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yenarae Lee
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Mukta Bagul
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rosy Liao
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Adrija Navarro
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tina L Yuan
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Raymond W S Ng
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Srivatsan Raghavan
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Aviad Tsherniak
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Jeff Settleman
- Calico Life Sciences, South San Francisco, CA 94080, USA
| | - William C Hahn
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 75 Francis Street, Boston, MA 02115, MA.
| | - Andrew J Aguirre
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 75 Francis Street, Boston, MA 02115, MA.
| |
Collapse
|
13
|
Georgiou A, Stewart A, Cunningham D, Banerji U, Whittaker SR. Inactivation of NF1 Promotes Resistance to EGFR Inhibition in KRAS/NRAS/BRAFV600 -Wild-Type Colorectal Cancer. Mol Cancer Res 2020; 18:835-846. [PMID: 32098826 PMCID: PMC7611272 DOI: 10.1158/1541-7786.mcr-19-1201] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/21/2020] [Accepted: 02/20/2020] [Indexed: 12/26/2022]
Abstract
Through the use of an unbiased, genome-scale CRISPR modifier screen, we identified NF1 suppression as a mechanism of resistance to EGFR inhibition in NRAS/KRAS/BRAFV600 -wild-type colorectal cancer cells. Reduced NF1 expression permitted sustained signaling through the MAPK pathway to promote cell proliferation in the presence of EGFR inhibition. Targeting of MEK in combination with EGFR inhibition leads to synergistic antiproliferative activity. Human KRAS/NRAS/BRAFV600 -wild-type colorectal cancer cell lines with NF1 mutations displayed reduced NF1 mRNA or protein expression and were resistant to EGFR blockade by gefitinib or cetuximab. Cooccurring loss-of-function mutations in PTEN were associated with resistance to dual EGFR/MEK inhibition but cotreatment with a PI3K inhibitor further suppressed proliferation. Loss of NF1 may be a useful biomarker to identify patients that are less likely to benefit from single-agent anti-EGFR therapy in colorectal cancer and may direct potential combination strategies. IMPLICATIONS: This study suggests that further clinical validation of NF1 status as predictor of response to anti-EGFR targeting antibodies in patients with colorectal cancer with KRAS/NRAS/BRAFV600 -wild-type tumors is warranted.
Collapse
Affiliation(s)
- Alexandros Georgiou
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
- Department of Medicine, The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Adam Stewart
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - David Cunningham
- Department of Medicine, The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Udai Banerji
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom.
- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Steven R Whittaker
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom.
| |
Collapse
|
14
|
Eller C, Heydmann L, Colpitts CC, El Saghire H, Piccioni F, Jühling F, Majzoub K, Pons C, Bach C, Lucifora J, Lupberger J, Nassal M, Cowley GS, Fujiwara N, Hsieh SY, Hoshida Y, Felli E, Pessaux P, Sureau C, Schuster C, Root DE, Verrier ER, Baumert TF. A genome-wide gain-of-function screen identifies CDKN2C as a HBV host factor. Nat Commun 2020; 11:2707. [PMID: 32483149 PMCID: PMC7264273 DOI: 10.1038/s41467-020-16517-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 05/03/2020] [Indexed: 12/21/2022] Open
Abstract
Chronic HBV infection is a major cause of liver disease and cancer worldwide. Approaches for cure are lacking, and the knowledge of virus-host interactions is still limited. Here, we perform a genome-wide gain-of-function screen using a poorly permissive hepatoma cell line to uncover host factors enhancing HBV infection. Validation studies in primary human hepatocytes identified CDKN2C as an important host factor for HBV replication. CDKN2C is overexpressed in highly permissive cells and HBV-infected patients. Mechanistic studies show a role for CDKN2C in inducing cell cycle G1 arrest through inhibition of CDK4/6 associated with the upregulation of HBV transcription enhancers. A correlation between CDKN2C expression and disease progression in HBV-infected patients suggests a role in HBV-induced liver disease. Taken together, we identify a previously undiscovered clinically relevant HBV host factor, allowing the development of improved infectious model systems for drug discovery and the study of the HBV life cycle.
Collapse
Affiliation(s)
- Carla Eller
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
| | - Laura Heydmann
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
| | - Che C Colpitts
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Houssein El Saghire
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
| | - Federica Piccioni
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Frank Jühling
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
| | - Karim Majzoub
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
| | - Caroline Pons
- Inserm, U1052, Cancer Research Center of Lyon (CRCL), Université de Lyon (UCBL1), CNRS UMR_5286, Centre Léon Bérard, Lyon, France
| | - Charlotte Bach
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
| | - Julie Lucifora
- Inserm, U1052, Cancer Research Center of Lyon (CRCL), Université de Lyon (UCBL1), CNRS UMR_5286, Centre Léon Bérard, Lyon, France
| | - Joachim Lupberger
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
| | - Michael Nassal
- Department of Internal Medicine II/Molecular Biology, University Hospital Freiburg, Freiburg, Germany
| | - Glenn S Cowley
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Naoto Fujiwara
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sen-Yung Hsieh
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Taipei, Taiwan
| | - Yujin Hoshida
- Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Emanuele Felli
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
- Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, 67000, Strasbourg, France
| | - Patrick Pessaux
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
- Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, 67000, Strasbourg, France
| | - Camille Sureau
- Laboratoire de Virologie Moléculaire, INTS, Paris, France
| | - Catherine Schuster
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France
| | - David E Root
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Eloi R Verrier
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France.
| | - Thomas F Baumert
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000, Strasbourg, France.
- Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, 67000, Strasbourg, France.
- Institut Universitaire de France (IUF), Paris, France.
| |
Collapse
|
15
|
Milton CK, Self AJ, Clarke PA, Banerji U, Piccioni F, Root DE, Whittaker SR. A Genome-scale CRISPR Screen Identifies the ERBB and mTOR Signaling Networks as Key Determinants of Response to PI3K Inhibition in Pancreatic Cancer. Mol Cancer Ther 2020; 19:1423-1435. [PMID: 32371585 DOI: 10.1158/1535-7163.mct-19-1131] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/17/2020] [Accepted: 04/06/2020] [Indexed: 12/21/2022]
Abstract
KRAS mutation is a key driver of pancreatic cancer and PI3K pathway activity is an additional requirement for Kras-induced tumorigenesis. Clinical trials of PI3K pathway inhibitors in pancreatic cancer have shown limited responses. Understanding the molecular basis for this lack of efficacy may direct future treatment strategies with emerging PI3K inhibitors. We sought new therapeutic approaches that synergize with PI3K inhibitors through pooled CRISPR modifier genetic screening and a drug combination screen. ERBB family receptor tyrosine kinase signaling and mTOR signaling were key modifiers of sensitivity to alpelisib and pictilisib. Inhibition of the ERBB family or mTOR was synergistic with PI3K inhibition in spheroid, stromal cocultures. Near-complete loss of ribosomal S6 phosphorylation was associated with synergy. Genetic alterations in the ERBB-PI3K signaling axis were associated with decreased survival of patients with pancreatic cancer. Suppression of the PI3K/mTOR axis is potentiated by dual PI3K and ERBB family or mTOR inhibition. Surprisingly, despite the presence of oncogenic KRAS, thought to bestow independence from receptor tyrosine kinase signaling, inhibition of the ERBB family blocks downstream pathway activation and synergizes with PI3K inhibitors. Further exploration of these therapeutic combinations is warranted for the treatment of pancreatic cancer.
Collapse
Affiliation(s)
- Charlotte K Milton
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Annette J Self
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Paul A Clarke
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Udai Banerji
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom.,The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | | | | | - Steven R Whittaker
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom.
| |
Collapse
|
16
|
Viswanatha R, Brathwaite R, Hu Y, Li Z, Rodiger J, Merckaert P, Chung V, Mohr SE, Perrimon N. Pooled CRISPR Screens in Drosophila Cells. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2019; 129:e111. [PMID: 31763777 PMCID: PMC6961806 DOI: 10.1002/cpmb.111] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
High-throughput screens in Drosophila melanogaster cell lines have led to discovery of conserved gene functions related to signal transduction, host-pathogen interactions, ion transport, and more. CRISPR/Cas9 technology has opened the door to new types of large-scale cell-based screens. Whereas array-format screens require liquid handling automation and assay miniaturization, pooled-format screens, in which reagents are introduced at random and in bulk, can be done in a standard lab setting. We provide a detailed protocol for conducting and evaluating genome-wide CRISPR single guide RNA (sgRNA) pooled screens in Drosophila S2R+ cultured cells. Specifically, we provide step-by-step instructions for library design and production, optimization of cytotoxin-based selection assays, genome-scale screening, and data analysis. This type of project takes ∼3 months to complete. Results can be used in follow-up studies performed in vivo in Drosophila, mammalian cells, and/or other systems. © 2019 by John Wiley & Sons, Inc. Basic Protocol: Pooled-format screening with Cas9-expressing Drosophila S2R+ cells in the presence of cytotoxin Support Protocol 1: Optimization of cytotoxin concentration for Drosophila cell screening Support Protocol 2: CRISPR sgRNA library design and production for Drosophila cell screening Support Protocol 3: Barcode deconvolution and analysis of screening data.
Collapse
Affiliation(s)
| | - Roderick Brathwaite
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Drosophila RNAi Screening Center, Harvard Medical School, Boston, Massachusetts
| | - Yanhui Hu
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Drosophila RNAi Screening Center, Harvard Medical School, Boston, Massachusetts
| | - Zhongchi Li
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Jonathan Rodiger
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Drosophila RNAi Screening Center, Harvard Medical School, Boston, Massachusetts
| | - Pierre Merckaert
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Drosophila RNAi Screening Center, Harvard Medical School, Boston, Massachusetts
| | - Verena Chung
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Drosophila RNAi Screening Center, Harvard Medical School, Boston, Massachusetts
| | - Stephanie E Mohr
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Drosophila RNAi Screening Center, Harvard Medical School, Boston, Massachusetts
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
- Drosophila RNAi Screening Center, Harvard Medical School, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston, Massachusetts
| |
Collapse
|
17
|
To TL, Cuadros AM, Shah H, Hung WHW, Li Y, Kim SH, Rubin DHF, Boe RH, Rath S, Eaton JK, Piccioni F, Goodale A, Kalani Z, Doench JG, Root DE, Schreiber SL, Vafai SB, Mootha VK. A Compendium of Genetic Modifiers of Mitochondrial Dysfunction Reveals Intra-organelle Buffering. Cell 2019; 179:1222-1238.e17. [PMID: 31730859 PMCID: PMC7053407 DOI: 10.1016/j.cell.2019.10.032] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 09/12/2019] [Accepted: 10/23/2019] [Indexed: 12/18/2022]
Abstract
Mitochondrial dysfunction is associated with a spectrum of human conditions, ranging from rare, inborn errors of metabolism to the aging process. To identify pathways that modify mitochondrial dysfunction, we performed genome-wide CRISPR screens in the presence of small-molecule mitochondrial inhibitors. We report a compendium of chemical-genetic interactions involving 191 distinct genetic modifiers, including 38 that are synthetic sick/lethal and 63 that are suppressors. Genes involved in glycolysis (PFKP), pentose phosphate pathway (G6PD), and defense against lipid peroxidation (GPX4) scored high as synthetic sick/lethal. A surprisingly large fraction of suppressors are pathway intrinsic and encode mitochondrial proteins. A striking example of such "intra-organelle" buffering is the alleviation of a chemical defect in complex V by simultaneous inhibition of complex I, which benefits cells by rebalancing redox cofactors, increasing reductive carboxylation, and promoting glycolysis. Perhaps paradoxically, certain forms of mitochondrial dysfunction may best be buffered with "second site" inhibitors to the organelle.
Collapse
Affiliation(s)
- Tsz-Leung To
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Hardik Shah
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Wendy H W Hung
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Yang Li
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Sharon H Kim
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Daniel H F Rubin
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ryan H Boe
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Sneha Rath
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - John K Eaton
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Amy Goodale
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Zohra Kalani
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - John G Doench
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - David E Root
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Stuart L Schreiber
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Scott B Vafai
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Vamsi K Mootha
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.
| |
Collapse
|
18
|
Stover EH, Baco MB, Cohen O, Li YY, Christie EL, Bagul M, Goodale A, Lee Y, Pantel S, Rees MG, Wei G, Presser AG, Gelbard MK, Zhang W, Zervantonakis IK, Bhola PD, Ryan J, Guerriero JL, Montero J, Liang FJ, Cherniack AD, Piccioni F, Matulonis UA, Bowtell DDL, Sarosiek KA, Letai A, Garraway LA, Johannessen CM, Meyerson M. Pooled Genomic Screens Identify Anti-apoptotic Genes as Targetable Mediators of Chemotherapy Resistance in Ovarian Cancer. Mol Cancer Res 2019; 17:2281-2293. [PMID: 31462500 DOI: 10.1158/1541-7786.mcr-18-1243] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 04/07/2019] [Accepted: 08/22/2019] [Indexed: 12/26/2022]
Abstract
High-grade serous ovarian cancer (HGSOC) is often sensitive to initial treatment with platinum and taxane combination chemotherapy, but most patients relapse with chemotherapy-resistant disease. To systematically identify genes modulating chemotherapy response, we performed pooled functional genomic screens in HGSOC cell lines treated with cisplatin, paclitaxel, or cisplatin plus paclitaxel. Genes in the intrinsic pathway of apoptosis were among the top candidate resistance genes in both gain-of-function and loss-of-function screens. In an open reading frame overexpression screen, followed by a mini-pool secondary screen, anti-apoptotic genes including BCL2L1 (BCL-XL) and BCL2L2 (BCL-W) were associated with chemotherapy resistance. In a CRISPR-Cas9 knockout screen, loss of BCL2L1 decreased cell survival whereas loss of proapoptotic genes promoted resistance. To dissect the role of individual anti-apoptotic proteins in HGSOC chemotherapy response, we evaluated overexpression or inhibition of BCL-2, BCL-XL, BCL-W, and MCL1 in HGSOC cell lines. Overexpression of anti-apoptotic proteins decreased apoptosis and modestly increased cell viability upon cisplatin or paclitaxel treatment. Conversely, specific inhibitors of BCL-XL, MCL1, or BCL-XL/BCL-2, but not BCL-2 alone, enhanced cell death when combined with cisplatin or paclitaxel. Anti-apoptotic protein inhibitors also sensitized HGSOC cells to the poly (ADP-ribose) polymerase inhibitor olaparib. These unbiased screens highlight anti-apoptotic proteins as mediators of chemotherapy resistance in HGSOC, and support inhibition of BCL-XL and MCL1, alone or combined with chemotherapy or targeted agents, in treatment of primary and recurrent HGSOC. IMPLICATIONS: Anti-apoptotic proteins modulate drug resistance in ovarian cancer, and inhibitors of BCL-XL or MCL1 promote cell death in combination with chemotherapy.
Collapse
Affiliation(s)
- Elizabeth H Stover
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts.,Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Maria B Baco
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Ofir Cohen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts.,Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Yvonne Y Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts.,Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Elizabeth L Christie
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | - Mukta Bagul
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Amy Goodale
- Genetic Perturbation Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Yenarae Lee
- Genetic Perturbation Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Sasha Pantel
- Genetic Perturbation Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Matthew G Rees
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Guo Wei
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Adam G Presser
- John B. Little Center for Radiation Sciences, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Maya K Gelbard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Weiqun Zhang
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Patrick D Bhola
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jeremy Ryan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jennifer L Guerriero
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Joan Montero
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Institute for Bioengineering of Catalonia, Barcelona, Spain
| | - Felice J Liang
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Andrew D Cherniack
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Federica Piccioni
- Genetic Perturbation Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Ursula A Matulonis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - David D L Bowtell
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | - Kristopher A Sarosiek
- John B. Little Center for Radiation Sciences, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Anthony Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | | | - Cory M Johannessen
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. .,Department of Medicine, Harvard Medical School, Boston, Massachusetts.,Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| |
Collapse
|