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Ueda MT, Inamo J, Miya F, Shimada M, Yamaguchi K, Kochi Y. Functional and dynamic profiling of transcript isoforms reveals essential roles of alternative splicing in interferon response. CELL GENOMICS 2024; 4:100654. [PMID: 39288763 DOI: 10.1016/j.xgen.2024.100654] [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: 06/21/2023] [Revised: 04/04/2024] [Accepted: 08/20/2024] [Indexed: 09/19/2024]
Abstract
Type I interferon (IFN-I) plays an important role in the innate immune response through inducing IFN-I-stimulated genes (ISGs). However, how alternative splicing (AS) events, especially over time, affect their function remains poorly understood. We generated an annotation (113,843 transcripts) for IFN-I-stimulated human B cells called isoISG using high-accuracy long-read sequencing data from PacBio Sequel II/IIe. Transcript isoform profiling using isoISG revealed that isoform switching occurred in the early response to IFN-I so that ISGs would gain functional domains (e.g., C4B) or higher protein production (e.g., IRF3). Conversely, isoforms lacking functional domains increased during the late phase of IFN-I response, mainly due to intron retention events. This suggests that isoform switching both triggers and terminates IFN-I responses at the translation and protein levels. Furthermore, genetic variants influencing the isoform ratio of ISGs were associated with immunological and infectious diseases. AS has essential roles in regulating innate immune response and associated diseases.
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Affiliation(s)
- Mahoko Takahashi Ueda
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Jun Inamo
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO, USA; Department of Biomedical Informatics, Center for Health Artificial Intelligence, University of Colorado School of Medicine, Aurora, CO, USA
| | - Fuyuki Miya
- Center for Medical Genetics, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Mihoko Shimada
- National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Kensuke Yamaguchi
- Biomedical Engineering Research Innovation Center, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo 113-8510, Japan; Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yuta Kochi
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan; Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
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van Haaren MJH, Steller LB, Vastert SJ, Calis JJA, van Loosdregt J. Get Spliced: Uniting Alternative Splicing and Arthritis. Int J Mol Sci 2024; 25:8123. [PMID: 39125692 PMCID: PMC11311815 DOI: 10.3390/ijms25158123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 07/21/2024] [Accepted: 07/22/2024] [Indexed: 08/12/2024] Open
Abstract
Immune responses demand the rapid and precise regulation of gene protein expression. Splicing is a crucial step in this process; ~95% of protein-coding gene transcripts are spliced during mRNA maturation. Alternative splicing allows for distinct functional regulation, as it can affect transcript degradation and can lead to alternative functional protein isoforms. There is increasing evidence that splicing can directly regulate immune responses. For several genes, immune cells display dramatic changes in isoform-level transcript expression patterns upon activation. Recent advances in long-read RNA sequencing assays have enabled an unbiased and complete description of transcript isoform expression patterns. With an increasing amount of cell types and conditions that have been analyzed with such assays, thousands of novel transcript isoforms have been identified. Alternative splicing has been associated with autoimmune diseases, including arthritis. Here, GWASs revealed that SNPs associated with arthritis are enriched in splice sites. In this review, we will discuss how alternative splicing is involved in immune responses and how the dysregulation of alternative splicing can contribute to arthritis pathogenesis. In addition, we will discuss the therapeutic potential of modulating alternative splicing, which includes examples of spliceform-based biomarkers for disease severity or disease subtype, splicing manipulation using antisense oligonucleotides, and the targeting of specific immune-related spliceforms using antibodies.
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Affiliation(s)
- Maurice J. H. van Haaren
- Center for Translational Immunology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Levina Bertina Steller
- Center for Translational Immunology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Sebastiaan J. Vastert
- Center for Translational Immunology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
- Division of Pediatric Rheumatology and Immunology, Wilhelmina Children’s Hospital, 3584 CX Utrecht, The Netherlands
| | - Jorg J. A. Calis
- Center for Translational Immunology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Jorg van Loosdregt
- Center for Translational Immunology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
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3
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Quinones-Valdez G, Amoah K, Xiao X. Long-read RNA-seq demarcates cis- and trans-directed alternative RNA splicing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.599101. [PMID: 38915585 PMCID: PMC11195283 DOI: 10.1101/2024.06.14.599101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Genetic regulation of alternative splicing constitutes an important link between genetic variation and disease. Nonetheless, RNA splicing is regulated by both cis-acting elements and trans-acting splicing factors. Determining splicing events that are directed primarily by the cis- or trans-acting mechanisms will greatly inform our understanding of the genetic basis of disease. Here, we show that long-read RNA-seq, combined with our new method isoLASER, enables a clear segregation of cis- and trans-directed splicing events for individual samples. The genetic linkage of splicing is largely individual-specific, in stark contrast to the tissue-specific pattern of splicing profiles. Analysis of long-read RNA-seq data from human and mouse revealed thousands of cis-directed splicing events susceptible to genetic regulation. We highlight such events in the HLA genes whose analysis was challenging with short-read data. We also highlight novel cis-directed splicing events in Alzheimer's disease-relevant genes such as MAPT and BIN1. Together, the clear demarcation of cis- and trans-directed splicing paves ways for future studies of the genetic basis of disease.
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Affiliation(s)
- Giovanni Quinones-Valdez
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kofi Amoah
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xinshu Xiao
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
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4
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Wang Y, Xu X, Zhang A, Yang S, Li H. Role of alternative splicing in fish immunity. FISH & SHELLFISH IMMUNOLOGY 2024; 149:109601. [PMID: 38701992 DOI: 10.1016/j.fsi.2024.109601] [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: 02/07/2024] [Revised: 04/22/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024]
Abstract
Alternative splicing serves as a pivotal source of complexity in the transcriptome and proteome, selectively connecting various coding elements to generate a diverse array of mRNAs. This process encodes multiple proteins with either similar or distinct functions, contributing significantly to the intricacies of cellular processes. The role of alternative splicing in mammalian immunity has been well studied. Remarkably, the immune system of fish shares substantial similarities with that of humans, and alternative splicing also emerges as a key player in the immune processes of fish. In this review, we offer an overview of alternative splicing and its associated functions in the immune processes of fish, and summarize the research progress on alternative splicing in the fish immunity. Furthermore, we review the impact of alternative splicing on the fish immune system's response to external stimuli. Finally, we present our perspectives on future directions in this field. Our aim is to provide valuable insights for the future investigations into the role of alternative splicing in immunity.
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Affiliation(s)
- Yunchao Wang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Xinyi Xu
- Hunan Fisheries Science Institute, Changsha, 410153, China
| | - Ailong Zhang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Shuaiqi Yang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
| | - Hongyan Li
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266003, China.
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5
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Holling GA, Chavel CA, Sharda AP, Lieberman MM, James CM, Lightman SM, Tong JH, Qiao G, Emmons TR, Giridharan T, Hou S, Intlekofer AM, Higashi RM, Fan TWM, Lane AN, Eng KH, Segal BH, Repasky EA, Lee KP, Olejniczak SH. CD8+ T cell metabolic flexibility elicited by CD28-ARS2 axis-driven alternative splicing of PKM supports antitumor immunity. Cell Mol Immunol 2024; 21:260-274. [PMID: 38233562 PMCID: PMC10902291 DOI: 10.1038/s41423-024-01124-2] [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: 07/14/2023] [Accepted: 12/26/2023] [Indexed: 01/19/2024] Open
Abstract
Metabolic flexibility has emerged as a critical determinant of CD8+ T-cell antitumor activity, yet the mechanisms driving the metabolic flexibility of T cells have not been determined. In this study, we investigated the influence of the nuclear cap-binding complex (CBC) adaptor protein ARS2 on mature T cells. In doing so, we discovered a novel signaling axis that endows activated CD8+ T cells with flexibility of glucose catabolism. ARS2 upregulation driven by CD28 signaling reinforced splicing factor recruitment to pre-mRNAs and affected approximately one-third of T-cell activation-induced alternative splicing events. Among these effects, the CD28-ARS2 axis suppressed the expression of the M1 isoform of pyruvate kinase in favor of PKM2, a key determinant of CD8+ T-cell glucose utilization, interferon gamma production, and antitumor effector function. Importantly, PKM alternative splicing occurred independently of CD28-driven PI3K pathway activation, revealing a novel means by which costimulation reprograms glucose metabolism in CD8+ T cells.
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Affiliation(s)
- G Aaron Holling
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
- University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Colin A Chavel
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Anand P Sharda
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Mackenzie M Lieberman
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Caitlin M James
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Shivana M Lightman
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Jason H Tong
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Guanxi Qiao
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
- Dana Farber Cancer Institute, Boston, MA, 02215, USA
| | - Tiffany R Emmons
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
- Massachusetts Institute of Technology, Boston, MA, 02139, USA
| | - Thejaswini Giridharan
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Shengqi Hou
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Andrew M Intlekofer
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Richard M Higashi
- Center for Environmental Systems Biochemistry, Department of Toxicology and Cancer Biology and Markey Cancer Center, Lexington, KY, 40536, USA
| | - Teresa W M Fan
- Center for Environmental Systems Biochemistry, Department of Toxicology and Cancer Biology and Markey Cancer Center, Lexington, KY, 40536, USA
| | - Andrew N Lane
- Center for Environmental Systems Biochemistry, Department of Toxicology and Cancer Biology and Markey Cancer Center, Lexington, KY, 40536, USA
| | - Kevin H Eng
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Brahm H Segal
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Elizabeth A Repasky
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Kelvin P Lee
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
- Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Scott H Olejniczak
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA.
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6
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Scott KA, Kojima H, Ropek N, Warren CD, Zhang TL, Hogg SJ, Webster C, Zhang X, Rahman J, Melillo B, Cravatt BF, Lyu J, Abdel-Wahab O, Vinogradova EV. Covalent Targeting of Splicing in T Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.572199. [PMID: 38187674 PMCID: PMC10769204 DOI: 10.1101/2023.12.18.572199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Despite significant interest in therapeutic targeting of splicing, few chemical probes are available for the proteins involved in splicing. Here, we show that elaborated stereoisomeric acrylamide chemical probe EV96 and its analogues lead to a selective T cell state-dependent loss of interleukin 2-inducible T cell kinase (ITK) by targeting one of the core splicing factors SF3B1. Mechanistic investigations suggest that the state-dependency stems from a combination of differential protein turnover rates and availability of functional mRNA pools that can be depleted due to extensive alternative splicing. We further introduce a comprehensive list of proteins involved in splicing and leverage both cysteine- and protein-directed activity-based protein profiling (ABPP) data with electrophilic scout fragments to demonstrate covalent ligandability for many classes of splicing factors and splicing regulators in primary human T cells. Taken together, our findings show how chemical perturbation of splicing can lead to immune state-dependent changes in protein expression and provide evidence for the broad potential to target splicing factors with covalent chemistry.
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Leal Y, Valenzuela-Muñoz V, Gallardo-Escárate C. Alternative splicing in Atlantic salmon head kidney and SHK-1 cell line during the Piscirickettsia salmonis infection: A comparative transcriptome survey. FISH & SHELLFISH IMMUNOLOGY 2023; 142:109127. [PMID: 37813155 DOI: 10.1016/j.fsi.2023.109127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/11/2023]
Abstract
Piscirickettsia salmonis, an intracellular bacterium in salmon aquaculture, is a big challenge because it is responsible for 54.2% of Atlantic salmon mortalities. In recent years, the high relevance of Alternative Splicing (AS) as a molecular mechanism associated with infectious conditions and host-pathogen interaction processes, especially in host immune activation, has been observed. Several studies have highlighted the role of AS in the host's immune response during viral, bacterial, and endoparasite infection. In the present study, we evaluated AS transcriptome profiles during P. salmonis infection in the two most used study models, SHK-1 cell line and salmon head kidney tissue. First, the SHK-1 cell line was exposed to P. salmonis infection at 0-, 7-, and 14-days post-infection (dpi). Following, total RNA was extracted for Illumina sequencing. On the other hand, RNA-Seq datasets of Atlantic salmon head kidney infected with the same P. salmonis strayingwase used. For both study models, the highest number of differentially alternative splicing (DAS) events was observed at 7 dpi, 16,830 DAS events derived from 9213 DAS genes in SHK-1 cells, and 13,820 DAS events from 7684 DAS genes in salmon HK. Alternative first exon (AF) was the most abundant AS type in the three infection times analyzed, representing 31% in SHK-1 cells and 228.6 in salmon HK; meanwhile, mutually exclusive exon (MX) was the least abundant. Notably, functional annotation of DAS genes in SHK-1 cells infected with P. salmonis showed a high presence of genes related to nucleotide metabolism. In contrast, the salmon head kidney exhibited many GO terms associated with immune response. Our findings reported the role of AS during P. salmonis infection in Atlantic salmon. These studies would contribute to a better understanding of the molecular bases that support the pathogen-host interaction, evidencing the contribution of AS regulating the transcriptional host response.
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Affiliation(s)
- Yeny Leal
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, P.O. Box 160-C, Concepción, 4030000, Chile
| | - Valentina Valenzuela-Muñoz
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, P.O. Box 160-C, Concepción, 4030000, Chile
| | - Cristian Gallardo-Escárate
- Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, P.O. Box 160-C, Concepción, 4030000, Chile.
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Dam SH, Olsen LR, Vitting-Seerup K. Expression and splicing mediate distinct biological signals. BMC Biol 2023; 21:220. [PMID: 37858135 PMCID: PMC10588054 DOI: 10.1186/s12915-023-01724-w] [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: 12/01/2022] [Accepted: 10/04/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Through alternative splicing, most human genes produce multiple isoforms in a cell-, tissue-, and disease-specific manner. Numerous studies show that alternative splicing is essential for development, diseases, and their treatments. Despite these important examples, the extent and biological relevance of splicing are currently unknown. RESULTS To solve this problem, we developed pairedGSEA and used it to profile transcriptional changes in 100 representative RNA-seq datasets. Our systematic analysis demonstrates that changes in splicing, on average, contribute to 48.1% of the biological signal in expression analyses. Gene-set enrichment analysis furthermore indicates that expression and splicing both convey shared and distinct biological signals. CONCLUSIONS These findings establish alternative splicing as a major regulator of the human condition and suggest that most contemporary RNA-seq studies likely miss out on critical biological insights. We anticipate our results will contribute to the transition from a gene-centric to an isoform-centric research paradigm.
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Affiliation(s)
- Søren Helweg Dam
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Lars Rønn Olsen
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Kristoffer Vitting-Seerup
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark.
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9
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Ner-Gaon H, Peleg R, Gazit R, Reiner-Benaim A, Shay T. Mapping the splicing landscape of the human immune system. Front Immunol 2023; 14:1116392. [PMID: 37711610 PMCID: PMC10499523 DOI: 10.3389/fimmu.2023.1116392] [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: 12/05/2022] [Accepted: 08/14/2023] [Indexed: 09/16/2023] Open
Abstract
Most human genes code for more than one transcript. Different ratios of transcripts of the same gene can be found in different cell types or states, indicating differential use of transcription start sites or differential splicing. Such differential transcript use (DTUs) events provide an additional layer of regulation and protein diversity. With the exceptions of PTPRC and CIITA, there are very few reported cases of DTU events in the immune system. To rigorously map DTUs between different human immune cell types, we leveraged four publicly available RNA sequencing datasets. We identified 282 DTU events between five human healthy immune cell types that appear in at least two datasets. The patterns of the DTU events were mostly cell-type-specific or lineage-specific, in the context of the five cell types tested. DTUs correlated with the expression pattern of potential regulators, namely, splicing factors and transcription factors. Of the several immune related conditions studied, only sepsis affected the splicing of more than a few genes and only in innate immune cells. Taken together, we map the DTUs landscape in human peripheral blood immune cell types, and present hundreds of genes whose transcript use changes between cell types or upon activation.
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Affiliation(s)
- Hadas Ner-Gaon
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Ronnie Peleg
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Roi Gazit
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Anat Reiner-Benaim
- Department of Epidemiology, Biostatistics and Community Health Sciences, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Tal Shay
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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Yang Y, Zhang YM, Wang Y, Liu K, Cui SY, Luo YQ, Zheng W, Xu J, Duan W, Wang JY. Genome-wide identification of aberrant alternative splicing and RNA-binding protein regulators in acute myeloid leukaemia which may contribute to immune microenvironment remodelling. Carcinogenesis 2023; 44:418-425. [PMID: 37209099 DOI: 10.1093/carcin/bgad032] [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: 11/30/2022] [Revised: 03/06/2023] [Accepted: 05/19/2023] [Indexed: 05/22/2023] Open
Abstract
Acute myeloid leukaemia (AML) is one of the most lethal cancers of the haematopoietic system with a poorly understood aetiology. Recent studies have shown that aberrant alternative splicing (AS) and a (RBP) regulators are highly associated with the pathogenesis of AML. This study presents an overview of the abnormal AS and differential expression of RNA-binding proteins (RBPs) in AML and further highlights their close relation to the remodelling of the immune microenvironment in AML patients. An in-depth understanding of the regulatory mechanism underlying AML will contribute to the future development of strategies for the prevention, diagnosis and therapy of AML and thus improve the overall survival of patients with AML.
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Affiliation(s)
- Ying Yang
- Department of Pharmacy, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250014, China
| | - Yu-Mei Zhang
- Department of Hematology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250014, China
- Institute of Hematology, Shandong University of Traditional Chinese Medicine, Jinan 250014, China
- Key Laboratory of Integrated Traditional Chinese and Western Medicine for Hematology, Health Commission of Shandong Province, Jinan 250014, China
| | - Yan Wang
- Department of Hematology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250014, China
- Institute of Hematology, Shandong University of Traditional Chinese Medicine, Jinan 250014, China
- Key Laboratory of Integrated Traditional Chinese and Western Medicine for Hematology, Health Commission of Shandong Province, Jinan 250014, China
| | - Kui Liu
- Department of Hematology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250014, China
- Institute of Hematology, Shandong University of Traditional Chinese Medicine, Jinan 250014, China
- Key Laboratory of Integrated Traditional Chinese and Western Medicine for Hematology, Health Commission of Shandong Province, Jinan 250014, China
| | - Si-Yuan Cui
- Department of Hematology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250014, China
- Institute of Hematology, Shandong University of Traditional Chinese Medicine, Jinan 250014, China
- Key Laboratory of Integrated Traditional Chinese and Western Medicine for Hematology, Health Commission of Shandong Province, Jinan 250014, China
| | - Ya-Qin Luo
- Department of Hematology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250014, China
- Institute of Hematology, Shandong University of Traditional Chinese Medicine, Jinan 250014, China
- Key Laboratory of Integrated Traditional Chinese and Western Medicine for Hematology, Health Commission of Shandong Province, Jinan 250014, China
| | - Wei Zheng
- Department of Hematology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250014, China
- Institute of Hematology, Shandong University of Traditional Chinese Medicine, Jinan 250014, China
- Key Laboratory of Integrated Traditional Chinese and Western Medicine for Hematology, Health Commission of Shandong Province, Jinan 250014, China
| | - Jie Xu
- Department of Hematology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250014, China
- Institute of Hematology, Shandong University of Traditional Chinese Medicine, Jinan 250014, China
- Key Laboratory of Integrated Traditional Chinese and Western Medicine for Hematology, Health Commission of Shandong Province, Jinan 250014, China
| | - Wei Duan
- School of Medicine, Faculty of Health, Deakin University, Waurn Ponds, Victoria, Australia
| | - Jing-Yi Wang
- Department of Hematology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250014, China
- Institute of Hematology, Shandong University of Traditional Chinese Medicine, Jinan 250014, China
- Key Laboratory of Integrated Traditional Chinese and Western Medicine for Hematology, Health Commission of Shandong Province, Jinan 250014, China
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11
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Bravo S, Leiva F, Moya J, Guzman O, Vidal R. Unveiling the Role of Dynamic Alternative Splicing Modulation After Infestation with Sea Lice (Caligus rogercresseyi) in Atlantic Salmon. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:223-234. [PMID: 36629943 DOI: 10.1007/s10126-023-10196-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 01/04/2023] [Indexed: 05/06/2023]
Abstract
Sea lice are pathogenic marine ectoparasite copepods that represent a severe risk to the worldwide salmon industry. Several transcriptomic investigations have characterized the regulation of gene expression response of Atlantic salmon to sea lice infestation. These studies have focused on the levels of transcript, overlooking the potentially relevant role of alternative splicing (AS), which corresponds to an essential control mechanism of gene expression through RNA processing. In the present study, we performed a genome-wide bioinformatics characterization of differential AS event dynamics in control and infested C. rogercresseyi Atlantic salmon and in resistant and susceptible phenotypes. We identified a significant rise of alternative splicing events and AS genes after infestation and 176 differential alternative splicing events (DASE) from 133 genes. In addition, a higher number of DASE and AS genes were observed among resistant and susceptible phenotypes. Functional annotation of AS genes shows several terms and pathways associated with behavior, RNA splicing, immune response, and RNA binding. Furthermore, three protein-coding genes were identified undergoing differential transcript usage events, among resistant and susceptible phenotypes. Our findings support AS performing a relevant regulatory role in the response of salmonids to sea lice infestation.
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Affiliation(s)
- Scarleth Bravo
- Laboratory of Molecular Ecology, Genomics and Evolutionary Studies, Department of Biology, Universidad de Santiago de Chile, Santiago, Chile
| | - Francisco Leiva
- Laboratory of Molecular Ecology, Genomics and Evolutionary Studies, Department of Biology, Universidad de Santiago de Chile, Santiago, Chile
| | - Javier Moya
- Benchmark Animal Health Chile, Santa Rosa 560 Of.26, Puerto Varas, Chile
| | - Osiel Guzman
- IDEVAC SpA, Francisco Bilbao 1129 Of. 306, Osorno, Chile
| | - Rodrigo Vidal
- Laboratory of Molecular Ecology, Genomics and Evolutionary Studies, Department of Biology, Universidad de Santiago de Chile, Santiago, Chile.
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12
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Zhang Z, Sauerwald N, Cappuccio A, Ramos I, Nair VD, Nudelman G, Zaslavsky E, Ge Y, Gaitas A, Ren H, Brockman J, Geis J, Ramalingam N, King D, McClain MT, Woods CW, Henao R, Burke TW, Tsalik EL, Goforth CW, Lizewski RA, Lizewski SE, Weir DL, Letizia AG, Sealfon SC, Troyanskaya OG. Blood RNA alternative splicing events as diagnostic biomarkers for infectious disease. CELL REPORTS METHODS 2023; 3:100395. [PMID: 36936082 PMCID: PMC10014279 DOI: 10.1016/j.crmeth.2023.100395] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/31/2022] [Accepted: 01/09/2023] [Indexed: 01/13/2023]
Abstract
Assays detecting blood transcriptome changes are studied for infectious disease diagnosis. Blood-based RNA alternative splicing (AS) events, which have not been well characterized in pathogen infection, have potential normalization and assay platform stability advantages over gene expression for diagnosis. Here, we present a computational framework for developing AS diagnostic biomarkers. Leveraging a large prospective cohort of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and whole-blood RNA sequencing (RNA-seq) data, we identify a major functional AS program switch upon viral infection. Using an independent cohort, we demonstrate the improved accuracy of AS biomarkers for SARS-CoV-2 diagnosis compared with six reported transcriptome signatures. We then optimize a subset of AS-based biomarkers to develop microfluidic PCR diagnostic assays. This assay achieves nearly perfect test accuracy (61/62 = 98.4%) using a naive principal component classifier, significantly more accurate than a gene expression PCR assay in the same cohort. Therefore, our RNA splicing computational framework enables a promising avenue for host-response diagnosis of infection.
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Affiliation(s)
- Zijun Zhang
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
- Division of Artificial Intelligence in Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Natalie Sauerwald
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
| | - Antonio Cappuccio
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Irene Ramos
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Venugopalan D. Nair
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - German Nudelman
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yongchao Ge
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Angelo Gaitas
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hui Ren
- Fluidigm Corporation, South San Francisco, CA 94080, USA
| | - Joel Brockman
- Fluidigm Corporation, South San Francisco, CA 94080, USA
| | - Jennifer Geis
- Fluidigm Corporation, South San Francisco, CA 94080, USA
| | | | - David King
- Fluidigm Corporation, South San Francisco, CA 94080, USA
| | - Micah T. McClain
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Christopher W. Woods
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ricardo Henao
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Thomas W. Burke
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ephraim L. Tsalik
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | | | | | | | - Dawn L. Weir
- Naval Medical Research Center, Silver Spring, MD, USA
| | | | - Stuart C. Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Olga G. Troyanskaya
- Center for Computational Biology, Flatiron Institute, New York, NY 10010, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Computer Science, Princeton University, Princeton, NJ 08544, USA
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13
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Matsushima S, Ajiro M, Iida K, Chamoto K, Honjo T, Hagiwara M. Chemical induction of splice-neoantigens attenuates tumor growth in a preclinical model of colorectal cancer. Sci Transl Med 2022; 14:eabn6056. [PMID: 36449604 DOI: 10.1126/scitranslmed.abn6056] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Neoantigen production is a determinant of cancer immunotherapy. However, the expansion of neoantigen abundance for cancer therapeutics is technically challenging. Here, we report that the synthetic compound RECTAS can induce the production of splice-neoantigens that could be used to boost antitumor immune responses. RECTAS suppressed tumor growth in a CD8+ T cell- and tumor major histocompatibility complex class I-dependent manner and enhanced immune checkpoint blockade efficacy. Subsequent transcriptome analysis and validation for immunogenicity identified six splice-neoantigen candidates whose expression was induced by RECTAS treatment. Vaccination of the identified neoepitopes elicited T cell responses capable of killing cancer cells in vitro, in addition to suppression of tumor growth in vivo upon sensitization with RECTAS. Collectively, these results provide support for the further development of splice variant-inducing treatments for cancer immunotherapy.
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Affiliation(s)
- Shingo Matsushima
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan.,Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan.,Pharmacology Research Laboratories, Watarase Research Center, Kyorin Pharmaceutical Co. Ltd, Tochigi 329-0114, Japan
| | - Masahiko Ajiro
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan.,Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Kei Iida
- Medical Research Support Center, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan.,Faculty of Science and Engineering, Kindai University, Osaka 577-8502, Japan
| | - Kenji Chamoto
- Department of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Tasuku Honjo
- Department of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan.,Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
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14
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IL-17D-induced inhibition of DDX5 expression in keratinocytes amplifies IL-36R-mediated skin inflammation. Nat Immunol 2022; 23:1577-1587. [PMID: 36271146 DOI: 10.1038/s41590-022-01339-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 09/14/2022] [Indexed: 11/08/2022]
Abstract
Aberrant RNA splicing in keratinocytes drives inflammatory skin disorders. In the present study, we found that the RNA helicase DDX5 was downregulated in keratinocytes from the inflammatory skin lesions in patients with atopic dermatitis and psoriasis, and that mice with keratinocyte-specific deletion of Ddx5 (Ddx5∆KC) were more susceptible to cutaneous inflammation. Inhibition of DDX5 expression in keratinocytes was induced by the cytokine interleukin (IL)-17D through activation of the CD93-p38 MAPK-AKT-SMAD2/3 signaling pathway and led to pre-messenger RNA splicing events that favored the production of membrane-bound, intact IL-36 receptor (IL-36R) at the expense of soluble IL-36R (sIL-36R) and to the selective amplification of IL-36R-mediated inflammatory responses and cutaneous inflammation. Restoration of sIL-36R in Ddx5∆KC mice with experimental atopic dermatitis or psoriasis suppressed skin inflammation and alleviated the disease phenotypes. These findings indicate that IL-17D modulation of DDX5 expression controls inflammation in keratinocytes during inflammatory skin diseases.
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15
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Llinas RJ, Xiong JQ, Clark NM, Burkhart SE, Bartel B. An Arabidopsis pre-RNA processing8a (prp8a) missense allele restores splicing of a subset of mis-spliced mRNAs. PLANT PHYSIOLOGY 2022; 189:2175-2192. [PMID: 35608297 PMCID: PMC9342983 DOI: 10.1093/plphys/kiac221] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/19/2022] [Indexed: 06/15/2023]
Abstract
Eukaryotic precursor mRNAs often harbor noncoding introns that must be removed prior to translation. Accurate splicing of precursor messenger RNA depends on placement and assembly of small nuclear ribonucleoprotein (snRNP) sub-complexes of the spliceosome. Yeast (Saccharomyces cerevisiae) studies established a role in splice-site selection for PRE-RNA PROCESSING8 (PRP8), a conserved spliceosome scaffolding protein of the U5 snRNP. However, analogous splice-site selection studies in multicellular eukaryotes are lacking. Such studies are crucial for a comprehensive understanding of alternative splicing, which is extensive in plants and animals but limited in yeast. In this work, we describe an Arabidopsis (Arabidopsis thaliana) prp8a mutant that modulates splice-site selection. We isolated prp8a-14 from a screen for suppressors of pex14-6, which carries a splice-site mutation in the PEROXIN14 (PEX14) peroxisome biogenesis gene. To elucidate Arabidopsis PRP8A function in spliceosome fidelity, we combined prp8a-14 with various pex14 splice-site mutations and monitored the double mutants for physiological and molecular consequences of dysfunctional and functional peroxisomes that correspond to impaired and recovered splicing, respectively. prp8a-14 restored splicing and PEX14 function to alleles with mutations in the exonic guanine of the 5'-splice site but did not restore splicing or function to alleles with mutations in the intronic guanine of 5'- or 3'-splice sites. We used RNA-seq to reveal the systemic impact of prp8a-14 and found hundreds of differentially spliced transcripts and thousands of transcripts with significantly altered levels. Among differentially spliced transcripts, prp8a-14 significantly altered 5'- and 3'-splice-site utilization to favor sites resulting in shorter introns. This study provides a genetic platform for probing splicing in plants and hints at a role for plant PRP8 in splice-site selection.
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Affiliation(s)
- Roxanna J Llinas
- Department of Biosciences, Rice University, Houston, Texas 77005, USA
| | | | - Natalie M Clark
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
| | - Sarah E Burkhart
- Department of Biosciences, Rice University, Houston, Texas 77005, USA
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16
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Charakopoulos E, Diamantopoulos PT, Zervakis K, Giannakopoulou N, Psichogiou M, Viniou NA. A case report of a fulminant Aeromonas hydrophila soft tissue infection in a patient with acute lymphoblastic leukemia harboring a rare translocation. Curr Med Res Opin 2022; 38:1125-1132. [PMID: 35575163 DOI: 10.1080/03007995.2022.2078079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
INTRODUCTION Aeromonads are gram-negative opportunistic bacteria, mainly found in aquatic environments. Hematologic patients are particularly at risk of Aeromonas soft tissue infections and septicemia, especially during chemotherapy-induced neutropenia. CASE DESCRIPTION A 46-year-old man was diagnosed with acute lymphoblastic leukemia characterized by the rare t(12;17)(p13;q21)/TAF15-ZNF384 aberration. On day 22 of chemotherapy, he developed febrile neutropenia followed by necrotizing fasciitis in his upper right extremity. Despite appropriate antibiotic therapy and prompt surgical intervention, he died within 36 h after the appearance of a fever. A multi-sensitive Aeromonas hydrophila was isolated from all cultural sites. DISCUSSION AND CONCLUSIONS In a previous paper we characterized the patient's aberration with cytogenetic and FISH analysis. Here, we provide details regarding the patient's rapidly progressing infection and underline the importance of maintaining high clinical suspicion of Aeromonas infections in acute leukemia. Given the unusually rapid progression of an infection caused by a rare non-resistant pathogen, and after considering data on the implication of metalloproteinase function in immune system regulation, a correlation between risk of severe infection and TAF15-ZNF384 aberrated acute lymphoblastic leukemia cannot be ruled out.
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Affiliation(s)
- Emmanouil Charakopoulos
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, Greece
| | - Panagiotis T Diamantopoulos
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, Greece
| | - Konstantinos Zervakis
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, Greece
| | - Nefeli Giannakopoulou
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, Greece
| | - Mina Psichogiou
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, Greece
| | - Nora-Athina Viniou
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, Greece
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17
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Inadvertent Transfer of Murine VL30 Retrotransposons to CAR-T Cells. ADVANCES IN CELL AND GENE THERAPY 2022; 2022. [PMID: 36081760 PMCID: PMC9450689 DOI: 10.1155/2022/6435077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
For more than a decade, genetically engineered autologous T-cells have been successfully employed as immunotherapy drugs for patients with incurable blood cancers. The active components in some of these game-changing medicines are autologous T-cells that express viral vector-delivered chimeric antigen receptors (CARs), which specifically target proteins that are preferentially expressed on cancer cells. Some of these therapeutic CAR expressing T-cells (CAR-Ts) are engineered via transduction with
-retroviral vectors (
-RVVs) produced in a stable producer cell line that was derived from murine PG13 packaging cells (ATCC CRL-10686). Earlier studies reported on the copackaging of murine virus-like 30S RNA (VL30) genomes with
-retroviral vectors generated in murine stable packaging cells. In an earlier study, VL30 mRNA was found to enhance the metastatic potential of human melanoma cells. These findings raise biosafety concerns regarding the possibility that therapeutic CAR-Ts have been inadvertently contaminated with potentially oncogenic VL30 retrotransposons. In this study, we demonstrated the presence of infectious VL30 particles in PG13 cell-conditioned media and observed the ability of these particles to deliver transcriptionally active VL30 genomes to human cells. Notably, VL30 genomes packaged by HIV-1-based vector particles transduced naïve human cells in culture. Furthermore, we detected the transfer and expression of VL30 genomes in clinical-grade CAR-T cells generated by transduction with PG13 cell-derived
-retroviral vectors. Our findings raise biosafety concerns regarding the use of murine packaging cell lines in ongoing clinical applications.
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18
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Wang C, Chen L, Chen Y, Jia W, Cai X, Liu Y, Ji F, Xiong P, Liang A, Liu R, Guan Y, Cheng Z, Weng Y, Wang W, Duan Y, Kuang D, Xu S, Cai H, Xia Q, Yang D, Wang MW, Yang X, Zhang J, Cheng C, Liu L, Liu Z, Liang R, Wang G, Li Z, Xia H, Xia T. Abnormal global alternative RNA splicing in COVID-19 patients. PLoS Genet 2022; 18:e1010137. [PMID: 35421082 PMCID: PMC9089920 DOI: 10.1371/journal.pgen.1010137] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 05/10/2022] [Accepted: 03/08/2022] [Indexed: 12/25/2022] Open
Abstract
Viral infections can alter host transcriptomes by manipulating host splicing machinery. Despite intensive transcriptomic studies on SARS-CoV-2, a systematic analysis of alternative splicing (AS) in severe COVID-19 patients remains largely elusive. Here we integrated proteomic and transcriptomic sequencing data to study AS changes in COVID-19 patients. We discovered that RNA splicing is among the major down-regulated proteomic signatures in COVID-19 patients. The transcriptome analysis showed that SARS-CoV-2 infection induces widespread dysregulation of transcript usage and expression, affecting blood coagulation, neutrophil activation, and cytokine production. Notably, CD74 and LRRFIP1 had increased skipping of an exon in COVID-19 patients that disrupts a functional domain, which correlated with reduced antiviral immunity. Furthermore, the dysregulation of transcripts was strongly correlated with clinical severity of COVID-19, and splice-variants may contribute to unexpected therapeutic activity. In summary, our data highlight that a better understanding of the AS landscape may aid in COVID-19 diagnosis and therapy.
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Affiliation(s)
- Changli Wang
- Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lijun Chen
- Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yaobin Chen
- Institute of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, China
| | - Wenwen Jia
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xunhui Cai
- Institute of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, China
| | - Yufeng Liu
- Institute of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, China
| | - Fenghu Ji
- Institute of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, China
| | - Peng Xiong
- Institute of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, China
| | - Anyi Liang
- Institute of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, China
| | - Ren Liu
- Department of Research and Development, Hugobiotech Co. Ltd., Beijing, China
| | - Yuanlin Guan
- Department of Research and Development, Hugobiotech Co. Ltd., Beijing, China
| | - Zhongyi Cheng
- Jingjie PTM BioLab (Hangzhou) Co. Ltd., Hangzhou, China
| | - Yejing Weng
- Jingjie PTM BioLab (Hangzhou) Co. Ltd., Hangzhou, China
| | - Weixin Wang
- Jingjie PTM BioLab (Hangzhou) Co. Ltd., Hangzhou, China
| | - Yaqi Duan
- Institute of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, China
| | - Dong Kuang
- Institute of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, China
| | - Sanpeng Xu
- Institute of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, China
| | - Hanghang Cai
- Institute of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, China
| | - Qin Xia
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dehua Yang
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Ming-Wei Wang
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xiangping Yang
- Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Chao Cheng
- Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Liang Liu
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhongmin Liu
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Ren Liang
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Guopin Wang
- Institute of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, China
| | | | - Han Xia
- Department of Research and Development, Hugobiotech Co. Ltd., Beijing, China
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, China
| | - Tian Xia
- Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, China
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19
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Alternative Splicing in Cancer and Immune Cells. Cancers (Basel) 2022; 14:cancers14071726. [PMID: 35406498 PMCID: PMC8996879 DOI: 10.3390/cancers14071726] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/22/2022] [Accepted: 03/25/2022] [Indexed: 12/31/2022] Open
Abstract
Splicing is a phenomenon enabling the excision of introns from pre-mRNA to give rise to mature mRNA. All the 20,000 genes of the human genome are concerned by this mechanism. Nevertheless, it is estimated that the proteome is composed of more than 100,000 proteins. How to go from 20,000 genes to more than 100,000 proteins? Alternative splicing (AS) is in charge of this diversity of proteins. AS which is found in most of the cells of an organism, participates in normal cells and in particular in immune cells, in the regulation of cellular behavior. In cancer, AS is highly dysregulated and involved in almost all of the hallmarks that characterize tumor cells. In view of the close link that exists between tumors and the immune system, we present in this review the literature relating to alternative splicing and immunotherapy. We also provide a global but not exhaustive view of AS in the immune system and tumor cells linked to the events that can lead to AS dysregulation in tumors.
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20
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Peng Q, Zhou Y, Oyang L, Wu N, Tang Y, Su M, Luo X, Wang Y, Sheng X, Ma J, Liao Q. Impacts and mechanisms of alternative mRNA splicing in cancer metabolism, immune response, and therapeutics. Mol Ther 2022; 30:1018-1035. [PMID: 34793975 PMCID: PMC8899522 DOI: 10.1016/j.ymthe.2021.11.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/29/2021] [Accepted: 11/11/2021] [Indexed: 02/08/2023] Open
Abstract
Alternative pre-mRNA splicing (AS) provides the potential to produce diversity at RNA and protein levels. Disruptions in the regulation of pre-mRNA splicing can lead to diseases. With the development of transcriptome and genome sequencing technology, increasing diseases have been identified to be associated with abnormal splicing of mRNAs. In tumors, abnormal alternative splicing frequently plays critical roles in cancer pathogenesis and may be considered as new biomarkers and therapeutic targets for cancer intervention. Metabolic abnormalities and immune disorders are important hallmarks of cancer. AS produces multiple different isoforms and diversifies protein expression, which is utilized by the immune and metabolic reprogramming systems to expand gene functions. The abnormal splicing events contributed to tumor progression, partially due to effects on immune response and metabolic reprogramming. Herein, we reviewed the vital role of alternative splicing in regulating cancer metabolism and immune response. We discussed how alternative splicing regulates metabolic reprogramming of cancer cells and antitumor immune response, and the possible strategies to targeting alternative splicing pathways or splicing-regulated metabolic pathway in the context of anticancer immunotherapy. Further, we highlighted the challenges and discuss the perspectives for RNA-based strategies for the treatment of cancer with abnormally alternative splicing isoforms.
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Affiliation(s)
- Qiu Peng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China,Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China
| | - Yujuan Zhou
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China,Hunan Key Laboratory of Translational Radiation Oncology, 283 Tongzipo Road, Changsha 410013, Hunan, China
| | - Linda Oyang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Nayiyuan Wu
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Yanyan Tang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Min Su
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Xia Luo
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Ying Wang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Xiaowu Sheng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Jian Ma
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China; Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China.
| | - Qianjin Liao
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China; Hunan Key Laboratory of Translational Radiation Oncology, 283 Tongzipo Road, Changsha 410013, Hunan, China.
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21
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Kim EY, Che Y, Dean HJ, Lorenzo-Redondo R, Stewart M, Keller CK, Whorf D, Mills D, Dulin NN, Kim T, Votoupal M, Walter M, Fernandez-Sesma A, Kim H, Wolinsky SM. Transcriptome-wide changes in gene expression, splicing, and lncRNAs in response to a live attenuated dengue virus vaccine. Cell Rep 2022; 38:110341. [PMID: 35139383 PMCID: PMC8994511 DOI: 10.1016/j.celrep.2022.110341] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/20/2021] [Accepted: 01/14/2022] [Indexed: 01/26/2023] Open
Abstract
The tetravalent dengue vaccine candidate, TAK-003, induces a functional antibody response, but the titers of antibodies against the four serotypes of the dengue virus (DENV) can vary. Here, through a transcriptomic analysis on whole blood collected from recipients of a two-dose schedule of TAK-003, we examine gene expression, splicing, and transcript isoform-level changes for both protein-coding and noncoding genes to broaden our understanding of the immune response. Our analysis reveals a dynamic pattern of vaccine-associated regulation of long noncoding RNAs (lncRNAs), differential splicing of interferon-stimulated gene exons, and gene expression changes related to multiple signaling pathways that detect viral infection. Co-expression networks isolate immune cell-type-related and interferon-response modules that represent specific biological processes that correlate with more robust antibody responses. These data provide insights into the early determinants of the variable immune response to the vaccine, highlighting the significance of splicing and isoform-level gene regulatory mechanisms in defining vaccine immunogenicity.
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Affiliation(s)
- Eun-Young Kim
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60011, USA
| | - Yan Che
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60011, USA
| | | | - Ramon Lorenzo-Redondo
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60011, USA
| | - Michael Stewart
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60011, USA
| | - Caroline K Keller
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60011, USA
| | - Daniel Whorf
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60011, USA
| | - Dawson Mills
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60011, USA
| | - Nikita N Dulin
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60011, USA
| | - Tiffany Kim
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60011, USA
| | - Megan Votoupal
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60011, USA
| | - Miriam Walter
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60011, USA
| | - Ana Fernandez-Sesma
- Department of Microbiology and Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Heejin Kim
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60011, USA
| | - Steven M Wolinsky
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60011, USA.
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22
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Guo S, Wang X, Zhou H, Gao Y, Wang P, Zhi H, Sun Y, Hao Y, Gan J, Zhang Y, Sun J, Zheng W, Zhao X, Xiao Y, Ning S. Identification and Characterization of Immunogene-Related Alternative Splicing Patterns and Tumor Microenvironment Infiltration Patterns in Breast Cancer. Cancers (Basel) 2022; 14:cancers14030595. [PMID: 35158863 PMCID: PMC8833331 DOI: 10.3390/cancers14030595] [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: 12/22/2021] [Accepted: 01/19/2022] [Indexed: 11/16/2022] Open
Abstract
Alternative splicing (AS) plays a crucial role in tumor development and tumor microenvironment (TME) formation. However, our current knowledge about AS, especially immunogene-related alternative splicing (IGAS) patterns in cancers, remains limited. Herein, we identified and characterized post-transcriptional mechanisms of breast cancer based on IGAS, TME, prognosis, and immuno/chemotherapy. We screened the differentially spliced IGAS events and constructed the IGAS prognostic model (p-values < 0.001, AUC = 0.939), which could be used as an independent prognostic factor. Besides, the AS regulatory network suggested a complex cooperative or competitive relationship between splicing factors and IGAS events, which explained the diversity of splice isoforms. In addition, more than half of the immune cells displayed varying degrees of infiltration in the IGAS risk groups, and the prognostic characteristics of IGAS demonstrated a remarkable and consistent trend correlation with the infiltration levels of immune cell types. The IGAS risk groups showed substantial differences in the sensitivity of immunotherapy and chemotherapy. Finally, IGAS clusters defined by unsupervised cluster analysis had distinct prognostic patterns, suggesting an essential heterogeneity of IGAS events. Significant differences in immune infiltration and unique prognostic capacity of immune cells were also detected in each IGAS cluster. In conclusion, our comprehensive analysis remarkably enhanced the understanding of IGAS patterns and TME in breast cancer, which may help clarify the underlying mechanisms of IGAS in neoplasia and provide clues to molecular mechanisms of oncogenesis and progression.
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23
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Naftaly AS, Pau S, White MA. Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish. Genome Res 2021; 31:1486-1497. [PMID: 34131005 PMCID: PMC8327910 DOI: 10.1101/gr.274282.120] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 06/15/2021] [Indexed: 01/07/2023]
Abstract
Alternate isoforms are important contributors to phenotypic diversity across eukaryotes. Although short-read RNA-sequencing has increased our understanding of isoform diversity, it is challenging to accurately detect full-length transcripts, preventing the identification of many alternate isoforms. Long-read sequencing technologies have made it possible to sequence full-length alternative transcripts, accurately characterizing alternative splicing events, alternate transcription start and end sites, and differences in UTR regions. Here, we use Pacific Biosciences (PacBio) long-read RNA-sequencing (Iso-Seq) to examine the transcriptomes of five organs in threespine stickleback fish (Gasterosteus aculeatus), a widely used genetic model species. The threespine stickleback fish has a refined genome assembly in which gene annotations are based on short-read RNA sequencing and predictions from coding sequence of other species. This suggests some of the existing annotations may be inaccurate or alternative transcripts may not be fully characterized. Using Iso-Seq we detected thousands of novel isoforms, indicating many isoforms are absent in the current Ensembl gene annotations. In addition, we refined many of the existing annotations within the genome. We noted many improperly positioned transcription start sites that were refined with long-read sequencing. The Iso-Seq-predicted transcription start sites were more accurate and verified through ATAC-seq. We also detected many alternative splicing events between sexes and across organs. We found a substantial number of genes in both somatic and gonadal samples that had sex-specific isoforms. Our study highlights the power of long-read sequencing to study the complexity of transcriptomes, greatly improving genomic resources for the threespine stickleback fish.
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Affiliation(s)
- Alice S Naftaly
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - Shana Pau
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
- Department of Biology, University of Texas Arlington, Arlington, Texas 76019, USA
| | - Michael A White
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
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24
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Tomita T, Kato M, Mishima T, Matsunaga Y, Sanjo H, Ito KI, Minagawa K, Matsui T, Oikawa H, Takahashi S, Takao T, Iwai N, Mino T, Takeuchi O, Maru Y, Hiratsuka S. Extracellular mRNA transported to the nucleus exerts translation-independent function. Nat Commun 2021; 12:3655. [PMID: 34135341 PMCID: PMC8208975 DOI: 10.1038/s41467-021-23969-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 05/27/2021] [Indexed: 12/19/2022] Open
Abstract
RNA in extracellular vesicles (EVs) are uptaken by cells, where they regulate fundamental cellular functions. EV-derived mRNA in recipient cells can be translated. However, it is still elusive whether “naked nonvesicular extracellular mRNA” (nex-mRNA) that are not packed in EVs can be uptaken by cells and, if so, whether they have any functions in recipient cells. Here, we show the entrance of nex-mRNA in the nucleus, where they exert a translation-independent function. Human nex-interleukin-1β (IL1β)-mRNA outside cells proved to be captured by RNA-binding zinc finger CCCH domain containing protein 12D (ZC3H12D)-expressing human natural killer (NK) cells. ZC3H12D recruited to the cell membrane binds to the 3′-untranslated region of nex-IL1β-mRNA and transports it to the nucleus. The nex-IL1β-mRNA in the NK cell nucleus upregulates antiapoptotic gene expression, migration activity, and interferon-γ production, leading to the killing of cancer cells and antimetastasis in mice. These results implicate the diverse actions of mRNA. Nonvesicular extracellular RNA (nex-RNA) that are not packed in extracellular vesicles is detected outside the cell, but it is poorly understood. Here the authors report that nex-RNA is captured by a zinc finger protein and transported to the nucleus to enhance antimetastatic characters of the cell.
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Affiliation(s)
- Takeshi Tomita
- Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, School of Medicine, Matsumoto, Nagano, Japan.,Department of Biochemistry and Molecular Biology, Shinshu University, School of Medicine, Matsumoto, Nagano, Japan
| | - Masayoshi Kato
- Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, School of Medicine, Matsumoto, Nagano, Japan.,Department of Biochemistry and Molecular Biology, Shinshu University, School of Medicine, Matsumoto, Nagano, Japan
| | - Taishi Mishima
- Department of Pharmacology, Tokyo Women's Medical University, Shinjuku, Tokyo, Japan
| | - Yuta Matsunaga
- Department of Pharmacology, Tokyo Women's Medical University, Shinjuku, Tokyo, Japan
| | - Hideki Sanjo
- Department of Molecular and Cellular Immunology, Shinshu University, School of Medicine, Matsumoto, Nagano, Japan
| | - Ken-Ichi Ito
- Division of Breast, Endocrine and Respiratory Surgery, Department of Surgery, Shinshu University, School of Medicine, Matsumoto, Nagano, Japan
| | - Kentaro Minagawa
- Department of Hematology/Oncology, Penn State College of Medicine, Hershey, PA, USA
| | - Toshimitsu Matsui
- Department of Hematology, Nishiwaki Municipal Hospital, Nishiwaki, Hyogo, Japan
| | - Hiroyuki Oikawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan
| | - Satoshi Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan
| | - Toshifumi Takao
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Noriki Iwai
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takashi Mino
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Osamu Takeuchi
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshiro Maru
- Department of Pharmacology, Tokyo Women's Medical University, Shinjuku, Tokyo, Japan.
| | - Sachie Hiratsuka
- Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, School of Medicine, Matsumoto, Nagano, Japan. .,Department of Biochemistry and Molecular Biology, Shinshu University, School of Medicine, Matsumoto, Nagano, Japan.
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25
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Robinson EK, Jagannatha P, Covarrubias S, Cattle M, Smaliy V, Safavi R, Shapleigh B, Abu-Shumays R, Jain M, Cloonan SM, Akeson M, Brooks AN, Carpenter S. Inflammation drives alternative first exon usage to regulate immune genes including a novel iron-regulated isoform of Aim2. eLife 2021; 10:69431. [PMID: 34047695 PMCID: PMC8260223 DOI: 10.7554/elife.69431] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 05/21/2021] [Indexed: 12/11/2022] Open
Abstract
Determining the layers of gene regulation within the innate immune response is critical to our understanding of the cellular responses to infection and dysregulation in disease. We identified a conserved mechanism of gene regulation in human and mouse via changes in alternative first exon (AFE) usage following inflammation, resulting in changes to the isoforms produced. Of these AFE events, we identified 95 unannotated transcription start sites in mice using a de novo transcriptome generated by long-read native RNA-sequencing, one of which is in the cytosolic receptor for dsDNA and known inflammatory inducible gene, Aim2. We show that this unannotated AFE isoform of Aim2 is the predominant isoform expressed during inflammation and contains an iron-responsive element in its 5′UTR enabling mRNA translation to be regulated by iron levels. This work highlights the importance of examining alternative isoform changes and translational regulation in the innate immune response and uncovers novel regulatory mechanisms of Aim2.
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Affiliation(s)
- Elektra K Robinson
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, United States
| | - Pratibha Jagannatha
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, United States.,Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, United States
| | - Sergio Covarrubias
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, United States
| | - Matthew Cattle
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, United States
| | - Valeriya Smaliy
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, United States
| | - Rojin Safavi
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, United States
| | - Barbara Shapleigh
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, United States
| | - Robin Abu-Shumays
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, United States
| | - Miten Jain
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, United States
| | - Suzanne M Cloonan
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, United States
| | - Mark Akeson
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, United States
| | - Angela N Brooks
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, United States
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, United States
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26
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Freen-van Heeren JJ. Post-transcriptional control of T-cell cytokine production: Implications for cancer therapy. Immunology 2021; 164:57-72. [PMID: 33884612 DOI: 10.1111/imm.13339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 03/22/2021] [Accepted: 03/30/2021] [Indexed: 01/05/2023] Open
Abstract
As part of the adaptive immune system, T cells are vital for the eradication of infected and malignantly transformed cells. To perform their protective function, T cells produce effector molecules that are either directly cytotoxic, such as granzymes, perforin, interferon-γ and tumour necrosis factor α, or attract and stimulate (immune) cells, such as interleukin-2. As these molecules can also induce immunopathology, tight control of their production is required. Indeed, inflammatory cytokine production is regulated on multiple levels. Firstly, locus accessibility and transcription factor availability and activity determine the amount of mRNA produced. Secondly, post-transcriptional mechanisms, influencing mRNA splicing/codon usage, stability, decay, localization and translation rate subsequently determine the amount of protein that is produced. In the immune suppressive environments of tumours, T cells gradually lose the capacity to produce effector molecules, resulting in tumour immune escape. Recently, the role of post-transcriptional regulation in fine-tuning T-cell effector function has become more appreciated. Furthermore, several groups have shown that exhausted or dysfunctional T cells from cancer patients or murine models possess mRNA for inflammatory mediators, but fail to produce effector molecules, hinting that post-transcriptional events also play a role in hampering tumour-infiltrating lymphocyte effector function. Here, the post-transcriptional regulatory events governing T-cell cytokine production are reviewed, with a specific focus on the importance of post-transcriptional regulation in anti-tumour responses. Furthermore, potential approaches to circumvent tumour-mediated dampening of T-cell effector function through the (dis)engagement of post-transcriptional events are explored, such as CRISPR/Cas9-mediated genome editing or chimeric antigen receptors.
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27
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Geng G, Xu C, Peng N, Li Y, Liu J, Wu J, Liang J, Zhu Y, Shi L. PTBP1 is necessary for dendritic cells to regulate T-cell homeostasis and antitumour immunity. Immunology 2021; 163:74-85. [PMID: 33421118 PMCID: PMC8044338 DOI: 10.1111/imm.13304] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 12/18/2020] [Accepted: 12/19/2020] [Indexed: 01/25/2023] Open
Abstract
Dendritic cells (DCs) play an important role in linking innate and adaptive immunity. DCs can sense endogenous and exogenous antigens and present those antigens to T cells to induce an immune response or immune tolerance. During activation, alternative splicing (AS) in DCs is dramatically changed to induce cytokine secretion and upregulation of surface marker expression. PTBP1, an RNA-binding protein, is essential in alternative splicing, but the function of PTBP1 in DCs is unknown. Here, we found that a specific deficiency of Ptbp1 in DCs could increase MHC II expression and perturb T-cell homeostasis without affecting DC development. Functionally, Ptbp1 deletion in DCs could enhance antitumour immunity and asthma exacerbation. Mechanistically, we found that Pkm alternative splicing and a subset of Ifn response genes could be regulated by PTBP1. These findings revealed the function of PTBP1 in DCs and indicated that PTBP1 might be a novel therapeutic target for antitumour treatment.
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Affiliation(s)
- Guangfeng Geng
- State Key Laboratory of Experimental HematologyState Key Laboratory of Medicinal Chemical BiologyCollege of Life SciencesNankai UniversityTianjinChina
| | - Changlu Xu
- State Key Laboratory of Experimental HematologyNational Clinical Research Center for Blood DiseasesInstitute of Hematology & Blood Diseases HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegeTianjinChina
| | - Nan Peng
- State Key Laboratory of Experimental HematologyNational Clinical Research Center for Blood DiseasesInstitute of Hematology & Blood Diseases HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegeTianjinChina
| | - Yue Li
- State Key Laboratory of Experimental HematologyNational Clinical Research Center for Blood DiseasesInstitute of Hematology & Blood Diseases HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegeTianjinChina
| | - Jinhua Liu
- State Key Laboratory of Experimental HematologyNational Clinical Research Center for Blood DiseasesInstitute of Hematology & Blood Diseases HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegeTianjinChina
| | - Jing Wu
- State Key Laboratory of Experimental HematologyNational Clinical Research Center for Blood DiseasesInstitute of Hematology & Blood Diseases HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegeTianjinChina
| | - Jing Liang
- State Key Laboratory of Experimental HematologyNational Clinical Research Center for Blood DiseasesInstitute of Hematology & Blood Diseases HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegeTianjinChina
| | - Yushan Zhu
- State Key Laboratory of Experimental HematologyState Key Laboratory of Medicinal Chemical BiologyCollege of Life SciencesNankai UniversityTianjinChina
| | - Lihong Shi
- State Key Laboratory of Experimental HematologyState Key Laboratory of Medicinal Chemical BiologyCollege of Life SciencesNankai UniversityTianjinChina
- State Key Laboratory of Experimental HematologyNational Clinical Research Center for Blood DiseasesInstitute of Hematology & Blood Diseases HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegeTianjinChina
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28
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Farkas C, Quiroz A, Alvarez C, Hermosilla V, Aylwin CF, Lomniczi A, Castro AF, Hepp MI, Pincheira R. Characterization of SALL2 Gene Isoforms and Targets Across Cell Types Reveals Highly Conserved Networks. Front Genet 2021; 12:613808. [PMID: 33692826 PMCID: PMC7937961 DOI: 10.3389/fgene.2021.613808] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 01/28/2021] [Indexed: 12/21/2022] Open
Abstract
The SALL2 transcription factor, an evolutionarily conserved gene through vertebrates, is involved in normal development and neuronal differentiation. In disease, SALL2 is associated with eye, kidney, and brain disorders, but mainly is related to cancer. Some studies support a tumor suppressor role and others an oncogenic role for SALL2, which seems to depend on the cancer type. An additional consideration is tissue-dependent expression of different SALL2 isoforms. Human and mouse SALL2 gene loci contain two promoters, each controlling the expression of a different protein isoform (E1 and E1A). Also, several improvements on the human genome assembly and gene annotation through next-generation sequencing technologies reveal correction and annotation of additional isoforms, obscuring dissection of SALL2 isoform-specific transcriptional targets and functions. We here integrated current data of normal/tumor gene expression databases along with ChIP-seq binding profiles to analyze SALL2 isoforms expression distribution and infer isoform-specific SALL2 targets. We found that the canonical SALL2 E1 isoform is one of the lowest expressed, while the E1A isoform is highly predominant across cell types. To dissect SALL2 isoform-specific targets, we analyzed publicly available ChIP-seq data from Glioblastoma tumor-propagating cells and in-house ChIP-seq datasets performed in SALL2 wild-type and E1A isoform knockout HEK293 cells. Another available ChIP-seq data in HEK293 cells (ENCODE Consortium Phase III) overexpressing a non-canonical SALL2 isoform (short_E1A) was also analyzed. Regardless of cell type, our analysis indicates that the SALL2 long E1 and E1A isoforms, but not short_E1A, are mostly contributing to transcriptional control, and reveals a highly conserved network of brain-specific transcription factors (i.e., SALL3, POU3F2, and NPAS3). Our data integration identified a conserved molecular network in which SALL2 regulates genes associated with neural function, cell differentiation, development, and cell adhesion between others. Also, we identified PODXL as a gene that is likely regulated by SALL2 across tissues. Our study encourages the validation of publicly available ChIP-seq datasets to assess a specific gene/isoform’s transcriptional targets. The knowledge of SALL2 isoforms expression and function in different tissue contexts is relevant to understanding its role in disease.
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Affiliation(s)
- Carlos Farkas
- Laboratorio de Transducción de Señales y Cáncer, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Aracelly Quiroz
- Laboratorio de Transducción de Señales y Cáncer, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Claudia Alvarez
- Laboratorio de Transducción de Señales y Cáncer, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Viviana Hermosilla
- Laboratorio de Transducción de Señales y Cáncer, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Carlos F Aylwin
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Portland, OR, United States
| | - Alejandro Lomniczi
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Portland, OR, United States
| | - Ariel F Castro
- Laboratorio de Transducción de Señales y Cáncer, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Matias I Hepp
- Laboratorio de Transducción de Señales y Cáncer, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile.,Laboratorio de Investigación en Ciencias Biomédicas, Departamento de Ciencias Básicas y Morfología, Facultad de Medicina, Universidad Católica de la Santísima Concepción, Concepción, Chile
| | - Roxana Pincheira
- Laboratorio de Transducción de Señales y Cáncer, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
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29
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García-Moreno JF, Romão L. Perspective in Alternative Splicing Coupled to Nonsense-Mediated mRNA Decay. Int J Mol Sci 2020; 21:ijms21249424. [PMID: 33321981 PMCID: PMC7764535 DOI: 10.3390/ijms21249424] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/03/2020] [Accepted: 12/07/2020] [Indexed: 12/19/2022] Open
Abstract
Alternative splicing (AS) of precursor mRNA (pre-mRNA) is a cellular post-transcriptional process that generates protein isoform diversity. Nonsense-mediated RNA decay (NMD) is an mRNA surveillance pathway that recognizes and selectively degrades transcripts containing premature translation-termination codons (PTCs), thereby preventing the production of truncated proteins. Nevertheless, NMD also fine-tunes the gene expression of physiological mRNAs encoding full-length proteins. Interestingly, around one third of all AS events results in PTC-containing transcripts that undergo NMD. Numerous studies have reported a coordinated action between AS and NMD, in order to regulate the expression of several genes, especially those coding for RNA-binding proteins (RBPs). This coupling of AS to NMD (AS-NMD) is considered a gene expression tool that controls the ratio of productive to unproductive mRNA isoforms, ultimately degrading PTC-containing non-functional mRNAs. In this review, we focus on the mechanisms underlying AS-NMD, and how this regulatory process is able to control the homeostatic expression of numerous RBPs, including splicing factors, through auto- and cross-regulatory feedback loops. Furthermore, we discuss the importance of AS-NMD in the regulation of biological processes, such as cell differentiation. Finally, we analyze interesting recent data on the relevance of AS-NMD to human health, covering its potential roles in cancer and other disorders.
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Affiliation(s)
- Juan F. García-Moreno
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal;
- Faculty of Science, BioISI—Biosystems and Integrative Sciences Institute, University of Lisboa, 1749-016 Lisboa, Portugal
| | - Luísa Romão
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016 Lisboa, Portugal;
- Faculty of Science, BioISI—Biosystems and Integrative Sciences Institute, University of Lisboa, 1749-016 Lisboa, Portugal
- Correspondence: ; Tel.: +351-217-508-155
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30
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Ram DR, Kroll K, Reeves RK. Skipped Over: Tuning Natural Killer Cells Toward HIV Through Alternative Splicing. AIDS Res Hum Retroviruses 2020; 36:969-972. [PMID: 32862656 PMCID: PMC7703092 DOI: 10.1089/aid.2020.0116] [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] [Indexed: 11/12/2022] Open
Abstract
Natural killer (NK) cells provide some of the earliest immune responses to infection, but when viruses manipulate or perturb the immune environment to alter NK cell function, this places the host at a disadvantage. Indeed, others and we observe that in the context of HIV/simian immunodeficiency virus (SIV) infection, although NK cells are not infected, they can become dysfunctional over time. Several studies have characterized protein and transcriptional profiles of NK cells during HIV/SIV infection, but none have examined whether the production of alternative transcripts and corresponding isoforms is modulated. This phenomenon occurs broadly in normal biology and in other disease states, and could provide a novel avenue of investigation that may yield better targets to restore or augment NK cell responses to HIV/SIV. Herein, we briefly summarize published and new data that may provide a perspective on how to target NK cell splice variants.
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Affiliation(s)
- Daniel R. Ram
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Kyle Kroll
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - R. Keith Reeves
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
- Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, Massachusetts, USA
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31
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Li J, Comeau HY, Zhang Z, Ren X. Landscape of transcript isoforms in single T cells infiltrating in non-small-cell lung cancer. J Genet Genomics 2020; 47:373-388. [PMID: 32998846 DOI: 10.1016/j.jgg.2020.06.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 06/08/2020] [Accepted: 06/21/2020] [Indexed: 01/14/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) has enabled high-resolution characterization of molecular signatures of tumor-infiltrating lymphocytes. However, analyses at the transcript isoform level are rarely reported. As alternative splicing is critical to T-cell differentiation and activation, here, we proposed a computational method named IDEA (Isoform Detection, Enrichment, and functional Annotation) to comprehensively detect and annotate differentially used isoforms across cell subtypes. We applied IDEA on a scRNA-seq data set of 12,346 T cells from non-small-cell lung cancer (NSCLC). We found that most genes tend to dominantly express one isoform in single T cells, enabling typing T cells based on the isotypes, given a gene. Isotype analysis suggested that tumor-infiltrating T cells significantly preferred specific isotypes for 245 genes in CD8+ T cells and 456 genes in CD4+ T cells. Functional annotation suggests that the preferred isoforms involved in coding/noncoding switches, transcription start site changes, gains/losses of domains, and subcellular translocation. Clonal analysis revealed that isoform switching occurred during T-cell activation/differentiation. Our analysis provides precise characterization of the molecular events in tumor-infiltrating T cells and sheds new light on the regulatory mechanisms of tumor-infiltrating T cells.
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Affiliation(s)
- Jiesheng Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Hannah Y Comeau
- BIOPIC, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Zemin Zhang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China; BIOPIC, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing, 100871, China.
| | - Xianwen Ren
- BIOPIC, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing, 100871, China.
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Dlamini Z, Alaouna M, Cholo MC, Hull R. Is targeting dysregulation in apoptosis splice variants in Mycobacterium tuberculosis (MTB) host interactions and splicing factors resulting in immune evasion by MTB strategies a possibility? Tuberculosis (Edinb) 2020; 124:101964. [PMID: 32829075 DOI: 10.1016/j.tube.2020.101964] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/22/2020] [Accepted: 06/29/2020] [Indexed: 12/17/2022]
Abstract
Mycobacterium tuberculosis (Mtb), is one of the foremost organisms causing mortality in humans, and has been for most of human history. When faced with an infection the human immune system is ordinarily very competent in killing both extracellular and intracellular bacilli. However, Mtb is able to evade the host immune system and is even able to establish a persistent infectious reservoir by "hiding" in the immune cells of the host. While the mechanisms by which the bacteria accomplishes this are not fully understood, it is known that the bacterium can subvert cellular processes in cells such as macrophages that prevent the lysis of the bacteria or the cell undergoing apoptosis. They are also able to interfere with immune cell signalling. One of the greatest effects that Mtb has is too alter the transcriptome of the macrophage. An easy way for the bacterium to accomplish this is to alter the alternative splicing patterns of the host. This can lead to a large change in the population of different protein isoforms, some of which have very different functions when compared to the original protein. At the same time the long history of Mtb infecting humans have led to specific immune reactions that occur in the host immune system in order to fight the infection. Many of these specific reactions involve new isoforms of host defence proteins. In this way the human host can use alternate splicing to create new isoforms of immune- related proteins that are more effective in defending against Mtb.
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Affiliation(s)
- Zodwa Dlamini
- SA-MRC/UP Precision Prevention & Novel Drug Targets for HIV-Associated Cancers Extramural Unit, Pan African Cancer Research Institute, University of Pretoria, Faculty of Health Sciences, Room 4.35 Pathology Building, Hatfield, 0028, South Africa.
| | - Mohammed Alaouna
- Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Moloko C Cholo
- Department of Immunology, Faculty of Health Sciences, University of Pretoria, Pretoria, 0001, South Africa
| | - Rodney Hull
- SA-MRC/UP Precision Prevention & Novel Drug Targets for HIV-Associated Cancers Extramural Unit, Pan African Cancer Research Institute, University of Pretoria, Faculty of Health Sciences, Room 4.35 Pathology Building, Hatfield, 0028, South Africa
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Patrick R, Humphreys DT, Janbandhu V, Oshlack A, Ho JW, Harvey RP, Lo KK. Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data. Genome Biol 2020; 21:167. [PMID: 32641141 PMCID: PMC7341584 DOI: 10.1186/s13059-020-02071-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 06/11/2020] [Indexed: 12/12/2022] Open
Abstract
High-throughput single-cell RNA-seq (scRNA-seq) is a powerful tool for studying gene expression in single cells. Most current scRNA-seq bioinformatics tools focus on analysing overall expression levels, largely ignoring alternative mRNA isoform expression. We present a computational pipeline, Sierra, that readily detects differential transcript usage from data generated by commonly used polyA-captured scRNA-seq technology. We validate Sierra by comparing cardiac scRNA-seq cell types to bulk RNA-seq of matched populations, finding significant overlap in differential transcripts. Sierra detects differential transcript usage across human peripheral blood mononuclear cells and the Tabula Muris, and 3 'UTR shortening in cardiac fibroblasts. Sierra is available at https://github.com/VCCRI/Sierra .
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Affiliation(s)
- Ralph Patrick
- Victor Chang Cardiac Research Institute, 405 Liverpool St., Darlinghurst, 2010 Australia
- St. Vincent’s Clinical School, UNSW Sydney, Kensington, 2052 Australia
| | - David T. Humphreys
- Victor Chang Cardiac Research Institute, 405 Liverpool St., Darlinghurst, 2010 Australia
- St. Vincent’s Clinical School, UNSW Sydney, Kensington, 2052 Australia
| | - Vaibhao Janbandhu
- Victor Chang Cardiac Research Institute, 405 Liverpool St., Darlinghurst, 2010 Australia
- St. Vincent’s Clinical School, UNSW Sydney, Kensington, 2052 Australia
| | - Alicia Oshlack
- Murdoch Children’s Research Institute, Parkville, 3052 Victoria Australia
- Peter MacCallum Cancer Centre, Research Division, 305 Grattan Street, Melbourne, 3000 Victoria Australia
| | - Joshua W.K. Ho
- Victor Chang Cardiac Research Institute, 405 Liverpool St., Darlinghurst, 2010 Australia
- St. Vincent’s Clinical School, UNSW Sydney, Kensington, 2052 Australia
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Richard P. Harvey
- Victor Chang Cardiac Research Institute, 405 Liverpool St., Darlinghurst, 2010 Australia
- St. Vincent’s Clinical School, UNSW Sydney, Kensington, 2052 Australia
- School of Biotechnology and Biomolecular Science, UNSW Sydney, Kensington, 2052 Australia
| | - Kitty K. Lo
- School of Mathematics and Statistics, Faculty of Science, The University of Sydney, Camperdown, 2006 Australia
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Guo G, Wang H, Shi X, Ye L, Yan K, Chen Z, Zhang H, Jin Z, Xue X. Disease Activity-Associated Alteration of mRNA m 5 C Methylation in CD4 + T Cells of Systemic Lupus Erythematosus. Front Cell Dev Biol 2020; 8:430. [PMID: 32582707 PMCID: PMC7291606 DOI: 10.3389/fcell.2020.00430] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/08/2020] [Indexed: 01/17/2023] Open
Abstract
Epigenetic processes including RNA methylation, post-translational modifications, and non-coding RNA expression have been associated with the heritable risks of systemic lupus erythematosus (SLE). In this study, we aimed to explore the dysregulated expression of 5-methylcytosine (m5C) in CD4+ T cells from patients with SLE and the potential function of affected mRNAs in SLE pathogenesis. mRNA methylation profiles were ascertained through chromatography-coupled triple quadrupole mass spectrometry in CD4+ T cells from two pools of patients with SLE exhibiting stable activity, two pools with moderate-to-major activity, and two pools of healthy controls (HCs). Simultaneously, mRNA methylation profiles and expression profiling were performed using RNA-Bis-Seq and RNA-Seq, respectively. Integrated mRNA methylation and mRNA expression bioinformatics analysis was comprehensively performed. mRNA methyltransferase NSUN2 expression was validated in CD4+ T cells from 27 patients with SLE and 28 HCs using real-time polymerase chain reaction and western blot analyses. Hypomethylated-mRNA profiles of NSUN2-knockdown HeLa cells and of CD4+ T cells of patients with SLE were jointly analyzed using bioinformatics. Eleven methylation modifications (including elevated Am, 3′OMeA, m1A, and m6A and decreased Ψ, m3C, m1G, m5U, and t6A levels) were detected in CD4+ T cells of patients with SLE. Additionally, decreased m5C levels, albeit increased number of m5C-containing mRNAs, were observed in CD4+ T cells of patients with SLE compared with that in CD4+ T cells of HCs. m5C site distribution in mRNA transcripts was highly conserved and enriched in mRNA translation initiation sites. In particular, hypermethylated m5C or/and significantly up-regulated genes in SLE were significantly involved in immune-related and inflammatory pathways, including immune system, cytokine signaling pathway, and interferon signaling. Compared to that in HCs, NSUN2 expression was significantly lower in SLE CD4+ T cells. Notably, hypomethylated m5C genes in SLE and in NSUN2-knockdown HeLa cells revealed linkage between eukaryotic translation elongation and termination, and mRNA metabolism. Our study identified novel aberrant m5C mRNAs relevant to critical immune pathways in CD4+ T cells from patients with SLE. These data provide valuable perspectives for future studies of the multifunctionality and post-transcriptional significance of mRNA m5C modification in SLE.
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Affiliation(s)
- Gangqiang Guo
- School of Life Sciences and Technology, Tongji University, Shanghai, China.,Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Huijing Wang
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xinyu Shi
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Lele Ye
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China.,Department of Gynecologic Oncology, Wenzhou Central Hospital, Wenzhou, China
| | - Kejing Yan
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Zhiyuan Chen
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Huidi Zhang
- Department of Nephrology, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Zibing Jin
- Laboratory for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research, Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Xiangyang Xue
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Institute of Tropical Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
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35
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Byun S, Han S, Zheng Y, Planelles V, Lee Y. The landscape of alternative splicing in HIV-1 infected CD4 T-cells. BMC Med Genomics 2020; 13:38. [PMID: 32241262 PMCID: PMC7118826 DOI: 10.1186/s12920-020-0680-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Background Elucidating molecular mechanisms that are altered during HIV-1 infection may provide a better understanding of the HIV-1 life cycle and how it interacts with infected T-cells. One such mechanism is alternative splicing (AS), which has been studied for HIV-1 itself, but no systematic analysis has yet been performed on infected T-cells. We hypothesized that AS patterns in infected T-cells may illuminate the molecular mechanisms underlying HIV-1 infection and identify candidate molecular markers for specifically targeting infected T-cells. Methods We downloaded previously published raw RNA-seq data obtained from HIV-1 infected and non-infected T-cells. We estimated percent spliced in (PSI) levels for each AS exon, then identified differential AS events in the infected cells (FDR < 0.05, PSI difference > 0.1). We performed functional gene set enrichment analysis on the genes with differentially expressed AS exons to identify their functional roles. In addition, we used RT-PCR to validate differential alternative splicing events in cyclin T1 (CCNT1) as a case study. Results We identified 427 candidate genes with differentially expressed AS exons in infected T-cells, including 20 genes related to cell surface, 35 to kinases, and 121 to immune-related genes. In addition, protein-protein interaction analysis identified six essential subnetworks related to the viral life cycle, including Transcriptional regulation by TP53, Class I MHC mediated antigen, G2/M transition, and late phase of HIV life cycle. CCNT1 exon 7 was more frequently skipped in infected T-cells, leading to loss of the key Cyclin_N motif and affecting HIV-1 transcriptional elongation. Conclusions Our findings may provide new insight into systemic host AS regulation under HIV-1 infection and may provide useful initial candidates for the discovery of new markers for specifically targeting infected T-cells.
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Affiliation(s)
- Seyoun Byun
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Seonggyun Han
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Yue Zheng
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Vicente Planelles
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Younghee Lee
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA. .,Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA.
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36
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Janssen WJ, Danhorn T, Harris C, Mould KJ, Lee FFY, Hedin BR, D'Alessandro A, Leach SM, Alper S. Inflammation-Induced Alternative Pre-mRNA Splicing in Mouse Alveolar Macrophages. G3 (BETHESDA, MD.) 2020; 10:555-567. [PMID: 31810980 PMCID: PMC7003074 DOI: 10.1534/g3.119.400935] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 11/26/2019] [Indexed: 12/16/2022]
Abstract
Alveolar macrophages serve as central orchestrators of inflammatory responses in the lungs, both initiating their onset and promoting their resolution. However, the mechanisms that program macrophages for these dynamic responses are not fully understood. Over 95% of all mammalian genes undergo alternative pre-mRNA splicing. While alternative splicing has been shown to regulate inflammatory responses in macrophages in vitro, it has not been investigated on a genome-wide scale in vivo Here we used RNAseq to investigate alternative pre-mRNA splicing in alveolar macrophages isolated from lipopolysaccharide (LPS)-treated mice during the peak of inflammation and during its resolution. We found that lung inflammation induced substantial alternative pre-mRNA splicing in alveolar macrophages. The number of changes in isoform usage was greatest at the peak of inflammation and involved multiple classes of alternative pre-mRNA splicing events. Comparative pathway analysis of inflammation-induced changes in alternative pre-mRNA splicing and differential gene expression revealed overlap of pathways enriched for immune responses such as chemokine signaling and cellular metabolism. Moreover, alternative pre-mRNA splicing of genes in metabolic pathways differed in tissue resident vs. recruited (blood monocyte-derived) alveolar macrophages and corresponded to changes in core metabolism, including a switch to Warburg-like metabolism in recruited macrophages with increased glycolysis and decreased flux through the tricarboxylic acid cycle.
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Affiliation(s)
- William J Janssen
- Department of Medicine
- Division of Pulmonary Sciences and Critical Care Medicine, and
| | | | - Chelsea Harris
- Center for Genes, Environment and Health, and
- Department of Biomedical Research, National Jewish Health, Denver, CO, 80206
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, 80045
| | - Kara J Mould
- Department of Medicine
- Division of Pulmonary Sciences and Critical Care Medicine, and
| | - Frank Fang-Yao Lee
- Center for Genes, Environment and Health, and
- Department of Biomedical Research, National Jewish Health, Denver, CO, 80206
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, 80045
| | - Brenna R Hedin
- Center for Genes, Environment and Health, and
- Department of Biomedical Research, National Jewish Health, Denver, CO, 80206
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, 80045
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO, 80045
| | - Sonia M Leach
- Center for Genes, Environment and Health, and
- Department of Biomedical Research, National Jewish Health, Denver, CO, 80206
| | - Scott Alper
- Center for Genes, Environment and Health, and
- Department of Biomedical Research, National Jewish Health, Denver, CO, 80206
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, 80045
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Sasanuma H, Ozawa M, Yoshida N. RNA-binding protein Ptbp1 is essential for BCR-mediated antibody production. Int Immunol 2020; 31:157-166. [PMID: 30476084 PMCID: PMC6400050 DOI: 10.1093/intimm/dxy077] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/21/2018] [Indexed: 11/22/2022] Open
Abstract
The RNA-binding protein polypyrimidine tract-binding protein-1 (Ptbp1) binds to the pyrimidine-rich sequence of target RNA and controls gene expression via post-transcriptional regulation such as alternative splicing. Although Ptbp1 is highly expressed in B lymphocytes, its role to date is largely unknown. To clarify the role of Ptbp1 in B-cell development and function, we generated B-cell-specific Ptbp1-deficient (P1BKO) mice. B-cell development in the bone marrow, spleen and peritoneal cavity of the P1BKO mice was nearly normal. However, the P1BKO mice had significantly lower levels of natural antibodies in serum compared with those of the control mice. To investigate the effect of Ptbp1 deficiency on the immune response in vivo, we immunized the P1BKO mice with T-cell-independent type-2 (TI-2) antigen NP-Ficoll and T-cell-dependent (TD) antigen NP-CGG. We found that B-cell-specific Ptbp1 deficiency causes an immunodeficiency phenotype due to defective production of antibody against both TI-2 and TD antigen. This immunodeficiency was accompanied by impaired B-cell receptor (BCR)-mediated B-cell activation and plasmablast generation. These findings demonstrate that Ptbp1 is essential for the humoral immune response.
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Affiliation(s)
- Hiroki Sasanuma
- Laboratory of Developmental Genetics, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Shirokanedai, Minato-ku, Tokyo, Japan
| | - Manabu Ozawa
- Laboratory of Reproductive Systems Biology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Shirokanedai, Minato-ku, Tokyo, Japan
| | - Nobuaki Yoshida
- Laboratory of Developmental Genetics, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Shirokanedai, Minato-ku, Tokyo, Japan
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38
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Kim TR, Jeong HH, Sohn KA. Topological integration of RPPA proteomic data with multi-omics data for survival prediction in breast cancer via pathway activity inference. BMC Med Genomics 2019; 12:94. [PMID: 31296204 PMCID: PMC6624183 DOI: 10.1186/s12920-019-0511-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The analysis of integrated multi-omics data enables the identification of disease-related biomarkers that cannot be identified from a single omics profile. Although protein-level data reflects the cellular status of cancer tissue more directly than gene-level data, past studies have mainly focused on multi-omics integration using gene-level data as opposed to protein-level data. However, the use of protein-level data (such as mass spectrometry) in multi-omics integration has some limitations. For example, the correlation between the characteristics of gene-level data (such as mRNA) and protein-level data is weak, and it is difficult to detect low-abundance signaling proteins that are used to target cancer. The reverse phase protein array (RPPA) is a highly sensitive antibody-based quantification method for signaling proteins. However, the number of protein features in RPPA data is extremely low compared to the number of gene features in gene-level data. In this study, we present a new method for integrating RPPA profiles with RNA-Seq and DNA methylation profiles for survival prediction based on the integrative directed random walk (iDRW) framework proposed in our previous study. In the iDRW framework, each omics profile is merged into a single pathway profile that reflects the topological information of the pathway. In order to address the sparsity of RPPA profiles, we employ the random walk with restart (RWR) approach on the pathway network. RESULTS Our model was validated using survival prediction analysis for a breast cancer dataset from The Cancer Genome Atlas. Our proposed model exhibited improved performance compared with other methods that utilize pathway information and also out-performed models that did not include the RPPA data utilized in our study. The risk pathways identified for breast cancer in this study were closely related to well-known breast cancer risk pathways. CONCLUSIONS Our results indicated that RPPA data is useful for survival prediction for breast cancer patients under our framework. We also observed that iDRW effectively integrates RNA-Seq, DNA methylation, and RPPA profiles, while variation in the composition of the omics data can affect both prediction performance and risk pathway identification. These results suggest that omics data composition is a critical parameter for iDRW.
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Affiliation(s)
- Tae Rim Kim
- Department of Computer Engineering, Ajou University, Suwon, 16499 South Korea
| | - Hyun-Hwan Jeong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030 USA
| | - Kyung-Ah Sohn
- Department of Computer Engineering, Ajou University, Suwon, 16499 South Korea
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Ashraf U, Benoit-Pilven C, Lacroix V, Navratil V, Naffakh N. Advances in Analyzing Virus-Induced Alterations of Host Cell Splicing. Trends Microbiol 2018; 27:268-281. [PMID: 30577974 DOI: 10.1016/j.tim.2018.11.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/19/2018] [Accepted: 11/09/2018] [Indexed: 12/14/2022]
Abstract
Alteration of host cell splicing is a common feature of many viral infections which is underappreciated because of the complexity and technical difficulty of studying alternative splicing (AS) regulation. Recent advances in RNA sequencing technologies revealed that up to several hundreds of host genes can show altered mRNA splicing upon viral infection. The observed changes in AS events can be either a direct consequence of viral manipulation of the host splicing machinery or result indirectly from the virus-induced innate immune response or cellular damage. Analysis at a higher resolution with single-cell RNAseq, and at a higher scale with the integration of multiple omics data sets in a systems biology perspective, will be needed to further comprehend this complex facet of virus-host interactions.
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Affiliation(s)
- Usama Ashraf
- Institut Pasteur, Unité de Génétique Moléculaire des Virus à ARN, Département de Virologie, F-75015 Paris, France; CNRS UMR3569, F-75015 Paris, France; Université Paris Diderot, Sorbonne Paris Cité EA302, F-75015 Paris, France
| | - Clara Benoit-Pilven
- INSERM U1028; CNRS UMR5292, Lyon Neuroscience Research Center, Genetic of Neuro-development Anomalies Team, F-69000 Lyon, France; Université Claude Bernard Lyon 1, CNRS UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France; EPI ERABLE, INRIA Grenoble Rhône-Alpes, F-38330 Montbonnot Saint-Martin, France
| | - Vincent Lacroix
- Université Claude Bernard Lyon 1, CNRS UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France; EPI ERABLE, INRIA Grenoble Rhône-Alpes, F-38330 Montbonnot Saint-Martin, France
| | - Vincent Navratil
- PRABI, Rhône Alpes Bioinformatics Center, UCBL, Université Claude Bernard Lyon 1, F-69000 Lyon, France; European Virus Bioinformatics Center, Leutragraben 1, D-07743 Jena, Germany
| | - Nadia Naffakh
- Institut Pasteur, Unité de Génétique Moléculaire des Virus à ARN, Département de Virologie, F-75015 Paris, France; CNRS UMR3569, F-75015 Paris, France; Université Paris Diderot, Sorbonne Paris Cité EA302, F-75015 Paris, France.
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40
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Valdes-Mora F, Handler K, Law AMK, Salomon R, Oakes SR, Ormandy CJ, Gallego-Ortega D. Single-Cell Transcriptomics in Cancer Immunobiology: The Future of Precision Oncology. Front Immunol 2018; 9:2582. [PMID: 30483257 PMCID: PMC6240655 DOI: 10.3389/fimmu.2018.02582] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 10/19/2018] [Indexed: 12/21/2022] Open
Abstract
Cancer is a heterogeneous and complex disease. Tumors are formed by cancer cells and a myriad of non-cancerous cell types that together with the extracellular matrix form the tumor microenvironment. These cancer-associated cells and components contribute to shape the progression of cancer and are deeply involved in patient outcome. The immune system is an essential part of the tumor microenvironment, and induction of cancer immunotolerance is a necessary step involved in tumor formation and growth. Immune mechanisms are intimately associated with cancer progression, invasion, and metastasis; as well as to tumor dormancy and modulation of sensitivity to drug therapy. Transcriptome analyses have been extensively used to understand the heterogeneity of tumors, classifying tumors into molecular subtypes and establishing signatures that predict response to therapy and patient outcomes. However, the classification of the tumor cell diversity and specially the identification of rare populations has been limited in these transcriptomic analyses of bulk tumor cell populations. Massively-parallel single-cell RNAseq analysis has emerged as a powerful method to unravel heterogeneity and to study rare cell populations in cancer, through unsupervised sampling and modeling of transcriptional states in single cells. In this context, the study of the role of the immune system in cancer would benefit from single cell approaches, as it will enable the characterization and/or discovery of the cell types and pathways involved in cancer immunotolerance otherwise missed in bulk transcriptomic information. Thus, the analysis of gene expression patterns at single cell resolution holds the potential to provide key information to develop precise and personalized cancer treatment including immunotherapy. This review is focused on the latest single-cell RNAseq methodologies able to agnostically study thousands of tumor cells as well as targeted single-cell RNAseq to study rare populations within tumors. In particular, we will discuss methods to study the immune system in cancer. We will also discuss the current challenges to the study of cancer at the single cell level and the potential solutions to the current approaches.
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Affiliation(s)
- Fatima Valdes-Mora
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Kristina Handler
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Andrew M K Law
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Robert Salomon
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Samantha R Oakes
- St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.,The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Christopher J Ormandy
- St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.,The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - David Gallego-Ortega
- St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.,The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
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41
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Han AL, Kim HR, Choi KH, Ryu JW, Hwang KE, So HS, Park MC, Zhu M, Huang Y, Lee YJ, Park DS. Expression Profile of Three Splicing Factors in Pleural Cells Based on the Underlying Etiology and Its Clinical Values in Patients with Pleural Effusion. Transl Oncol 2018; 11:147-156. [PMID: 29288986 PMCID: PMC6002346 DOI: 10.1016/j.tranon.2017.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 12/07/2017] [Indexed: 11/20/2022] Open
Abstract
Splicing factors (SFs) are involved in oncogenesis or immune modulation, the common underlying processes giving rise to pleural effusion (PE). The expression profiles of three SFs (HNRNPA1, SRSF1, and SRSF3) and their clinical values have never been assessed in PE. The three SFs (in pellets of PE) and conventional tumor markers were analyzed using PE samples in patients with PE (N = 336). The sum of higher-molecular weight (Mw) forms of HNRNPA1 (Sum-HMws-HNRNPA1) and SRSF1 (Sum-HMws-SRSF1) and SRSF3 levels were upregulated in malignant PE (MPE) compared to benign PE (BPE); they were highest in cytology-positive MPE, followed by tuberculous PE and parapneumonic PE. Meanwhile, the lowest-Mw HNRNPA1 (LMw-HNRNPA1) and SRSF1 (LMw-SRSF1) levels were not upregulated in MPE. Sum-HMws-HNRNPA1, Sum-HMws-SRSF1, and SRSF3, but neither LMw-HNRNPA1 nor LMw-SRSF1, showed positive correlations with cancer cell percentages in MPE. The detection accuracy for MPE was high in the order of carcinoembryonic antigen (CEA, 85%), Sum-HMws-HNRNPA1 (76%), Sum-HMws-SRSF1 (68%), SRSF3, cytokeratin-19 fragments (CYFRA 21-1), LMw-HNRNPA1, and LMw-SRSF1. Sum-HMws-HNRNPA1 detected more than half of the MPE cases that were undetected by cytology and CEA. Sum-HMws-HNRNPA1, but not other SFs or conventional tumor markers, showed an association with longer overall survival among patients with MPE receiving chemotherapy. Our results demonstrated different levels of the three SFs with their Mw-specific profiles depending on the etiology of PE. We suggest that Sum-HMws-HNRNPA1 is a supplementary diagnostic marker for MPE and a favorable prognostic indicator for patients with MPE receiving chemotherapy.
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Affiliation(s)
- A-Lum Han
- Department of Family Medicine, School of Medicine, Wonkwang University, Iksan, 54538, Korea
| | - Hak-Ryul Kim
- Department of Internal Medicine, School of Medicine, Wonkwang University, Iksan, 54538, Korea
| | - Keum-Ha Choi
- Department of Pathology, School of Medicine, Wonkwang University, Iksan, 54538, Korea
| | - Jae-Won Ryu
- School of Medicine, Catholic University of Daegu, Daegu 42472, Korea
| | - Ki-Eun Hwang
- Department of Internal Medicine, School of Medicine, Wonkwang University, Iksan, 54538, Korea
| | - Hong-Seob So
- Department of Microbiology, School of Medicine, Wonkwang University, Iksan, 54538, Korea
| | - Min-Cheol Park
- Department of Oriental Medical Ophthalmology & Otolaryngology & Dermatology, College of Oriental Medicine, Wonkwang University, Iksan, 54538, Korea
| | - Mengyu Zhu
- Department of Laboratory Medicine, School of Medicine, Wonkwang University, Iksan, 54538, Korea
| | - Yuya Huang
- Department of Laboratory Medicine, School of Medicine, Wonkwang University, Iksan, 54538, Korea
| | - Young-Jin Lee
- Department of Laboratory Medicine, School of Medicine, Wonkwang University, Iksan, 54538, Korea
| | - Do-Sim Park
- Department of Laboratory Medicine, School of Medicine, Wonkwang University, Iksan, 54538, Korea; Wonkwang Institute of Clinical Medicine, Wonkwang University Hospital, Iksan, 54538, Korea; Institute of Wonkwang Medical Science, School of Medicine, Wonkwang University, Iksan, 54538, Korea.
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42
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RNA-binding proteins control gene expression and cell fate in the immune system. Nat Immunol 2018; 19:120-129. [PMID: 29348497 DOI: 10.1038/s41590-017-0028-4] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 11/29/2017] [Indexed: 12/19/2022]
Abstract
RNA-binding proteins (RBPs) are essential for the development and function of the immune system. They interact dynamically with RNA to control its biogenesis and turnover by transcription-dependent and transcription-independent mechanisms. In this Review, we discuss the molecular mechanisms by which RBPs allow gene expression changes to occur at different speeds and to varying degrees, and which RBPs regulate the diversity of the transcriptome and proteome. These proteins are nodes for integration of transcriptional and signaling networks and are intimately linked to intermediary metabolism. They are essential components of regulatory feedback mechanisms that maintain immune tolerance and limit inflammation. The role of RBPs in malignancy and autoimmunity has led to their emergence as targets for the development of new therapeutic modalities.
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43
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Monzón-Casanova E, Screen M, Díaz-Muñoz MD, Coulson RMR, Bell SE, Lamers G, Solimena M, Smith CWJ, Turner M. The RNA-binding protein PTBP1 is necessary for B cell selection in germinal centers. Nat Immunol 2018; 19:267-278. [PMID: 29358707 PMCID: PMC5842895 DOI: 10.1038/s41590-017-0035-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 12/12/2017] [Indexed: 12/17/2022]
Abstract
Antibody affinity maturation occurs in germinal centres (GC) where B
cells cycle between the light zone (LZ) and the dark zone. In the LZ GC B cells
bearing immunoglobulins with the highest affinity for antigen receive positive
selection signals from T helper cells that promotes their rapid proliferation.
Here we show that the RNA binding protein PTBP1 is necessary for the progression
of GC B cells through late S-phase of the cell cycle and for affinity
maturation. PTBP1 is required for the proper expression of the c-MYC-dependent
gene program induced in GC B cells receiving T cell help and directly regulates
the alternative splicing and abundance of transcripts increased during positive
selection to promote proliferation.
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Affiliation(s)
- Elisa Monzón-Casanova
- Laboratory of Lymphocyte Signaling and Development, The Babraham Institute, Cambridge, UK.,Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Michael Screen
- Laboratory of Lymphocyte Signaling and Development, The Babraham Institute, Cambridge, UK
| | - Manuel D Díaz-Muñoz
- Laboratory of Lymphocyte Signaling and Development, The Babraham Institute, Cambridge, UK
| | - Richard M R Coulson
- Laboratory of Lymphocyte Signaling and Development, The Babraham Institute, Cambridge, UK
| | - Sarah E Bell
- Laboratory of Lymphocyte Signaling and Development, The Babraham Institute, Cambridge, UK
| | - Greta Lamers
- Laboratory of Lymphocyte Signaling and Development, The Babraham Institute, Cambridge, UK
| | - Michele Solimena
- Molecular Diabetology, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany.,Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany.,Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany.,German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | | | - Martin Turner
- Laboratory of Lymphocyte Signaling and Development, The Babraham Institute, Cambridge, UK.
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44
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Lichti J, Gallus C, Glasmacher E. Immune Responses – Transcriptional and Post-Transcriptional Networks Pass the Baton. Trends Biochem Sci 2018; 43:1-4. [DOI: 10.1016/j.tibs.2017.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/31/2017] [Accepted: 11/03/2017] [Indexed: 12/17/2022]
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