1
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Coan M, Haefliger S, Ounzain S, Johnson R. Targeting and engineering long non-coding RNAs for cancer therapy. Nat Rev Genet 2024; 25:578-595. [PMID: 38424237 DOI: 10.1038/s41576-024-00693-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2024] [Indexed: 03/02/2024]
Abstract
RNA therapeutics (RNATx) aim to treat diseases, including cancer, by targeting or employing RNA molecules for therapeutic purposes. Amongst the most promising targets are long non-coding RNAs (lncRNAs), which regulate oncogenic molecular networks in a cell type-restricted manner. lncRNAs are distinct from protein-coding genes in important ways that increase their therapeutic potential yet also present hurdles to conventional clinical development. Advances in genome editing, oligonucleotide chemistry, multi-omics and RNA engineering are paving the way for efficient and cost-effective lncRNA-focused drug discovery pipelines. In this Review, we present the emerging field of lncRNA therapeutics for oncology, with emphasis on the unique strengths and challenges of lncRNAs within the broader RNATx framework. We outline the necessary steps for lncRNA therapeutics to deliver effective, durable, tolerable and personalized treatments for cancer.
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Affiliation(s)
- Michela Coan
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Simon Haefliger
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | | | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland.
- Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland.
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
- Department for BioMedical Research, University of Bern, Bern, Switzerland.
- FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, Dublin, Ireland.
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2
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Xiao MS, Damodaran AP, Kumari B, Dickson E, Xing K, On TA, Parab N, King HE, Perez AR, Guiblet WM, Duncan G, Che A, Chari R, Andresson T, Vidigal JA, Weatheritt RJ, Aregger M, Gonatopoulos-Pournatzis T. Genome-scale exon perturbation screens uncover exons critical for cell fitness. Mol Cell 2024; 84:2553-2572.e19. [PMID: 38917794 PMCID: PMC11246229 DOI: 10.1016/j.molcel.2024.05.024] [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: 10/01/2023] [Revised: 04/04/2024] [Accepted: 05/24/2024] [Indexed: 06/27/2024]
Abstract
CRISPR-Cas technology has transformed functional genomics, yet understanding of how individual exons differentially shape cellular phenotypes remains limited. Here, we optimized and conducted massively parallel exon deletion and splice-site mutation screens in human cell lines to identify exons that regulate cellular fitness. Fitness-promoting exons are prevalent in essential and highly expressed genes and commonly overlap with protein domains and interaction interfaces. Conversely, fitness-suppressing exons are enriched in nonessential genes, exhibiting lower inclusion levels, and overlap with intrinsically disordered regions and disease-associated mutations. In-depth mechanistic investigation of the screen-hit TAF5 alternative exon-8 revealed that its inclusion is required for assembly of the TFIID general transcription initiation complex, thereby regulating global gene expression output. Collectively, our orthogonal exon perturbation screens established a comprehensive repository of phenotypically important exons and uncovered regulatory mechanisms governing cellular fitness and gene expression.
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Affiliation(s)
- Mei-Sheng Xiao
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Arun Prasath Damodaran
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA.
| | - Bandana Kumari
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Ethan Dickson
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Kun Xing
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Tyler A On
- Molecular Targets Program, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Nikhil Parab
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Helen E King
- EMBL Australia and Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Alexendar R Perez
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA; Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Wilfried M Guiblet
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA
| | - Gerard Duncan
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21701, USA
| | - Anney Che
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21701, USA
| | - Raj Chari
- Genome Modification Core, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21702, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD 21701, USA
| | - Joana A Vidigal
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Robert J Weatheritt
- EMBL Australia and Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2010, Australia
| | - Michael Aregger
- Molecular Targets Program, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA.
| | - Thomas Gonatopoulos-Pournatzis
- RNA Biology Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Frederick, MD 21702, USA.
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3
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Li Y, Tan M, Akkari-Henić A, Zhang L, Kip M, Sun S, Sepers JJ, Xu N, Ariyurek Y, Kloet SL, Davis RP, Mikkers H, Gruber JJ, Snyder MP, Li X, Pang B. Genome-wide Cas9-mediated screening of essential non-coding regulatory elements via libraries of paired single-guide RNAs. Nat Biomed Eng 2024; 8:890-908. [PMID: 38778183 DOI: 10.1038/s41551-024-01204-8] [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: 09/05/2023] [Accepted: 03/27/2024] [Indexed: 05/25/2024]
Abstract
The functions of non-coding regulatory elements (NCREs), which constitute a major fraction of the human genome, have not been systematically studied. Here we report a method involving libraries of paired single-guide RNAs targeting both ends of an NCRE as a screening system for the Cas9-mediated deletion of thousands of NCREs genome-wide to study their functions in distinct biological contexts. By using K562 and 293T cell lines and human embryonic stem cells, we show that NCREs can have redundant functions, and that many ultra-conserved elements have silencer activity and play essential roles in cell growth and in cellular responses to drugs (notably, the ultra-conserved element PAX6_Tarzan may be critical for heart development, as removing it from human embryonic stem cells led to defects in cardiomyocyte differentiation). The high-throughput screen, which is compatible with single-cell sequencing, may allow for the identification of druggable NCREs.
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Affiliation(s)
- Yufeng Li
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Minkang Tan
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Almira Akkari-Henić
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Limin Zhang
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Maarten Kip
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Shengnan Sun
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Jorian J Sepers
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ningning Xu
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Yavuz Ariyurek
- Leiden Genome Technology Center, Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Susan L Kloet
- Leiden Genome Technology Center, Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Richard P Davis
- Department of Anatomy and Embryology, The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, the Netherlands
| | - Harald Mikkers
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Joshua J Gruber
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Xiao Li
- Department of Biochemistry, The Center for RNA Science and Therapeutics, Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, OH, USA.
| | - Baoxu Pang
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands.
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4
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Wu P, Yao M, Wang W. Differential impact of quiescent non-coding loci on chromatin entropy. Nucleic Acids Res 2024:gkae535. [PMID: 38908026 DOI: 10.1093/nar/gkae535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/17/2024] [Accepted: 06/12/2024] [Indexed: 06/24/2024] Open
Abstract
Non-coding regions of the human genome are important for functional regulations, but their mechanisms remain elusive. We used machine learning to guide a CRISPR screening on hubs (i.e. non-coding loci forming many 3D contacts) and significantly increased the discovery rate of hubs essential for cell growth. We found no clear genetic or epigenetic differences between essential and nonessential hubs, but we observed that some neighboring hubs in the linear genome have distinct spatial contacts and opposite effects on cell growth. One such pair in an epigenetically quiescent region showed different impacts on gene expression, chromatin accessibility and chromatin organization. We also found that deleting the essential hub altered the genetic network activity and increased the entropy of chromatin accessibility, more severe than that caused by deletion of the nonessential hub, suggesting that they are critical for maintaining an ordered chromatin structure. Our study reveals new insights into the system-level roles of non-coding regions in the human genome.
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Affiliation(s)
- Peiyao Wu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0359, USA
| | - Mina Yao
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0359, USA
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0359, USA
- Bioinformatics and Systems Biology program, University of California, San Diego, La Jolla, CA 92093-0359, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0359, USA
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5
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Li K, Xie T, Li Y, Huang X. LncRNAs act as modulators of macrophages within the tumor microenvironment. Carcinogenesis 2024; 45:363-377. [PMID: 38459912 DOI: 10.1093/carcin/bgae021] [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: 11/16/2023] [Revised: 02/21/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) have been established as pivotal players in various cellular processes, encompassing the regulation of transcription, translation and post-translational modulation of proteins, thereby influencing cellular functions. Notably, lncRNAs exert a regulatory influence on diverse biological processes, particularly in the context of tumor development. Tumor-associated macrophages (TAMs) exhibit the M2 phenotype, exerting significant impact on crucial processes such as tumor initiation, angiogenesis, metastasis and immune evasion. Elevated infiltration of TAMs into the tumor microenvironment (TME) is closely associated with a poor prognosis in various cancers. LncRNAs within TAMs play a direct role in regulating cellular processes. Functioning as integral components of tumor-derived exosomes, lncRNAs prompt the M2-like polarization of macrophages. Concurrently, reports indicate that lncRNAs in tumor cells contribute to the expression and release of molecules that modulate TAMs within the TME. These actions of lncRNAs induce the recruitment, infiltration and M2 polarization of TAMs, thereby providing critical support for tumor development. In this review, we survey recent studies elucidating the impact of lncRNAs on macrophage recruitment, polarization and function across different types of cancers.
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Affiliation(s)
- Kangning Li
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Jiangxi Medical College, Nanchang University, Nanchang, China
- HuanKui Academy, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Tao Xie
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Yong Li
- Department of Anesthesiology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Xuan Huang
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Jiangxi Medical College, Nanchang University, Nanchang, China
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6
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Halasz H, Malekos E, Covarrubias S, Yitiz S, Montano C, Sudek L, Katzman S, Liu SJ, Horlbeck MA, Namvar L, Weissman JS, Carpenter S. CRISPRi screens identify the lncRNA, LOUP, as a multifunctional locus regulating macrophage differentiation and inflammatory signaling. Proc Natl Acad Sci U S A 2024; 121:e2322524121. [PMID: 38781216 PMCID: PMC11145268 DOI: 10.1073/pnas.2322524121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/16/2024] [Indexed: 05/25/2024] Open
Abstract
Long noncoding RNAs (lncRNAs) account for the largest portion of RNA from the transcriptome, yet most of their functions remain unknown. Here, we performed two independent high-throughput CRISPRi screens to understand the role of lncRNAs in monocyte function and differentiation. The first was a reporter-based screen to identify lncRNAs that regulate TLR4-NFkB signaling in human monocytes and the second screen identified lncRNAs involved in monocyte to macrophage differentiation. We successfully identified numerous noncoding and protein-coding genes that can positively or negatively regulate inflammation and differentiation. To understand the functional roles of lncRNAs in both processes, we chose to further study the lncRNA LOUP [lncRNA originating from upstream regulatory element of SPI1 (also known as PU.1)], as it emerged as a top hit in both screens. Not only does LOUP regulate its neighboring gene, the myeloid fate-determining factor SPI1, thereby affecting monocyte to macrophage differentiation, but knockdown of LOUP leads to a broad upregulation of NFkB-targeted genes at baseline and upon TLR4-NFkB activation. LOUP also harbors three small open reading frames capable of being translated and are responsible for LOUP's ability to negatively regulate TLR4/NFkB signaling. This work emphasizes the value of high-throughput screening to rapidly identify functional lncRNAs in the innate immune system.
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Affiliation(s)
- Haley Halasz
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, CA95064
| | - Eric Malekos
- Department of Biomolecular Engineering, University of California Santa Cruz, CA95064
| | - Sergio Covarrubias
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, CA95064
| | - Samira Yitiz
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, CA95064
| | - Christy Montano
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, CA95064
| | - Lisa Sudek
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, CA95064
| | - Sol Katzman
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, CA95064
| | - S. John Liu
- Department of Radiation Oncology, University of California, San Francisco, CA94158
- Department of Neurological Surgery, University of California, San Francisco, CA94158
| | - Max A. Horlbeck
- Department of Radiation Oncology, University of California, San Francisco, CA94158
- Department of Neurological Surgery, University of California, San Francisco, CA94158
- Department of Pediatrics, Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA02115
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA02138
| | - Leila Namvar
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, CA95064
| | - Jonathan S. Weissman
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA02142
- HHMI, Chevy Chase, MD20815
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA02142
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, CA95064
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7
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Fang Y, Li X, Tian R. Unlocking Glioblastoma Vulnerabilities with CRISPR-Based Genetic Screening. Int J Mol Sci 2024; 25:5702. [PMID: 38891890 PMCID: PMC11171782 DOI: 10.3390/ijms25115702] [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: 03/31/2024] [Revised: 05/17/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
Glioblastoma (GBM) is the most common malignant brain tumor in adults. Despite advancements in treatment, the prognosis for patients with GBM remains poor due to its aggressive nature and resistance to therapy. CRISPR-based genetic screening has emerged as a powerful tool for identifying genes crucial for tumor progression and treatment resistance, offering promising targets for tumor therapy. In this review, we provide an overview of the recent advancements in CRISPR-based genetic screening approaches and their applications in GBM. We highlight how these approaches have been used to uncover the genetic determinants of GBM progression and responsiveness to various therapies. Furthermore, we discuss the ongoing challenges and future directions of CRISPR-based screening methods in advancing GBM research.
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Affiliation(s)
- Yitong Fang
- Department of Medical Neuroscience, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China; (Y.F.); (X.L.)
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xing Li
- Department of Medical Neuroscience, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China; (Y.F.); (X.L.)
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ruilin Tian
- Department of Medical Neuroscience, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China; (Y.F.); (X.L.)
- Key University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen 518055, China
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8
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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.
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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
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9
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Peralta-Alvarez CA, Núñez-Martínez HN, Cerecedo-Castillo ÁJ, Poot-Hernández AC, Tapia-Urzúa G, Garza-Manero S, Guerrero G, Recillas-Targa F. A Bidirectional Non-Coding RNA Promoter Mediates Long-Range Gene Expression Regulation. Genes (Basel) 2024; 15:549. [PMID: 38790178 PMCID: PMC11120797 DOI: 10.3390/genes15050549] [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: 03/21/2024] [Revised: 04/18/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024] Open
Abstract
Recent evidence suggests that human gene promoters display gene expression regulatory mechanisms beyond the typical single gene local transcription modulation. In mammalian genomes, genes with an associated bidirectional promoter are abundant; bidirectional promoter architecture serves as a regulatory hub for a gene pair expression. However, it has been suggested that its contribution to transcriptional regulation might exceed local transcription initiation modulation. Despite their abundance, the functional consequences of bidirectional promoter architecture remain largely unexplored. This work studies the long-range gene expression regulatory role of a long non-coding RNA gene promoter using chromosome conformation capture methods. We found that this particular bidirectional promoter contributes to distal gene expression regulation in a target-specific manner by establishing promoter-promoter interactions. In particular, we validated that the promoter-promoter interactions of this regulatory element with the promoter of distal gene BBX contribute to modulating the transcription rate of this gene; removing the bidirectional promoter from its genomic context leads to a rearrangement of BBX promoter-enhancer interactions and to increased gene expression. Moreover, long-range regulatory functionality is not directly dependent on its associated non-coding gene pair expression levels.
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Affiliation(s)
- Carlos Alberto Peralta-Alvarez
- Instituto de Fisiología Celular, Departaménto de Genética Molecular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (C.A.P.-A.); (H.N.N.-M.)
- Instituto de Fisiología Celular, Unidad de Bioinformática y Manejo de la Información, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Hober Nelson Núñez-Martínez
- Instituto de Fisiología Celular, Departaménto de Genética Molecular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (C.A.P.-A.); (H.N.N.-M.)
| | - Ángel Josué Cerecedo-Castillo
- Instituto de Fisiología Celular, Departaménto de Genética Molecular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (C.A.P.-A.); (H.N.N.-M.)
| | - Augusto César Poot-Hernández
- Instituto de Fisiología Celular, Unidad de Bioinformática y Manejo de la Información, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Gustavo Tapia-Urzúa
- Instituto de Fisiología Celular, Departaménto de Genética Molecular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (C.A.P.-A.); (H.N.N.-M.)
| | - Sylvia Garza-Manero
- Instituto de Fisiología Celular, Departaménto de Genética Molecular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (C.A.P.-A.); (H.N.N.-M.)
| | - Georgina Guerrero
- Instituto de Fisiología Celular, Departaménto de Genética Molecular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (C.A.P.-A.); (H.N.N.-M.)
| | - Félix Recillas-Targa
- Instituto de Fisiología Celular, Departaménto de Genética Molecular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (C.A.P.-A.); (H.N.N.-M.)
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10
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Wang Y, Peng Y, Zi G, Chen J, Peng B. Co-delivery of Cas9 mRNA and guide RNAs for editing of LGMN gene represses breast cancer cell metastasis. Sci Rep 2024; 14:8095. [PMID: 38582932 PMCID: PMC10998893 DOI: 10.1038/s41598-024-58765-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 04/03/2024] [Indexed: 04/08/2024] Open
Abstract
Legumain (or asparagine endopeptidase/AEP) is a lysosomal cysteine endopeptidase associated with increased invasive and migratory behavior in a variety of cancers. In this study, co-delivery of Cas9 mRNA and guide RNA (gRNA) by lipid nanoparticles (LNP) for editing of LGMN gene was performed. For in-vitro transcription (IVT) of gRNA, two templates were designed: linearized pUC57-T7-gRNA and T7-gRNA oligos, and the effectiveness of gRNA was verified in multiple ways. Cas9 plasmid was modified and optimized for IVT of Cas9 mRNA. The effects of LGMN gene editing on lysosomal/autophagic function and cancer cell metastasis were investigated. Co-delivery of Cas9 mRNA and gRNA resulted in impaired lysosomal/autophagic degradation, clone formation, migration, and invasion capacity of cancer cells in-vitro. Experimental lung metastasis experiment indicates co-delivery of Cas9 mRNA and gRNA by LNP reduced the migration and invasion capacity of cancer cells in-vivo. These results indicate that co-delivery of Cas9 mRNA and gRNA can enhance the efficiency of CRISPR/Cas9-mediated gene editing in-vitro and in-vivo, and suggest that Cas9 mRNA and gRNA gene editing of LGMN may be a potential treatment for breast tumor metastasis.
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Affiliation(s)
- Yue Wang
- College of Pharmacy, Dali University, 2 HongShen Road, Dali, 671003, Yunnan, China
| | - Yatu Peng
- JinCai High School, 2788 Yang Gao Middle Road, Pudong New District, Shanghai, 200135, China
| | - Guanghui Zi
- College of Pharmacy, Dali University, 2 HongShen Road, Dali, 671003, Yunnan, China
| | - Jin Chen
- College of Pharmacy, Dali University, 2 HongShen Road, Dali, 671003, Yunnan, China
| | - Baowei Peng
- College of Pharmacy, Dali University, 2 HongShen Road, Dali, 671003, Yunnan, China.
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11
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Ijee S, Chambayil K, Chaudhury AD, Bagchi A, Modak K, Das S, Benjamin ESB, Rani S, Paul DZ, Nath A, Roy D, Palani D, Priyanka S, Ravichandran R, Kumary BK, Sivamani Y, S. V, Babu D, Nakamura Y, Thamodaran V, Balasubramanian P, Velayudhan SR. Efficient deletion of microRNAs using CRISPR/Cas9 with dual guide RNAs. Front Mol Biosci 2024; 10:1295507. [PMID: 38628442 PMCID: PMC11020096 DOI: 10.3389/fmolb.2023.1295507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 12/27/2023] [Indexed: 04/19/2024] Open
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs that play crucial roles in gene regulation, exerting post-transcriptional silencing, thereby influencing cellular function, development, and disease. Traditional loss-of-function methods for studying miRNA functions, such as miRNA inhibitors and sponges, present limitations in terms of specificity, transient effects, and off-target effects. Similarly, CRISPR/Cas9-based editing of miRNAs using single guide RNAs (sgRNAs) also has limitations in terms of design space for generating effective gRNAs. In this study, we introduce a novel approach that utilizes CRISPR/Cas9 with dual guide RNAs (dgRNAs) for the rapid and efficient generation of short deletions within miRNA genomic regions. Through the expression of dgRNAs through single-copy lentiviral integration, this approach achieves over a 90% downregulation of targeted miRNAs within a week. We conducted a comprehensive analysis of various parameters influencing efficient deletion formation. In addition, we employed doxycycline (Dox)-inducible expression of Cas9 from the AAVS1 locus, enabling homogeneous, temporal, and stage-specific editing during cellular differentiation. Compared to miRNA inhibitory methods, the dgRNA-based approach offers higher specificity, allowing for the deletion of individual miRNAs with similar seed sequences, without affecting other miRNAs. Due to the increased design space, the dgRNA-based approach provides greater flexibility in gRNA design compared to the sgRNA-based approach. We successfully applied this approach in two human cell lines, demonstrating its applicability for studying the mechanisms of human erythropoiesis and pluripotent stem cell (iPSC) biology and differentiation. Efficient deletion of miR-451 and miR-144 resulted in blockage of erythroid differentiation, and the deletion of miR-23a and miR-27a significantly affected iPSC survival. We have validated the highly efficient deletion of genomic regions by editing protein-coding genes, resulting in a significant impact on protein expression. This protocol has the potential to be extended to delete multiple miRNAs within miRNA clusters, allowing for future investigations into the cooperative effects of the cluster members on cellular functions. The protocol utilizing dgRNAs for miRNA deletion can be employed to generate efficient pooled libraries for high-throughput comprehensive analysis of miRNAs involved in different biological processes.
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Affiliation(s)
- Smitha Ijee
- Centre for Stem Cell Research (A Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, India
| | - Karthik Chambayil
- Centre for Stem Cell Research (A Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
- Sree Chitra Tirunal Institute of Science and Medical Technology, Thiruvananthapuram, India
| | - Anurag Dutta Chaudhury
- Department of Haematology, Christian Medical College Campus, Vellore, India
- Regional Centre for Biotechnology, New Delhi, India
| | - Abhirup Bagchi
- Centre for Stem Cell Research (A Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
| | - Kirti Modak
- Department of Haematology, Christian Medical College Campus, Vellore, India
- Regional Centre for Biotechnology, New Delhi, India
| | - Saswati Das
- Department of Biotechnology, Thiruvalluvar University, Vellore, India
- Department of Haematology, Christian Medical College Campus, Vellore, India
| | - Esther Sathya Bama Benjamin
- Sree Chitra Tirunal Institute of Science and Medical Technology, Thiruvananthapuram, India
- Department of Haematology, Christian Medical College Campus, Vellore, India
| | - Sonam Rani
- Centre for Stem Cell Research (A Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
- Department of Biotechnology, Thiruvalluvar University, Vellore, India
| | - Daniel Zechariah Paul
- Department of Haematology, Christian Medical College Campus, Vellore, India
- Manipal Academy of Higher Education, Manipal, India
| | - Aneesha Nath
- Centre for Stem Cell Research (A Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
| | - Debanjan Roy
- Department of Haematology, Christian Medical College Campus, Vellore, India
- Manipal Academy of Higher Education, Manipal, India
| | - Dhavapriya Palani
- Centre for Stem Cell Research (A Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
| | - Sweety Priyanka
- Department of Haematology, Christian Medical College Campus, Vellore, India
| | | | - Betty K. Kumary
- Department of Haematology, Christian Medical College Campus, Vellore, India
| | - Yazhini Sivamani
- Department of Haematology, Christian Medical College Campus, Vellore, India
| | - Vijayanand S.
- Department of Biotechnology, Thiruvalluvar University, Vellore, India
| | - Dinesh Babu
- Centre for Stem Cell Research (A Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Vasanth Thamodaran
- Centre for Stem Cell Research (A Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
- Tata Institute of Genetics and Society, Bengaluru, India
| | | | - Shaji R. Velayudhan
- Centre for Stem Cell Research (A Unit of inStem, Bengaluru), Christian Medical College Campus, Vellore, India
- Department of Haematology, Christian Medical College Campus, Vellore, India
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12
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Srinivas T, Siqueira E, Guil S. Techniques for investigating lncRNA transcript functions in neurodevelopment. Mol Psychiatry 2024; 29:874-890. [PMID: 38145986 PMCID: PMC11176085 DOI: 10.1038/s41380-023-02377-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 12/05/2023] [Accepted: 12/12/2023] [Indexed: 12/27/2023]
Abstract
Long noncoding RNAs (lncRNAs) are sequences of 200 nucleotides or more that are transcribed from a large portion of the mammalian genome. While hypothesized to have a variety of biological roles, many lncRNAs remain largely functionally uncharacterized due to unique challenges associated with their investigation. For example, some lncRNAs overlap with other genomic loci, are expressed in a cell-type-specific manner, and/or are differentially processed at the post-transcriptional level. The mammalian CNS contains a vast diversity of lncRNAs, and lncRNAs are highly abundant in the mammalian brain. However, interrogating lncRNA function in models of the CNS, particularly in vivo, can be complex and challenging. Here we review the breadth of methods used to investigate lncRNAs in the CNS, their merits, and the understanding they can provide with respect to neurodevelopment and pathophysiology. We discuss remaining challenges in the field and provide recommendations to assay lncRNAs based on current methods.
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Affiliation(s)
- Tara Srinivas
- Josep Carreras Leukaemia Research Institute (IJC), 08916, Badalona, Barcelona, Catalonia, Spain
| | - Edilene Siqueira
- Josep Carreras Leukaemia Research Institute (IJC), 08916, Badalona, Barcelona, Catalonia, Spain
| | - Sonia Guil
- Josep Carreras Leukaemia Research Institute (IJC), 08916, Badalona, Barcelona, Catalonia, Spain.
- Germans Trias i Pujol Health Science Research Institute, 08916, Badalona, Barcelona, Catalonia, Spain.
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13
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Montero JJ, Trozzo R, Sugden M, Öllinger R, Belka A, Zhigalova E, Waetzig P, Engleitner T, Schmidt-Supprian M, Saur D, Rad R. Genome-scale pan-cancer interrogation of lncRNA dependencies using CasRx. Nat Methods 2024; 21:584-596. [PMID: 38409225 PMCID: PMC11009108 DOI: 10.1038/s41592-024-02190-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 01/19/2024] [Indexed: 02/28/2024]
Abstract
Although long noncoding RNAs (lncRNAs) dominate the transcriptome, their functions are largely unexplored. The extensive overlap of lncRNAs with coding and regulatory sequences restricts their systematic interrogation by DNA-directed perturbation. Here we developed genome-scale lncRNA transcriptome screening using Cas13d/CasRx. We show that RNA targeting overcomes limitations inherent to other screening methods, thereby considerably expanding the explorable space of the lncRNAome. By evolving the screening system toward pan-cancer applicability, it supports molecular and phenotypic data integration to contextualize screening hits or infer lncRNA function. We thereby addressed challenges posed by the enormous transcriptome size and tissue specificity through a size-reduced multiplexed gRNA library termed Albarossa, targeting 24,171 lncRNA genes. Its rational design incorporates target prioritization based on expression, evolutionary conservation and tissue specificity, thereby reconciling high discovery power and pan-cancer representation with scalable experimental throughput. Applied across entities, the screening platform identified numerous context-specific and common essential lncRNAs. Our work sets the stage for systematic exploration of lncRNA biology in health and disease.
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Affiliation(s)
- Juan J Montero
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany.
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany.
| | - Riccardo Trozzo
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Maya Sugden
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Rupert Öllinger
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Alexander Belka
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Ekaterina Zhigalova
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Paul Waetzig
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Thomas Engleitner
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Marc Schmidt-Supprian
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 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
| | - Dieter Saur
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technische Universität München, Munich, Germany
- Institute for Experimental Cancer Therapy, School of Medicine, Technische Universität München, Munich, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany.
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany.
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
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14
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Yao D, Tycko J, Oh JW, Bounds LR, Gosai SJ, Lataniotis L, Mackay-Smith A, Doughty BR, Gabdank I, Schmidt H, Guerrero-Altamirano T, Siklenka K, Guo K, White AD, Youngworth I, Andreeva K, Ren X, Barrera A, Luo Y, Yardımcı GG, Tewhey R, Kundaje A, Greenleaf WJ, Sabeti PC, Leslie C, Pritykin Y, Moore JE, Beer MA, Gersbach CA, Reddy TE, Shen Y, Engreitz JM, Bassik MC, Reilly SK. Multicenter integrated analysis of noncoding CRISPRi screens. Nat Methods 2024; 21:723-734. [PMID: 38504114 PMCID: PMC11009116 DOI: 10.1038/s41592-024-02216-7] [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: 12/02/2022] [Accepted: 02/18/2024] [Indexed: 03/21/2024]
Abstract
The ENCODE Consortium's efforts to annotate noncoding cis-regulatory elements (CREs) have advanced our understanding of gene regulatory landscapes. Pooled, noncoding CRISPR screens offer a systematic approach to investigate cis-regulatory mechanisms. The ENCODE4 Functional Characterization Centers conducted 108 screens in human cell lines, comprising >540,000 perturbations across 24.85 megabases of the genome. Using 332 functionally confirmed CRE-gene links in K562 cells, we established guidelines for screening endogenous noncoding elements with CRISPR interference (CRISPRi), including accurate detection of CREs that exhibit variable, often low, transcriptional effects. Benchmarking five screen analysis tools, we find that CASA produces the most conservative CRE calls and is robust to artifacts of low-specificity single guide RNAs. We uncover a subtle DNA strand bias for CRISPRi in transcribed regions with implications for screen design and analysis. Together, we provide an accessible data resource, predesigned single guide RNAs for targeting 3,275,697 ENCODE SCREEN candidate CREs with CRISPRi and screening guidelines to accelerate functional characterization of the noncoding genome.
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Affiliation(s)
- David Yao
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Josh Tycko
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA.
| | - Jin Woo Oh
- Departments of Biomedical Engineering and Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Lexi R Bounds
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Sager J Gosai
- Broad Institute of Harvard & MIT, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Center for System Biology, Harvard University, Cambridge, MA, USA
- Harvard Graduate Program in Biological and Biomedical Science, Boston, MA, USA
| | - Lazaros Lataniotis
- Department of Neurology, Institute for Human Genetics, University of California, San Franscisco, San Francisco, CA, USA
| | - Ava Mackay-Smith
- University Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC, USA
| | | | - Idan Gabdank
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Henri Schmidt
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tania Guerrero-Altamirano
- University Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC, USA
- Department of Biology, Duke University, Durham, NC, USA
| | - Keith Siklenka
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
| | - Katherine Guo
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Alexander D White
- Department of Electrical Engineering, Stanford University, Stanford, CA, USA
| | | | - Kalina Andreeva
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Xingjie Ren
- Department of Neurology, Institute for Human Genetics, University of California, San Franscisco, San Francisco, CA, USA
| | - Alejandro Barrera
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
| | - Yunhai Luo
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | | | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Pardis C Sabeti
- Broad Institute of Harvard & MIT, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Center for System Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Christina Leslie
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yuri Pritykin
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Jill E Moore
- Program in Bioinformatics and Integrative Biology, RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Michael A Beer
- Departments of Biomedical Engineering and Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Timothy E Reddy
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
| | - Yin Shen
- Department of Neurology, Institute for Human Genetics, University of California, San Franscisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Jesse M Engreitz
- Department of Genetics, Stanford University, Stanford, CA, USA
- BASE Initiative, Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford, CA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Steven K Reilly
- Department of Genetics, Yale University, New Haven, CT, USA.
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15
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Jin Y, Wu H, Liu J, Cho WC, Song G. Application and progress of CRISPR/Cas9 gene editing in B-cell lymphoma: a narrative review. Transl Cancer Res 2024; 13:1584-1595. [PMID: 38617522 PMCID: PMC11009809 DOI: 10.21037/tcr-23-1146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 01/23/2024] [Indexed: 04/16/2024]
Abstract
Background and Objective Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) gene editing and CRISPR/Cas9 screening libraries are hot topics, and have high application values in the diagnosis and treatment of genetic diseases, and the improvement of prognosis. The major treatment of B-cell lymphoma is chemotherapy combined with biological therapy. Due to the individual specificity and the emergence of drug resistance, the therapeutic efficacy varies. The objective of this article is to explore potential targets to enhance therapeutic effects, optimize treatment plans, and improve the prognosis of patients with B-cell lymphoma. Methods We undertook a comprehensive, narrative review of the latest literature to define the current application and progress of CRISPR/Cas9 in B-cell lymphoma. Key Content and Findings The concepts of CRISPR/Cas9, the mechanism of gene editing, and the procedures of CRISPR/Cas9 screening libraries are investigated for candidate genes. We mainly focus on application and progress of CRISPR/Cas9 in B-cell lymphoma and screen out some genes, signaling pathways, and cytokines, which may become potential targets for clinical treatment. Conclusions CRISPR/Cas9 gene editing has great promise in the treatment of B-cell lymphoma. This article reviews some genes, signaling pathways, and cytokines related to the progression and prognosis of B-cell lymphoma to provide a strong theoretical basis.
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Affiliation(s)
- Ying Jin
- Department of Hematology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Haiyi Wu
- Department of Hematology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Jianzhao Liu
- Department of Hematology, Affiliated Hospital of Nantong University, Dalian Medical University, Dalian, China
| | - William C. Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong, China
| | - Guoqi Song
- Department of Hematology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
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16
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Jiang H, Tang M, Xu Z, Wang Y, Li M, Zheng S, Zhu J, Lin Z, Zhang M. CRISPR/Cas9 system and its applications in nervous system diseases. Genes Dis 2024; 11:675-686. [PMID: 37692518 PMCID: PMC10491921 DOI: 10.1016/j.gendis.2023.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/05/2023] [Indexed: 09/12/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system is an acquired immune system of many bacteria and archaea, comprising CRISPR loci, Cas genes, and its associated proteins. This system can recognize exogenous DNA and utilize the Cas9 protein's nuclease activity to break DNA double-strand and to achieve base insertion or deletion by subsequent DNA repair. In recent years, multiple laboratory and clinical studies have revealed the therapeutic role of the CRISPR/Cas9 system in neurological diseases. This article reviews the CRISPR/Cas9-mediated gene editing technology and its potential for clinical application against neurological diseases.
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Affiliation(s)
- Haibin Jiang
- The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Mengyan Tang
- The First School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Zidi Xu
- The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Yanan Wang
- The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Mopu Li
- The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Shuyin Zheng
- The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Jianghu Zhu
- Department of Pediatrics, The Second School of Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Key Laboratory of Perinatal Medicine of Wenzhou, Wenzhou, Zhejiang 325027, China
- Key Laboratory of Structural Malformations in Children of Zhejiang Province, Wenzhou, Zhejiang 325000, China
- Zhejiang Provincial Clinical Research Center for Pediatric Disease, Wenzhou, Zhejiang 325027, China
| | - Zhenlang Lin
- Department of Pediatrics, The Second School of Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Key Laboratory of Perinatal Medicine of Wenzhou, Wenzhou, Zhejiang 325027, China
- Key Laboratory of Structural Malformations in Children of Zhejiang Province, Wenzhou, Zhejiang 325000, China
- Zhejiang Provincial Clinical Research Center for Pediatric Disease, Wenzhou, Zhejiang 325027, China
| | - Min Zhang
- Department of Pediatrics, The Second School of Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
- Key Laboratory of Perinatal Medicine of Wenzhou, Wenzhou, Zhejiang 325027, China
- Key Laboratory of Structural Malformations in Children of Zhejiang Province, Wenzhou, Zhejiang 325000, China
- Zhejiang Provincial Clinical Research Center for Pediatric Disease, Wenzhou, Zhejiang 325027, China
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17
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Hazan JM, Amador R, Ali-Nasser T, Lahav T, Shotan SR, Steinberg M, Cohen Z, Aran D, Meiri D, Assaraf YG, Guigó R, Bester AC. Integration of transcription regulation and functional genomic data reveals lncRNA SNHG6's role in hematopoietic differentiation and leukemia. J Biomed Sci 2024; 31:27. [PMID: 38419051 PMCID: PMC10900714 DOI: 10.1186/s12929-024-01015-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 02/22/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are pivotal players in cellular processes, and their unique cell-type specific expression patterns render them attractive biomarkers and therapeutic targets. Yet, the functional roles of most lncRNAs remain enigmatic. To address the need to identify new druggable lncRNAs, we developed a comprehensive approach integrating transcription factor binding data with other genetic features to generate a machine learning model, which we have called INFLAMeR (Identifying Novel Functional LncRNAs with Advanced Machine Learning Resources). METHODS INFLAMeR was trained on high-throughput CRISPR interference (CRISPRi) screens across seven cell lines, and the algorithm was based on 71 genetic features. To validate the predictions, we selected candidate lncRNAs in the human K562 leukemia cell line and determined the impact of their knockdown (KD) on cell proliferation and chemotherapeutic drug response. We further performed transcriptomic analysis for candidate genes. Based on these findings, we assessed the lncRNA small nucleolar RNA host gene 6 (SNHG6) for its role in myeloid differentiation. Finally, we established a mouse K562 leukemia xenograft model to determine whether SNHG6 KD attenuates tumor growth in vivo. RESULTS The INFLAMeR model successfully reconstituted CRISPRi screening data and predicted functional lncRNAs that were previously overlooked. Intensive cell-based and transcriptomic validation of nearly fifty genes in K562 revealed cell type-specific functionality for 85% of the predicted lncRNAs. In this respect, our cell-based and transcriptomic analyses predicted a role for SNHG6 in hematopoiesis and leukemia. Consistent with its predicted role in hematopoietic differentiation, SNHG6 transcription is regulated by hematopoiesis-associated transcription factors. SNHG6 KD reduced the proliferation of leukemia cells and sensitized them to differentiation. Treatment of K562 leukemic cells with hemin and PMA, respectively, demonstrated that SNHG6 inhibits red blood cell differentiation but strongly promotes megakaryocyte differentiation. Using a xenograft mouse model, we demonstrate that SNHG6 KD attenuated tumor growth in vivo. CONCLUSIONS Our approach not only improved the identification and characterization of functional lncRNAs through genomic approaches in a cell type-specific manner, but also identified new lncRNAs with roles in hematopoiesis and leukemia. Such approaches can be readily applied to identify novel targets for precision medicine.
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Affiliation(s)
- Joshua M Hazan
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Raziel Amador
- Centre for Genomic Regulation (CRG), Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain
- Universitat de Barcelona (UB), Barcelona, Catalonia, Spain
| | - Tahleel Ali-Nasser
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Tamar Lahav
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Stav Roni Shotan
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Miryam Steinberg
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Ziv Cohen
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
- The Taub Faculty of Computer Science, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Dvir Aran
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
- The Taub Faculty of Computer Science, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - David Meiri
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Yehuda G Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Assaf C Bester
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel.
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18
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Fukuda K. The role of transposable elements in human evolution and methods for their functional analysis: current status and future perspectives. Genes Genet Syst 2024; 98:289-304. [PMID: 37866889 DOI: 10.1266/ggs.23-00140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023] Open
Abstract
Transposable elements (TEs) are mobile DNA sequences that can insert themselves into various locations within the genome, causing mutations that may provide advantages or disadvantages to individuals and species. The insertion of TEs can result in genetic variation that may affect a wide range of human traits including genetic disorders. Understanding the role of TEs in human biology is crucial for both evolutionary and medical research. This review discusses the involvement of TEs in human traits and disease susceptibility, as well as methods for functional analysis of TEs.
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Affiliation(s)
- Kei Fukuda
- Integrative Genomics Unit, The University of Melbourne
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19
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Li H, Bartke R, Zhao L, Verma Y, Horacek A, Rechav Ben-Natan A, Pangilinan GR, Krishnappa N, Nielsen R, Hockemeyer D. Functional annotation of variants of the BRCA2 gene via locally haploid human pluripotent stem cells. Nat Biomed Eng 2024; 8:165-176. [PMID: 37488236 PMCID: PMC10878975 DOI: 10.1038/s41551-023-01065-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 06/15/2023] [Indexed: 07/26/2023]
Abstract
Mutations in the BRCA2 gene are associated with sporadic and familial cancer, cause genomic instability and sensitize cancer cells to inhibition by the poly(ADP-ribose) polymerase (PARP). Here we show that human pluripotent stem cells (hPSCs) with one copy of BRCA2 deleted can be used to annotate variants of this gene and to test their sensitivities to PARP inhibition. By using Cas9 to edit the functional BRCA2 allele in the locally haploid hPSCs and in fibroblasts differentiated from them, we characterized essential regions in the gene to identify permissive and loss-of-function mutations. We also used Cas9 to directly test the function of individual amino acids, including amino acids encoded by clinical BRCA2 variants of uncertain significance, and identified alleles that are sensitive to PARP inhibitors used as a standard of care in BRCA2-deficient cancers. Locally haploid human pluripotent stem cells can facilitate detailed structure-function analyses of genes and the rapid functional evaluation of clinically observed mutations.
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Affiliation(s)
- Hanqin Li
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Rebecca Bartke
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Lei Zhao
- Section for GeoGenetics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Yogendra Verma
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Anna Horacek
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Alma Rechav Ben-Natan
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Gabriella R Pangilinan
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | | | - Rasmus Nielsen
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
- Section for GeoGenetics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Dirk Hockemeyer
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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20
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Yang Z, Zhang Z, Li J, Chen W, Liu C. CRISPRlnc: a machine learning method for lncRNA-specific single-guide RNA design of CRISPR/Cas9 system. Brief Bioinform 2024; 25:bbae066. [PMID: 38426328 PMCID: PMC10905519 DOI: 10.1093/bib/bbae066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/22/2024] [Accepted: 02/03/2024] [Indexed: 03/02/2024] Open
Abstract
CRISPR/Cas9 is a promising RNA-guided genome editing technology, which consists of a Cas9 nuclease and a single-guide RNA (sgRNA). So far, a number of sgRNA prediction softwares have been developed. However, they were usually designed for protein-coding genes without considering that long non-coding RNA (lncRNA) genes may have different characteristics. In this study, we first evaluated the performances of a series of known sgRNA-designing tools in the context of both coding and non-coding datasets. Meanwhile, we analyzed the underpinnings of their varied performances on the sgRNA's specificity for lncRNA including nucleic acid sequence, genome location and editing mechanism preference. Furthermore, we introduce a support vector machine-based machine learning algorithm named CRISPRlnc, which aims to model both CRISPR knock-out (CRISPRko) and CRISPR inhibition (CRISPRi) mechanisms to predict the on-target activity of targets. CRISPRlnc combined the paired-sgRNA design and off-target analysis to achieve one-stop design of CRISPR/Cas9 sgRNAs for non-coding genes. Performance comparison on multiple datasets showed that CRISPRlnc was far superior to existing methods for both CRISPRko and CRISPRi mechanisms during the lncRNA-specific sgRNA design. To maximize the availability of CRISPRlnc, we developed a web server (http://predict.crisprlnc.cc) and made it available for download on GitHub.
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Affiliation(s)
- Zitian Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zexin Zhang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Jing Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
| | - Wen Chen
- Hunan Provincial Key Laboratory of Vascular Biology and Translational Medicine, School of Medicine, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China
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21
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Mahato RK, Bhattacharya S, Khullar N, Sidhu IS, Reddy PH, Bhatti GK, Bhatti JS. Targeting long non-coding RNAs in cancer therapy using CRISPR-Cas9 technology: A novel paradigm for precision oncology. J Biotechnol 2024; 379:98-119. [PMID: 38065367 DOI: 10.1016/j.jbiotec.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/30/2023] [Accepted: 12/03/2023] [Indexed: 12/25/2023]
Abstract
Cancer is the second leading cause of death worldwide, despite recent advances in its identification and management. To improve cancer patient diagnosis and care, it is necessary to identify new biomarkers and molecular targets. In recent years, long non-coding RNAs (lncRNAs) have surfaced as important contributors to various cellular activities, with growing proof indicating their substantial role in the genesis, development, and spread of cancer. Their unique expression profiles within specific tissues and their wide-ranging functionalities make lncRNAs excellent candidates for potential therapeutic intervention in cancer management. They are implicated in multiple hallmarks of cancer, such as uncontrolled proliferation, angiogenesis, and immune evasion. This review article explores the innovative application of CRISPR-Cas9 technology in targeting lncRNAs as a cancer therapeutic strategy. The CRISPR-Cas9 system has been widely applied in functional genomics, gene therapy, and cancer research, offering a versatile platform for lncRNA targeting. CRISPR-Cas9-mediated targeting of lncRNAs can be achieved through CRISPR interference, activation or the complete knockout of lncRNA loci. Combining CRISPR-Cas9 technology with high-throughput functional genomics makes it possible to identify lncRNAs critical for the survival of specific cancer subtypes, opening the door for tailored treatments and personalised cancer therapies. CRISPR-Cas9-mediated lncRNA targeting with other cutting-edge cancer therapies, such as immunotherapy and targeted molecular therapeutics can be used to overcome the drug resistance in cancer. The synergy of lncRNA research and CRISPR-Cas9 technology presents immense potential for individualized cancer treatment, offering renewed hope in the battle against this disease.
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Affiliation(s)
- Rahul Kumar Mahato
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Srinjan Bhattacharya
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Naina Khullar
- Department of Zoology, Mata Gujri College, Fatehgarh Sahib, Punjab, India
| | - Inderpal Singh Sidhu
- Department of Zoology, Sri Guru Gobind Singh College, Sector 26, Chandigarh, India
| | - P Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Department of Pharmacology & Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Departments of Neurology, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Public Health Department of Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Department of Speech, Language and Hearing Sciences, School Health Professions, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Gurjit Kaur Bhatti
- Department of Medical Lab Technology, University Institute of Applied Health Sciences, Chandigarh University, Mohali, India.
| | - Jasvinder Singh Bhatti
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India.
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22
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Dziubańska-Kusibab PJ, Nevedomskaya E, Haendler B. Preclinical Anticipation of On- and Off-Target Resistance Mechanisms to Anti-Cancer Drugs: A Systematic Review. Int J Mol Sci 2024; 25:705. [PMID: 38255778 PMCID: PMC10815614 DOI: 10.3390/ijms25020705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/22/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
The advent of targeted therapies has led to tremendous improvements in treatment options and their outcomes in the field of oncology. Yet, many cancers outsmart precision drugs by developing on-target or off-target resistance mechanisms. Gaining the ability to resist treatment is the rule rather than the exception in tumors, and it remains a major healthcare challenge to achieve long-lasting remission in most cancer patients. Here, we discuss emerging strategies that take advantage of innovative high-throughput screening technologies to anticipate on- and off-target resistance mechanisms before they occur in treated cancer patients. We divide the methods into non-systematic approaches, such as random mutagenesis or long-term drug treatment, and systematic approaches, relying on the clustered regularly interspaced short palindromic repeats (CRISPR) system, saturated mutagenesis, or computational methods. All these new developments, especially genome-wide CRISPR-based screening platforms, have significantly accelerated the processes for identification of the mechanisms responsible for cancer drug resistance and opened up new avenues for future treatments.
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Affiliation(s)
| | | | - Bernard Haendler
- Research and Early Development Oncology, Pharmaceuticals, Bayer AG, Müllerstr. 178, 13353 Berlin, Germany; (P.J.D.-K.); (E.N.)
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23
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Chanchal DK, Chaudhary JS, Kumar P, Agnihotri N, Porwal P. CRISPR-Based Therapies: Revolutionizing Drug Development and Precision Medicine. Curr Gene Ther 2024; 24:193-207. [PMID: 38310456 DOI: 10.2174/0115665232275754231204072320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/26/2023] [Accepted: 11/15/2023] [Indexed: 02/05/2024]
Abstract
With the discovery of CRISPR-Cas9, drug development and precision medicine have undergone a major change. This review article looks at the new ways that CRISPR-based therapies are being used and how they are changing the way medicine is done. CRISPR technology's ability to precisely and flexibly edit genes has opened up new ways to find, validate, and develop drug targets. Also, it has made way for personalized gene therapies, precise gene editing, and advanced screening techniques, all of which hold great promise for treating a wide range of diseases. In this article, we look at the latest research and clinical trials that show how CRISPR could be used to treat genetic diseases, cancer, infectious diseases, and other hard-to-treat conditions. However, ethical issues and problems with regulations are also discussed in relation to CRISPR-based therapies, which shows how important it is to use them safely and responsibly. As CRISPR continues to change how drugs are made and used, this review shines a light on the amazing things that have been done and what the future might hold in this rapidly changing field.
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Affiliation(s)
- Dilip Kumar Chanchal
- Department of Pharmacy, Smt. Vidyawati College of Pharmacy, Jhansi, Uttar Pradesh, India
- Glocal School of Pharmacy, Glocal University Mirzapur Pole, Saharanpur - 247121, Uttar Pradesh, India
| | | | - Pushpendra Kumar
- Faculty of Pharmacy, Uttar Pradesh University of Medical Sciences, Saifai, Etawah 206130, Uttar Pradesh, India
| | - Neha Agnihotri
- Department of Pharmacy, Maharana Pratap College of Pharmacy, Kothi, Mandhana, Kanpur-209217, Uttar Pradesh, India
| | - Prateek Porwal
- Glocal School of Pharmacy, Glocal University Mirzapur Pole, Saharanpur - 247121, Uttar Pradesh, India
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24
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Huang W, Xiong T, Zhao Y, Heng J, Han G, Wang P, Zhao Z, Shi M, Li J, Wang J, Wu Y, Liu F, Xi JJ, Wang Y, Zhang QC. Computational prediction and experimental validation identify functionally conserved lncRNAs from zebrafish to human. Nat Genet 2024; 56:124-135. [PMID: 38195860 PMCID: PMC10786727 DOI: 10.1038/s41588-023-01620-7] [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: 08/19/2022] [Accepted: 11/21/2023] [Indexed: 01/11/2024]
Abstract
Functional studies of long noncoding RNAs (lncRNAs) have been hindered by the lack of methods to assess their evolution. Here we present lncRNA Homology Explorer (lncHOME), a computational pipeline that identifies a unique class of long noncoding RNAs (lncRNAs) with conserved genomic locations and patterns of RNA-binding protein (RBP) binding sites (coPARSE-lncRNAs). Remarkably, several hundred human coPARSE-lncRNAs can be evolutionarily traced to zebrafish. Using CRISPR-Cas12a knockout and rescue assays, we found that knocking out many human coPARSE-lncRNAs led to cell proliferation defects, which were subsequently rescued by predicted zebrafish homologs. Knocking down coPARSE-lncRNAs in zebrafish embryos caused severe developmental delays that were rescued by human homologs. Furthermore, we verified that human, mouse and zebrafish coPARSE-lncRNA homologs tend to bind similar RBPs with their conserved functions relying on specific RBP-binding sites. Overall, our study demonstrates a comprehensive approach for studying the functional conservation of lncRNAs and implicates numerous lncRNAs in regulating vertebrate physiology.
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Affiliation(s)
- Wenze Huang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Tuanlin Xiong
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Yuting Zhao
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Jian Heng
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Ge Han
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Pengfei Wang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Zhihua Zhao
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Ming Shi
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Juan Li
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Jiazhen Wang
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Yixia Wu
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, Shandong University, Qingdao, China
| | - Jianzhong Jeff Xi
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China.
| | - Yangming Wang
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China.
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China.
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
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25
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Costa V, Giovannetti E, Lonardo E. Revolutionizing Cancer Treatment: Unveiling New Frontiers by Targeting the (Un)Usual Suspects. Cancers (Basel) 2023; 16:132. [PMID: 38201558 PMCID: PMC10778478 DOI: 10.3390/cancers16010132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
This Special Issue includes original articles and reviews on both established and innovative approaches to cancer targeting, showcased at the 29th IGB Workshop titled "Targeting the (un)usual suspects in cancer" "https://29thigbworkshop [...].
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Affiliation(s)
- Valerio Costa
- Institute of Genetics and Biophysics (IGB), National Research Council of Italy (CNR), 80131 Naples, Italy;
| | - Elisa Giovannetti
- Department of Medical Oncology, Amsterdam UMC, VU University, Cancer Center Amsterdam, 1081 HV Amsterdam, The Netherlands;
- Fondazione Pisana per la Scienza, San Giuliano Terme, 56124 Pisa, Italy
| | - Enza Lonardo
- Institute of Genetics and Biophysics (IGB), National Research Council of Italy (CNR), 80131 Naples, Italy;
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26
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Xu D, Tang L, Zhou J, Wang F, Cao H, Huang Y, Kapranov P. Evidence for widespread existence of functional novel and non-canonical human transcripts. BMC Biol 2023; 21:271. [PMID: 38001496 PMCID: PMC10675921 DOI: 10.1186/s12915-023-01753-5] [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: 01/24/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND Fraction of functional sequence in the human genome remains a key unresolved question in Biology and the subject of vigorous debate. While a plethora of studies have connected a significant fraction of human DNA to various biochemical processes, the classical definition of function requires evidence of effects on cellular or organismal fitness that such studies do not provide. Although multiple high-throughput reverse genetics screens have been developed to address this issue, they are limited to annotated genomic elements and suffer from non-specific effects, arguing for a strong need to develop additional functional genomics approaches. RESULTS In this work, we established a high-throughput lentivirus-based insertional mutagenesis strategy as a forward genetics screen tool in aneuploid cells. Application of this approach to human cell lines in multiple phenotypic screens suggested the presence of many yet uncharacterized functional elements in the human genome, represented at least in part by novel exons of known and novel genes. The novel transcripts containing these exons can be massively, up to thousands-fold, induced by specific stresses, and at least some can represent bi-cistronic protein-coding mRNAs. CONCLUSIONS Altogether, these results argue that many unannotated and non-canonical human transcripts, including those that appear as aberrant splice products, have biological relevance under specific biological conditions.
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Affiliation(s)
- Dongyang Xu
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Lu Tang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Junjun Zhou
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Fang Wang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Huifen Cao
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Yu Huang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China.
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China.
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27
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Li Y, Huang B, Chen J, Huang L, Xu J, Wang Y, Cui G, Zhao H, Xin B, Song W, Zhu J, Lai J. Targeted large fragment deletion in plants using paired crRNAs with type I CRISPR system. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2196-2208. [PMID: 37641539 PMCID: PMC10579709 DOI: 10.1111/pbi.14122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/19/2023] [Accepted: 06/25/2023] [Indexed: 08/31/2023]
Abstract
The CRISPR-Cas systems have been widely used as genome editing tools, with type II and V systems typically introducing small indels, and type I system mediating long-range deletions. However, the precision of type I systems for large fragment deletion is still remained to be optimized. Here, we developed a compact Cascade-Cas3 Dvu I-C system with Cas11c for plant genome editing. The Dvu I-C system was efficient to introduce controllable large fragment deletion up to at least 20 kb using paired crRNAs. The paired-crRNAs design also improved the controllability of deletions for the type I-E system. Dvu I-C system was sensitive to spacer length and mismatch, which was benefit for target specificity. In addition, we showed that the Dvu I-C system was efficient for generating stable transgenic lines in maize and rice with the editing efficiency up to 86.67%. Overall, Dvu I-C system we developed here is powerful for achieving controllable large fragment deletions.
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Affiliation(s)
- Yingnan Li
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Boyu Huang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jian Chen
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Liangliang Huang
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Jianghai Xu
- College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Yingying Wang
- College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Guanghui Cui
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Haiming Zhao
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Beibei Xin
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Weibin Song
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Jian‐Kang Zhu
- Institute of Advanced Biotechnology and School of Life SciencesSouthern University of Science and TechnologyShenzhenChina
- Center for Advanced Bioindustry TechnologiesChinese Academy of Agricultural SciencesBeijingChina
| | - Jinsheng Lai
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
- Frontiers Science Center for Molecular Design BreedingChina Agricultural UniversityBeijingChina
- Center for Crop Functional Genomics and Molecular BreedingChina Agricultural UniversityBeijingChina
- Sanya Institute of China Agricultural UniversitySanyaChina
- Hainan Yazhou Bay Seed LaboratorySanyaChina
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28
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Bin Wang, Yuan C, Qie Y, Dang S. Long non-coding RNAs and pancreatic cancer: A multifaceted view. Biomed Pharmacother 2023; 167:115601. [PMID: 37774671 DOI: 10.1016/j.biopha.2023.115601] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/17/2023] [Accepted: 09/25/2023] [Indexed: 10/01/2023] Open
Abstract
Pancreatic cancer (PC) is a highly malignant disease with a 5-year survival rate of only 10%. Families with PC are at greater risk, as are type 2 diabetes, pancreatitis, and other factors. Insufficient early detection methods make this cancer have a poor prognosis. Additionally, the molecular mechanisms underlying PC development remain unclear. Increasing evidence suggests that long non-coding RNAs (lncRNAs) contribute to PC pathology,which may control gene expression by recruiting histone modification complexes to chromatin and interacting with proteins and RNAs. In recent studies, abnormal regulation of lncRNAs has been implicated in PC proliferation, metastasis, invasion, angiogenesis, apoptosis, and chemotherapy resistance suggesting potential clinical implications. The paper reviews the progress of lncRNA research in PC about diabetes mellitus, pancreatitis, cancer metastasis, tumor microenvironment regulation, and chemoresistance. Furthermore, lncRNAs may serve as potential therapeutic targets and biomarkers for PC diagnosis and prognosis. This will help improve PC patients' survival rate from a lncRNA perspective.
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Affiliation(s)
- Bin Wang
- General Surgery Department, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, Jiangsu 212000, China
| | - Chang Yuan
- General Surgery Department, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, Jiangsu 212000, China
| | - Yinyin Qie
- General Surgery Department, Yixing People's Hospital, Wuxi, Jiangsu 214200, China
| | - Shengchun Dang
- General Surgery Department, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, Jiangsu 212000, China; Siyang Hospital, Suqian, Jiangsu 223700, China.
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29
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Fadul SM, Arshad A, Mehmood R. CRISPR-based epigenome editing: mechanisms and applications. Epigenomics 2023; 15:1137-1155. [PMID: 37990877 DOI: 10.2217/epi-2023-0281] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
Abstract
Epigenomic anomalies contribute significantly to the development of numerous human disorders. The development of epigenetic research tools is essential for understanding how epigenetic marks contribute to gene expression. A gene-editing technique known as CRISPR (clustered regularly interspaced short palindromic repeats) typically targets a particular DNA sequence using a guide RNA (gRNA). CRISPR/Cas9 technology has been remodeled for epigenome editing by generating a 'dead' Cas9 protein (dCas9) that lacks nuclease activity and juxtaposing it with an epigenetic effector domain. Based on fusion partners of dCas9, a specific epigenetic state can be achieved. CRISPR-based epigenome editing has widespread application in drug screening, cancer treatment and regenerative medicine. This paper discusses the tools developed for CRISPR-based epigenome editing and their applications.
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Affiliation(s)
- Shaima M Fadul
- Department of Life Sciences, College of Science & General Studies, Alfaisal University, Riyadh, 11533, Kingdom of Saudi Arabia
| | - Aleeza Arshad
- Medical Teaching Insitute, Ayub Teaching Hospital, Abbottabad, 22020, Pakistan
| | - Rashid Mehmood
- Department of Life Sciences, College of Science & General Studies, Alfaisal University, Riyadh, 11533, Kingdom of Saudi Arabia
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Tao S, Hou Y, Diao L, Hu Y, Xu W, Xie S, Xiao Z. Long noncoding RNA study: Genome-wide approaches. Genes Dis 2023; 10:2491-2510. [PMID: 37554208 PMCID: PMC10404890 DOI: 10.1016/j.gendis.2022.10.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 10/09/2022] [Accepted: 10/23/2022] [Indexed: 11/30/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have been confirmed to play a crucial role in various biological processes across several species. Though many efforts have been devoted to the expansion of the lncRNAs landscape, much about lncRNAs is still unknown due to their great complexity. The development of high-throughput technologies and the constantly improved bioinformatic methods have resulted in a rapid expansion of lncRNA research and relevant databases. In this review, we introduced genome-wide research of lncRNAs in three parts: (i) novel lncRNA identification by high-throughput sequencing and computational pipelines; (ii) functional characterization of lncRNAs by expression atlas profiling, genome-scale screening, and the research of cancer-related lncRNAs; (iii) mechanism research by large-scale experimental technologies and computational analysis. Besides, primary experimental methods and bioinformatic pipelines related to these three parts are summarized. This review aimed to provide a comprehensive and systemic overview of lncRNA genome-wide research strategies and indicate a genome-wide lncRNA research system.
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Affiliation(s)
- Shuang Tao
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Yarui Hou
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Liting Diao
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Yanxia Hu
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Wanyi Xu
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Shujuan Xie
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
- Institute of Vaccine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Zhendong Xiao
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
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Ng M, Verboon L, Issa H, Bhayadia R, Vermunt MW, Winkler R, Schüler L, Alejo O, Schuschel K, Regenyi E, Borchert D, Heuser M, Reinhardt D, Yaspo ML, Heckl D, Klusmann JH. Myeloid leukemia vulnerabilities embedded in long noncoding RNA locus MYNRL15. iScience 2023; 26:107844. [PMID: 37766974 PMCID: PMC10520325 DOI: 10.1016/j.isci.2023.107844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 05/02/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
The noncoding genome presents a largely untapped source of new biological insights, including thousands of long noncoding RNA (lncRNA) loci. While lncRNA dysregulation has been reported in myeloid malignancies, their functional relevance remains to be systematically interrogated. We performed CRISPRi screens of lncRNA signatures from normal and malignant hematopoietic cells and identified MYNRL15 as a myeloid leukemia dependency. Functional dissection suggests an RNA-independent mechanism mediated by two regulatory elements embedded in the locus. Genetic perturbation of these elements triggered a long-range chromatin interaction and downregulation of leukemia dependency genes near the gained interaction sites, as well as overall suppression of cancer dependency pathways. Thus, this study describes a new noncoding myeloid leukemia vulnerability and mechanistic concept for myeloid leukemia. Importantly, MYNRL15 perturbation caused strong and selective impairment of leukemia cells of various genetic backgrounds over normal hematopoietic stem and progenitor cells in vitro, and depletion of patient-derived xenografts in vivo.
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Affiliation(s)
- Michelle Ng
- Department of Pediatric Hematology and Oncology, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Lonneke Verboon
- Department of Pediatrics, Goethe University Frankfurt, 60323 Frankfurt (Main), Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, 60323 Frankfurt (Main), Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hasan Issa
- Department of Pediatrics, Goethe University Frankfurt, 60323 Frankfurt (Main), Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, 60323 Frankfurt (Main), Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Raj Bhayadia
- Department of Pediatrics, Goethe University Frankfurt, 60323 Frankfurt (Main), Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, 60323 Frankfurt (Main), Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marit Willemijn Vermunt
- Department of Pediatrics, Goethe University Frankfurt, 60323 Frankfurt (Main), Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Robert Winkler
- Department of Pediatrics, Goethe University Frankfurt, 60323 Frankfurt (Main), Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, 60323 Frankfurt (Main), Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Leah Schüler
- Department of Pediatrics, Goethe University Frankfurt, 60323 Frankfurt (Main), Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, 60323 Frankfurt (Main), Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oriol Alejo
- Department of Pediatric Hematology and Oncology, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Konstantin Schuschel
- Department of Pediatrics, Goethe University Frankfurt, 60323 Frankfurt (Main), Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, 60323 Frankfurt (Main), Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Eniko Regenyi
- Department of Pediatric Hematology and Oncology, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Dorit Borchert
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Michael Heuser
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - Dirk Reinhardt
- Clinic for Pediatrics III, University Hospital Essen, 45147 Essen, Germany
| | - Marie-Laure Yaspo
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Dirk Heckl
- Institute for Experimental Pediatric Hematology and Oncology, Goethe University Frankfurt, 60323 Frankfurt (Main), Germany
| | - Jan-Henning Klusmann
- Department of Pediatrics, Goethe University Frankfurt, 60323 Frankfurt (Main), Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, 60323 Frankfurt (Main), Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany
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Wu P, Wang W. Distinct 3D contacts and phenotypic consequences of adjacent non-coding loci in the epigenetically quiescent regions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.11.557110. [PMID: 37745584 PMCID: PMC10515877 DOI: 10.1101/2023.09.11.557110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Non-coding regions of the human genome are important for functional regulations, but their mechanisms remain elusive. We used machine learning to guide a CRISPR screening on hubs (i.e. non-coding loci forming many 3D contacts) and significantly increased the discovery rate of hubs essential for cell growth. We found no clear genetic or epigenetic differences between essential and nonessential hubs, but we observed that some neighboring hubs in the linear genome have distinct spatial contacts and opposite effects on cell growth. One such pair in an epigenetically quiescent region showed different impacts on gene expression, chromatin accessibility and chromatin organization. We also found that deleting the essential hub altered the genetic network activity and increased the entropy of chromatin accessibility, more severe than that caused by deletion of the nonessential hub, suggesting that they are critical for maintaining an ordered chromatin structure. Our study reveals new insights into the system-level roles of non-coding regions in the human genome.
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Affiliation(s)
- Peiyao Wu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0359
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0359
- Bioinformatics and Systems Biology program, University of California, San Diego, La Jolla, CA 92093-0359
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0359
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Farzaneh M, Abouali Gale Dari M, Anbiyaiee A, Najafi S, Dayer D, Mousavi Salehi A, Keivan M, Ghafourian M, Uddin S, Azizidoost S. Emerging roles of the long non-coding RNA NEAT1 in gynecologic cancers. J Cell Commun Signal 2023; 17:531-547. [PMID: 37310654 PMCID: PMC10409959 DOI: 10.1007/s12079-023-00746-x] [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: 10/27/2022] [Accepted: 04/10/2023] [Indexed: 06/14/2023] Open
Abstract
Gynecologic cancers are a worldwide problem among women. Recently, molecular targeted therapy opened up an avenue for cancer diagnosis and treatment. Long non-coding RNAs (lncRNAs) are RNA molecules (> 200 nt) that are not translated into protein, and interact with DNA, RNA, and proteins. LncRNAs were found to play pivotal roles in cancer tumorigenesis and progression. Nuclear paraspeckle assembly transcript 1 (NEAT1) is a lncRNA that mediates cell proliferation, migration, and EMT in gynecologic cancers by targeting several miRNAs/mRNA axes. Therefore, NEAT1 may function as a potent biomarker for the prediction and treatment of breast, ovarian, cervical, and endometrial cancers. In this narrative review, we summarized various NEAT1-related signaling pathways that are critical in gynecologic cancers. Long non-coding RNA (lncRNA) by targeting various signaling pathways involved in its target genes can regulate the occurrence of gynecologic cancers.
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Affiliation(s)
- Maryam Farzaneh
- Fertility, Infertility and Perinatology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mahrokh Abouali Gale Dari
- Department of Obstetrics and Gynecology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Amir Anbiyaiee
- Department of Surgery, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Dian Dayer
- Fertility and Infertility Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Abdolah Mousavi Salehi
- Cellular and Molecular Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mona Keivan
- Department of Immunology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mehri Ghafourian
- Fertility, Infertility and Perinatology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Cellular and Molecular Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Shahab Uddin
- Translational Research Institute and Dermatology Institute, Academic Health System, Hamad Medical Corporation, 3050, Doha, Qatar
- Department of Biosciences, Integral University, Lucknow, Uttar Pradesh 22602 India
| | - Shirin Azizidoost
- Atherosclerosis Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Lyu QR, Zhang S, Zhang Z, Tang Z. Functional knockout of long non-coding RNAs with genome editing. Front Genet 2023; 14:1242129. [PMID: 37705609 PMCID: PMC10495571 DOI: 10.3389/fgene.2023.1242129] [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: 06/18/2023] [Accepted: 08/16/2023] [Indexed: 09/15/2023] Open
Abstract
An effective loss-of-function study is necessary to investigate the biological function of long non-coding RNA (lncRNA). Various approaches are available, including RNA silencing, antisense oligos, and CRISPR-based genome editing. CRISPR-based genome editing is the most widely used for inactivating lncRNA function at the genomic level. Knocking out the lncRNA function can be achieved by removing the promoter and the first exon (PE1), introducing pre-termination poly(A) signals, or deleting the entire locus, unlike frameshift strategies used for messenger RNA (mRNA). However, the intricate genomic interplay between lncRNA and neighbor genes makes it challenging to interpret lncRNA function accurately. This article discusses the advantages and disadvantages of each lncRNA knockout method and envisions the potential future directions to facilitate lncRNA functional study.
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Affiliation(s)
- Qing Rex Lyu
- Medical Research Center, Chongqing General Hospital, Chongqing, China
- Chongqing Academy of Medical Sciences, Chongqing, China
| | - Shikuan Zhang
- Key Lab in Healthy Science and Technology of Shenzhen, Tsinghua Shenzhen International Graduate School, Shenzhen, China
| | - Zhe Zhang
- Department of Chinese Medical Gastrointestinal of China-Japan Friendship Hospital, Beijing, China
| | - Zhiyu Tang
- Medical Research Center, Chongqing General Hospital, Chongqing, China
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35
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Ahmad M, Weiswald LB, Poulain L, Denoyelle C, Meryet-Figuiere M. Involvement of lncRNAs in cancer cells migration, invasion and metastasis: cytoskeleton and ECM crosstalk. J Exp Clin Cancer Res 2023; 42:173. [PMID: 37464436 PMCID: PMC10353155 DOI: 10.1186/s13046-023-02741-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/26/2023] [Indexed: 07/20/2023] Open
Abstract
Cancer is the main cause of death worldwide and metastasis is a major cause of poor prognosis and cancer-associated mortality. Metastatic conversion of cancer cells is a multiplex process, including EMT through cytoskeleton remodeling and interaction with TME. Tens of thousands of putative lncRNAs have been identified, but the biological functions of most are still to be identified. However, lncRNAs have already emerged as key regulators of gene expression at transcriptional and post-transcriptional level to control gene expression in a spatio-temporal fashion. LncRNA-dependent mechanisms can control cell fates during development and their perturbed expression is associated with the onset and progression of many diseases including cancer. LncRNAs have been involved in each step of cancer cells metastasis through different modes of action. The investigation of lncRNAs different roles in cancer metastasis could possibly lead to the identification of new biomarkers and innovative cancer therapeutic options.
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Affiliation(s)
- Mohammad Ahmad
- (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Baclesse Cancer Centre, Université de Caen Normandie Inserm Anticipe UMR 1086, Normandie Univ, Research Building, F-14000 François 3 Avenue Général Harris, BP 45026, 14 076, cedex 05, Caen, France
- Comprehensive Cancer Center François Baclesse, UNICANCER, Caen, France
- Biochemistry Division, Chemistry Department, Faculty of Science, Damanhour University, Damanhour, 14000, Egypt
| | - Louis-Bastien Weiswald
- (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Baclesse Cancer Centre, Université de Caen Normandie Inserm Anticipe UMR 1086, Normandie Univ, Research Building, F-14000 François 3 Avenue Général Harris, BP 45026, 14 076, cedex 05, Caen, France
- Comprehensive Cancer Center François Baclesse, UNICANCER, Caen, France
| | - Laurent Poulain
- (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Baclesse Cancer Centre, Université de Caen Normandie Inserm Anticipe UMR 1086, Normandie Univ, Research Building, F-14000 François 3 Avenue Général Harris, BP 45026, 14 076, cedex 05, Caen, France
- Comprehensive Cancer Center François Baclesse, UNICANCER, Caen, France
| | - Christophe Denoyelle
- (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Baclesse Cancer Centre, Université de Caen Normandie Inserm Anticipe UMR 1086, Normandie Univ, Research Building, F-14000 François 3 Avenue Général Harris, BP 45026, 14 076, cedex 05, Caen, France
- Comprehensive Cancer Center François Baclesse, UNICANCER, Caen, France
| | - Matthieu Meryet-Figuiere
- (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Baclesse Cancer Centre, Université de Caen Normandie Inserm Anticipe UMR 1086, Normandie Univ, Research Building, F-14000 François 3 Avenue Général Harris, BP 45026, 14 076, cedex 05, Caen, France.
- Comprehensive Cancer Center François Baclesse, UNICANCER, Caen, France.
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Iaffaldano BJ, Marino MP, Reiser J. CRISPR library screening to develop HEK293-derived cell lines with improved lentiviral vector titers. Front Genome Ed 2023; 5:1218328. [PMID: 37520398 PMCID: PMC10373892 DOI: 10.3389/fgeed.2023.1218328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 07/03/2023] [Indexed: 08/01/2023] Open
Abstract
Lentiviral (LV) vectors have emerged as powerful tools for treating genetic and acquired human diseases. As clinical studies and commercial demands have progressed, there has been a growing need for large amounts of purified LV vectors. To help meet this demand, we developed CRISPR library screening methods to identify genetic perturbations in human embryonic kidney 293 (HEK293) cells and their derivatives that may increase LV vector titers. Briefly, LV vector-based Human CRISPR Activation and Knockout libraries (Calabrese and Brunello) were used to modify HEK293 and HEK293T cells. These cell populations were then expanded, and integrated LV vector genomes were rescued by transfection. LV vectors were harvested, and the process of sequential transduction and rescue-transfection was iterated. Through this workflow, guide RNAs (gRNAs) that target genes that may suppress or enhance LV vector production were enriched and identified with Next-Generation Sequencing (NGS). Though more work is needed to test genes identified in this screen, we expect that perturbations of genes we identified here, such as TTLL12, which is an inhibitor of antiviral innate immunity may be introduced and multiplexed to yield cell lines with improved LV vector productivity.
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Yang F, Li J, Ge Q, Zhang Y, Zhang M, Zhou J, Wang H, Du J, Gao S, Liang C, Meng J. Non-coding RNAs: emerging roles in the characterization of immune microenvironment and immunotherapy of prostate cancer. Biochem Pharmacol 2023:115669. [PMID: 37364622 DOI: 10.1016/j.bcp.2023.115669] [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: 02/10/2023] [Revised: 06/17/2023] [Accepted: 06/20/2023] [Indexed: 06/28/2023]
Abstract
Prostate cancer is the most common tumor among men. Although the prognosis for early-stage prostate cancer is good, patients with advanced disease often progress to metastatic castration-resistant prostate cancer (mCRPC), which usually leads to death owing to resistance to existing treatments and lack of long-term effective therapy. In recent years, immunotherapy, especially immune checkpoint inhibitors (ICIs), has made great progress in the treatment of various solid tumors, including prostate cancer. However, the ICIs have only shown modest outcomes in mCRPC compared with other tumors. Previous studies have suggested that the suppressive tumor immune microenvironment (TIME) of prostate cancer leads to poor anti-tumor immune response and tumor resistance to immunotherapy. It has been reported that non-coding RNAs (ncRNAs) are capable of regulating upstream signaling at the transcriptional level, leading to a "cascade of changes" in downstream molecules. As a result, ncRNAs have been identified as an ideal class of molecules for cancer treatment. The discovery of ncRNAs provides a new perspective on TIME regulation in prostate cancer. ncRNAs have been associated with establishing an immunosuppressive microenvironment in prostate cancer through multiple pathways to modulate the immune escape of tumor cells which can promote resistance of prostate cancer to immunotherapy. Targeting these related ncRNAs presents an opportunity to improve the effectiveness of immunotherapy in this patient population.
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Affiliation(s)
- Feixiang Yang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei 230022, China.
| | - Jiawei Li
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei 230022, China
| | - Qintao Ge
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei 230022, China
| | - Yuchen Zhang
- First School of Clinical Medicine, Anhui Medical University, Hefei 230022, China.
| | - Meng Zhang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei 230022, China
| | - Jun Zhou
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei 230022, China
| | - Haitao Wang
- Center for Cancer Research, Clinical Research/NCI/NIH, Bethesda, MD 20892, USA
| | - Juan Du
- The Second Affiliated Hospital, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, Guangdong, China.
| | - Shenglin Gao
- Department of Urology, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou 213003, Jiangsu, China; Gonghe County Hospital of Traditional Chinese Medicine, Hainan 813099, Qinghai, China
| | - Chaozhao Liang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei 230022, China
| | - Jialin Meng
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei 230022, China.
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Pal A, Ghosh PK, Das S. The "LINC" between Δ40p53-miRNA Axis in the Regulation of Cellular Homeostasis. Mol Cell Biol 2023; 43:335-353. [PMID: 37283188 PMCID: PMC10348045 DOI: 10.1080/10985549.2023.2213147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 04/25/2023] [Indexed: 06/08/2023] Open
Abstract
Previous research has shown that Δ40p53, the translational isoform of p53, can inhibit cell growth independently of p53 by regulating microRNAs. Here, we explored the role of Δ40p53 in regulating the long noncoding RNA-micro-RNA-cellular process axis, specifically focusing on LINC00176. Interestingly, LINC00176 levels were predominantly affected by the overexpression/stress-mediated induction and knockdown of Δ40p53 rather than p53 levels. Additional assays revealed that Δ40p53 transactivates LINC00176 transcriptionally and could also regulate its stability. RNA immunoprecipitation experiments revealed that LINC00176 sequesters several putative microRNA targets, which could further titrate several mRNA targets involved in different cellular processes. To understand the downstream effects of this regulation, we ectopically overexpressed and knocked down LINC00176 in HCT116 p53-/- (harboring only Δ40p53) cells, which affected their proliferation, cell viability, and expression of epithelial markers. Our results provide essential insights into the pivotal role of Δ40p53 in regulating the novel LINC00176 RNA-microRNA-mRNA axis independent of FL-p53 and in maintaining cellular homeostasis.
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Affiliation(s)
- Apala Pal
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Pritam Kumar Ghosh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Saumitra Das
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
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Rafat M, Kohsarian M, Bahiraei M, Nikpoor AR. A Comprehensive Study on Signal Transduction and Therapeutic Role of miR-877 in Human Cancers. Adv Biomed Res 2023; 12:118. [PMID: 37434921 PMCID: PMC10331537 DOI: 10.4103/abr.abr_412_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 05/07/2022] [Accepted: 05/16/2022] [Indexed: 07/13/2023] Open
Abstract
MicroRNAs are a group of short non-coding RNAs (miRNAs), which are epigenetically involved in gene expression and other cellular biological processes and can be considered as potential biomarkers for cancer detection and support for treatment management. This review aims to amass the evidence in order to reach the molecular mechanism and clinical significance of miR-877 in different types of cancer. Dysregulation of miR-877 level in various types of malignancies as bladder cancer, cervical cancer, cholangiocarcinoma, colorectal cancer (CRC), gastric cancer, glioblastoma, head and neck squamous cell carcinoma (HNSCC), hepatocellular carcinoma, laryngeal squamous cell carcinoma, melanoma, non-small cell lung cancer (NSCLC), oral squamous cell carcinoma, ovarian cancer (OC), pancreatic ductal adenocarcinoma, and renal cell carcinoma (RCC) have reported, significantly increase or decrease in its level, which can be indicated to its function as oncogene or tumor suppressor. MiR-877 is involved in cell proliferation, migration, and invasion through cell cycle pathways in cancer. MiR-877 could be potential a candidate as a valuable biomarker for prognosis in various cancers. Through this study, we proposed that miR-877 can potentially be a candidate as a prognostic marker for early detection of tumor development, progression, as well as metastasis.
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Affiliation(s)
- Milad Rafat
- Student Research Committee, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Mahdis Kohsarian
- Department of Biology, Faculty of Science, Guilan University, Rasht, Iran
| | - Mohamad Bahiraei
- Department of Radiology, Besat Hospital, Hamedan University of Medical Sciences, Hamedan, Iran
| | - Amin R. Nikpoor
- Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
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Guo R, Su Y, Zhang Q, Xiu B, Huang S, Chi W, Zhang L, Li L, Hou J, Wang J, Chen J, Chi Y, Xue J, Wu J. LINC00478-derived novel cytoplasmic lncRNA LacRNA stabilizes PHB2 and suppresses breast cancer metastasis via repressing MYC targets. J Transl Med 2023; 21:120. [PMID: 36782197 PMCID: PMC9926633 DOI: 10.1186/s12967-023-03967-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 02/04/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND Metastasis is the predominant cause of mortality in patients with breast cancer. Long noncoding RNAs (lncRNAs) have been shown to drive important phenotypes in tumors, including invasion and metastasis. However, the lncRNAs involved in metastasis and their molecular and cellular mechanisms are still largely unknown. METHODS The transcriptional and posttranscriptional processing of LINC00478-associated cytoplasmic RNA (LacRNA) was determined by RT-qPCR, semiquantitative PCR and 5'/3' RACE. Paired-guide CRISPR/cas9 and CRISPR/dead-Cas9 systems was used to knock out or activate the expression of LacRNA. Cell migration and invasion assay was performed to confirm the phenotype of LacRNA. Tail vein model and mammary fat pad model were used for in vivo study. The LacRNA-PHB2-cMyc axis were screened and validated by RNA pulldown, mass spectrometry, RNA immunoprecipitation and RNA-seq assays. RESULTS Here, we identified a novel cytoplasmic lncRNA, LacRNA (LINC00478-associated cytoplasmic RNA), derived from nucleus-located lncRNA LINC00478. The nascent transcript of LINC00478 full-length (LINC00478_FL) was cleaved and polyadenylated, simultaneously yielding 5' ends stable expressing LacRNA, which is released into the cytoplasm, and long 3' ends of nuclear-retained lncRNA. LINC00478_3'RNA was rapidly degraded. LacRNA significantly inhibited breast cancer invasion and metastasis in vitro and in vivo. Mechanistically, LacRNA physically interacted with the PHB domain of PHB2 through its 61-140-nt region. This specific binding affected the formation of the autophagy degradation complex of PHB2 and LC3, delaying the degradation of the PHB2 protein. Unexpectedly, LacRNA specifically interacted with PHB2, recruited c-Myc and promoted c-Myc ubiquitination and degradation. The negatively regulation of Myc signaling ultimately inhibited breast cancer metastasis. Furthermore, LacRNA and LacRNA-mediated c-Myc signaling downregulation are significantly associated with good clinical outcomes, take advantage of these factors we constructed a prognostic predict model. CONCLUSION Therefore, our findings propose LacRNA as a potential prognostic biomarker and a new therapeutic strategy.
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Affiliation(s)
- Rong Guo
- grid.452404.30000 0004 1808 0942Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032 People’s Republic of China ,Department of Breast Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, 650000 People’s Republic of China ,grid.11841.3d0000 0004 0619 8943Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 People’s Republic of China
| | - Yonghui Su
- grid.452404.30000 0004 1808 0942Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032 People’s Republic of China ,grid.11841.3d0000 0004 0619 8943Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 People’s Republic of China
| | - Qi Zhang
- grid.452404.30000 0004 1808 0942Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032 People’s Republic of China ,grid.11841.3d0000 0004 0619 8943Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 People’s Republic of China
| | - Bingqiu Xiu
- grid.452404.30000 0004 1808 0942Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032 People’s Republic of China ,grid.11841.3d0000 0004 0619 8943Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 People’s Republic of China
| | - Sheng Huang
- grid.452404.30000 0004 1808 0942Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032 People’s Republic of China ,Department of Breast Surgery, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, Kunming, 650000 People’s Republic of China ,grid.11841.3d0000 0004 0619 8943Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 People’s Republic of China
| | - Weiru Chi
- grid.452404.30000 0004 1808 0942Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032 People’s Republic of China ,grid.11841.3d0000 0004 0619 8943Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 People’s Republic of China
| | - Liyi Zhang
- grid.452404.30000 0004 1808 0942Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032 People’s Republic of China ,grid.11841.3d0000 0004 0619 8943Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 People’s Republic of China
| | - Lun Li
- grid.452404.30000 0004 1808 0942Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032 People’s Republic of China ,grid.11841.3d0000 0004 0619 8943Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 People’s Republic of China
| | - Jianjing Hou
- grid.452404.30000 0004 1808 0942Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032 People’s Republic of China ,grid.11841.3d0000 0004 0619 8943Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 People’s Republic of China
| | - Jia Wang
- grid.452404.30000 0004 1808 0942Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032 People’s Republic of China ,grid.11841.3d0000 0004 0619 8943Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 People’s Republic of China
| | - Jiajian Chen
- grid.452404.30000 0004 1808 0942Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032 People’s Republic of China ,grid.11841.3d0000 0004 0619 8943Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 People’s Republic of China
| | - Yayun Chi
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, People's Republic of China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China.
| | - Jingyan Xue
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, People's Republic of China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China.
| | - Jiong Wu
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, People's Republic of China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, People's Republic of China.
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Fang Z, Fan M, Yuan D, Jin L, Wang Y, Ding L, Xu S, Tu J, Zhang E, Wu X, Chen ZB, Huang W. Downregulation of hepatic lncRNA Gm19619 improves gluconeogenesis and lipogenesis following vertical sleeve gastrectomy in mice. Commun Biol 2023; 6:105. [PMID: 36707678 PMCID: PMC9883214 DOI: 10.1038/s42003-023-04483-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 01/13/2023] [Indexed: 01/28/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are emerging important epigenetic regulators in metabolic processes. Whether they contribute to the metabolic effects of vertical sleeve gastrectomy (VSG), one of the most effective treatments for sustainable weight loss and metabolic improvement, is unknown. Herein, we identify a hepatic lncRNA Gm19619, which is strongly repressed by VSG but highly up-regulated by diet-induced obesity and overnight-fasting in mice. Forced transcription of Gm19619 in the mouse liver significantly promotes hepatic gluconeogenesis with the elevated expression of G6pc and Pck1. In contrast, AAV-CasRx mediated knockdown of Gm19619 in high-fat diet-fed mice significantly improves hepatic glucose and lipid metabolism. Mechanistically, Gm19619 is enriched along genomic regions encoding leptin receptor (Lepr) and transcription factor Foxo1, as revealed in chromatin isolation by RNA purification (ChIRP) assay and is confirmed to modulate their transcription in the mouse liver. In conclusion, Gm19619 may enhance gluconeogenesis and lipid accumulation in the liver.
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Affiliation(s)
- Zhipeng Fang
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Mingjie Fan
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
- Department of Pediatric, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Dongqiang Yuan
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Lihua Jin
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Yangmeng Wang
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Lili Ding
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Senlin Xu
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
- Irell & Manella Graduate School of Biological Science, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Jui Tu
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
- Irell & Manella Graduate School of Biological Science, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Eryun Zhang
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Xiwei Wu
- Integrated Genomic Core, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Zhen Bouman Chen
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
- Irell & Manella Graduate School of Biological Science, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Wendong Huang
- Department of Diabetes Complications and Metabolism, Arthur Riggs-Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA.
- Irell & Manella Graduate School of Biological Science, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA.
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Furtado CLM, da Silva Santos R, Sales SLA, Teixeira LPR, Pessoa CDÓ. Long Non-coding RNAs and CRISPR-Cas Edition in Tumorigenesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1429:41-58. [PMID: 37486515 DOI: 10.1007/978-3-031-33325-5_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Long non-coding RNAs (lncRNAs) are one of the most abundant and heterogeneous transcripts with key roles in chromatin remodeling and gene regulation at the transcriptional and post-transcriptional levels. Due to their role in cell growth and differentiation, lncRNAs have emerged as an important biomarker in cancer diagnosis, prognosis, and targeted treatment. Recent studies have focused on elucidating lncRNA function during malignant transformation, tumor progression and drug resistance. The advent of the CRISPR system has made it possible to precisely edit complex genomic loci such as lncRNAs. Thus, we summarized the advances in CRISPR-Cas approaches for functional studies of lncRNAs including gene knockout, knockdown, overexpression and RNA targeting in tumorigenesis and drug resistance. Additionally, we highlighted the perspectives and potential applications of CRISPR approaches to treat cancer, as an emerging and promising target therapy.
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Affiliation(s)
- Cristiana Libardi Miranda Furtado
- University of Fortaleza, Experimental Biology Center, Fortaleza, Ceara, Brazil.
- Drug Research and Development Center, Postgraduate Program in Translational Medicine, Federal University of Ceara, Fortaleza, Brazil.
| | - Renan da Silva Santos
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceara, Fortaleza, Brazil
| | - Sarah Leyenne Alves Sales
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceara, Fortaleza, Brazil
| | | | - Claudia do Ó Pessoa
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceara, Fortaleza, Brazil
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He L, He Z, Li Y, Sun H, Wang H. In Vivo Investigation of Gene Function in Muscle Stem Cells by CRISPR/Cas9-Mediated Genome Editing. Methods Mol Biol 2023; 2640:287-311. [PMID: 36995603 DOI: 10.1007/978-1-0716-3036-5_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Skeletal muscle satellite cells (SCs) are adult stem cells responsible for muscle development and injury-induced muscle regeneration. Functional elucidation of intrinsic regulatory factors governing SC activity is constrained partially by the technological limitations in editing SCs in vivo. Although the power of CRISPR/Cas9 in genome manipulation has been widely documented, its application in endogenous SCs remains largely untested. Our recent study generates a muscle-specific genome editing system leveraging the Cre-dependent Cas9 knockin mice and AAV9-mediated sgRNAs delivery, which allows gene disruption in SCs in vivo. Here, we illustrate the step-by-step procedure for achieving efficient editing using the above system.
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Affiliation(s)
- Liangqiang He
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Zhiming He
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yuying Li
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Hao Sun
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Huating Wang
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.
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Kretzmer C, Narasimhan RL, Lal RD, Balassi V, Ravellette J, Kotekar Manjunath AK, Koshy JJ, Viano M, Torre S, Zanda VM, Kumravat M, Saldanha KMR, Chandranpillai H, Nihad I, Zhong F, Sun Y, Gustin J, Borgschulte T, Liu J, Razafsky D. De novo assembly and annotation of the CHOZN® GS -/- genome supports high-throughput genome-scale screening. Biotechnol Bioeng 2022; 119:3632-3646. [PMID: 36073082 PMCID: PMC9825924 DOI: 10.1002/bit.28226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/20/2022] [Accepted: 08/28/2022] [Indexed: 01/11/2023]
Abstract
Chinese hamster ovary (CHO) cells have been used as the industry standard for the production of therapeutic monoclonal antibodies for several decades. Despite significant improvements in commercial-scale production processes and media, the CHO cell has remained largely unchanged. Due to the cost and complexity of whole-genome sequencing and gene-editing it has been difficult to obtain the tools necessary to improve the CHO cell line. With the advent of next-generation sequencing and the discovery of the CRISPR/Cas9 system it has become more cost effective to sequence and manipulate the CHO genome. Here, we provide a comprehensive de novo assembly and annotation of the CHO-K1 based CHOZN® GS-/- genome. Using this platform, we designed, built, and confirmed the functionality of a whole genome CRISPR guide RNA library that will allow the bioprocessing community to design a more robust CHO cell line leading to the production of life saving medications in a more cost-effective manner.
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Affiliation(s)
- Corey Kretzmer
- Upstream Research and Development, MilliporeSigmaSt. LouisMissouriUSA
| | - Rajagopalan Lakshmi Narasimhan
- Bioinformatics, IT R&D Applications, Merck (Sigma‐Aldrich Chemicals Pvt. Ltd., A subsidiary of Merck KGaA, Darmstadt, Germany)BangaloreIndia
| | - Rahul Deva Lal
- Bioinformatics, IT R&D Applications, Merck (Sigma‐Aldrich Chemicals Pvt. Ltd., A subsidiary of Merck KGaA, Darmstadt, Germany)BangaloreIndia
| | - Vincent Balassi
- Upstream Research and Development, MilliporeSigmaSt. LouisMissouriUSA
| | - James Ravellette
- Upstream Research and Development, MilliporeSigmaSt. LouisMissouriUSA
| | - Ajaya Kumar Kotekar Manjunath
- Bioinformatics, IT R&D Applications, Merck (Sigma‐Aldrich Chemicals Pvt. Ltd., A subsidiary of Merck KGaA, Darmstadt, Germany)BangaloreIndia
| | - Jesvin Joy Koshy
- Bioinformatics, IT R&D Applications, Merck (Sigma‐Aldrich Chemicals Pvt. Ltd., A subsidiary of Merck KGaA, Darmstadt, Germany)BangaloreIndia
| | - Marta Viano
- Istituto di Ricerche Biomediche “A. Marxer” RBM S.p.A.IvreaItaly
| | - Serena Torre
- Istituto di Ricerche Biomediche “A. Marxer” RBM S.p.A.IvreaItaly
| | - Valeria M. Zanda
- Istituto di Ricerche Biomediche “A. Marxer” RBM S.p.A.IvreaItaly
| | - Mausam Kumravat
- Bioinformatics, IT R&D Applications, Merck (Sigma‐Aldrich Chemicals Pvt. Ltd., A subsidiary of Merck KGaA, Darmstadt, Germany)BangaloreIndia
| | - Keith Metelo Raul Saldanha
- Bioinformatics, IT R&D Applications, Merck (Sigma‐Aldrich Chemicals Pvt. Ltd., A subsidiary of Merck KGaA, Darmstadt, Germany)BangaloreIndia
| | - Harikrishnan Chandranpillai
- Bioinformatics, IT R&D Applications, Merck (Sigma‐Aldrich Chemicals Pvt. Ltd., A subsidiary of Merck KGaA, Darmstadt, Germany)BangaloreIndia
| | - Ifra Nihad
- Bioinformatics, IT R&D Applications, Merck (Sigma‐Aldrich Chemicals Pvt. Ltd., A subsidiary of Merck KGaA, Darmstadt, Germany)BangaloreIndia
| | - Fei Zhong
- Life Science Bioinformatics, IT, MilliporeSigmaSt. LouisMissouriUSA
| | - Yi Sun
- Bioinformatics, IT R&D Applications, MilliporeSigmaSt. LouisMissouriUSA
| | - Jason Gustin
- Upstream Research and Development, MilliporeSigmaSt. LouisMissouriUSA
| | | | - Jiajian Liu
- Life Science Bioinformatics, IT, MilliporeSigmaSt. LouisMissouriUSA
| | - David Razafsky
- Upstream Research and Development, MilliporeSigmaSt. LouisMissouriUSA
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Glycation-Associated Diabetic Nephropathy and the Role of Long Noncoding RNAs. Biomedicines 2022; 10:biomedicines10102623. [PMID: 36289886 PMCID: PMC9599575 DOI: 10.3390/biomedicines10102623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/12/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022] Open
Abstract
The glycation of various biomolecules is the root cause of many pathological conditions associated with diabetic nephropathy and end-stage kidney disease. Glycation imbalances metabolism and increases renal cell injury. Numerous therapeutic measures have narrowed down the adverse effects of endogenous glycation, but efficient and potent measures are miles away. Recent advances in the identification and characterization of noncoding RNAs, especially the long noncoding RNAs (lncRNAs), have opened a mammon of new biology to explore the mitigations for glycation-associated diabetic nephropathy. Furthermore, tissue-specific distribution and condition-specific expression make lncRNA a promising key for second-generation therapeutic interventions. Though the techniques to identify and exemplify noncoding RNAs are rapidly evolving, the lncRNA study encounters multiple methodological constraints. This review will discuss lncRNAs and their possible involvement in glycation and advanced glycation end products (AGEs) signaling pathways. We further highlight the possible approaches for lncRNA-based therapeutics and their working mechanism for perturbing glycation and conclude our review with lncRNAs biology-related future opportunities.
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Rittiner J, Cumaran M, Malhotra S, Kantor B. Therapeutic modulation of gene expression in the disease state: Treatment strategies and approaches for the development of next-generation of the epigenetic drugs. Front Bioeng Biotechnol 2022; 10:1035543. [PMID: 36324900 PMCID: PMC9620476 DOI: 10.3389/fbioe.2022.1035543] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/05/2022] [Indexed: 11/18/2022] Open
Abstract
Epigenetic dysregulation is an important determinant of many pathological conditions and diseases. Designer molecules that can specifically target endogenous DNA sequences provide a means to therapeutically modulate gene function. The prokaryote-derived CRISPR/Cas editing systems have transformed our ability to manipulate the expression program of genes through specific DNA and RNA targeting in living cells and tissues. The simplicity, utility, and robustness of this technology have revolutionized epigenome editing for research and translational medicine. Initial success has inspired efforts to discover new systems for targeting and manipulating nucleic acids on the epigenetic level. The evolution of nuclease-inactive and RNA-targeting Cas proteins fused to a plethora of effector proteins to regulate gene expression, epigenetic modifications and chromatin interactions opened up an unprecedented level of possibilities for the development of “next-generation” gene therapy therapeutics. The rational design and construction of different types of designer molecules paired with viral-mediated gene-to-cell transfers, specifically using lentiviral vectors (LVs) and adeno-associated vectors (AAVs) are reviewed in this paper. Furthermore, we explore and discuss the potential of these molecules as therapeutic modulators of endogenous gene function, focusing on modulation by stable gene modification and by regulation of gene transcription. Notwithstanding the speedy progress of CRISPR/Cas-based gene therapy products, multiple challenges outlined by undesirable off-target effects, oncogenicity and other virus-induced toxicities could derail the successful translation of these new modalities. Here, we review how CRISPR/Cas—based gene therapy is translated from research-grade technological system to therapeutic modality, paying particular attention to the therapeutic flow from engineering sophisticated genome and epigenome-editing transgenes to delivery vehicles throughout efficient and safe manufacturing and administration of the gene therapy regimens. In addition, the potential solutions to some of the obstacles facing successful CRISPR/Cas utility in the clinical research are discussed in this review. We believe, that circumventing these challenges will be essential for advancing CRISPR/Cas-based tools towards clinical use in gene and cell therapies.
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Affiliation(s)
- Joseph Rittiner
- Department of Neurobiology, Duke University Medical Center, Durham, NC, United States
- Viral Vector Core, Duke University Medical Center, Durham, NC, United States
- Duke Center for Advanced Genomic Technologies, Durham, NC, United States
| | - Mohanapriya Cumaran
- Department of Neurobiology, Duke University Medical Center, Durham, NC, United States
- Viral Vector Core, Duke University Medical Center, Durham, NC, United States
- Duke Center for Advanced Genomic Technologies, Durham, NC, United States
| | - Sahil Malhotra
- Department of Neurobiology, Duke University Medical Center, Durham, NC, United States
- Viral Vector Core, Duke University Medical Center, Durham, NC, United States
- Duke Center for Advanced Genomic Technologies, Durham, NC, United States
| | - Boris Kantor
- Department of Neurobiology, Duke University Medical Center, Durham, NC, United States
- Viral Vector Core, Duke University Medical Center, Durham, NC, United States
- Duke Center for Advanced Genomic Technologies, Durham, NC, United States
- *Correspondence: Boris Kantor,
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Allemailem KS, Alsahli MA, Almatroudi A, Alrumaihi F, Alkhaleefah FK, Rahmani AH, Khan AA. Current updates of CRISPR/Cas9-mediated genome editing and targeting within tumor cells: an innovative strategy of cancer management. CANCER COMMUNICATIONS (LONDON, ENGLAND) 2022; 42:1257-1287. [PMID: 36209487 PMCID: PMC9759771 DOI: 10.1002/cac2.12366] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 05/19/2022] [Accepted: 09/21/2022] [Indexed: 01/25/2023]
Abstract
Clustered regularly interspaced short palindromic repeats-associated protein (CRISPR/Cas9), an adaptive microbial immune system, has been exploited as a robust, accurate, efficient and programmable method for genome targeting and editing. This innovative and revolutionary technique can play a significant role in animal modeling, in vivo genome therapy, engineered cell therapy, cancer diagnosis and treatment. The CRISPR/Cas9 endonuclease system targets a specific genomic locus by single guide RNA (sgRNA), forming a heteroduplex with target DNA. The Streptococcus pyogenes Cas9/sgRNA:DNA complex reveals a bilobed architecture with target recognition and nuclease lobes. CRISPR/Cas9 assembly can be hijacked, and its nanoformulation can be engineered as a delivery system for different clinical utilizations. However, the efficient and safe delivery of the CRISPR/Cas9 system to target tissues and cancer cells is very challenging, limiting its clinical utilization. Viral delivery strategies of this system may have many advantages, but disadvantages such as immune system stimulation, tumor promotion risk and small insertion size outweigh these advantages. Thus, there is a desperate need to develop an efficient non-viral physical delivery system based on simple nanoformulations. The delivery strategies of CRISPR/Cas9 by a nanoparticle-based system have shown tremendous potential, such as easy and large-scale production, combination therapy, large insertion size and efficient in vivo applications. This review aims to provide in-depth updates on Streptococcus pyogenic CRISPR/Cas9 structure and its mechanistic understanding. In addition, the advances in its nanoformulation-based delivery systems, including lipid-based, polymeric structures and rigid NPs coupled to special ligands such as aptamers, TAT peptides and cell-penetrating peptides, are discussed. Furthermore, the clinical applications in different cancers, clinical trials and future prospects of CRISPR/Cas9 delivery and genome targeting are also discussed.
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Affiliation(s)
- Khaled S. Allemailem
- Department of Medical Laboratories, College of Applied Medical SciencesQassim UniversityBuraydahSaudi Arabia
| | - Mohammed A Alsahli
- Department of Medical Laboratories, College of Applied Medical SciencesQassim UniversityBuraydahSaudi Arabia
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical SciencesQassim UniversityBuraydahSaudi Arabia
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical SciencesQassim UniversityBuraydahSaudi Arabia
| | | | - Arshad Husain Rahmani
- Department of Medical Laboratories, College of Applied Medical SciencesQassim UniversityBuraydahSaudi Arabia
| | - Amjad Ali Khan
- Department of Basic Health SciencesCollege of Applied Medical SciencesQassim UniversityBuraydahSaudi Arabia
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Geng K, Merino LG, Wedemann L, Martens A, Sobota M, Sanchez YP, Søndergaard JN, White RJ, Kutter C. Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells. Genome Res 2022; 32:1876-1891. [PMID: 36180232 PMCID: PMC9712622 DOI: 10.1101/gr.276901.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/19/2022] [Indexed: 11/24/2022]
Abstract
The CRISPR-Cas9 system is widely used to permanently delete genomic regions via dual guide RNAs. Genomic rearrangements induced by CRISPR-Cas9 can occur, but continuous technical developments make it possible to characterize complex on-target effects. We combined an innovative droplet-based target enrichment approach with long-read sequencing and coupled it to a customized de novo sequence assembly. This approach enabled us to dissect the sequence content at kilobase scale within an on-target genomic locus. We here describe extensive genomic disruptions by Cas9, involving the allelic co-occurrence of a genomic duplication and inversion of the target region, as well as integrations of exogenous DNA and clustered interchromosomal DNA fragment rearrangements. Furthermore, we found that these genomic alterations led to functional aberrant DNA fragments and can alter cell proliferation. Our findings broaden the consequential spectrum of the Cas9 deletion system, reinforce the necessity of meticulous genomic validations, and introduce a data-driven workflow enabling detailed dissection of the on-target sequence content with superior resolution.
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Affiliation(s)
- Keyi Geng
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 65, Stockholm, Sweden
| | - Lara G Merino
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 65, Stockholm, Sweden
| | - Linda Wedemann
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 65, Stockholm, Sweden
| | - Aniek Martens
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 65, Stockholm, Sweden
| | - Małgorzata Sobota
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 65, Stockholm, Sweden
| | - Yerma P Sanchez
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 65, Stockholm, Sweden
| | - Jonas Nørskov Søndergaard
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 65, Stockholm, Sweden
| | - Robert J White
- Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Claudia Kutter
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 65, Stockholm, Sweden
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49
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Al-Darraji MN, Jasim SَA, Salah Aldeen ODA, Ghasemian A, Rasheed M. The Effect of LL37 Antimicrobial Peptide on FOXE1 and lncRNA PTCSC 2 Genes Expression in Colorectal Cancer (CRC) and Normal Cells. Asian Pac J Cancer Prev 2022; 23:3437-3442. [PMID: 36308369 PMCID: PMC9924353 DOI: 10.31557/apjcp.2022.23.10.3437] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Indexed: 12/29/2022] Open
Abstract
OBJECTIVE As an innate immune system component, antimicrobial peptides (AMPs) exert various effects, such as anticancer properties. This study aimed to evaluate the LL37 AMP anticancer effect against colorectal cancer (CRC) cells and the expression of FOXE1 and lncRNA PTCSC2 genes. METHODS The LL37 AMP was purchased from GenScript USA, Inc. Various CRC cell lines (HCT-116, HT29, WiDr, and SW742) were cultured in the DMEM medium. Various concentrations ranging from (5-400) μg/mL of LL37 AMP were prepared, added to cell cultures, and incubated for (24 and 48) hours. A nontoxic level of 30 µg/mL of LL37 was investigated for FOXE1 and lncRNA PTCSC2 gene expression. RESULTS At 24 hours, the (50 and 90) % lethal concentrations of LC50 and LC90, respectively, of LL37 against NCM460 normal cells were (640 and > 640) g/mL. Additionally, these values at 48 hours included (160 and > 640) µg/mL, respectively. After 24 hours of treatment, the LC50 and LC90 of LL37 AMP against CRC cell lines included (20 and 200) µg/mL. The LC50 and LC90 of the LL37 at 48 hours included (20 and 50) µg/mL and at 72 hours. they included (~10 and 40) μg/mL, respectively. FOXE1 but not the PTCSC 2 gene expression was significantly higher in CRC cells than normal cells (NCM460 and HaCaT). The LL37 AMP significantly decreased FOXE1 gene expression by 1.95-fold in CRC cells (p < 0.001). CONCLUSION The FOXE1 gene can be considered a biomarker of CRC development. The expression of FOXE1 but not the PTCSC2 gene was significantly affected by the LL37 AMP. The effects of LL37 AMP against CRC cells were time and dose-dependent. Future studies are warranted to verify these effects.
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Affiliation(s)
| | | | | | - Abdolmajid Ghasemian
- Noncommunicable Diseases Research Center, School of Medicine, Fasa University of Medical Sciences, Fasa, Iran.
| | - Mohammed Rasheed
- Applied Sciences Department, University of Technology, Iraq. ,For Correspondence:
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50
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Pandey GK, Kanduri C. Long Non-Coding RNAs: Tools for Understanding and Targeting Cancer Pathways. Cancers (Basel) 2022; 14:cancers14194760. [PMID: 36230680 PMCID: PMC9564174 DOI: 10.3390/cancers14194760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/24/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
The regulatory nature of long non-coding RNAs (lncRNAs) has been well established in various processes of cellular growth, development, and differentiation. Therefore, it is vital to examine their contribution to cancer development. There are ample examples of lncRNAs whose cellular levels are significantly associated with clinical outcomes. However, whether these non-coding molecules can work as either key drivers or barriers to cancer development remains unknown. The current review aims to discuss some well-characterised lncRNAs in the process of oncogenesis and extrapolate the extent of their decisive contribution to tumour development. We ask if these lncRNAs can independently initiate neoplastic lesions or they always need the modulation of well characterized oncogenes or tumour suppressors to exert their functional properties. Finally, we discuss the emerging genetic approaches and appropriate animal and humanised models that can significantly contribute to the functional dissection of lncRNAs in cancer development and progression.
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Affiliation(s)
- Gaurav Kumar Pandey
- Department of Zoology, Banaras Hindu University, Varanasi 221005, India
- Correspondence: (G.K.P.); (C.K.)
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, The Sahlgrenska Academy, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Correspondence: (G.K.P.); (C.K.)
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