1
|
Moffa JC, Bland IN, Tooley JR, Kalyanaraman V, Heitmeier M, Creed MC, Copits BA. Cell-Specific Single Viral Vector CRISPR/Cas9 Editing and Genetically Encoded Tool Delivery in the Central and Peripheral Nervous Systems. eNeuro 2024; 11:ENEURO.0438-23.2024. [PMID: 38871457 PMCID: PMC11228695 DOI: 10.1523/eneuro.0438-23.2024] [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: 10/24/2023] [Revised: 03/20/2024] [Accepted: 04/18/2024] [Indexed: 06/15/2024] Open
Abstract
CRISPR/Cas9 gene editing represents an exciting avenue to study genes of unknown function and can be combined with genetically encoded tools such as fluorescent proteins, channelrhodopsins, DREADDs, and various biosensors to more deeply probe the function of these genes in different cell types. However, current strategies to also manipulate or visualize edited cells are challenging due to the large size of Cas9 proteins and the limited packaging capacity of adeno-associated viruses (AAVs). To overcome these constraints, we developed an alternative gene editing strategy using a single AAV vector and mouse lines that express Cre-dependent Cas9 to achieve efficient cell-type specific editing across the nervous system. Expressing Cre-dependent Cas9 from a genomic locus affords space to package guide RNAs for gene editing together with Cre-dependent, genetically encoded tools to manipulate, map, or monitor neurons using a single virus. We validated this strategy with three common tools in neuroscience: ChRonos, a channelrhodopsin, for studying synaptic transmission using optogenetics, GCaMP8f for recording Ca2+ transients using photometry, and mCherry for tracing axonal projections. We tested these tools in multiple brain regions and cell types, including GABAergic neurons in the nucleus accumbens, glutamatergic neurons projecting from the ventral pallidum to the lateral habenula, dopaminergic neurons in the ventral tegmental area, and proprioceptive neurons in the periphery. This flexible approach could help identify and test the function of novel genes affecting synaptic transmission, circuit activity, or morphology with a single viral injection.
Collapse
Affiliation(s)
- Jamie C Moffa
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri 63110
- Washington University Medical Scientist Training Program, Washington University School of Medicine, St. Louis, Missouri 63110
| | - India N Bland
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Jessica R Tooley
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri 63110
- Washington University Division of Biological and Behavioral Sciences, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Vani Kalyanaraman
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Monique Heitmeier
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Meaghan C Creed
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri 63110
- Departments of Neuroscience, Psychiatry, and Biomedical Engineering, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Bryan A Copits
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri 63110
| |
Collapse
|
2
|
Martinez S, Wu S, Geuenich M, Malik A, Weber R, Woo T, Zhang A, Jang GH, Dervovic D, Al-Zahrani KN, Tsai R, Fodil N, Gros P, Gallinger S, Neely GG, Notta F, Sendoel A, Campbell K, Elling U, Schramek D. In vivo CRISPR screens reveal SCAF1 and USP15 as drivers of pancreatic cancer. Nat Commun 2024; 15:5266. [PMID: 38902237 PMCID: PMC11189927 DOI: 10.1038/s41467-024-49450-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 06/05/2024] [Indexed: 06/22/2024] Open
Abstract
Functionally characterizing the genetic alterations that drive pancreatic cancer is a prerequisite for precision medicine. Here, we perform somatic CRISPR/Cas9 mutagenesis screens to assess the transforming potential of 125 recurrently mutated pancreatic cancer genes, which revealed USP15 and SCAF1 as pancreatic tumor suppressors. Mechanistically, we find that USP15 functions in a haploinsufficient manner and that loss of USP15 or SCAF1 leads to reduced inflammatory TNFα, TGF-β and IL6 responses and increased sensitivity to PARP inhibition and Gemcitabine. Furthermore, we find that loss of SCAF1 leads to the formation of a truncated, inactive USP15 isoform at the expense of full-length USP15, functionally coupling SCAF1 and USP15. Notably, USP15 and SCAF1 alterations are observed in 31% of pancreatic cancer patients. Our results highlight the utility of in vivo CRISPR screens to integrate human cancer genomics and mouse modeling for the discovery of cancer driver genes with potential prognostic and therapeutic implications.
Collapse
Affiliation(s)
- Sebastien Martinez
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Shifei Wu
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Michael Geuenich
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Ahmad Malik
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Ramona Weber
- Institute for Regenerative Medicine (IREM), University of Zurich, Zurich, Switzerland
| | - Tristan Woo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Amy Zhang
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Gun Ho Jang
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Dzana Dervovic
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Khalid N Al-Zahrani
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Ricky Tsai
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Nassima Fodil
- Department of Biochemistry, Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, QC, Canada
| | - Philippe Gros
- Department of Biochemistry, Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, QC, Canada
| | - Steven Gallinger
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - G Gregory Neely
- Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre, and School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Faiyaz Notta
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Ataman Sendoel
- Institute for Regenerative Medicine (IREM), University of Zurich, Zurich, Switzerland
| | - Kieran Campbell
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Daniel Schramek
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
3
|
Aulston BD, Gimse K, Bazick HO, Kramar EA, Pizzo DP, Parra-Rivas LA, Sun J, Branes-Guerrero K, Checka N, Bagheri N, Satyadev N, Carlson-Stevermer J, Saito T, Saido TC, Audhya A, Wood MA, Zylka MJ, Saha K, Roy S. Long term rescue of Alzheimer's deficits in vivo by one-time gene-editing of App C-terminus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.08.598099. [PMID: 38895278 PMCID: PMC11185791 DOI: 10.1101/2024.06.08.598099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Gene-editing technologies promise to create a new class of therapeutics that can achieve permanent correction with a single intervention. Besides eliminating mutant alleles in familial disease, gene-editing can also be used to favorably manipulate upstream pathophysiologic events and alter disease-course in wider patient populations, but few such feasible therapeutic avenues have been reported. Here we use CRISPR-Cas9 to edit the last exon of amyloid precursor protein (App), relevant for Alzheimer's disease (AD). Our strategy effectively eliminates an endocytic (YENPTY) motif at APP C-terminus, while preserving the N-terminus and compensatory APP-homologues. This manipulation favorably alters events along the amyloid-pathway - inhibiting toxic APP-β-cleavage fragments (including Aβ) and upregulating neuroprotective APP-α-cleavage products. AAV-driven editing ameliorates neuropathologic, electrophysiologic, and behavioral deficits in an AD knockin mouse model. Effects persist for many months, and no abnormalities are seen in WT mice even after germline App-editing; underlining overall efficacy and safety. Pathologic alterations in the glial-transcriptome of App-KI mice, as seen by single nuclei RNA-sequencing (sNuc-Seq), are also normalized by App C-terminus editing. Our strategy takes advantage of innate transcriptional rules that render terminal exons insensitive to nonsense-decay, and the upstream manipulation is expected to be effective for all forms of AD. These studies offer a path for a one-time disease-modifying treatment for AD.
Collapse
Affiliation(s)
- Brent D. Aulston
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - Kirstan Gimse
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, 53715, USA; Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Hannah O. Bazick
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Eniko A. Kramar
- Department of Neurobiology and Behavior, School of Biological Sciences University of California, Irvine 92697-2695, USA
| | - Donald P. Pizzo
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - Leonardo A. Parra-Rivas
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - Jichao Sun
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
- Present address: Department of Geriatrics and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People’s Hospital, The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Kristen Branes-Guerrero
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
- Present address: Eli Lilly Pharmaceuticals, Indianapolis, IN, USA
| | - Nidhi Checka
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - Neda Bagheri
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| | - Nihal Satyadev
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
- Present address: Department of Neurology, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Jared Carlson-Stevermer
- Synthego Corporation, 3696 Haven Ave Suite A, Redwood City, CA 94063
- Present address: Serotiny Inc., 329 Oyster Point Boulevard, 3rd Floor, South San Francisco, CA 94080
| | - Takashi Saito
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Department of Neurocognitive Science, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi 467-8601, Japan
| | - Takaomi C. Saido
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Anjon Audhya
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Marcelo A. Wood
- Department of Neurobiology and Behavior, School of Biological Sciences University of California, Irvine 92697-2695, USA
| | - Mark J. Zylka
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Krishanu Saha
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, 53715, USA; Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Subhojit Roy
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
- Department of Neurosciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| |
Collapse
|
4
|
Teh S, Bowland K, Halper-Stromberg E, Kotwal A, Bennett A, Skaist A, Tang J, Cai F, Macoretta A, Liang H, Kamiyama H, Wheelan S, Lin MT, Hruban R, Hung CF, Goldstein M, Scharpf R, Roberts N, Eshleman J. CRISPR-Cas9 for selective targeting of somatic mutations in pancreatic cancers. NAR Cancer 2024; 6:zcae028. [PMID: 38915758 PMCID: PMC11195629 DOI: 10.1093/narcan/zcae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 05/23/2024] [Accepted: 06/03/2024] [Indexed: 06/26/2024] Open
Abstract
Somatic mutations are desirable targets for selective elimination of cancer, yet most are found within noncoding regions. We have adapted the CRISPR-Cas9 gene editing tool as a novel, cancer-specific killing strategy by targeting the subset of somatic mutations that create protospacer adjacent motifs (PAMs), which have evolutionally allowed bacterial cells to distinguish between self and non-self DNA for Cas9-induced double strand breaks. Whole genome sequencing (WGS) of paired tumor minus normal (T-N) samples from three pancreatic cancer patients (Panc480, Panc504, and Panc1002) showed an average of 417 somatic PAMs per tumor produced from single base substitutions. Further analyses of 591 paired T-N samples from The International Cancer Genome Consortium found medians of ∼455 somatic PAMs per tumor in pancreatic, ∼2800 in lung, and ∼3200 in esophageal cancer cohorts. Finally, we demonstrated 69-99% selective cell death of three targeted pancreatic cancer cell lines using 4-9 sgRNAs designed using the somatic PAM discovery approach. We also showed no off-target activity from these tumor-specific sgRNAs in either the patient's normal cells or an irrelevant cancer using WGS. This study demonstrates the potential of CRISPR-Cas9 as a novel and selective anti-cancer strategy, and supports the genetic targeting of adult cancers.
Collapse
Affiliation(s)
- Selina Shiqing K Teh
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kirsten Bowland
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Eitan Halper-Stromberg
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Akhil Kotwal
- Department of Radiation Oncology and Molecular Radiation Sciences, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alexis Bennett
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alyza Skaist
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jacqueline Tang
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fidel Cai
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Antonella Macoretta
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hong Liang
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Sarah Wheelan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Scientific Review Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Ming-Tseh Lin
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ralph H Hruban
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chien-Fu Hung
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael Goldstein
- Department of Radiation Oncology and Molecular Radiation Sciences, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert B Scharpf
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nicholas J Roberts
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James R Eshleman
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| |
Collapse
|
5
|
Shuldiner EG, Karmakar S, Tsai MK, Hebert JD, Tang YJ, Andrejka L, Wang M, Detrick CR, Cai H, Tang R, Petrov DA, Winslow MM. Aging represses lung tumorigenesis and alters tumor suppression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596319. [PMID: 38853826 PMCID: PMC11160591 DOI: 10.1101/2024.05.28.596319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Most cancers are diagnosed in persons over the age of sixty, but little is known about how age impacts tumorigenesis. While aging is accompanied by mutation accumulation - widely understood to contribute to cancer risk - it is also associated with numerous other cellular and molecular changes likely to impact tumorigenesis. Moreover, cancer incidence decreases in the oldest part of the population, suggesting that very old age may reduce carcinogenesis. Here we show that aging represses tumor initiation and growth in genetically engineered mouse models of human lung cancer. Moreover, aging dampens the impact of inactivating many, but not all, tumor suppressor genes with the impact of inactivating PTEN, a negative regulator of the PI3K/AKT pathway, weakened to a disproportionate extent. Single-cell transcriptomic analysis revealed that neoplastic cells from tumors in old mice retain many age-related transcriptomic changes, showing that age has an enduring impact that persists through oncogenic transformation. Furthermore, the consequences of PTEN inactivation were strikingly age-dependent, with PTEN deficiency reducing signatures of aging in cancer cells and the tumor microenvironment. Our findings suggest that the relationship between age and lung cancer incidence may reflect an integration of the competing effects of driver mutation accumulation and tumor suppressive effects of aging.
Collapse
|
6
|
Hebert JD, Xu H, Tang YJ, Ruiz PA, Detrick CR, Wang J, Hughes NW, Donosa O, Andrejka L, Karmakar S, Aboiralor I, Tang R, Sage J, Cong L, Petrov DA, Winslow MM. Efficient and multiplexed somatic genome editing with Cas12a mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583774. [PMID: 38496463 PMCID: PMC10942438 DOI: 10.1101/2024.03.07.583774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Somatic genome editing in mouse models has increased our understanding of the in vivo effects of genetic alterations in areas ranging from neuroscience to cancer biology and beyond. However, existing models are limited in their ability to create multiple targeted edits. Thus, our understanding of the complex genetic interactions that underlie development, homeostasis, and disease remains incomplete. Cas12a is an RNA-guided endonuclease with unique attributes that enable simple targeting of multiple genes with crRNA arrays containing tandem guides. To accelerate and expand the generation of complex genotypes in somatic cells, we generated transgenic mice with Cre-regulated and constitutive expression of enhanced Acidaminococcus sp. Cas12a (enAsCas12a). In these mice, enAsCas12a-mediated somatic genome editing robustly generated compound genotypes, as exemplified by the initiation of diverse cancer types driven by homozygous inactivation of trios of tumor suppressor genes. We further integrated these modular crRNA arrays with clonal barcoding to quantify the size and number of tumors with each array, as well as the efficiency of each crRNA. These Cas12a alleles will enable the rapid generation of disease models and broadly facilitate the high-throughput investigation of coincident genomic alterations in somatic cells in vivo .
Collapse
|
7
|
Sánchez Rivera FJ, Dow LE. How CRISPR Is Revolutionizing the Generation of New Models for Cancer Research. Cold Spring Harb Perspect Med 2024; 14:a041384. [PMID: 37487630 PMCID: PMC11065179 DOI: 10.1101/cshperspect.a041384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Cancers arise through acquisition of mutations in genes that regulate core biological processes like cell proliferation and cell death. Decades of cancer research have led to the identification of genes and mutations causally involved in disease development and evolution, yet defining their precise function across different cancer types and how they influence therapy responses has been challenging. Mouse models have helped define the in vivo function of cancer-associated alterations, and genome-editing approaches using CRISPR have dramatically accelerated the pace at which these models are developed and studied. Here, we highlight how CRISPR technologies have impacted the development and use of mouse models for cancer research and discuss the many ways in which these rapidly evolving platforms will continue to transform our understanding of this disease.
Collapse
Affiliation(s)
- Francisco J Sánchez Rivera
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Lukas E Dow
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York 10065, USA
- Department of Biochemistry, Weill Cornell Medicine, New York, New York 10065, USA
- Department of Medicine, Weill Cornell Medicine, New York, New York 10065, USA
| |
Collapse
|
8
|
Hebert JD, Tang YJ, Andrejka L, Lopez SS, Petrov DA, Boross G, Winslow MM. Combinatorial in vivo genome editing identifies widespread epistasis during lung tumorigenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583981. [PMID: 38496564 PMCID: PMC10942407 DOI: 10.1101/2024.03.07.583981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Lung adenocarcinoma, the most common subtype of lung cancer, is genomically complex, with tumors containing tens to hundreds of non-synonymous mutations. However, little is understood about how genes interact with each other to enable tumorigenesis in vivo , largely due to a lack of methods for investigating genetic interactions in a high-throughput and multiplexed manner. Here, we employed a novel platform to generate tumors with all pairwise inactivation of ten tumor suppressor genes within an autochthonous mouse model of oncogenic KRAS-driven lung cancer. By quantifying the fitness of tumors with every single and double mutant genotype, we show that most tumor suppressor genetic interactions exhibited negative epistasis, with diminishing returns on tumor fitness. In contrast, Apc inactivation showed positive epistasis with the inactivation of several other genes, including dramatically synergistic effects on tumor fitness in combination with Lkb1 or Nf1 inactivation. This approach has the potential to expand the scope of genetic interactions that may be functionally characterized in vivo , which could lead to a better understanding of how complex tumor genotypes impact each step of carcinogenesis.
Collapse
|
9
|
Ely ZA, Mathey-Andrews N, Naranjo S, Gould SI, Mercer KL, Newby GA, Cabana CM, Rideout WM, Jaramillo GC, Khirallah JM, Holland K, Randolph PB, Freed-Pastor WA, Davis JR, Kulstad Z, Westcott PMK, Lin L, Anzalone AV, Horton BL, Pattada NB, Shanahan SL, Ye Z, Spranger S, Xu Q, Sánchez-Rivera FJ, Liu DR, Jacks T. A prime editor mouse to model a broad spectrum of somatic mutations in vivo. Nat Biotechnol 2024; 42:424-436. [PMID: 37169967 PMCID: PMC11120832 DOI: 10.1038/s41587-023-01783-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 04/05/2023] [Indexed: 05/13/2023]
Abstract
Genetically engineered mouse models only capture a small fraction of the genetic lesions that drive human cancer. Current CRISPR-Cas9 models can expand this fraction but are limited by their reliance on error-prone DNA repair. Here we develop a system for in vivo prime editing by encoding a Cre-inducible prime editor in the mouse germline. This model allows rapid, precise engineering of a wide range of mutations in cell lines and organoids derived from primary tissues, including a clinically relevant Kras mutation associated with drug resistance and Trp53 hotspot mutations commonly observed in pancreatic cancer. With this system, we demonstrate somatic prime editing in vivo using lipid nanoparticles, and we model lung and pancreatic cancer through viral delivery of prime editing guide RNAs or orthotopic transplantation of prime-edited organoids. We believe that this approach will accelerate functional studies of cancer-associated mutations and complex genetic combinations that are challenging to construct with traditional models.
Collapse
Affiliation(s)
- Zackery A Ely
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicolas Mathey-Andrews
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Santiago Naranjo
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Samuel I Gould
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kim L Mercer
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Christina M Cabana
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - William M Rideout
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Grissel Cervantes Jaramillo
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Katie Holland
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Angelo State University, San Angelo, TX, USA
| | - Peyton B Randolph
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - William A Freed-Pastor
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jessie R Davis
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Zachary Kulstad
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Peter M K Westcott
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Cold Spring Harbor Laboratory, Huntington, NY, USA
| | - Lin Lin
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrew V Anzalone
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Brendan L Horton
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nimisha B Pattada
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sean-Luc Shanahan
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zhongfeng Ye
- Department of Biomedical Engineering, Tufts University, Medford, MA, USA
| | - Stefani Spranger
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Qiaobing Xu
- Department of Biomedical Engineering, Tufts University, Medford, MA, USA
| | - Francisco J Sánchez-Rivera
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Tyler Jacks
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
10
|
Oser MG, MacPherson D, Oliver TG, Sage J, Park KS. Genetically-engineered mouse models of small cell lung cancer: the next generation. Oncogene 2024; 43:457-469. [PMID: 38191672 PMCID: PMC11180418 DOI: 10.1038/s41388-023-02929-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/10/2024]
Abstract
Small cell lung cancer (SCLC) remains the most fatal form of lung cancer, with patients in dire need of new and effective therapeutic approaches. Modeling SCLC in an immunocompetent host is essential for understanding SCLC pathogenesis and ultimately discovering and testing new experimental therapeutic strategies. Human SCLC is characterized by near universal genetic loss of the RB1 and TP53 tumor suppressor genes. Twenty years ago, the first genetically-engineered mouse model (GEMM) of SCLC was generated using conditional deletion of both Rb1 and Trp53 in the lungs of adult mice. Since then, several other GEMMs of SCLC have been developed coupling genomic alterations found in human SCLC with Rb1 and Trp53 deletion. Here we summarize how GEMMs of SCLC have contributed significantly to our understanding of the disease in the past two decades. We also review recent advances in modeling SCLC in mice that allow investigators to bypass limitations of the previous generation of GEMMs while studying new genes of interest in SCLC. In particular, CRISPR/Cas9-mediated somatic gene editing can accelerate how new genes of interest are functionally interrogated in SCLC tumorigenesis. Notably, the development of allograft models and precancerous precursor models from SCLC GEMMs provides complementary approaches to GEMMs to study tumor cell-immune microenvironment interactions and test new therapeutic strategies to enhance response to immunotherapy. Ultimately, the new generation of SCLC models can accelerate research and help develop new therapeutic strategies for SCLC.
Collapse
Affiliation(s)
- Matthew G Oser
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA.
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
| | - David MacPherson
- Division of Human Biology, Fred Hutch Cancer Center, Seattle, WA, 98109, USA
| | - Trudy G Oliver
- Department of Pharmacology & Cancer Biology, Duke University, Durham, NC, 27708, USA
| | - Julien Sage
- Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Kwon-Sik Park
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, 22903, USA.
| |
Collapse
|
11
|
Gong X, Du J, Peng RW, Chen C, Yang Z. CRISPRing KRAS: A Winding Road with a Bright Future in Basic and Translational Cancer Research. Cancers (Basel) 2024; 16:460. [PMID: 38275900 PMCID: PMC10814442 DOI: 10.3390/cancers16020460] [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: 01/02/2024] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
Once considered "undruggable" due to the strong affinity of RAS proteins for GTP and the structural lack of a hydrophobic "pocket" for drug binding, the development of proprietary therapies for KRAS-mutant tumors has long been a challenging area of research. CRISPR technology, the most successful gene-editing tool to date, is increasingly being utilized in cancer research. Here, we provide a comprehensive review of the application of the CRISPR system in basic and translational research in KRAS-mutant cancer, summarizing recent advances in the mechanistic understanding of KRAS biology and the underlying principles of drug resistance, anti-tumor immunity, epigenetic regulatory networks, and synthetic lethality co-opted by mutant KRAS.
Collapse
Affiliation(s)
- Xian Gong
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, 29 Xinquan Road, Fuzhou 350001, China; (X.G.); (J.D.)
- Key Laboratory of Cardio-Thoracic Surgery, Fujian Medical University, Fuzhou 350001, China
| | - Jianting Du
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, 29 Xinquan Road, Fuzhou 350001, China; (X.G.); (J.D.)
- Key Laboratory of Cardio-Thoracic Surgery, Fujian Medical University, Fuzhou 350001, China
| | - Ren-Wang Peng
- Division of General Thoracic Surgery, Department of BioMedical Research (DBMR), Inselspital, Bern University Hospital, University of Bern, Murtenstrasse 28, 3008 Bern, Switzerland;
| | - Chun Chen
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, 29 Xinquan Road, Fuzhou 350001, China; (X.G.); (J.D.)
- Key Laboratory of Cardio-Thoracic Surgery, Fujian Medical University, Fuzhou 350001, China
| | - Zhang Yang
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, 29 Xinquan Road, Fuzhou 350001, China; (X.G.); (J.D.)
- Key Laboratory of Cardio-Thoracic Surgery, Fujian Medical University, Fuzhou 350001, China
| |
Collapse
|
12
|
LaFleur MW, Lemmen AM, Streeter ISL, Nguyen TH, Milling LE, Derosia NM, Hoffman ZM, Gillis JE, Tjokrosurjo Q, Markson SC, Huang AY, Anekal PV, Montero Llopis P, Haining WN, Doench JG, Sharpe AH. X-CHIME enables combinatorial, inducible, lineage-specific and sequential knockout of genes in the immune system. Nat Immunol 2024; 25:178-188. [PMID: 38012416 PMCID: PMC10881062 DOI: 10.1038/s41590-023-01689-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 10/20/2023] [Indexed: 11/29/2023]
Abstract
Annotation of immunologic gene function in vivo typically requires the generation of knockout mice, which is time consuming and low throughput. We previously developed CHimeric IMmune Editing (CHIME), a CRISPR-Cas9 bone marrow delivery system for constitutive, ubiquitous deletion of single genes. Here we describe X-CHIME, four new CHIME-based systems for modular and rapid interrogation of gene function combinatorially (C-CHIME), inducibly (I-CHIME), lineage-specifically (L-CHIME) or sequentially (S-CHIME). We use C-CHIME and S-CHIME to assess the consequences of combined deletion of Ptpn1 and Ptpn2, an embryonic lethal gene pair, in adult mice. We find that constitutive deletion of both PTPN1 and PTPN2 leads to bone marrow hypoplasia and lethality, while inducible deletion after immune development leads to enteritis and lethality. These findings demonstrate that X-CHIME can be used for rapid mechanistic evaluation of genes in distinct in vivo contexts and that PTPN1 and PTPN2 have some functional redundancy important for viability in adult mice.
Collapse
Affiliation(s)
- Martin W LaFleur
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ashlyn M Lemmen
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ivy S L Streeter
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Thao H Nguyen
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Lauren E Milling
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Nicole M Derosia
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Zachary M Hoffman
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jacob E Gillis
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Qin Tjokrosurjo
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Samuel C Markson
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Amy Y Huang
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | | | - John G Doench
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Arlene H Sharpe
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
13
|
Ravichandran M, Maddalo D. Applications of CRISPR-Cas9 for advancing precision medicine in oncology: from target discovery to disease modeling. Front Genet 2023; 14:1273994. [PMID: 37908590 PMCID: PMC10613999 DOI: 10.3389/fgene.2023.1273994] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/27/2023] [Indexed: 11/02/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) (CRISPR/Cas9) system is a powerful tool that enables precise and efficient gene manipulation. In a relatively short time, CRISPR has risen to become the preferred gene-editing system due to its high efficiency, simplicity, and programmability at low costs. Furthermore, in the recent years, the CRISPR toolkit has been rapidly expanding, and the emerging advancements have shown tremendous potential in uncovering molecular mechanisms and new therapeutic strategies for human diseases. In this review, we provide our perspectives on the recent advancements in CRISPR technology and its impact on precision medicine, ranging from target identification, disease modeling, and diagnostics. We also discuss the impact of novel approaches such as epigenome, base, and prime editing on preclinical cancer drug discovery.
Collapse
Affiliation(s)
- Mirunalini Ravichandran
- Department of Translational Oncology, Genentech, Inc., South San Francisco, CA, United States
| | - Danilo Maddalo
- Department of Translational Oncology, Genentech, Inc., South San Francisco, CA, United States
| |
Collapse
|
14
|
Blair LM, Juan JM, Sebastian L, Tran VB, Nie W, Wall GD, Gerceker M, Lai IK, Apilado EA, Grenot G, Amar D, Foggetti G, Do Carmo M, Ugur Z, Deng D, Chenchik A, Paz Zafra M, Dow LE, Politi K, MacQuitty JJ, Petrov DA, Winslow MM, Rosen MJ, Winters IP. Oncogenic context shapes the fitness landscape of tumor suppression. Nat Commun 2023; 14:6422. [PMID: 37828026 PMCID: PMC10570323 DOI: 10.1038/s41467-023-42156-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: 01/30/2023] [Accepted: 10/02/2023] [Indexed: 10/14/2023] Open
Abstract
Tumors acquire alterations in oncogenes and tumor suppressor genes in an adaptive walk through the fitness landscape of tumorigenesis. However, the interactions between oncogenes and tumor suppressor genes that shape this landscape remain poorly resolved and cannot be revealed by human cancer genomics alone. Here, we use a multiplexed, autochthonous mouse platform to model and quantify the initiation and growth of more than one hundred genotypes of lung tumors across four oncogenic contexts: KRAS G12D, KRAS G12C, BRAF V600E, and EGFR L858R. We show that the fitness landscape is rugged-the effect of tumor suppressor inactivation often switches between beneficial and deleterious depending on the oncogenic context-and shows no evidence of diminishing-returns epistasis within variants of the same oncogene. These findings argue against a simple linear signaling relationship amongst these three oncogenes and imply a critical role for off-axis signaling in determining the fitness effects of inactivating tumor suppressors.
Collapse
Affiliation(s)
| | | | | | - Vy B Tran
- D2G Oncology, Mountain View, CA, USA
| | | | | | | | - Ian K Lai
- D2G Oncology, Mountain View, CA, USA
| | | | | | - David Amar
- D2G Oncology, Mountain View, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
- Department of Cardiovascular Medicine and the Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Mariana Do Carmo
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Zeynep Ugur
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | | | | | - Maria Paz Zafra
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Excellence Research Unit "Modeling Nature" (MNat), University of Granada, E-18016, Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), E-18071, Granada, Spain
| | - Lukas E Dow
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Katerina Politi
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Section of Medical Oncology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | | | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, CA, USA
- Chan Zuckerberg BioHub, San Francisco, CA, USA
| | - Monte M Winslow
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | | |
Collapse
|
15
|
Moffa JC, Bland IN, Tooley JR, Kalyanaraman V, Heitmeier M, Creed MC, Copits BA. Cell specific single viral vector CRISPR/Cas9 editing and genetically encoded tool delivery in the central and peripheral nervous systems. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.10.561249. [PMID: 37873336 PMCID: PMC10592710 DOI: 10.1101/2023.10.10.561249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Gene manipulation strategies using germline knockout, conditional knockout, and more recently CRISPR/Cas9 are crucial tools for advancing our understanding of the nervous system. However, traditional gene knockout approaches can be costly and time consuming, may lack cell-type specificity, and can induce germline recombination. Viral gene editing presents and an exciting alternative to more rapidly study genes of unknown function; however, current strategies to also manipulate or visualize edited cells are challenging due to the large size of Cas9 proteins and the limited packaging capacity of adeno-associated viruses (AAVs). To overcome these constraints, we have developed an alternative gene editing strategy using a single AAV vector and mouse lines that express Cre-dependent Cas9 to achieve efficient cell-type specific editing across the nervous system. Expressing Cre-dependent Cas9 in specific cell types in transgenic mouse lines affords more space to package guide RNAs for gene editing together with Cre-dependent, genetically encoded tools to manipulate, map, or monitor neurons using a single virus. We validated this strategy with three commonly used tools in neuroscience: ChRonos, a channelrhodopsin, for manipulating synaptic transmission using optogenetics; GCaMP8f for recording Ca2+ transients using fiber photometry, and mCherry for anatomical tracing of axonal projections. We tested these tools in multiple brain regions and cell types, including GABAergic neurons in the nucleus accumbens (NAc), glutamatergic neurons projecting from the ventral pallidum (VP) to the lateral habenula (LHb), dopaminergic neurons in the ventral tegmental area (VTA), and parvalbumin (PV)-positive proprioceptive neurons in the periphery. This flexible approach should be useful to identify novel genes that affect synaptic transmission, circuit activity, or morphology with a single viral injection.
Collapse
Affiliation(s)
- Jamie C. Moffa
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine; St. Louis, MO
- Washington University Medical Scientist Training Program, Washington University School of Medicine; St. Louis, MO
| | - India N. Bland
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine; St. Louis, MO
| | - Jessica R. Tooley
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine; St. Louis, MO
- Washington University Division of Biological and Behavioral Sciences, Washington University School of Medicine; St. Louis, MO
| | - Vani Kalyanaraman
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine; St. Louis, MO
| | - Monique Heitmeier
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine; St. Louis, MO
| | - Meaghan C. Creed
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine; St. Louis, MO
- Departments of Neuroscience, Psychiatry, and Biomedical Engineering, Washington University School of Medicine, St. Louis, MO
| | - Bryan A. Copits
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine; St. Louis, MO
| |
Collapse
|
16
|
Yousefi M, Andrejka L, Szamecz M, Winslow MM, Petrov DA, Boross G. Fully accessible fitness landscape of oncogene-negative lung adenocarcinoma. Proc Natl Acad Sci U S A 2023; 120:e2303224120. [PMID: 37695905 PMCID: PMC10515140 DOI: 10.1073/pnas.2303224120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/12/2023] [Indexed: 09/13/2023] Open
Abstract
Cancer genomes are almost invariably complex with genomic alterations cooperating during each step of carcinogenesis. In cancers that lack a single dominant oncogene mutation, cooperation between the inactivation of multiple tumor suppressor genes can drive tumor initiation and growth. Here, we shed light on how the sequential acquisition of genomic alterations generates oncogene-negative lung tumors. We couple tumor barcoding with combinatorial and multiplexed somatic genome editing to characterize the fitness landscapes of three tumor suppressor genes NF1, RASA1, and PTEN, the inactivation of which jointly drives oncogene-negative lung adenocarcinoma initiation and growth. The fitness landscape was surprisingly accessible, with each additional mutation leading to growth advantage. Furthermore, the fitness landscapes remained fully accessible across backgrounds with the inactivation of additional tumor suppressor genes. These results suggest that while predicting cancer evolution will be challenging, acquiring the multiple alterations that drive the growth of oncogene-negative tumors can be facilitated by the lack of constraints on mutational order.
Collapse
Affiliation(s)
- Maryam Yousefi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA94305
| | - Laura Andrejka
- Department of Genetics, Stanford University School of Medicine, Stanford, CA94305
| | - Márton Szamecz
- Eötvös Loránd University, Faculty of Informatics, Budapest1053, Hungary
| | - Monte M. Winslow
- Department of Genetics, Stanford University School of Medicine, Stanford, CA94305
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA94305
- Department of Pathology, Stanford University School of Medicine, Stanford, CA94305
| | - Dmitri A. Petrov
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA94305
- Department of Biology, Stanford University, Stanford, CA94305
| | - Gábor Boross
- Department of Biology, Stanford University, Stanford, CA94305
| |
Collapse
|
17
|
Perelli L, Zhang L, Mangiameli S, Russell AJC, Giannese F, Peng F, Carbone F, Le C, Khan H, Citron F, Soeung M, Lam TNA, Lundgren S, Zhu C, Catania D, Feng N, Gurreri E, Sgambato A, Tortora G, Draetta GF, Tonon G, Futreal A, Giuliani V, Carugo A, Viale A, Heffernan TP, Wang L, Cittaro D, Chen F, Genovese G. Evolutionary fingerprints of EMT in pancreatic cancers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558231. [PMID: 37786705 PMCID: PMC10541589 DOI: 10.1101/2023.09.18.558231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Mesenchymal plasticity has been extensively described in advanced and metastatic epithelial cancers; however, its functional role in malignant progression, metastatic dissemination and therapy response is controversial. More importantly, the role of epithelial mesenchymal transition (EMT) and cell plasticity in tumor heterogeneity, clonal selection and clonal evolution is poorly understood. Functionally, our work clarifies the contribution of EMT to malignant progression and metastasis in pancreatic cancer. We leveraged ad hoc somatic mosaic genome engineering, lineage tracing and ablation technologies and dynamic genetic reporters to trace and ablate tumor-specific lineages along the phenotypic spectrum of epithelial to mesenchymal plasticity. The experimental evidences clarify the essential contribution of mesenchymal lineages to pancreatic cancer evolution and metastatic dissemination. Spatial genomic analysis combined with single cell transcriptomic and epigenomic profiling of epithelial and mesenchymal lineages reveals that EMT promotes with the emergence of chromosomal instability (CIN). Specifically tumor lineages with mesenchymal features display highly conserved patterns of genomic evolution including complex structural genomic rearrangements and chromotriptic events. Genetic ablation of mesenchymal lineages robustly abolished these mutational processes and evolutionary patterns, as confirmed by cross species analysis of pancreatic and other human epithelial cancers. Mechanistically, we discovered that malignant cells with mesenchymal features display increased chromatin accessibility, particularly in the pericentromeric and centromeric regions, which in turn results in delayed mitosis and catastrophic cell division. Therefore, EMT favors the emergence of high-fitness tumor cells, strongly supporting the concept of a cell-state, lineage-restricted patterns of evolution, where cancer cell sub-clonal speciation is propagated to progenies only through restricted functional compartments. Restraining those evolutionary routes through genetic ablation of clones capable of mesenchymal plasticity and extinction of the derived lineages completely abrogates the malignant potential of one of the most aggressive form of human cancer.
Collapse
|
18
|
Brockman QR, Scherer A, McGivney GR, Gutierrez WR, Rytlewski J, Sheehan A, Warrier A, Laverty EA, Roughton G, Carnevale NC, Knepper-Adrian V, Dodd RD. Discrepancies in indel software resolution with somatic CRISPR/Cas9 tumorigenesis models. Sci Rep 2023; 13:14798. [PMID: 37684258 PMCID: PMC10491828 DOI: 10.1038/s41598-023-41109-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
CRISPR/Cas9 gene editing has evolved from a simple laboratory tool to a powerful method of in vivo genomic engineering. As the applications of CRISPR/Cas9 technology have grown, the need to characterize the breadth and depth of indels generated by editing has expanded. Traditionally, investigators use one of several publicly-available platforms to determine CRISPR/Cas9-induced indels in an edited sample. However, to our knowledge, there has not been a cross-platform comparison of available indel analysis software in samples generated from somatic in vivo mouse models. Our group has pioneered using CRISPR/Cas9 to generate somatic primary mouse models of malignant peripheral nerve sheath tumors (MPNSTs) through genetic editing of Nf1. Here, we used sequencing data from the in vivo editing of the Nf1 gene in our CRISPR/Cas9 tumorigenesis model to directly compare results across four different software platforms. By analyzing the same genetic target across a wide panel of cell lines with the same sequence file, we are able to draw systematic conclusions about the differences in these software programs for analysis of in vivo-generated indels. Surprisingly, we report high variability in the reported number, size, and frequency of indels across each software platform. These data highlight the importance of selecting indel analysis platforms specific to the context that the gene editing approach is being applied. Taken together, this analysis shows that different software platforms can report widely divergent indel data from the same sample, particularly if larger indels are present, which are common in somatic, in vivo CRISPR/Cas9 tumor models.
Collapse
Affiliation(s)
- Qierra R Brockman
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, 375 Newton Rd, 5206 MERF, Iowa City, IA, 52246, USA
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
| | - Amanda Scherer
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, 375 Newton Rd, 5206 MERF, Iowa City, IA, 52246, USA
| | - Gavin R McGivney
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, 375 Newton Rd, 5206 MERF, Iowa City, IA, 52246, USA
- Cancer Biology Training Program, University of Iowa, Iowa City, IA, USA
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, USA
| | - Wade R Gutierrez
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, 375 Newton Rd, 5206 MERF, Iowa City, IA, 52246, USA
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
- Cancer Biology Training Program, University of Iowa, Iowa City, IA, USA
- Medical Scientist Training Program, University of Iowa, Iowa City, IA, USA
| | - Jeffrey Rytlewski
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, 375 Newton Rd, 5206 MERF, Iowa City, IA, 52246, USA
| | - Alexa Sheehan
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, 375 Newton Rd, 5206 MERF, Iowa City, IA, 52246, USA
| | - Akshaya Warrier
- Cancer Biology Training Program, University of Iowa, Iowa City, IA, USA
- Medical Scientist Training Program, University of Iowa, Iowa City, IA, USA
| | - Emily A Laverty
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, 375 Newton Rd, 5206 MERF, Iowa City, IA, 52246, USA
| | - Grace Roughton
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, 375 Newton Rd, 5206 MERF, Iowa City, IA, 52246, USA
| | - Nina C Carnevale
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, 375 Newton Rd, 5206 MERF, Iowa City, IA, 52246, USA
| | - Vickie Knepper-Adrian
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, 375 Newton Rd, 5206 MERF, Iowa City, IA, 52246, USA
| | - Rebecca D Dodd
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, 375 Newton Rd, 5206 MERF, Iowa City, IA, 52246, USA.
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA.
- Cancer Biology Training Program, University of Iowa, Iowa City, IA, USA.
| |
Collapse
|
19
|
Ebrahimi S, Khosravi MA, Raz A, Karimipoor M, Parvizi P. CRISPR-Cas Technology as a Revolutionary Genome Editing tool: Mechanisms and Biomedical Applications. IRANIAN BIOMEDICAL JOURNAL 2023; 27:219-46. [PMID: 37873636 PMCID: PMC10707817 DOI: 10.61186/ibj.27.5.219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/14/2023] [Indexed: 12/17/2023]
Abstract
Programmable nucleases are powerful genomic tools for precise genome editing. These tools precisely recognize, remove, or change DNA at a defined site, thereby, stimulating cellular DNA repair pathways that can cause mutations or accurate replacement or deletion/insertion of a sequence. CRISPR-Cas9 system is the most potent and useful genome editing technique adapted from the defense immune system of certain bacteria and archaea against viruses and phages. In the past decade, this technology made notable progress, and at present, it has largely been used in genome manipulation to make precise gene editing in plants, animals, and human cells. In this review, we aim to explain the basic principle, mechanisms of action, and applications of this system in different areas of medicine, with emphasizing on the detection and treatment of parasitic diseases.
Collapse
Affiliation(s)
- Sahar Ebrahimi
- Molecular Systematics Laboratory, Parasitology Department, Pasteur Institute of Iran, Tehran, Iran
- Molecular Medicine Department, Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Ali Khosravi
- Molecular Medicine Department, Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abbasali Raz
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
| | - Morteza Karimipoor
- Molecular Medicine Department, Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
| | - Parviz Parvizi
- Molecular Systematics Laboratory, Parasitology Department, Pasteur Institute of Iran, Tehran, Iran
| |
Collapse
|
20
|
Wollenzien H, Tecleab YA, Szczepaniak-Sloane R, Restaino A, Kareta MS. Single-Cell Evolutionary Analysis Reveals Drivers of Plasticity and Mediators of Chemoresistance in Small Cell Lung Cancer. Mol Cancer Res 2023; 21:892-907. [PMID: 37256926 PMCID: PMC10527088 DOI: 10.1158/1541-7786.mcr-22-0881] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/11/2023] [Accepted: 05/24/2023] [Indexed: 06/02/2023]
Abstract
Small cell lung cancer (SCLC) is often a heterogeneous tumor, where dynamic regulation of key transcription factors can drive multiple populations of phenotypically different cells which contribute differentially to tumor dynamics. This tumor is characterized by a very low 2-year survival rate, high rates of metastasis, and rapid acquisition of chemoresistance. The heterogeneous nature of this tumor makes it difficult to study and to treat, as it is not clear how or when this heterogeneity arises. Here we describe temporal, single-cell analysis of SCLC to investigate tumor initiation and chemoresistance in both SCLC xenografts and an autochthonous SCLC model. We identify an early population of tumor cells with high expression of AP-1 network genes that are critical for tumor growth. Furthermore, we have identified and validated the cancer testis antigens (CTA) PAGE5 and GAGE2A as mediators of chemoresistance in human SCLC. CTAs have been successfully targeted in other tumor types and may be a promising avenue for targeted therapy in SCLC. IMPLICATIONS Understanding the evolutionary dynamics of SCLC can shed light on key mechanisms such as cellular plasticity, heterogeneity, and chemoresistance.
Collapse
Affiliation(s)
- Hannah Wollenzien
- Cancer Biology and Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota, USA
- Genetics & Genomics Group, Sanford Research, Sioux Falls, South Dakota, USA
- Division of Basic Biomedical Sciences, University of South Dakota, Vermillion, South Dakota, USA
| | | | - Robert Szczepaniak-Sloane
- Cancer Biology and Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota, USA
- Genetics & Genomics Group, Sanford Research, Sioux Falls, South Dakota, USA
| | - Anthony Restaino
- Cancer Biology and Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota, USA
- Department of Pediatrics, Sanford School of Medicine, Sioux Falls, South Dakota, USA
| | - Michael S. Kareta
- Cancer Biology and Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota, USA
- Genetics & Genomics Group, Sanford Research, Sioux Falls, South Dakota, USA
- Division of Basic Biomedical Sciences, University of South Dakota, Vermillion, South Dakota, USA
- Functional Genomics & Bioinformatics Core, Sanford Research, Sioux Falls, SD, USA
- Department of Pediatrics, Sanford School of Medicine, Sioux Falls, South Dakota, USA
- Department of Biochemistry, South Dakota State University, Brookings, South Dakota, USA
| |
Collapse
|
21
|
Thomsen MK, Busk M. Pre-Clinical Models to Study Human Prostate Cancer. Cancers (Basel) 2023; 15:4212. [PMID: 37686488 PMCID: PMC10486646 DOI: 10.3390/cancers15174212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/16/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
Prostate cancer is a common cancer among men and typically progresses slowly for several decades before becoming aggressive and spreading to other organs, leaving few treatment options. While large animals have been studied, the dog's prostate is anatomically similar to humans and has been used to study spontaneous prostate cancer. However, most research currently focuses on the mouse as a model organism due to the ability to genetically modify their prostatic tissues for molecular analysis. One milestone in this research was the identification of the prostate-specific promoter Probasin, which allowed for the prostate-specific expression of transgenes. This has led to the generation of mice with aggressive prostatic tumors through overexpression of the SV40 oncogene. The Probasin promoter is also used to drive Cre expression and has allowed researchers to generate prostate-specific loss-of-function studies. Another landmark moment in the process of modeling prostate cancer in mice was the orthoptic delivery of viral particles. This technology allows the selective overexpression of oncogenes from lentivirus or the use of CRISPR to generate complex loss-of-function studies. These genetically modified models are complemented by classical xenografts of human prostate tumor cells in immune-deficient mice. Overall, pre-clinical models have provided a portfolio of model systems to study and address complex mechanisms in prostate cancer for improved treatment options. This review will focus on the advances in each technique.
Collapse
Affiliation(s)
| | - Morten Busk
- Department of Experimental Clinical Oncology, Aarhus University Hospital, 8200 Aarhus, Denmark;
- Danish Centre for Particle Therapy, Aarhus University Hospital, 8200 Aarhus, Denmark
| |
Collapse
|
22
|
Chacko L, Chaudhary A, Singh B, Dewanjee S, Kandimalla R. CRISPR-Cas9 in Alzheimer's disease: Therapeutic trends, modalities, and challenges. Drug Discov Today 2023; 28:103652. [PMID: 37290639 DOI: 10.1016/j.drudis.2023.103652] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/24/2023] [Accepted: 06/01/2023] [Indexed: 06/10/2023]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder with no known cure, which has prompted the exploration of novel therapeutic approaches. The clustered regularly interspaced palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) tool has generated significant interest for its potential in AD therapeutics by correcting faulty genes. Our report comprehensively reviews emerging applications for CRISPR-Cas9 in developing in vitro and in vivo models for AD research and therapeutics. We further assess its ability to identify and validate genetic markers and potential therapeutic targets for AD. Moreover, we review the current challenges and delivery strategies for the in vivo application of CRISPR-Cas9 in AD therapeutics.
Collapse
Affiliation(s)
- Leena Chacko
- BioAnalytical Lab, Meso Scale Discovery, 1601 Research Blvd, Rockville, MD, USA
| | - Anupama Chaudhary
- Orinin-BioSystems, LE-52, Lotus Road 4, CHD City, Karnal, Haryana 132 001, India
| | - Birbal Singh
- ICAR-Indian Veterinary Research Institute (IVRI), Regional Station, Palampur, Himachal Pradesh 176 061, India
| | - Saikat Dewanjee
- Advanced Pharmacognosy Research Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700 032, India.
| | - Ramesh Kandimalla
- Department of Biochemistry, Kakatiya Medical College, Warangal 506 007, Telangana, India; Department of Applied Biology, CSIR-Indian Institute of Technology, Uppal Road, Tarnaka, Hyderabad 500 007, India.
| |
Collapse
|
23
|
Rieskamp JD, Rosado-Burgos I, Christofi JE, Ansar E, Einstein D, Walters AE, Valentini V, Bruno JP, Kirby ED. Excitatory amino acid transporter 1 supports adult hippocampal neural stem cell self-renewal. iScience 2023; 26:107068. [PMID: 37534178 PMCID: PMC10391730 DOI: 10.1016/j.isci.2023.107068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 05/01/2023] [Accepted: 06/05/2023] [Indexed: 08/04/2023] Open
Abstract
Within the adult mammalian dentate gyrus (DG) of the hippocampus, glutamate stimulates neural stem cell (NSC) self-renewing proliferation, providing a link between adult neurogenesis and local circuit activity. Here, we show that glutamate-induced self-renewal of adult DG NSCs requires glutamate transport via excitatory amino acid transporter 1 (EAAT1) to stimulate lipogenesis. Loss of EAAT1 prevented glutamate-induced self-renewing proliferation of NSCs in vitro and in vivo, with little role evident for canonical glutamate receptors. Transcriptomics and further pathway manipulation revealed that glutamate simulation of NSCs relied on EAAT1 transport-stimulated lipogenesis. Our findings demonstrate a critical, direct role for EAAT1 in stimulating NSCs to support neurogenesis in adulthood, thereby providing insights into a non-canonical mechanism by which NSCs sense and respond to their niche.
Collapse
Affiliation(s)
- Joshua D. Rieskamp
- Department of Psychology, The Ohio State University, Columbus, OH 43210, USA
| | | | - Jacob E. Christofi
- Department of Psychology, The Ohio State University, Columbus, OH 43210, USA
| | - Eliza Ansar
- Department of Psychology, The Ohio State University, Columbus, OH 43210, USA
| | - Dalia Einstein
- Department of Psychology, The Ohio State University, Columbus, OH 43210, USA
| | - Ashley E. Walters
- Department of Psychology, The Ohio State University, Columbus, OH 43210, USA
| | - Valentina Valentini
- Department of Psychology, The Ohio State University, Columbus, OH 43210, USA
- Department of Biomedical Sciences, University of Cagliari, 09124 Cagliari, Italy
| | - John P. Bruno
- Department of Psychology, The Ohio State University, Columbus, OH 43210, USA
- Department of Neuroscience, The Ohio State University, Columbus, OH 43210, USA
| | - Elizabeth D. Kirby
- Department of Psychology, The Ohio State University, Columbus, OH 43210, USA
- Department of Neuroscience, The Ohio State University, Columbus, OH 43210, USA
- Chronic Brain Injury Program, The Ohio State University, Columbus, OH 43210, USA
| |
Collapse
|
24
|
Tang YJ, Shuldiner EG, Karmakar S, Winslow MM. High-Throughput Identification, Modeling, and Analysis of Cancer Driver Genes In Vivo. Cold Spring Harb Perspect Med 2023; 13:a041382. [PMID: 37277208 PMCID: PMC10317066 DOI: 10.1101/cshperspect.a041382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The vast number of genomic and molecular alterations in cancer pose a substantial challenge to uncovering the mechanisms of tumorigenesis and identifying therapeutic targets. High-throughput functional genomic methods in genetically engineered mouse models allow for rapid and systematic investigation of cancer driver genes. In this review, we discuss the basic concepts and tools for multiplexed investigation of functionally important cancer genes in vivo using autochthonous cancer models. Furthermore, we highlight emerging technical advances in the field, potential opportunities for future investigation, and outline a vision for integrating multiplexed genetic perturbations with detailed molecular analyses to advance our understanding of the genetic and molecular basis of cancer.
Collapse
Affiliation(s)
- Yuning J Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Emily G Shuldiner
- Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Saswati Karmakar
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Monte M Winslow
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| |
Collapse
|
25
|
Perelli L, Carbone F, Zhang L, Huang JK, Le C, Khan H, Citron F, Del Poggetto E, Gutschner T, Tomihara H, Soeung M, Minelli R, Srinivasan S, Peoples M, Lam TNA, Lundgren S, Xia R, Zhu C, Mohamed AMT, Zhang J, Sircar K, Sgambato A, Gao J, Jonasch E, Draetta GF, Futreal A, Bakouny Z, Van Allen EM, Choueiri T, Signoretti S, Msaouel P, Litchfield K, Turajlic S, Wang L, Chen YB, Di Natale RG, Hakimi AA, Giuliani V, Heffernan TP, Viale A, Bristow CA, Tannir NM, Carugo A, Genovese G. Interferon signaling promotes tolerance to chromosomal instability during metastatic evolution in renal cancer. NATURE CANCER 2023; 4:984-1000. [PMID: 37365326 PMCID: PMC10368532 DOI: 10.1038/s43018-023-00584-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/18/2023] [Indexed: 06/28/2023]
Abstract
Molecular routes to metastatic dissemination are critical determinants of aggressive cancers. Through in vivo CRISPR-Cas9 genome editing, we generated somatic mosaic genetically engineered models that faithfully recapitulate metastatic renal tumors. Disruption of 9p21 locus is an evolutionary driver to systemic disease through the rapid acquisition of complex karyotypes in cancer cells. Cross-species analysis revealed that recurrent patterns of copy number variations, including 21q loss and dysregulation of the interferon pathway, are major drivers of metastatic potential. In vitro and in vivo genomic engineering, leveraging loss-of-function studies, along with a model of partial trisomy of chromosome 21q, demonstrated a dosage-dependent effect of the interferon receptor genes cluster as an adaptive mechanism to deleterious chromosomal instability in metastatic progression. This work provides critical knowledge on drivers of renal cell carcinoma progression and defines the primary role of interferon signaling in constraining the propagation of aneuploid clones in cancer evolution.
Collapse
Affiliation(s)
- Luigi Perelli
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Federica Carbone
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Nerviano Medical Sciences, NMS Group Spa, Milan, Italy
| | - Li Zhang
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Justin K Huang
- TRACTION platform, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Courtney Le
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hania Khan
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Francesca Citron
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Edoardo Del Poggetto
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tony Gutschner
- Junior Research Group 'RNA Biology and Pathogenesis', Medical Faculty, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Hideo Tomihara
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Melinda Soeung
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rosalba Minelli
- TRACTION platform, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sanjana Srinivasan
- TRACTION platform, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Peoples
- TRACTION platform, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Truong Nguyen Anh Lam
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sebastian Lundgren
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ruohan Xia
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cihui Zhu
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alaa M T Mohamed
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kanishka Sircar
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alessandro Sgambato
- Dipartimento Universitario di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - JianJun Gao
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Eric Jonasch
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Giulio F Draetta
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ziad Bakouny
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Toni Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sabina Signoretti
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Pavlos Msaouel
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA
| | | | | | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ying Bei Chen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Renzo G Di Natale
- Department of Urology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A Ari Hakimi
- Department of Urology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Virginia Giuliani
- TRACTION platform, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Timothy P Heffernan
- TRACTION platform, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andrea Viale
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher A Bristow
- TRACTION platform, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nizar M Tannir
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alessandro Carugo
- TRACTION platform, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Biology, IRBM S.p.A., Rome, Italy.
| | - Giannicola Genovese
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- TRACTION platform, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| |
Collapse
|
26
|
Yang X, Zhang B. A review on CRISPR/Cas: a versatile tool for cancer screening, diagnosis, and clinic treatment. Funct Integr Genomics 2023; 23:182. [PMID: 37231285 DOI: 10.1007/s10142-023-01117-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023]
Abstract
Cancer is one of the leading causes of death worldwide and it has the trend of increase incidence. However, in the past decades, as quickly developed new technologies and modified old techniques for cancer screening, diagnosis, and treatment, the cancer-caused mortality rates dropped quickly, and the survival times of cancer patients are enhanced. However, the current death rate is still about 50% and the survival patients always suffer from the side effect of current cancer treatments. Recently developed Nobel Prize-winning CRISPR/Cas technology provides new hope on cancer screening, early diagnosis, and clinic treatment as well as new drug development. Currently, four major CRISPR/Cas9-derived genome editors, CRISPR/Cas9 nucleotide sequence editor, CRISPR/Cas base editor (BE), CRISPR prime editor (PE), and CRISPR interference (CRISPRi) (including both CRISPRa and CRISPRr), were well developed and used to various research and applications, including cancer biology study and cancer screening, diagnosis, and treatment. Additionally, CRISPR/Cas12 and CRISPR/Cas13 genome editors were also widely used in cancer-related basic and applied research as well as treatment. Cancer-associated SNPs and genetic mutations as well as both oncogenes and tumor suppressor genes are perfect targets for CRISPR/Cas-based gene therapy for cancer treatment. CRISPR/Cas is also employed to modify and generate new Chimeric antigen receptor (CAR) T-cells for improving its safety, efficiency, and longer-time last for treating various cancers. Currently, there are many clinic trails of CRISPR-based gene therapy for cancer treatments. Although all CRISPR/Cas-derived genome and epigenome tools are promising methods for cancer biology study and treatment, the efficiency and long term-safety are still the major concerns for CRISPR-based gene therapy. Developing new CRISPR/Cas delivery methods and reducing the potential side effects, including off-target impacts, will enhance CRISPR/Cas application in cancer-related research, diagnosis, and therapeutical treatment.
Collapse
Affiliation(s)
- Xianguang Yang
- College of Life Science, Henan Normal University, Xinxiang, 453007, Henan, China.
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA.
| |
Collapse
|
27
|
Kalamakis G, Platt RJ. CRISPR for neuroscientists. Neuron 2023:S0896-6273(23)00306-9. [PMID: 37201524 DOI: 10.1016/j.neuron.2023.04.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 03/14/2023] [Accepted: 04/18/2023] [Indexed: 05/20/2023]
Abstract
Genome engineering technologies provide an entry point into understanding and controlling the function of genetic elements in health and disease. The discovery and development of the microbial defense system CRISPR-Cas yielded a treasure trove of genome engineering technologies and revolutionized the biomedical sciences. Comprising diverse RNA-guided enzymes and effector proteins that evolved or were engineered to manipulate nucleic acids and cellular processes, the CRISPR toolbox provides precise control over biology. Virtually all biological systems are amenable to genome engineering-from cancer cells to the brains of model organisms to human patients-galvanizing research and innovation and giving rise to fundamental insights into health and powerful strategies for detecting and correcting disease. In the field of neuroscience, these tools are being leveraged across a wide range of applications, including engineering traditional and non-traditional transgenic animal models, modeling disease, testing genomic therapies, unbiased screening, programming cell states, and recording cellular lineages and other biological processes. In this primer, we describe the development and applications of CRISPR technologies while highlighting outstanding limitations and opportunities.
Collapse
Affiliation(s)
- Georgios Kalamakis
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland; Novartis Institutes for BioMedical Research, 4056 Basel, Switzerland
| | - Randall J Platt
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland; Department of Chemistry, University of Basel, Petersplatz 1, 4003 Basel, Switzerland; NCCR MSE, Mattenstrasse 24a, 4058 Basel, Switzerland; Botnar Research Center for Child Health, Mattenstrasse 24a, 4058 Basel, Switzerland.
| |
Collapse
|
28
|
Farzanehpour M, Miri A, Ghorbani Alvanegh A, Esmaeili Gouvarchinghaleh H. Viral Vectors, Exosomes, and Vexosomes: Potential Armamentarium for Delivering CRISPR/Cas to Cancer Cells. Biochem Pharmacol 2023; 212:115555. [PMID: 37075815 DOI: 10.1016/j.bcp.2023.115555] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 04/21/2023]
Abstract
The underlying cause of cancer is genetic disruption, so gene editing technologies, particularly CRISPR/Cas systems can be used to go against cancer. The field of gene therapy has undergone many transitions over its 40-year history. Despite its many successes, it has also suffered many failures in the battle against malignancies, causing really adverse effects instead of therapeutic outcomes. At the tip of this double-edged sword are viral and non-viral-based vectors, which have profoundly transformed the way scientists and clinicians develop therapeutic platforms. Viruses such as lentivirus, adenovirus, and adeno-associated viruses are the most common viral vectors used for delivering the CRISPR/Cas system into human cells. In addition, among non-viral vectors, exosomes, especially tumor-derived exosomes (TDEs), have proven to be quite effective at delivering this gene editing tool. The combined use of viral vectors and exosomes, called vexosomes, seems to be a solution to overcoming the obstacles of both delivery systems.
Collapse
Affiliation(s)
- Mahdieh Farzanehpour
- Applied Virology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Miri
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | | | | |
Collapse
|
29
|
Teh SSK, Halper-Stromberg E, Morsberger L, Bennett A, Bowland K, Skaist A, Cai F, Liang H, Hruban RH, Roberts NJ, Scharpf RB, Zou YS, Eshleman JR. Mechanism of delayed cell death following simultaneous CRISPR-Cas9 targeting in pancreatic cancers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.03.535384. [PMID: 37066222 PMCID: PMC10103988 DOI: 10.1101/2023.04.03.535384] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
When we transduced pancreatic cancers with sgRNAs that targeted 2-16 target sites in the human genome, we found that increasing the number of CRISPR-Cas9 target sites produced greater cytotoxicity, with >99% growth inhibition observed by targeting only 12 sites. However, cell death was delayed by 2-3 weeks after sgRNA transduction, in contrast to the repair of double strand DNA breaks (DSBs) that happened within 3 days after transduction. To explain this discrepancy, we used both cytogenetics and whole genome sequencing to interrogate the genome. We first detected chromatid and chromosome breaks, followed by radial formations, dicentric, ring chromosomes, and other chromosomal aberrations that peaked at 14 days after transduction. Structural variants (SVs) were detected at sites that were directly targeted by CRISPR-Cas9, including SVs generated from two sites that were targeted, but the vast majority of SVs (89.4%) were detected elsewhere in the genome that arose later than those directly targeted. Cells also underwent polyploidization that peaked at day 10 as detected by XY FISH assay, and ultimately died via apoptosis. Overall, we found that the simultaneous DSBs induced by CRISPR-Cas9 in pancreatic cancers caused chromosomal instability and polyploidization that ultimately led to delayed cell death.
Collapse
Affiliation(s)
- Selina Shiqing K. Teh
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Eitan Halper-Stromberg
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Laura Morsberger
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alexis Bennett
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kirsten Bowland
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alyza Skaist
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fidel Cai
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hong Liang
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ralph H. Hruban
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nicholas J. Roberts
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert B. Scharpf
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ying S. Zou
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James R. Eshleman
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| |
Collapse
|
30
|
Vudatha V, Herremans KM, Freudenberger DC, Liu C, Trevino JG. In vivo models of pancreatic ductal adenocarcinoma. Adv Cancer Res 2023; 159:75-112. [PMID: 37268402 DOI: 10.1016/bs.acr.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy with high mortality rate. Within the next decade, PDAC is projected to become the second leading cause of cancer-associated death in the United States. Understanding the pathophysiology of PDAC tumorigenesis and metastases is crucial toward developing new therapeutics. One of the challenges in cancer research is generating in vivo models that closely recapitulate the genomic, histological, and clinical characteristics of human tumors. An ideal model for PDAC not only captures the tumor and stromal environment of human disease, but also allows for mutational control and is easy to reproduce in terms of time and cost. In this review, we highlight evolution of in vivo models for PDAC including spontaneous tumors models (i.e., chemical induction, genetic modification, viral delivery), implantation models including patient derived xenografts (PDX), and humanized PDX. We discuss the implementation of each system and evaluate the benefits and shortcomings of these models. Overall, this review provides a broad overview of prior and current techniques of in vivo PDAC modeling and their associated challenges.
Collapse
Affiliation(s)
- Vignesh Vudatha
- Department of Surgery, Virginia Commonwealth University School of Medicine, Richmond, VA, United States
| | - Kelly M Herremans
- Department of Surgery, University of Florida College of Medicine, Gainesville, FL, United States
| | - Devon C Freudenberger
- Department of Surgery, Virginia Commonwealth University School of Medicine, Richmond, VA, United States
| | - Christopher Liu
- Department of Surgery, Virginia Commonwealth University School of Medicine, Richmond, VA, United States
| | - Jose G Trevino
- Department of Surgery, Virginia Commonwealth University School of Medicine, Richmond, VA, United States; Division of Surgical Oncology, VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States.
| |
Collapse
|
31
|
Zhang P, Xiao Y, Sun X, Lin X, Koo S, Yaremenko AV, Qin D, Kong N, Farokhzad OC, Tao W. Cancer nanomedicine toward clinical translation: Obstacles, opportunities, and future prospects. MED 2023; 4:147-167. [PMID: 36549297 DOI: 10.1016/j.medj.2022.12.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 10/03/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022]
Abstract
With the integration of nanotechnology into the medical field at large, great strides have been made in the development of nanomedicines for tackling different diseases, including cancers. To date, various cancer nanomedicines have demonstrated success in preclinical studies, improving therapeutic outcomes, prolonging survival, and/or decreasing side effects. However, the translation from bench to bedside remains challenging. While a number of nanomedicines have entered clinical trials, only a few have been approved for clinical applications. In this review, we highlight the most recent progress in cancer nanomedicine, discuss current clinical advances and challenges for the translation of cancer nanomedicines, and provide our viewpoints on accelerating clinical translation. We expect this review to benefit the future development of cancer nanotherapeutics specifically from the clinical perspective.
Collapse
Affiliation(s)
- Pengfei Zhang
- Institute of Molecular Immunology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510080, China
| | - Yufen Xiao
- Center for Nanomedicine, Department of Anesthesiology, Perioperative, and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Xue Sun
- Department of Neurosurgery, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361004, China
| | - Xiaoning Lin
- Department of Neurosurgery, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361004, China
| | - Seyoung Koo
- Center for Nanomedicine, Department of Anesthesiology, Perioperative, and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Alexey V Yaremenko
- Center for Nanomedicine, Department of Anesthesiology, Perioperative, and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Duotian Qin
- Center for Nanomedicine, Department of Anesthesiology, Perioperative, and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Na Kong
- Center for Nanomedicine, Department of Anesthesiology, Perioperative, and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Omid C Farokhzad
- Center for Nanomedicine, Department of Anesthesiology, Perioperative, and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Seer, Inc., Redwood City, CA 94065, USA
| | - Wei Tao
- Center for Nanomedicine, Department of Anesthesiology, Perioperative, and Pain Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
32
|
Yousefi M, Andrejka L, Winslow MM, Petrov DA, Boross G. Fully accessible fitness landscape of oncogene-negative lung adenocarcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.30.526178. [PMID: 36778226 PMCID: PMC9915475 DOI: 10.1101/2023.01.30.526178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Cancer genomes are almost invariably complex with genomic alterations cooperating during each step of carcinogenesis. In cancers that lack a single dominant oncogene mutation, cooperation between the inactivation of multiple tumor suppressor genes can drive tumor initiation and growth. Here, we shed light on how the sequential acquisition of genomic alterations generates oncogene-negative lung tumors. We couple tumor barcoding with combinatorial and multiplexed somatic genome editing to characterize the fitness landscapes of three tumor suppressor genes NF1, RASA1, and PTEN, the inactivation of which jointly drives oncogene-negative lung adenocarcinoma initiation and growth. The fitness landscape was surprisingly accessible, with each additional mutation leading to growth advantage. Furthermore, the fitness landscapes remained fully accessible across backgrounds with additional tumor suppressor mutations. These results suggest that while predicting cancer evolution will be challenging, acquiring the multiple alterations required for the growth of oncogene-negative tumors can be facilitated by the lack of constraints on mutational order.
Collapse
|
33
|
Lee MC, Cai H, Murray CW, Li C, Shue YT, Andrejka L, He AL, Holzem AME, Drainas AP, Ko JH, Coles GL, Kong C, Zhu S, Zhu C, Wang J, van de Rijn M, Petrov DA, Winslow MM, Sage J. A multiplexed in vivo approach to identify driver genes in small cell lung cancer. Cell Rep 2023; 42:111990. [PMID: 36640300 PMCID: PMC9972901 DOI: 10.1016/j.celrep.2023.111990] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 10/24/2022] [Accepted: 01/04/2023] [Indexed: 01/15/2023] Open
Abstract
Small cell lung cancer (SCLC) is a lethal form of lung cancer. Here, we develop a quantitative multiplexed approach on the basis of lentiviral barcoding with somatic CRISPR-Cas9-mediated genome editing to functionally investigate candidate regulators of tumor initiation and growth in genetically engineered mouse models of SCLC. We found that naphthalene pre-treatment enhances lentiviral vector-mediated SCLC initiation, enabling high multiplicity of tumor clones for analysis through high-throughput sequencing methods. Candidate drivers of SCLC identified from a meta-analysis across multiple human SCLC genomic datasets were tested using this approach, which defines both positive and detrimental impacts of inactivating 40 genes across candidate pathways on SCLC development. This analysis and subsequent validation in human SCLC cells establish TSC1 in the PI3K-AKT-mTOR pathway as a robust tumor suppressor in SCLC. This approach should illuminate drivers of SCLC, facilitate the development of precision therapies for defined SCLC genotypes, and identify therapeutic targets.
Collapse
Affiliation(s)
- Myung Chang Lee
- Department of Pediatrics, Stanford University, 265 Campus Drive, SIM1 G2078, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Hongchen Cai
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | | | - Chuan Li
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Yan Ting Shue
- Department of Pediatrics, Stanford University, 265 Campus Drive, SIM1 G2078, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Laura Andrejka
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Andy L He
- Department of Pediatrics, Stanford University, 265 Campus Drive, SIM1 G2078, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Alessandra M E Holzem
- Department of Pediatrics, Stanford University, 265 Campus Drive, SIM1 G2078, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Alexandros P Drainas
- Department of Pediatrics, Stanford University, 265 Campus Drive, SIM1 G2078, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Julie H Ko
- Department of Pediatrics, Stanford University, 265 Campus Drive, SIM1 G2078, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Garry L Coles
- Department of Pediatrics, Stanford University, 265 Campus Drive, SIM1 G2078, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Christina Kong
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Shirley Zhu
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - ChunFang Zhu
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Jason Wang
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Matt van de Rijn
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Monte M Winslow
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Julien Sage
- Department of Pediatrics, Stanford University, 265 Campus Drive, SIM1 G2078, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
34
|
Bindu DS, Tan CX, Savage JT, Eroglu C. GEARBOCS: An Adeno Associated Virus Tool for In Vivo Gene Editing in Astrocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.17.524433. [PMID: 36711516 PMCID: PMC9884502 DOI: 10.1101/2023.01.17.524433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
In the mammalian central nervous system (CNS), astrocytes are indispensable for brain development, function, and health. However, non-invasive tools to study astrocyte biology and function in vivo have been limited to genetically modified mice. CRISPR/Cas9-based genome engineering enables rapid and precise gene manipulations in the CNS. Here, we developed a non-invasive astrocyte-specific method utilizing a single AAV vector, GEARBOCS (Gene Editing in AstRocytes Based On CRISPR/Cas9 System). We verified GEARBOCS' specificity to mouse cortical astrocytes and demonstrated its utility for three types of gene manipulations: knockout (KO); tagging (TagIN); and reporter gene knock-in (Gene-TRAP) strategies. We deployed GEARBOCS to determine whether cortical astrocytes express Vamp2 protein. The presence of Vamp2-positive vesicles in cultured astrocytes is well-established, however, Vamp2 protein expression in astrocytes in vivo has proven difficult to ascertain due to its overwhelming abundance in neurons. Using GEARBOCS, we delineated the in vivo astrocytic Vamp2 expression and found that it is required for maintaining excitatory and inhibitory synapse numbers in the visual cortex. GEARBOCS strategy provides fast and efficient means to study astrocyte biology in vivo.
Collapse
Affiliation(s)
| | - Christabel Xin Tan
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Justin T. Savage
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Cagla Eroglu
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA
- Duke Institute for Brain Sciences (DIBS), Durham, NC 27710, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC, 27710, USA
| |
Collapse
|
35
|
An HW, Seok SH, Kwon JW, Choudhury AD, Oh JS, Voon DC, Kim DY, Park JW. The loss of epithelial Smad4 drives immune evasion via CXCL1 while displaying vulnerability to combinatorial immunotherapy in gastric cancer. Cell Rep 2022; 41:111878. [PMID: 36577366 DOI: 10.1016/j.celrep.2022.111878] [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: 03/28/2022] [Revised: 10/17/2022] [Accepted: 12/02/2022] [Indexed: 12/29/2022] Open
Abstract
SMAD4 is frequently mutated and inactivated in human gastric cancer (GC). Although the epithelial cell-autonomous functions of Smad4 have been extensively studied, its contribution to tumor immunity is largely undetermined. Here, we report that the loss of Smad4 expression in GC cells endows them with the ability to evade tumor immunity. Unlike their Smad4-proficient counterparts, Smad4-deficient stomach organoids can evade host immunity to form tumors in immunocompetent mice. Smad4-deficient GC cells show expanded CD133+ cancer stem-like cells while suppressing dendritic cell (DC) differentiation and cytotoxic T cells with granulocytic myeloid-derived suppressor cell (G-MDSC) accumulation through a secretome containing CXCL1. Moreover, Smad4 deficiency increases programmed cell death ligand-1 (PD-L1) and decreases 4-1BBL expressions, indicating a change in immunogenicity. Combinatorial immune checkpoint blockade (ICB) of anti-PD-L1 and anti-CTLA-4 or agonistic anti-4-1BB antibodies effectively treats ICB monotherapy-resistant Smad4-deficient allografts, exposing a specific vulnerability. Collectively, these data provide a rational basis for ICB strategies in treating advanced GC with Smad4 deficiency.
Collapse
Affiliation(s)
- Hyeok-Won An
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, 1 Kangwondaehak-gil, ChunCheon-si, Gangwon-do 24341, South Korea
| | - Sang Hyeok Seok
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, 1 Kangwondaehak-gil, ChunCheon-si, Gangwon-do 24341, South Korea
| | - Jong-Wan Kwon
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, 1 Kangwondaehak-gil, ChunCheon-si, Gangwon-do 24341, South Korea
| | - Anahita Dev Choudhury
- Innovative Cancer Model Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Jeong-Seop Oh
- Department of Veterinary Pathology, College of Veterinary Medicine, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Dominic C Voon
- Innovative Cancer Model Research Unit, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan; Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan.
| | - Dae-Yong Kim
- Department of Veterinary Pathology, College of Veterinary Medicine, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea.
| | - Jun Won Park
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, 1 Kangwondaehak-gil, ChunCheon-si, Gangwon-do 24341, South Korea.
| |
Collapse
|
36
|
In vivo genome editing using novel AAV-PHP variants rescues motor function deficits and extends survival in a SOD1-ALS mouse model. Gene Ther 2022; 30:443-454. [PMID: 36450833 PMCID: PMC9713118 DOI: 10.1038/s41434-022-00375-w] [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: 01/15/2022] [Revised: 10/10/2022] [Accepted: 11/08/2022] [Indexed: 12/03/2022]
Abstract
CRISPR-based gene editing technology represents a promising approach to deliver therapies for inherited disorders, including amyotrophic lateral sclerosis (ALS). Toxic gain-of-function superoxide dismutase 1 (SOD1) mutations are responsible for ~20% of familial ALS cases. Thus, current clinical strategies to treat SOD1-ALS are designed to lower SOD1 levels. Here, we utilized AAV-PHP.B variants to deliver CRISPR-Cas9 guide RNAs designed to disrupt the human SOD1 (huSOD1) transgene in SOD1G93A mice. A one-time intracerebroventricular injection of AAV.PHP.B-huSOD1-sgRNA into neonatal H11Cas9 SOD1G93A mice caused robust and sustained mutant huSOD1 protein reduction in the cortex and spinal cord, and restored motor function. Neonatal treatment also reduced spinal motor neuron loss, denervation at neuromuscular junction (NMJ) and muscle atrophy, diminished axonal damage and preserved compound muscle action potential throughout the lifespan of treated mice. SOD1G93A treated mice achieved significant disease-free survival, extending lifespan by more than 110 days. Importantly, a one-time intrathecal or intravenous injection of AAV.PHP.eB-huSOD1-sgRNA in adult H11Cas9 SOD1G93A mice, immediately before symptom onset, also extended lifespan by at least 170 days. We observed substantial protection against disease progression, demonstrating the utility of our CRISPR editing preclinical approach for target evaluation. Our approach uncovered key parameters (e.g., AAV capsid, Cas9 expression) that resulted in improved efficacy compared to similar approaches and can also serve to accelerate drug target validation.
Collapse
|
37
|
Vaishnavi A, Juan J, Jacob M, Stehn C, Gardner EE, Scherzer MT, Schuman S, Van Veen JE, Murphy B, Hackett CS, Dupuy AJ, Chmura SA, van der Weyden L, Newberg JY, Liu A, Mann K, Rust AG, Weiss WA, Kinsey CG, Adams DJ, Grossmann A, Mann MB, McMahon M. Transposon Mutagenesis Reveals RBMS3 Silencing as a Promoter of Malignant Progression of BRAFV600E-Driven Lung Tumorigenesis. Cancer Res 2022; 82:4261-4273. [PMID: 36112789 PMCID: PMC9664136 DOI: 10.1158/0008-5472.can-21-3214] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 06/29/2022] [Accepted: 09/13/2022] [Indexed: 01/09/2023]
Abstract
Mutationally activated BRAF is detected in approximately 7% of human lung adenocarcinomas, with BRAFT1799A serving as a predictive biomarker for treatment of patients with FDA-approved inhibitors of BRAFV600E oncoprotein signaling. In genetically engineered mouse (GEM) models, expression of BRAFV600E in the lung epithelium initiates growth of benign lung tumors that, without additional genetic alterations, rarely progress to malignant lung adenocarcinoma. To identify genes that cooperate with BRAFV600E for malignant progression, we used Sleeping Beauty-mediated transposon mutagenesis, which dramatically accelerated the emergence of lethal lung cancers. Among the genes identified was Rbms3, which encodes an RNA-binding protein previously implicated as a putative tumor suppressor. Silencing of RBMS3 via CRISPR/Cas9 gene editing promoted growth of BRAFV600E lung organoids and promoted development of malignant lung cancers with a distinct micropapillary architecture in BRAFV600E and EGFRL858R GEM models. BRAFV600E/RBMS3Null lung tumors displayed elevated expression of Ctnnb1, Ccnd1, Axin2, Lgr5, and c-Myc mRNAs, suggesting that RBMS3 silencing elevates signaling through the WNT/β-catenin signaling axis. Although RBMS3 silencing rendered BRAFV600E-driven lung tumors resistant to the effects of dabrafenib plus trametinib, the tumors were sensitive to inhibition of porcupine, an acyltransferase of WNT ligands necessary for their secretion. Analysis of The Cancer Genome Atlas patient samples revealed that chromosome 3p24, which encompasses RBMS3, is frequently lost in non-small cell lung cancer and correlates with poor prognosis. Collectively, these data reveal the role of RBMS3 as a lung cancer suppressor and suggest that RBMS3 silencing may contribute to malignant NSCLC progression. SIGNIFICANCE Loss of RBMS3 cooperates with BRAFV600E to induce lung tumorigenesis, providing a deeper understanding of the molecular mechanisms underlying mutant BRAF-driven lung cancer and potential strategies to more effectively target this disease.
Collapse
Affiliation(s)
- Aria Vaishnavi
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Joseph Juan
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Maebh Jacob
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | | | - Eric E. Gardner
- Meyer Cancer Center, Weill Cornell Medicine, New York City, New York
- Palo Alto Wellness, Menlo Park, California
| | - Michael T. Scherzer
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Department of Oncological Sciences, University of Utah, Salt Lake City, Utah
| | - Sophia Schuman
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - J. Edward Van Veen
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Brandon Murphy
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Christopher S. Hackett
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Adam J. Dupuy
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa
| | - Steven A. Chmura
- Meyer Cancer Center, Weill Cornell Medicine, New York City, New York
- Palo Alto Wellness, Menlo Park, California
| | - Louise van der Weyden
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Justin Y. Newberg
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Annie Liu
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Karen Mann
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Alistair G. Rust
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - William A. Weiss
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
- Department of Neurology, University of California, San Francisco, California
- Department of Dermatology, University of Utah, Salt Lake City, Utah
- Department of Pediatrics, University of California, San Francisco, California
- Department of Neurological Surgery, University of California, San Francisco, California
| | - Conan G. Kinsey
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah
| | - David J. Adams
- Department of Dermatology, University of Utah, Salt Lake City, Utah
- Department of Pediatrics, University of California, San Francisco, California
| | - Allie Grossmann
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Department of Pathology, University of Utah, Salt Lake City, Utah
| | - Michael B. Mann
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Martin McMahon
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
- Department of Oncological Sciences, University of Utah, Salt Lake City, Utah
- Department of Dermatology, University of Utah, Salt Lake City, Utah
- Department of Pediatrics, University of California, San Francisco, California
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California
| |
Collapse
|
38
|
Shen Y, Zhang K, Wang R, Sun S, Yang Y, Yao Y, Liu H, Ren Z. MCPIP1 alleviated alcohol-induced immune dysfunction via the MAPK/ERK signaling pathway. Psychopharmacology (Berl) 2022; 239:3485-3493. [PMID: 36129492 DOI: 10.1007/s00213-022-06214-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/13/2022] [Indexed: 11/26/2022]
Abstract
RATIONALE In recent years, monocyte chemotactic protein-induced protein 1 (MCPIP1) has been reported to control inflammation via IL-10. OBJECTIVES The aims of this study were to determine (1) whether MCPIP1 can repair damage to the immune system after alcohol use and (2) whether MCPIP1 can repair the immune function impaired by alcohol use through the MAPK/ERK signaling pathway. Our results will inform the treatment of immune dysfunction caused by alcohol consumption. METHODS Scrambled shRNA or MCPIP-1-shRNA carried by the lentiviral vector (50μl each at 1×108TU/ml) was injected retrogradely through the pancreatic duct to pretreat male C57BL/6 mice. Five days after the injection, mice were exposed to intragastric ethanol infusion (5g/kg, 25% ethanol w/v) daily or vehicle for 10 days. RESULTS MCPIP-1 protein was increased in the pancreas after alcohol exposure. MCPIP-1 shRNA specifically decreased MCPIP-1 protein expression and mRNA level in the pancreas. Specific knockdown of MCPIP-1 exacerbates pancreatic necrosis, interstitial edema, and inflammatory infiltrates after alcohol exposure. Meanwhile, specific knockdown of MCPIP-1 also increased pancreatic pro-inflammatory cytokine (IL-6 and IL-1β), chemokine MCP-1, and chemokine receptor 2 (CCR2) after alcohol exposure. What's more, p-JNK and p-ERK in the pancreas were all similarly increased in response to pancreas-specific knockdown of MCPIP-1 during alcohol exposure. CONCLUSIONS Taken together, the results above suggested that MCPIP1 repairs the immune function impaired by alcohol use via stimulating JNK and ERK pathways. Our results will inform the treatment of immune dysfunction caused by alcohol consumption.
Collapse
Affiliation(s)
- Yanjie Shen
- Department of Anatomy, Anhui Medical University, Hefei, 230032, China
| | - Kai Zhang
- Department of Psychiatry, Chaohu Hospital of Anhui Medical University, Hefei, 238000, China
- Anhui Mental Health Center, Anhui Medical University, Hefei, China
| | - Rui Wang
- Department of Anatomy, Anhui Medical University, Hefei, 230032, China
| | - Shuaichen Sun
- Department of Anatomy, Anhui Medical University, Hefei, 230032, China
| | - Yating Yang
- Department of Psychiatry, Chaohu Hospital of Anhui Medical University, Hefei, 238000, China
- Anhui Mental Health Center, Anhui Medical University, Hefei, China
| | - Yitan Yao
- Department of Psychiatry, Chaohu Hospital of Anhui Medical University, Hefei, 238000, China
- Anhui Mental Health Center, Anhui Medical University, Hefei, China
| | - Huanzhong Liu
- Department of Psychiatry, Chaohu Hospital of Anhui Medical University, Hefei, 238000, China.
- Anhui Mental Health Center, Anhui Medical University, Hefei, China.
| | - Zhenhua Ren
- Department of Anatomy, Anhui Medical University, Hefei, 230032, China.
| |
Collapse
|
39
|
Shi DD, Savani MR, Levitt MM, Wang AC, Endress JE, Bird CE, Buehler J, Stopka SA, Regan MS, Lin YF, Puliyappadamba VT, Gao W, Khanal J, Evans L, Lee JH, Guo L, Xiao Y, Xu M, Huang B, Jennings RB, Bonal DM, Martin-Sandoval MS, Dang T, Gattie LC, Cameron AB, Lee S, Asara JM, Kornblum HI, Mak TW, Looper RE, Nguyen QD, Signoretti S, Gradl S, Sutter A, Jeffers M, Janzer A, Lehrman MA, Zacharias LG, Mathews TP, Losman JA, Richardson TE, Cahill DP, DeBerardinis RJ, Ligon KL, Xu L, Ly P, Agar NYR, Abdullah KG, Harris IS, Kaelin WG, McBrayer SK. De novo pyrimidine synthesis is a targetable vulnerability in IDH mutant glioma. Cancer Cell 2022; 40:939-956.e16. [PMID: 35985343 PMCID: PMC9515386 DOI: 10.1016/j.ccell.2022.07.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 06/09/2022] [Accepted: 07/26/2022] [Indexed: 12/30/2022]
Abstract
Mutations affecting isocitrate dehydrogenase (IDH) enzymes are prevalent in glioma, leukemia, and other cancers. Although mutant IDH inhibitors are effective against leukemia, they seem to be less active in aggressive glioma, underscoring the need for alternative treatment strategies. Through a chemical synthetic lethality screen, we discovered that IDH1-mutant glioma cells are hypersensitive to drugs targeting enzymes in the de novo pyrimidine nucleotide synthesis pathway, including dihydroorotate dehydrogenase (DHODH). We developed a genetically engineered mouse model of mutant IDH1-driven astrocytoma and used it and multiple patient-derived models to show that the brain-penetrant DHODH inhibitor BAY 2402234 displays monotherapy efficacy against IDH-mutant gliomas. Mechanistically, this reflects an obligate dependence of glioma cells on the de novo pyrimidine synthesis pathway and mutant IDH's ability to sensitize to DNA damage upon nucleotide pool imbalance. Our work outlines a tumor-selective, biomarker-guided therapeutic strategy that is poised for clinical translation.
Collapse
Affiliation(s)
- Diana D Shi
- Department of Radiation Oncology, Dana-Farber/Brigham and Women's Cancer Center, Harvard Medical School, Boston, MA 02215, USA; Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Milan R Savani
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Medical Scientist Training Program, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Michael M Levitt
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Adam C Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Jennifer E Endress
- Ludwig Cancer Center, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Cylaina E Bird
- Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | - Joseph Buehler
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sylwia A Stopka
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Michael S Regan
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yu-Fen Lin
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vinesh T Puliyappadamba
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wenhua Gao
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Januka Khanal
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Laura Evans
- Bayer HealthCare Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Joyce H Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Lei Guo
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yi Xiao
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Min Xu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bofu Huang
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Rebecca B Jennings
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Dennis M Bonal
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, MA 02210, USA
| | - Misty S Martin-Sandoval
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tammie Dang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lauren C Gattie
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | - Amy B Cameron
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, MA 02210, USA
| | - Sungwoo Lee
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, Republic of Korea
| | - John M Asara
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Harley I Kornblum
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Psychiatry and Behavioral Sciences, and Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90024, USA
| | - Tak W Mak
- The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, ON M5G 2M9, Canada; The Princess Margaret Cancer Centre and Ontario Cancer Institute, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Ryan E Looper
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Quang-De Nguyen
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, MA 02210, USA
| | - Sabina Signoretti
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Stefan Gradl
- Bayer AG, Muellerstrasse 178, 13353 Berlin, Germany
| | | | - Michael Jeffers
- Bayer HealthCare Pharmaceuticals, Inc., Whippany, NJ 07981, USA
| | | | - Mark A Lehrman
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lauren G Zacharias
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Thomas P Mathews
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Julie-Aurore Losman
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Timothy E Richardson
- Department of Pathology, Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Daniel P Cahill
- Department of Neurosurgery, Translational Neuro-Oncology Laboratory, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Ralph J DeBerardinis
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | - Keith L Ligon
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Pathology, Children's Hospital Boston, Boston, MA 02115, USA
| | - Lin Xu
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | - Peter Ly
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nathalie Y R Agar
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Kalil G Abdullah
- Department of Neurosurgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA; Hillman Comprehensive Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA 15232, USA
| | - Isaac S Harris
- Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - William G Kaelin
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Samuel K McBrayer
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA.
| |
Collapse
|
40
|
Thege FI, Rupani DN, Barathi BB, Manning SL, Maitra A, Rhim AD, Wörmann SM. A Programmable In Vivo CRISPR Activation Model Elucidates the Oncogenic and Immunosuppressive Functions of MYC in Lung Adenocarcinoma. Cancer Res 2022; 82:2761-2776. [PMID: 35666804 PMCID: PMC9357118 DOI: 10.1158/0008-5472.can-21-4009] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 04/18/2022] [Accepted: 06/01/2022] [Indexed: 02/05/2023]
Abstract
Conventional genetically engineered mouse models (GEMM) are time-consuming, laborious, and offer limited spatiotemporal control. Here, we describe the development of a streamlined platform for in vivo gene activation using CRISPR activation (CRISPRa) technology. Unlike conventional GEMMs, this model system allows for flexible, sustained, and timed activation of one or more target genes using single or pooled lentiviral guides. Myc and Yap1 were used as model oncogenes to demonstrate gene activation in primary pancreatic organoid cultures in vitro and enhanced tumorigenic potential in Myc-activated organoids when transplanted orthotopically in vivo. Implementation of this model as an autochthonous lung cancer model showed that transduction-mediated activation of Myc led to accelerated tumor progression and significantly reduced overall survival relative to nontargeted tumor controls. Furthermore, Myc activation led to the acquisition of an immune suppressive, "cold" tumor microenvironment. Cross-species validation of these results using publicly available RNA/DNA-seq datasets linked MYC to a previously described immunosuppressive molecular subtype in patient tumors, thus identifying a patient cohort that may benefit from combined MYC- and immune-targeted therapies. Overall, this work demonstrates how CRISPRa can be used for rapid functional validation of putative oncogenes and may allow for the identification and evaluation of potential metastatic and oncogenic drivers through competitive screening. SIGNIFICANCE A streamlined platform for programmable CRISPR gene activation enables rapid evaluation and functional validation of putative oncogenes in vivo.
Collapse
Affiliation(s)
- Fredrik I. Thege
- Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, University of Texas, Houston, TX 77030, USA
- CORRESPONDANCE: Fredrik I. Thege, , Sonja M. Wörmann, , MD Anderson Cancer Center, Zayed Building, Z3.2065, 6565 MD Anderson Blvd., Houston, TX 77030, USA
| | - Dhwani N. Rupani
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bhargavi B. Barathi
- Department of Gastroenterology, Hepatology & Nutrition, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sara L. Manning
- Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Gastroenterology, Hepatology & Nutrition, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Anirban Maitra
- Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, University of Texas, Houston, TX 77030, USA
| | - Andrew D. Rhim
- Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Gastroenterology, Hepatology & Nutrition, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sonja M. Wörmann
- Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, University of Texas, Houston, TX 77030, USA
- CORRESPONDANCE: Fredrik I. Thege, , Sonja M. Wörmann, , MD Anderson Cancer Center, Zayed Building, Z3.2065, 6565 MD Anderson Blvd., Houston, TX 77030, USA
| |
Collapse
|
41
|
Braun CJ, Adames AC, Saur D, Rad R. Tutorial: design and execution of CRISPR in vivo screens. Nat Protoc 2022; 17:1903-1925. [PMID: 35840661 DOI: 10.1038/s41596-022-00700-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 03/22/2022] [Indexed: 11/09/2022]
Abstract
Here we provide a detailed tutorial on CRISPR in vivo screening. Using the mouse as the model organism, we introduce a range of CRISPR tools and applications, delineate general considerations for 'transplantation-based' or 'direct in vivo' screening design, and provide details on technical execution, sequencing readouts, computational analyses and data interpretation. In vivo screens face unique pitfalls and limitations, such as delivery issues or library bottlenecking, which must be counteracted to avoid screening failure or flawed conclusions. A broad variety of in vivo phenotypes can be interrogated such as organ development, hematopoietic lineage decision and evolutionary licensing in oncogenesis. We describe experimental strategies to address various biological questions and provide an outlook on emerging CRISPR applications, such as genetic interaction screening. These technological advances create potent new opportunities to dissect the molecular underpinnings of complex organismal phenotypes.
Collapse
Affiliation(s)
- Christian J Braun
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany. .,Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany. .,Hopp Children's Cancer Center Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Andrés Carbonell Adames
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Dieter Saur
- Institute of Experimental Cancer Therapy, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.,Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany. .,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany. .,Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany. .,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
| |
Collapse
|
42
|
Liu H, Wang HG, Pitt G, Liu Z. Direct Observation of Compartment-Specific Localization and Dynamics of Voltage-Gated Sodium Channels. J Neurosci 2022; 42:5482-5498. [PMID: 35672149 PMCID: PMC9295844 DOI: 10.1523/jneurosci.0086-22.2022] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/15/2022] [Accepted: 05/18/2022] [Indexed: 11/21/2022] Open
Abstract
Brain enriched voltage-gated sodium channel (VGSC) Nav1.2 and Nav1.6 are critical for electrical signaling in the CNS. Previous studies have extensively characterized cell-type-specific expression and electrophysiological properties of these two VGSCs and how their differences contribute to fine-tuning of neuronal excitability. However, because of a lack of reliable labeling and imaging methods, the subcellular localization and dynamics of these homologous Nav1.2 and Nav1.6 channels remain understudied. To overcome this challenge, we combined genome editing, super-resolution, and live-cell single-molecule imaging to probe subcellular composition, relative abundances, and trafficking dynamics of Nav1.2 and Nav1.6 in cultured mouse and rat neurons and in male and female mouse brain. We discovered a previously uncharacterized trafficking pathway that targets Nav1.2 to the distal axon of unmyelinated neurons. This pathway uses distinct signals residing in the intracellular loop 1 between transmembrane domain I and II to suppress the retention of Nav1.2 in the axon initial segment and facilitate its membrane loading at the distal axon. As mouse pyramidal neurons undergo myelination, Nav1.2 is gradually excluded from the distal axon as Nav1.6 becomes the dominant VGSC in the axon initial segment and nodes of Ranvier. In addition, we revealed exquisite developmental regulation of Nav1.2 and Nav1.6 localizations in the axon initial segment and dendrites, clarifying the molecular identity of sodium channels in these subcellular compartments. Together, these results unveiled compartment-specific localizations and trafficking mechanisms for VGSCs, which could be regulated separately to modulate membrane excitability in the brain.SIGNIFICANCE STATEMENT Direct observation of endogenous voltage-gated sodium channels reveals a previously uncharacterized distal axon targeting mechanism and the molecular identity of sodium channels in distinct subcellular compartments.
Collapse
Affiliation(s)
- Hui Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147
| | - Hong-Gang Wang
- Weill Cornell Medicine, Cardiovascular Research Institute, New York, New York 10021
| | - Geoffrey Pitt
- Weill Cornell Medicine, Cardiovascular Research Institute, New York, New York 10021
| | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147
| |
Collapse
|
43
|
The Mettl3 epitranscriptomic writer amplifies p53 stress responses. Mol Cell 2022; 82:2370-2384.e10. [PMID: 35512709 PMCID: PMC9807187 DOI: 10.1016/j.molcel.2022.04.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 01/05/2022] [Accepted: 04/06/2022] [Indexed: 01/04/2023]
Abstract
The p53 transcription factor drives anti-proliferative gene expression programs in response to diverse stressors, including DNA damage and oncogenic signaling. Here, we seek to uncover new mechanisms through which p53 regulates gene expression using tandem affinity purification/mass spectrometry to identify p53-interacting proteins. This approach identified METTL3, an m6A RNA-methyltransferase complex (MTC) constituent, as a p53 interactor. We find that METTL3 promotes p53 protein stabilization and target gene expression in response to DNA damage and oncogenic signals, by both catalytic activity-dependent and independent mechanisms. METTL3 also enhances p53 tumor suppressor activity in in vivo mouse cancer models and human cancer cells. Notably, METTL3 only promotes tumor suppression in the context of intact p53. Analysis of human cancer genome data further supports the notion that the MTC reinforces p53 function in human cancer. Together, these studies reveal a fundamental role for METTL3 in amplifying p53 signaling in response to cellular stress.
Collapse
|
44
|
Jaeger AM, Stopfer LE, Ahn R, Sanders EA, Sandel DA, Freed-Pastor WA, Rideout WM, Naranjo S, Fessenden T, Nguyen KB, Winter PS, Kohn RE, Westcott PMK, Schenkel JM, Shanahan SL, Shalek AK, Spranger S, White FM, Jacks T. Deciphering the immunopeptidome in vivo reveals new tumour antigens. Nature 2022; 607:149-155. [PMID: 35705813 PMCID: PMC9945857 DOI: 10.1038/s41586-022-04839-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 05/06/2022] [Indexed: 11/09/2022]
Abstract
Immunosurveillance of cancer requires the presentation of peptide antigens on major histocompatibility complex class I (MHC-I) molecules1-5. Current approaches to profiling of MHC-I-associated peptides, collectively known as the immunopeptidome, are limited to in vitro investigation or bulk tumour lysates, which limits our understanding of cancer-specific patterns of antigen presentation in vivo6. To overcome these limitations, we engineered an inducible affinity tag into the mouse MHC-I gene (H2-K1) and targeted this allele to the KrasLSL-G12D/+Trp53fl/fl mouse model (KP/KbStrep)7. This approach enabled us to precisely isolate MHC-I peptides from autochthonous pancreatic ductal adenocarcinoma and from lung adenocarcinoma (LUAD) in vivo. In addition, we profiled the LUAD immunopeptidome from the alveolar type 2 cell of origin up to late-stage disease. Differential peptide presentation in LUAD was not predictable by mRNA expression or translation efficiency and is probably driven by post-translational mechanisms. Vaccination with peptides presented by LUAD in vivo induced CD8+ T cell responses in naive mice and tumour-bearing mice. Many peptides specific to LUAD, including immunogenic peptides, exhibited minimal expression of the cognate mRNA, which prompts the reconsideration of antigen prediction pipelines that triage peptides according to transcript abundance8. Beyond cancer, the KbStrep allele is compatible with other Cre-driver lines to explore antigen presentation in vivo in the pursuit of understanding basic immunology, infectious disease and autoimmunity.
Collapse
Affiliation(s)
- Alex M Jaeger
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Lauren E Stopfer
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ryuhjin Ahn
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Emma A Sanders
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Demi A Sandel
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - William A Freed-Pastor
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - William M Rideout
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Santiago Naranjo
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Tim Fessenden
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Kim B Nguyen
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peter S Winter
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ryan E Kohn
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Peter M K Westcott
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Jason M Schenkel
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Sean-Luc Shanahan
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Alex K Shalek
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of MGH, Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Stefani Spranger
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Forest M White
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tyler Jacks
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
45
|
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
|
46
|
Jauch-Speer SL, Herrera-Rivero M, Ludwig N, Véras De Carvalho BC, Martens L, Wolf J, Imam Chasan A, Witten A, Markus B, Schieffer B, Vogl T, Rossaint J, Stoll M, Roth J, Fehler O. C/EBPδ-induced epigenetic changes control the dynamic gene transcription of S100a8 and S100a9. eLife 2022; 11:75594. [PMID: 35543413 PMCID: PMC9122501 DOI: 10.7554/elife.75594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 05/06/2022] [Indexed: 11/25/2022] Open
Abstract
The proinflammatory alarmins S100A8 and S100A9 are among the most abundant proteins in neutrophils and monocytes but are completely silenced after differentiation to macrophages. The molecular mechanisms of the extraordinarily dynamic transcriptional regulation of S100a8 and S100a9 genes, however, are only barely understood. Using an unbiased genome-wide CRISPR/Cas9 knockout (KO)-based screening approach in immortalized murine monocytes, we identified the transcription factor C/EBPδ as a central regulator of S100a8 and S100a9 expression. We showed that S100A8/A9 expression and thereby neutrophil recruitment and cytokine release were decreased in C/EBPδ KO mice in a mouse model of acute lung inflammation. S100a8 and S100a9 expression was further controlled by the C/EBPδ antagonists ATF3 and FBXW7. We confirmed the clinical relevance of this regulatory network in subpopulations of human monocytes in a clinical cohort of cardiovascular patients. Moreover, we identified specific C/EBPδ-binding sites within S100a8 and S100a9 promoter regions, and demonstrated that C/EBPδ-dependent JMJD3-mediated demethylation of H3K27me3 is indispensable for their expression. Overall, our work uncovered C/EBPδ as a novel regulator of S100a8 and S100a9 expression. Therefore, C/EBPδ represents a promising target for modulation of inflammatory conditions that are characterized by S100a8 and S100a9 overexpression.
Collapse
Affiliation(s)
| | | | - Nadine Ludwig
- Department of Anesthesiology, Intensive Care and Pain Medicine, University Hospital Münster, Münster, Germany
| | | | - Leonie Martens
- Institute of Immunology, University of Münster, Münster, Germany
| | - Jonas Wolf
- Institute of Immunology, University of Münster, Münster, Germany
| | | | - Anika Witten
- Department of Genetic Epidemiology, University of Münster, Münster, Germany
| | - Birgit Markus
- Clinic for Cardiology, Angiology and Internal Intensive Medicine, University Hospital Marburg, Marburg, Germany
| | - Bernhard Schieffer
- Clinic for Cardiology, Angiology and Internal Intensive Medicine, University Hospital Marburg, Marburg, Germany
| | - Thomas Vogl
- Institute of Immunology, University of Münster, Münster, Germany
| | - Jan Rossaint
- Department of Anesthesiology, Intensive Care and Pain Medicine, University Hospital Münster, Münster, Germany
| | - Monika Stoll
- Department of Genetic Epidemiology, University of Münster, Münster, Germany
| | - Johannes Roth
- Institute of Immunology, University of Münster, Münster, Germany
| | - Olesja Fehler
- Institute of Immunology, University of Münster, Münster, Germany
| |
Collapse
|
47
|
Tsai NY, Wang F, Toma K, Yin C, Takatoh J, Pai EL, Wu K, Matcham AC, Yin L, Dang EJ, Marciano DK, Rubenstein JL, Wang F, Ullian EM, Duan X. Trans-Seq maps a selective mammalian retinotectal synapse instructed by Nephronectin. Nat Neurosci 2022; 25:659-674. [PMID: 35524141 PMCID: PMC9172271 DOI: 10.1038/s41593-022-01068-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 03/30/2022] [Indexed: 12/21/2022]
Abstract
The mouse visual system serves as an accessible model to understand mammalian circuit wiring. Despite rich knowledge in retinal circuits, the long-range connectivity map from distinct retinal ganglion cell (RGC) types to diverse brain neuron types remains unknown. In this study, we developed an integrated approach, called Trans-Seq, to map RGCs to superior collicular (SC) circuits. Trans-Seq combines a fluorescent anterograde trans-synaptic tracer, consisting of codon-optimized wheat germ agglutinin fused to mCherry, with single-cell RNA sequencing. We used Trans-Seq to classify SC neuron types innervated by genetically defined RGC types and predicted a neuronal pair from αRGCs to Nephronectin-positive wide-field neurons (NPWFs). We validated this connection using genetic labeling, electrophysiology and retrograde tracing. We then used transcriptomic data from Trans-Seq to identify Nephronectin as a determinant for selective synaptic choice from αRGC to NPWFs via binding to Integrin α8β1. The Trans-Seq approach can be broadly applied for post-synaptic circuit discovery from genetically defined pre-synaptic neurons.
Collapse
Affiliation(s)
- Nicole Y Tsai
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA
- Medical Scientist Training Program and Biomedical Science Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Fei Wang
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA
| | - Kenichi Toma
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA
| | - Chen Yin
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA
| | - Jun Takatoh
- McGovern Institute for Brain Research, MIT Brain and Cognitive Sciences, Cambridge, MA, USA
| | - Emily L Pai
- Neuroscience Graduate Program, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA
| | - Kongyan Wu
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA
| | - Angela C Matcham
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA
- Neuroscience Graduate Program, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Luping Yin
- McGovern Institute for Brain Research, MIT Brain and Cognitive Sciences, Cambridge, MA, USA
| | - Eric J Dang
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA
| | - Denise K Marciano
- Departments of Cell Biology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - John L Rubenstein
- Neuroscience Graduate Program, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA
| | - Fan Wang
- McGovern Institute for Brain Research, MIT Brain and Cognitive Sciences, Cambridge, MA, USA
| | - Erik M Ullian
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA
| | - Xin Duan
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA.
- Department of Physiology, University of California, San Francisco, San Francisco, CA, USA.
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA, USA.
| |
Collapse
|
48
|
Abstract
Over the past decade, CRISPR has become as much a verb as it is an acronym, transforming biomedical research and providing entirely new approaches for dissecting all facets of cell biology. In cancer research, CRISPR and related tools have offered a window into previously intractable problems in our understanding of cancer genetics, the noncoding genome and tumour heterogeneity, and provided new insights into therapeutic vulnerabilities. Here, we review the progress made in the development of CRISPR systems as a tool to study cancer, and the emerging adaptation of these technologies to improve diagnosis and treatment.
Collapse
Affiliation(s)
- Alyna Katti
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Science, Weill Cornell Medicine, New York, NY, USA
| | - Bianca J Diaz
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Science, Weill Cornell Medicine, New York, NY, USA
| | - Christina M Caragine
- Department of Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Neville E Sanjana
- Department of Biology, New York University, New York, NY, USA.
- New York Genome Center, New York, NY, USA.
| | - Lukas E Dow
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
| |
Collapse
|
49
|
Yousefi M, Boross G, Weiss C, Murray CW, Hebert JD, Cai H, Ashkin EL, Karmakar S, Andrejka L, Chen L, Wang M, Tsai MK, Lin WY, Li C, Yakhchalian P, Colón CI, Chew SK, Chu P, Swanton C, Kunder CA, Petrov DA, Winslow MM. Combinatorial Inactivation of Tumor Suppressors Efficiently Initiates Lung Adenocarcinoma with Therapeutic Vulnerabilities. Cancer Res 2022; 82:1589-1602. [PMID: 35425962 PMCID: PMC9022333 DOI: 10.1158/0008-5472.can-22-0059] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/07/2022] [Accepted: 02/09/2022] [Indexed: 11/16/2022]
Abstract
Lung cancer is the leading cause of cancer death worldwide, with lung adenocarcinoma being the most common subtype. Many oncogenes and tumor suppressor genes are altered in this cancer type, and the discovery of oncogene mutations has led to the development of targeted therapies that have improved clinical outcomes. However, a large fraction of lung adenocarcinomas lacks mutations in known oncogenes, and the genesis and treatment of these oncogene-negative tumors remain enigmatic. Here, we perform iterative in vivo functional screens using quantitative autochthonous mouse model systems to uncover the genetic and biochemical changes that enable efficient lung tumor initiation in the absence of oncogene alterations. Generation of hundreds of diverse combinations of tumor suppressor alterations demonstrates that inactivation of suppressors of the RAS and PI3K pathways drives the development of oncogene-negative lung adenocarcinoma. Human genomic data and histology identified RAS/MAPK and PI3K pathway activation as a common feature of an event in oncogene-negative human lung adenocarcinomas. These Onc-negativeRAS/PI3K tumors and related cell lines are vulnerable to pharmacologic inhibition of these signaling axes. These results transform our understanding of this prevalent yet understudied subtype of lung adenocarcinoma. SIGNIFICANCE To address the large fraction of lung adenocarcinomas lacking mutations in proto-oncogenes for which targeted therapies are unavailable, this work uncovers driver pathways of oncogene-negative lung adenocarcinomas and demonstrates their therapeutic vulnerabilities.
Collapse
Affiliation(s)
- Maryam Yousefi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- These authors contributed equally
| | - Gábor Boross
- Department of Biology, Stanford University, Stanford, CA, USA
- These authors contributed equally
| | - Carly Weiss
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | - Jess D. Hebert
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Hongchen Cai
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Emily L. Ashkin
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Saswati Karmakar
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Laura Andrejka
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Leo Chen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Minwei Wang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Min K. Tsai
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Wen-Yang Lin
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Chuan Li
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Pegah Yakhchalian
- Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA
| | - Caterina I. Colón
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Su-Kit Chew
- Cancer Evolution and Genome Instability Laboratory, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Pauline Chu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Christian A. Kunder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Dmitri A. Petrov
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Monte M. Winslow
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| |
Collapse
|
50
|
Kaltenbacher T, Löprich J, Maresch R, Weber J, Müller S, Oellinger R, Groß N, Griger J, de Andrade Krätzig N, Avramopoulos P, Ramanujam D, Brummer S, Widholz SA, Bärthel S, Falcomatà C, Pfaus A, Alnatsha A, Mayerle J, Schmidt-Supprian M, Reichert M, Schneider G, Ehmer U, Braun CJ, Saur D, Engelhardt S, Rad R. CRISPR somatic genome engineering and cancer modeling in the mouse pancreas and liver. Nat Protoc 2022; 17:1142-1188. [PMID: 35288718 DOI: 10.1038/s41596-021-00677-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/07/2021] [Indexed: 12/23/2022]
Abstract
Genetically engineered mouse models (GEMMs) transformed the study of organismal disease phenotypes but are limited by their lengthy generation in embryonic stem cells. Here, we describe methods for rapid and scalable genome engineering in somatic cells of the liver and pancreas through delivery of CRISPR components into living mice. We introduce the spectrum of genetic tools, delineate viral and nonviral CRISPR delivery strategies and describe a series of applications, ranging from gene editing and cancer modeling to chromosome engineering or CRISPR multiplexing and its spatio-temporal control. Beyond experimental design and execution, the protocol describes quantification of genetic and functional editing outcomes, including sequencing approaches, data analysis and interpretation. Compared to traditional knockout mice, somatic GEMMs face an increased risk for mouse-to-mouse variability because of the higher experimental demands of the procedures. The robust protocols described here will help unleash the full potential of somatic genome manipulation. Depending on the delivery method and envisaged application, the protocol takes 3-5 weeks.
Collapse
Affiliation(s)
- Thorsten Kaltenbacher
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Jessica Löprich
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Roman Maresch
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Julia Weber
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Sebastian Müller
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Rupert Oellinger
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Nina Groß
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Joscha Griger
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Niklas de Andrade Krätzig
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Petros Avramopoulos
- Institute of Pharmacology and Toxicology, Technical University of Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Deepak Ramanujam
- Institute of Pharmacology and Toxicology, Technical University of Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Sabine Brummer
- Institute of Pharmacology and Toxicology, Technical University of Munich, Munich, Germany
| | - Sebastian A Widholz
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Stefanie Bärthel
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.,Institute of Experimental Cancer Therapy, Technical University of Munich, Munich, Germany
| | - Chiara Falcomatà
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.,Institute of Experimental Cancer Therapy, Technical University of Munich, Munich, Germany
| | - Anja Pfaus
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Ahmed Alnatsha
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany
| | - Julia Mayerle
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marc Schmidt-Supprian
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Experimental Hematology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Maximilian Reichert
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Günter Schneider
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Ursula Ehmer
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Christian J Braun
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany.,Hopp Children's Cancer Center Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dieter Saur
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.,Institute of Experimental Cancer Therapy, Technical University of Munich, Munich, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Stefan Engelhardt
- Institute of Pharmacology and Toxicology, Technical University of Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany. .,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany. .,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.
| |
Collapse
|