1
|
Halasz H, Malekos E, Covarrubias S, Yitiz S, Montano C, Sudek L, Katzman S, Liu SJ, Horlbeck MA, Namvar L, Weissman JS, Carpenter S. CRISPRi screens identify the lncRNA, LOUP, as a multifunctional locus regulating macrophage differentiation and inflammatory signaling. Proc Natl Acad Sci U S A 2024; 121:e2322524121. [PMID: 38781216 PMCID: PMC11145268 DOI: 10.1073/pnas.2322524121] [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: 12/20/2023] [Accepted: 04/16/2024] [Indexed: 05/25/2024] Open
Abstract
Long noncoding RNAs (lncRNAs) account for the largest portion of RNA from the transcriptome, yet most of their functions remain unknown. Here, we performed two independent high-throughput CRISPRi screens to understand the role of lncRNAs in monocyte function and differentiation. The first was a reporter-based screen to identify lncRNAs that regulate TLR4-NFkB signaling in human monocytes and the second screen identified lncRNAs involved in monocyte to macrophage differentiation. We successfully identified numerous noncoding and protein-coding genes that can positively or negatively regulate inflammation and differentiation. To understand the functional roles of lncRNAs in both processes, we chose to further study the lncRNA LOUP [lncRNA originating from upstream regulatory element of SPI1 (also known as PU.1)], as it emerged as a top hit in both screens. Not only does LOUP regulate its neighboring gene, the myeloid fate-determining factor SPI1, thereby affecting monocyte to macrophage differentiation, but knockdown of LOUP leads to a broad upregulation of NFkB-targeted genes at baseline and upon TLR4-NFkB activation. LOUP also harbors three small open reading frames capable of being translated and are responsible for LOUP's ability to negatively regulate TLR4/NFkB signaling. This work emphasizes the value of high-throughput screening to rapidly identify functional lncRNAs in the innate immune system.
Collapse
Affiliation(s)
- Haley Halasz
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, CA95064
| | - Eric Malekos
- Department of Biomolecular Engineering, University of California Santa Cruz, CA95064
| | - Sergio Covarrubias
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, CA95064
| | - Samira Yitiz
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, CA95064
| | - Christy Montano
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, CA95064
| | - Lisa Sudek
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, CA95064
| | - Sol Katzman
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, CA95064
| | - S. John Liu
- Department of Radiation Oncology, University of California, San Francisco, CA94158
- Department of Neurological Surgery, University of California, San Francisco, CA94158
| | - Max A. Horlbeck
- Department of Radiation Oncology, University of California, San Francisco, CA94158
- Department of Neurological Surgery, University of California, San Francisco, CA94158
- Department of Pediatrics, Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA02115
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA02138
| | - Leila Namvar
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, CA95064
| | - Jonathan S. Weissman
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA02142
- HHMI, Chevy Chase, MD20815
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA02142
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, CA95064
| |
Collapse
|
2
|
Munir M, Embry A, Doench JG, Heaton NS, Wilen CB, Orchard RC. Genome-wide CRISPR activation screen identifies JADE3 as an antiviral activator of NF-kB-dependent IFITM3 expression. J Biol Chem 2024; 300:107153. [PMID: 38462163 PMCID: PMC11001640 DOI: 10.1016/j.jbc.2024.107153] [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: 09/29/2023] [Revised: 02/29/2024] [Accepted: 03/05/2024] [Indexed: 03/12/2024] Open
Abstract
The innate immune system features a web of interacting pathways that require exquisite regulation. To identify novel nodes in this immune landscape, we conducted a gain-of-function, genome-wide CRISPR activation screen with influenza A virus. We identified both appreciated and novel antiviral genes, including Jade family PHD zinc finger 3 (JADE3) a protein involved in directing the histone acetyltransferase histone acetyltransferase binding to ORC1 complex to modify chromatin and regulate transcription. JADE3 is both necessary and sufficient to restrict influenza A virus infection. Our results suggest a distinct function for JADE3 as expression of the closely related paralogs JADE1 and JADE2 does not confer resistance to influenza A virus infection. JADE3 is required for both constitutive and inducible expression of the well-characterized antiviral gene interferon-induced transmembrane protein 3 (IFITM3). Furthermore, we find JADE3 activates the NF-kB signaling pathway, which is required for the promotion of IFITM3 expression by JADE3. Therefore, we propose JADE3 activates an antiviral genetic program involving NF-kB-dependent IFITM3 expression to restrict influenza A virus infection.
Collapse
Affiliation(s)
- Moiz Munir
- Departments of Immunology and Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Aaron Embry
- Departments of Immunology and Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Nicholas S Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Craig B Wilen
- Department of Laboratory Medicine and Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Robert C Orchard
- Departments of Immunology and Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
| |
Collapse
|
3
|
Wilson EL, Yu Y, Leal NS, Woodward JA, Patikas N, Morris JL, Field SF, Plumbly W, Paupe V, Chowdhury SR, Antrobus R, Lindop GE, Adia YM, Loh SHY, Prudent J, Martins LM, Metzakopian E. Genome-wide CRISPR/Cas9 screen shows that loss of GET4 increases mitochondria-endoplasmic reticulum contact sites and is neuroprotective. Cell Death Dis 2024; 15:203. [PMID: 38467609 PMCID: PMC10928201 DOI: 10.1038/s41419-024-06568-y] [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: 06/26/2023] [Revised: 02/13/2024] [Accepted: 02/19/2024] [Indexed: 03/13/2024]
Abstract
Organelles form membrane contact sites between each other, allowing for the transfer of molecules and signals. Mitochondria-endoplasmic reticulum (ER) contact sites (MERCS) are cellular subdomains characterized by close apposition of mitochondria and ER membranes. They have been implicated in many diseases, including neurodegenerative, metabolic, and cardiac diseases. Although MERCS have been extensively studied, much remains to be explored. To uncover novel regulators of MERCS, we conducted a genome-wide, flow cytometry-based screen using an engineered MERCS reporter cell line. We found 410 genes whose downregulation promotes MERCS and 230 genes whose downregulation decreases MERCS. From these, 29 genes were selected from each population for arrayed screening and 25 were validated from the high population and 13 from the low population. GET4 and BAG6 were highlighted as the top 2 genes that upon suppression increased MERCS from both the pooled and arrayed screens, and these were subjected to further investigation. Multiple microscopy analyses confirmed that loss of GET4 or BAG6 increased MERCS. GET4 and BAG6 were also observed to interact with the known MERCS proteins, inositol 1,4,5-trisphosphate receptors (IP3R) and glucose-regulated protein 75 (GRP75). In addition, we found that loss of GET4 increased mitochondrial calcium uptake upon ER-Ca2+ release and mitochondrial respiration. Finally, we show that loss of GET4 rescues motor ability, improves lifespan and prevents neurodegeneration in a Drosophila model of Alzheimer's disease (Aβ42Arc). Together, these results suggest that GET4 is involved in decreasing MERCS and that its loss is neuroprotective.
Collapse
Affiliation(s)
- Emma L Wilson
- UK Dementia Research Institute, University of Cambridge, Clifford Albutt building, Cambridge biomedical campus, Cambridge, CB2 0AH, UK
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters building, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Yizhou Yu
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Nuno S Leal
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - James A Woodward
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Nikolaos Patikas
- UK Dementia Research Institute, University of Cambridge, Clifford Albutt building, Cambridge biomedical campus, Cambridge, CB2 0AH, UK
| | - Jordan L Morris
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters building, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK
| | - Sarah F Field
- UK Dementia Research Institute, University of Cambridge, Clifford Albutt building, Cambridge biomedical campus, Cambridge, CB2 0AH, UK
| | - William Plumbly
- UK Dementia Research Institute, University of Cambridge, Clifford Albutt building, Cambridge biomedical campus, Cambridge, CB2 0AH, UK
| | - Vincent Paupe
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters building, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK
| | - Suvagata R Chowdhury
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters building, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Rd, Cambridge, CB2 0XY, UK
| | - Georgina E Lindop
- Cambridge Advanced Imaging Centre, University of Cambridge, Anatomy Building, Downing Site, Cambridge, CB2 3DY, UK
| | - Yusuf M Adia
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Samantha H Y Loh
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Julien Prudent
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters building, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK.
| | - L Miguel Martins
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK.
| | - Emmanouil Metzakopian
- UK Dementia Research Institute, University of Cambridge, Clifford Albutt building, Cambridge biomedical campus, Cambridge, CB2 0AH, UK.
- bit bio, The Dorothy Hodgkin Building, Babraham Research Campus, Cambridge, CB22 3FH, UK.
| |
Collapse
|
4
|
Li X, Chen Z, Ye W, Yu J, Zhang X, Li Y, Niu Y, Ran S, Wang S, Luo Z, Zhao J, Hao Y, Zong J, Xia C, Xia J, Wu J. High-throughput CRISPR technology: a novel horizon for solid organ transplantation. Front Immunol 2024; 14:1295523. [PMID: 38239344 PMCID: PMC10794540 DOI: 10.3389/fimmu.2023.1295523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 12/12/2023] [Indexed: 01/22/2024] Open
Abstract
Organ transplantation is the gold standard therapy for end-stage organ failure. However, the shortage of available grafts and long-term graft dysfunction remain the primary barriers to organ transplantation. Exploring approaches to solve these issues is urgent, and CRISPR/Cas9-based transcriptome editing provides one potential solution. Furthermore, combining CRISPR/Cas9-based gene editing with an ex vivo organ perfusion system would enable pre-implantation transcriptome editing of grafts. How to determine effective intervention targets becomes a new problem. Fortunately, the advent of high-throughput CRISPR screening has dramatically accelerated the effective targets. This review summarizes the current advancements, utilization, and workflow of CRISPR screening in various immune and non-immune cells. It also discusses the ongoing applications of CRISPR/Cas-based gene editing in transplantation and the prospective applications of CRISPR screening in solid organ transplantation.
Collapse
Affiliation(s)
- Xiaohan Li
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhang Chen
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Weicong Ye
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jizhang Yu
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xi Zhang
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuan Li
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuqing Niu
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shuan Ran
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Song Wang
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zilong Luo
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiulu Zhao
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yanglin Hao
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Junjie Zong
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chengkun Xia
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiahong Xia
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Organ Transplantation, Ministry of Education, National Health Commission (NHC) Key Laboratory of Organ Transplantation, Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
| | - Jie Wu
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Organ Transplantation, Ministry of Education, National Health Commission (NHC) Key Laboratory of Organ Transplantation, Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
| |
Collapse
|
5
|
Binan L, Danquah S, Valakh V, Simonton B, Bezney J, Nehme R, Cleary B, Farhi SL. Simultaneous CRISPR screening and spatial transcriptomics reveals intracellular, intercellular, and functional transcriptional circuits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569494. [PMID: 38076932 PMCID: PMC10705493 DOI: 10.1101/2023.11.30.569494] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Pooled optical screens have enabled the study of cellular interactions, morphology, or dynamics at massive scale, but have not yet leveraged the power of highly-plexed single-cell resolved transcriptomic readouts to inform molecular pathways. Here, we present Perturb-FISH, which bridges these approaches by combining imaging spatial transcriptomics with parallel optical detection of in situ amplified guide RNAs. We show that Perturb-FISH recovers intracellular effects that are consistent with Perturb-seq results in a screen of lipopolysaccharide response in cultured monocytes, and uncover new intercellular and density-dependent regulation of the innate immune response. We further pair Perturb-FISH with a functional readout in a screen of autism spectrum disorder risk genes, showing common calcium activity phenotypes in induced pluripotent stem cell derived astrocytes and their associated genetic interactions and dysregulated molecular pathways. Perturb-FISH is thus a generally applicable method for studying the genetic and molecular associations of spatial and functional biology at single-cell resolution.
Collapse
Affiliation(s)
- Loϊc Binan
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Serwah Danquah
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Vera Valakh
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Brooke Simonton
- Present address: The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. (Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA)
| | - Jon Bezney
- Present address: Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. (Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA)
| | - Ralda Nehme
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Brian Cleary
- Faculty of Computing and Data Sciences, Boston University, Boston, MA, USA; Department of Biology, Boston University, Boston, MA, USA; Department of Biomedical Engineering, Boston University, Boston, MA, USA; Program in Bioinformatics, Boston University, Boston, MA, USA; Biological Design Center, Boston University, Boston, MA, USA
| | - Samouil L Farhi
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| |
Collapse
|
6
|
Munir M, Embry A, Doench JG, Heaton NS, Wilen CB, Orchard RC. Genome-wide CRISPR activation screen identifies JADE3 as an antiviral activator of NF-kB. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.29.560128. [PMID: 37808733 PMCID: PMC10557722 DOI: 10.1101/2023.09.29.560128] [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
The innate immune system features a web of interacting pathways that require exquisite regulation. To identify novel nodes in this immune landscape we conducted a gain of function, genome-wide CRISPR activation screen with influenza A virus. We identified both appreciated and novel antiviral genes, including JADE3 a protein involved in directing the histone acetyltransferase HBO1 complex to modify chromatin and regulate transcription. JADE3 is both necessary and sufficient to restrict influenza A virus infection. Interestingly, expression of the closely related paralogues JADE1 and JADE2 are unable to restrict influenza A virus infection, suggesting a distinct function of JADE3. We identify both shared and unique transcriptional signatures between uninfected cells expressing JADE3 and JADE2. These data provide a framework for understanding the overlapping and distinct functions of the JADE family of paralogues. Specifically, we find that JADE3 expression activates the NF-kB signaling pathway, consistent with an antiviral function. Therefore, we propose JADE3, but not JADE1 or JADE2, activates an antiviral genetic program involving the NF-kB pathway to restrict influenza A virus infection.
Collapse
Affiliation(s)
- Moiz Munir
- Departments of Immunology and Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Aaron Embry
- Departments of Immunology and Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - John G. Doench
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Nicholas S. Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Craig B. Wilen
- Departments of Laboratory Medicine and Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Robert C. Orchard
- Departments of Immunology and Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| |
Collapse
|
7
|
Riley-Gillis B, Tsaih SW, King E, Wollenhaupt S, Reeb J, Peck AR, Wackman K, Lemke A, Rui H, Dezso Z, Flister MJ. Machine learning reveals genetic modifiers of the immune microenvironment of cancer. iScience 2023; 26:107576. [PMID: 37664640 PMCID: PMC10470213 DOI: 10.1016/j.isci.2023.107576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 05/01/2023] [Accepted: 08/04/2023] [Indexed: 09/05/2023] Open
Abstract
Heritability in the immune tumor microenvironment (iTME) has been widely observed yet remains largely uncharacterized. Here, we developed a machine learning approach to map iTME modifiers within loci from genome-wide association studies (GWASs) for breast cancer (BrCa) incidence. A random forest model was trained on a positive set of immune-oncology (I-O) targets, and then used to assign I-O target probability scores to 1,362 candidate genes in linkage disequilibrium with 155 BrCa GWAS loci. Cluster analysis of the most probable candidates revealed two subfamilies of genes related to effector functions and adaptive immune responses, suggesting that iTME modifiers impact multiple aspects of anticancer immunity. Two of the top ranking BrCa candidates, LSP1 and TLR1, were orthogonally validated as iTME modifiers using BrCa patient biopsies and comparative mapping studies, respectively. Collectively, these data demonstrate a robust and flexible framework for functionally fine-mapping GWAS risk loci to identify translatable therapeutic targets.
Collapse
Affiliation(s)
- Bridget Riley-Gillis
- Genomics Research Center, AbbVie Inc, 1 North Waukegan Road, North Chicago, IL 60064, USA
| | - Shirng-Wern Tsaih
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Emily King
- Genomics Research Center, AbbVie Inc, 1 North Waukegan Road, North Chicago, IL 60064, USA
| | - Sabrina Wollenhaupt
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Jonas Reeb
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Amy R. Peck
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Kelsey Wackman
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Angela Lemke
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Hallgeir Rui
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Zoltan Dezso
- Genomics Research Center, AbbVie Bay Area, 1000 Gateway Boulevard, South San Francisco, CA 94080, USA
| | - Michael J. Flister
- Genomics Research Center, AbbVie Inc, 1 North Waukegan Road, North Chicago, IL 60064, USA
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| |
Collapse
|
8
|
Mishra AK, Malonia SK. Advancing cellular immunotherapy with macrophages. Life Sci 2023:121857. [PMID: 37307965 DOI: 10.1016/j.lfs.2023.121857] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/01/2023] [Accepted: 06/09/2023] [Indexed: 06/14/2023]
Abstract
Cell-based immunotherapies have become an exciting avenue for cancer treatment, particularly CAR T cells, which have shown great success in treating hematological malignancies. However, the limited success of T cell-based approaches in treating solid tumors has sparked interest in alternative cell types that could be used for solid tumor immunotherapy. Recent research has pointed to macrophages as a potential solution, given their ability to infiltrate solid tumors, exhibit a strong anti-tumor response, and persist long-term in the tumor microenvironment. Although early attempts with ex-vivo activated macrophage-based therapies failed to translate into clinical success, the field has revolutionized with the recent development of chimeric antigen receptor-expressing macrophages (CAR-M). While CAR-M therapy has reached the clinical trial stage, several challenges still need to be overcome before the therapy can become a reality. Here we review the evolution of macrophage-based cell therapy and evaluate recent studies and developments, emphasizing the potential of macrophages as cellular therapeutics. Furthermore, we also discuss the challenges and opportunities associated with using macrophages as a basis for therapeutic interventions.
Collapse
Affiliation(s)
- Alok K Mishra
- Department of Molecular, Cell, and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA.
| | - Sunil K Malonia
- Department of Molecular, Cell, and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA.
| |
Collapse
|
9
|
Palos K, Yu L, Railey CE, Nelson Dittrich AC, Nelson ADL. Linking discoveries, mechanisms, and technologies to develop a clearer perspective on plant long noncoding RNAs. THE PLANT CELL 2023; 35:1762-1786. [PMID: 36738093 PMCID: PMC10226578 DOI: 10.1093/plcell/koad027] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 05/30/2023]
Abstract
Long noncoding RNAs (lncRNAs) are a large and diverse class of genes in eukaryotic genomes that contribute to a variety of regulatory processes. Functionally characterized lncRNAs play critical roles in plants, ranging from regulating flowering to controlling lateral root formation. However, findings from the past decade have revealed that thousands of lncRNAs are present in plant transcriptomes, and characterization has lagged far behind identification. In this setting, distinguishing function from noise is challenging. However, the plant community has been at the forefront of discovery in lncRNA biology, providing many functional and mechanistic insights that have increased our understanding of this gene class. In this review, we examine the key discoveries and insights made in plant lncRNA biology over the past two and a half decades. We describe how discoveries made in the pregenomics era have informed efforts to identify and functionally characterize lncRNAs in the subsequent decades. We provide an overview of the functional archetypes into which characterized plant lncRNAs fit and speculate on new avenues of research that may uncover yet more archetypes. Finally, this review discusses the challenges facing the field and some exciting new molecular and computational approaches that may help inform lncRNA comparative and functional analyses.
Collapse
Affiliation(s)
- Kyle Palos
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Li’ang Yu
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Caylyn E Railey
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- Plant Biology Graduate Field, Cornell University, Ithaca, NY 14853, USA
| | | | | |
Collapse
|
10
|
Zein-Eddine R, Refrégier G, Cervantes J, Yokobori NK. The future of CRISPR in Mycobacterium tuberculosis infection. J Biomed Sci 2023; 30:34. [PMID: 37245014 DOI: 10.1186/s12929-023-00932-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/23/2023] [Indexed: 05/29/2023] Open
Abstract
Clustered Regularly Interspaced Short Palindromic repeats (CRISPR)-Cas systems rapidly raised from a bacterial genetic curiosity to the most popular tool for genetic modifications which revolutionized the study of microbial physiology. Due to the highly conserved nature of the CRISPR locus in Mycobacterium tuberculosis, the etiological agent of one of the deadliest infectious diseases globally, initially, little attention was paid to its CRISPR locus, other than as a phylogenetic marker. Recent research shows that M. tuberculosis has a partially functional Type III CRISPR, which provides a defense mechanism against foreign genetic elements mediated by the ancillary RNAse Csm6. With the advent of CRISPR-Cas based gene edition technologies, our possibilities to explore the biology of M. tuberculosis and its interaction with the host immune system are boosted. CRISPR-based diagnostic methods can lower the detection threshold to femtomolar levels, which could contribute to the diagnosis of the still elusive paucibacillary and extrapulmonary tuberculosis cases. In addition, one-pot and point-of-care tests are under development, and future challenges are discussed. We present in this literature review the potential and actual impact of CRISPR-Cas research on human tuberculosis understanding and management. Altogether, the CRISPR-revolution will revitalize the fight against tuberculosis with more research and technological developments.
Collapse
Affiliation(s)
- Rima Zein-Eddine
- Laboratoire d'Optique et Biosciences (LOB), Ecole Polytechnique, Route de Saclay 91120, Palaiseau, France
| | - Guislaine Refrégier
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, 91190, Gif-Sur-Yvette, France
| | - Jorge Cervantes
- Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, 79905, USA
| | - Noemí Kaoru Yokobori
- Servicio de Micobacterias, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS and CONICET, C1282AFF, Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| |
Collapse
|
11
|
Patterson AR, Needle GA, Sugiura A, Chi C, Steiner KK, Fisher EL, Robertson GL, Bodnya C, Markle JG, Gama V, Rathmell JC. Functional Overlap of Inborn Errors of Immunity and Metabolism Genes Define T Cell Immunometabolic Vulnerabilities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.24.525419. [PMID: 36747715 PMCID: PMC9900827 DOI: 10.1101/2023.01.24.525419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Inborn Errors of Metabolism (IEM) and Immunity (IEI) are Mendelian diseases in which complex phenotypes and patient rarity can limit clinical annotations. Few genes are assigned to both IEM and IEI, but immunometabolic demands suggest functional overlap is underestimated. We applied CRISPR screens to test IEM genes for immunologic roles and IEI genes for metabolic effects and found considerable crossover. Analysis of IEM showed N-linked glycosylation and the de novo hexosamine synthesis enzyme, Gfpt1 , are critical for T cell expansion and function. Interestingly, Gfpt1 -deficient T H 1 cells were more affected than T H 17 cells, which had increased Nagk for salvage UDP-GlcNAc synthesis. Screening IEI genes showed the transcription factor Bcl11b promotes CD4 + T cell mitochondrial activity and Mcl1 expression necessary to prevent metabolic stress. These data illustrate a high degree of functional overlap of IEM and IEI genes and point to potential immunometabolic mechanisms for a previously unappreciated set of these disorders. HIGHLIGHTS Inborn errors of immunity and metabolism have greater overlap than previously known Gfpt1 deficiency causes an IEM but also selectively regulates T cell subset fate Loss of Bcl11b causes a T cell deficiency IEI but also harms mitochondrial function Many IEM may have immune defects and IEI may be driven by metabolic mechanisms.
Collapse
|
12
|
Shi H, Doench JG, Chi H. CRISPR screens for functional interrogation of immunity. Nat Rev Immunol 2022:10.1038/s41577-022-00802-4. [DOI: 10.1038/s41577-022-00802-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2022] [Indexed: 12/13/2022]
|
13
|
Holcomb EA, Pearson AN, Jungles KM, Tate A, James J, Jiang L, Huber AK, Green MD. High-content CRISPR screening in tumor immunology. Front Immunol 2022; 13:1041451. [PMID: 36479127 PMCID: PMC9721350 DOI: 10.3389/fimmu.2022.1041451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 10/21/2022] [Indexed: 11/22/2022] Open
Abstract
CRISPR screening is a powerful tool that links specific genetic alterations to corresponding phenotypes, thus allowing for high-throughput identification of novel gene functions. Pooled CRISPR screens have enabled discovery of innate and adaptive immune response regulators in the setting of viral infection and cancer. Emerging methods couple pooled CRISPR screens with parallel high-content readouts at the transcriptomic, epigenetic, proteomic, and optical levels. These approaches are illuminating cancer immune evasion mechanisms as well as nominating novel targets that augment T cell activation, increase T cell infiltration into tumors, and promote enhanced T cell cytotoxicity. This review details recent methodological advances in high-content CRISPR screens and highlights the impact this technology is having on tumor immunology.
Collapse
Affiliation(s)
- Erin A. Holcomb
- Graduate Program in Immunology, School of Medicine, University of Michigan, Ann Arbor, MI, United States,Department of Radiation Oncology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Ashley N. Pearson
- Graduate Program in Immunology, School of Medicine, University of Michigan, Ann Arbor, MI, United States,Department of Radiation Oncology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Kassidy M. Jungles
- Department of Radiation Oncology, School of Medicine, University of Michigan, Ann Arbor, MI, United States,Department of Pharmacology, School of Medicine, University of Michigan, Ann Arbor, MI, United States,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, United States
| | - Akshay Tate
- Department of Radiation Oncology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Jadyn James
- Department of Radiation Oncology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Long Jiang
- Department of Radiation Oncology, School of Medicine, University of Michigan, Ann Arbor, MI, United States,Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, China
| | - Amanda K. Huber
- Department of Radiation Oncology, School of Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Michael D. Green
- Graduate Program in Immunology, School of Medicine, University of Michigan, Ann Arbor, MI, United States,Department of Radiation Oncology, School of Medicine, University of Michigan, Ann Arbor, MI, United States,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, United States,Department of Microbiology and Immunology, School of Medicine, University of Michigan, Ann Arbor, MI, United States,Department of Radiation Oncology, Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, MI, United States,*Correspondence: Michael D. Green,
| |
Collapse
|
14
|
Tsai HC, Pietrobon V, Peng M, Wang S, Zhao L, Marincola FM, Cai Q. Current strategies employed in the manipulation of gene expression for clinical purposes. J Transl Med 2022; 20:535. [PMID: 36401279 PMCID: PMC9673226 DOI: 10.1186/s12967-022-03747-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 09/29/2022] [Indexed: 11/19/2022] Open
Abstract
Abnormal gene expression level or expression of genes containing deleterious mutations are two of the main determinants which lead to genetic disease. To obtain a therapeutic effect and thus to cure genetic diseases, it is crucial to regulate the host's gene expression and restore it to physiological conditions. With this purpose, several molecular tools have been developed and are currently tested in clinical trials. Genome editing nucleases are a class of molecular tools routinely used in laboratories to rewire host's gene expression. Genome editing nucleases include different categories of enzymes: meganucleses (MNs), zinc finger nucleases (ZFNs), clustered regularly interspaced short palindromic repeats (CRISPR)- CRISPR associated protein (Cas) and transcription activator-like effector nuclease (TALENs). Transposable elements are also a category of molecular tools which includes different members, for example Sleeping Beauty (SB), PiggyBac (PB), Tol2 and TcBuster. Transposons have been used for genetic studies and can serve as gene delivery tools. Molecular tools to rewire host's gene expression also include episomes, which are divided into different categories depending on their molecular structure. Finally, RNA interference is commonly used to regulate gene expression through the administration of small interfering RNA (siRNA), short hairpin RNA (shRNA) and bi-functional shRNA molecules. In this review, we will describe the different molecular tools that can be used to regulate gene expression and discuss their potential for clinical applications. These molecular tools are delivered into the host's cells in the form of DNA, RNA or protein using vectors that can be grouped into physical or biochemical categories. In this review we will also illustrate the different types of payloads that can be used, and we will discuss recent developments in viral and non-viral vector technology.
Collapse
Affiliation(s)
| | | | - Maoyu Peng
- Kite Pharma Inc, Santa Monica, CA, 90404, USA
| | - Suning Wang
- Kite Pharma Inc, Santa Monica, CA, 90404, USA
| | - Lihong Zhao
- Kite Pharma Inc, Santa Monica, CA, 90404, USA
| | | | - Qi Cai
- Kite Pharma Inc, Santa Monica, CA, 90404, USA.
| |
Collapse
|
15
|
Malekos E, Carpenter S. Short open reading frame genes in innate immunity: from discovery to characterization. Trends Immunol 2022; 43:741-756. [PMID: 35965152 PMCID: PMC10118063 DOI: 10.1016/j.it.2022.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 12/27/2022]
Abstract
Next-generation sequencing (NGS) technologies have greatly expanded the size of the known transcriptome. Many newly discovered transcripts are classified as long noncoding RNAs (lncRNAs) which are assumed to affect phenotype through sequence and structure and not via translated protein products despite the vast majority of them harboring short open reading frames (sORFs). Recent advances have demonstrated that the noncoding designation is incorrect in many cases and that sORF-encoded peptides (SEPs) translated from these transcripts are important contributors to diverse biological processes. Interest in SEPs is at an early stage and there is evidence for the existence of thousands of SEPs that are yet unstudied. We hope to pique interest in investigating this unexplored proteome by providing a discussion of SEP characterization generally and describing specific discoveries in innate immunity.
Collapse
Affiliation(s)
- Eric Malekos
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA; Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Susan Carpenter
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA; Department of Molecular Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, USA.
| |
Collapse
|
16
|
Ochsner SA, Pillich RT, Rawool D, Grethe JS, McKenna NJ. Transcriptional regulatory networks of circulating immune cells in type 1 diabetes: A community knowledgebase. iScience 2022; 25:104581. [PMID: 35832893 PMCID: PMC9272393 DOI: 10.1016/j.isci.2022.104581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 12/02/2022] Open
Abstract
Investigator-generated transcriptomic datasets interrogating circulating immune cell (CIC) gene expression in clinical type 1 diabetes (T1D) have underappreciated re-use value. Here, we repurposed these datasets to create an open science environment for the generation of hypotheses around CIC signaling pathways whose gain or loss of function contributes to T1D pathogenesis. We firstly computed sets of genes that were preferentially induced or repressed in T1D CICs and validated these against community benchmarks. We then inferred and validated signaling node networks regulating expression of these gene sets, as well as differentially expressed genes in the original underlying T1D case:control datasets. In a set of three use cases, we demonstrated how informed integration of these networks with complementary digital resources supports substantive, actionable hypotheses around signaling pathway dysfunction in T1D CICs. Finally, we developed a federated, cloud-based web resource that exposes the entire data matrix for unrestricted access and re-use by the research community. Re-use of transcriptomic type 1 diabetes (T1D) circulating immune cells (CICs) datasets We generated transcriptional regulatory networks for T1D CICs Use cases generate substantive hypotheses around signaling pathway dysfunction in T1D CICs Networks are freely accessible on the web for re-use by the research community
Collapse
Affiliation(s)
- Scott A. Ochsner
- Department of Molecular, Baylor College of Medicine, Houston, TX 77030, USA
- Cellular Biology and Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rudolf T. Pillich
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Deepali Rawool
- Center for Research in Biological Systems, University of California San Diego, La Jolla, CA 92093, USA
| | - Jeffrey S. Grethe
- Center for Research in Biological Systems, University of California San Diego, La Jolla, CA 92093, USA
| | - Neil J. McKenna
- Department of Molecular, Baylor College of Medicine, Houston, TX 77030, USA
- Cellular Biology and Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Corresponding author
| |
Collapse
|
17
|
Shin S, Kim SH, Park JH, Lee JS, Lee GM. Recombinase-mediated cassette exchange-based screening of a CRISPR/Cas9 library for enhanced recombinant protein production in human embryonic kidney cells: Improving resistance to hyperosmotic stress. Metab Eng 2022; 72:247-258. [DOI: 10.1016/j.ymben.2022.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/23/2022] [Accepted: 03/30/2022] [Indexed: 10/18/2022]
|
18
|
Worthington AK, Forsberg EC. A CRISPR view of hematopoietic stem cells: Moving innovative bioengineering into the clinic. Am J Hematol 2022; 97:1226-1235. [PMID: 35560111 PMCID: PMC9378712 DOI: 10.1002/ajh.26588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/26/2022] [Accepted: 05/02/2022] [Indexed: 12/14/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas genome engineering has emerged as a powerful tool to modify precise genomic sequences with unparalleled accuracy and efficiency. Major advances in CRISPR technologies over the last 5 years have fueled the development of novel techniques in hematopoiesis research to interrogate the complexities of hematopoietic stem cell (HSC) biology. In particular, high throughput CRISPR based screens using various "flavors" of Cas coupled with sequencing and/or functional outputs are becoming increasingly efficient and accessible. In this review, we discuss recent achievements in CRISPR-mediated genomic engineering and how these new tools have advanced the understanding of HSC heterogeneity and function throughout life. Additionally, we highlight how these techniques can be used to answer previously inaccessible questions and the challenges to implement them. Finally, we focus on their translational potential to both model and treat hematological diseases in the clinic.
Collapse
Affiliation(s)
- Atesh K. Worthington
- Institute for the Biology of Stem Cells University of California‐Santa Cruz Santa Cruz California USA
- Program in Biomedical Sciences and Engineering, Department of Molecular, Cell, and Developmental Biology University of California‐Santa Cruz Santa Cruz California USA
| | - E. Camilla Forsberg
- Institute for the Biology of Stem Cells University of California‐Santa Cruz Santa Cruz California USA
- Biomolecular Engineering University of California‐Santa Cruz Santa Cruz California USA
| |
Collapse
|
19
|
Dong MB, Tang K, Zhou X, Zhou JJ, Chen S. Tumor immunology CRISPR screening: present, past, and future. Trends Cancer 2022; 8:210-225. [PMID: 34920978 PMCID: PMC8854335 DOI: 10.1016/j.trecan.2021.11.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 11/21/2021] [Accepted: 11/22/2021] [Indexed: 02/08/2023]
Abstract
Recent advances in immunotherapy have fundamentally changed the landscape of cancer treatment by leveraging the specificity and selectivity of the adaptive immune system to kill cancer cells. These successes have ushered in a new wave of research aimed at understanding immune recognition with the hope of developing newer immunotherapies. The advent of clustered regularly interspaced short palindromic repeats (CRISPR) technologies and advancement of multiomics modalities have greatly accelerated the discovery process. Here, we review the current literature surrounding CRISPR screens within the context of tumor immunology, provide essential components needed to conduct immune-specific CRISPR screens, and present avenues for future research.
Collapse
Affiliation(s)
- Matthew B. Dong
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA,System Biology Institute, Yale University, West Haven, CT, USA,Center for Cancer Systems Biology, Yale University, West Haven, CT, USA,Immunobiology Program, Yale University, New Haven, CT, USA,Department of Immunobiology, Yale University, New Haven, CT, USA,M.D.-Ph.D. Program, Yale University, West Haven, CT, USA
| | - Kaiyuan Tang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA,System Biology Institute, Yale University, West Haven, CT, USA,Center for Cancer Systems Biology, Yale University, West Haven, CT, USA,Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, CT, USA
| | - Xiaoyu Zhou
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA,System Biology Institute, Yale University, West Haven, CT, USA,Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Jingjia J. Zhou
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA,System Biology Institute, Yale University, West Haven, CT, USA,Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Sidi Chen
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; System Biology Institute, Yale University, West Haven, CT, USA; Center for Cancer Systems Biology, Yale University, West Haven, CT, USA; Immunobiology Program, Yale University, New Haven, CT, USA; M.D.-Ph.D. Program, Yale University, West Haven, CT, USA; Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, CT, USA; Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA; Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA; Yale Center for Biomedical Data Science, Yale University School of Medicine, New Haven, CT, USA.
| |
Collapse
|
20
|
Bock C, Datlinger P, Chardon F, Coelho MA, Dong MB, Lawson KA, Lu T, Maroc L, Norman TM, Song B, Stanley G, Chen S, Garnett M, Li W, Moffat J, Qi LS, Shapiro RS, Shendure J, Weissman JS, Zhuang X. High-content CRISPR screening. NATURE REVIEWS. METHODS PRIMERS 2022; 2:9. [PMID: 37214176 PMCID: PMC10200264 DOI: 10.1038/s43586-022-00098-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
CRISPR screens are a powerful source of biological discovery, enabling the unbiased interrogation of gene function in a wide range of applications and species. In pooled CRISPR screens, various genetically encoded perturbations are introduced into pools of cells. The targeted cells proliferate under a biological challenge such as cell competition, drug treatment or viral infection. Subsequently, the perturbation-induced effects are evaluated by sequencing-based counting of the guide RNAs that specify each perturbation. The typical results of such screens are ranked lists of genes that confer sensitivity or resistance to the biological challenge of interest. Contributing to the broad utility of CRISPR screens, adaptations of the core CRISPR technology make it possible to activate, silence or otherwise manipulate the target genes. Moreover, high-content read-outs such as single-cell RNA sequencing and spatial imaging help characterize screened cells with unprecedented detail. Dedicated software tools facilitate bioinformatic analysis and enhance reproducibility. CRISPR screening has unravelled various molecular mechanisms in basic biology, medical genetics, cancer research, immunology, infectious diseases, microbiology and other fields. This Primer describes the basic and advanced concepts of CRISPR screening and its application as a flexible and reliable method for biological discovery, biomedical research and drug development - with a special emphasis on high-content methods that make it possible to obtain detailed biological insights directly as part of the screen.
Collapse
Affiliation(s)
- Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Institute of Artificial Intelligence, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Paul Datlinger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Florence Chardon
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Matthew B. Dong
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Systems Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Keith A. Lawson
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Tian Lu
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Department of Physics, Harvard University, Cambridge, MA, USA
| | - Laetitia Maroc
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Thomas M. Norman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, CA, USA
- Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bicna Song
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC, USA
- Department of Genomics and Precision Medicine, George Washington University, Washington, DC, USA
| | - Geoff Stanley
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Sidi Chen
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Systems Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
| | - Mathew Garnett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Wei Li
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC, USA
- Department of Genomics and Precision Medicine, George Washington University, Washington, DC, USA
| | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Lei S. Qi
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
| | - Rebecca S. Shapiro
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Jonathan S. Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, CA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Department of Physics, Harvard University, Cambridge, MA, USA
| |
Collapse
|
21
|
Mohammed Salih M, Carpenter S. What sequencing technologies can teach us about innate immunity. Immunol Rev 2022; 305:9-28. [PMID: 34747035 PMCID: PMC8865538 DOI: 10.1111/imr.13033] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/22/2021] [Accepted: 10/16/2021] [Indexed: 01/03/2023]
Abstract
For years, we have taken a reductionist approach to understanding gene regulation through the study of one gene in one cell at a time. While this approach has been fruitful it is laborious and fails to provide a global picture of what is occurring in complex situations involving tightly coordinated immune responses. The emergence of whole-genome techniques provides a system-level view of a response and can provide a plethora of information on events occurring in a cell from gene expression changes to splicing changes and chemical modifications. As with any technology, this often results in more questions than answers, but this wealth of knowledge is providing us with an unprecedented view of what occurs inside our cells during an immune response. In this review, we will discuss the current RNA-sequencing technologies and what they are helping us learn about the innate immune system.
Collapse
Affiliation(s)
- Mays Mohammed Salih
- Department of Molecular Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, USA
| | - Susan Carpenter
- Department of Molecular Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, USA
| |
Collapse
|