1
|
Zhang J, Xu X, Deng H, Liu L, Xiang Y, Feng J. Overcoming cancer drug-resistance calls for novel strategies targeting abnormal alternative splicing. Pharmacol Ther 2024; 261:108697. [PMID: 39025436 DOI: 10.1016/j.pharmthera.2024.108697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 05/12/2024] [Accepted: 07/15/2024] [Indexed: 07/20/2024]
Abstract
Abnormal gene alternative splicing (AS) events are strongly associated with cancer progression. Here, we summarize AS events that contribute to the development of drug resistance and classify them into three categories: alternative cis-splicing (ACS), alternative trans-splicing (ATS), and alternative back-splicing (ABS). The regulatory mechanisms underlying AS processes through cis-acting regulatory elements and trans-acting factors are comprehensively described, and the distinct functions of spliced variants, including linear spliced variants derived from ACS, chimeric spliced variants arising from ATS, and circRNAs generated through ABS, are discussed. The identification of dysregulated spliced variants, which contribute to drug resistance and hinder effective cancer treatment, suggests that abnormal AS processes may together serve as a precise regulatory mechanism enabling drug-resistant cancer cell survival or, alternatively, represent an evolutionary pathway for cancer cells to adapt to changes in the external environment. Moreover, this review summarizes recent advancements in treatment approaches targeting AS-associated drug resistance, focusing on cis-acting regulatory elements, trans-acting factors, and specific spliced variants. Collectively, gaining an in-depth understanding of the mechanisms underlying aberrant alternative splicing events and developing strategies to target this process hold great promise for overcoming cancer drug resistance.
Collapse
Affiliation(s)
- Ji Zhang
- Department of Anesthesiology, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan Province 646000, China; Anesthesiology and Critical Care Medicine Key Laboratory of Luzhou, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan Province 646000, China
| | - Xinyu Xu
- Department of Anesthesiology, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan Province 646000, China; Anesthesiology and Critical Care Medicine Key Laboratory of Luzhou, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan Province 646000, China
| | - Hongwei Deng
- Department of Anesthesiology, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan Province 646000, China; Anesthesiology and Critical Care Medicine Key Laboratory of Luzhou, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan Province 646000, China
| | - Li Liu
- Department of Anesthesiology, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan Province 646000, China; Anesthesiology and Critical Care Medicine Key Laboratory of Luzhou, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan Province 646000, China
| | - Yuancai Xiang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou city, Sichuan 646000, China.
| | - Jianguo Feng
- Department of Anesthesiology, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan Province 646000, China; Anesthesiology and Critical Care Medicine Key Laboratory of Luzhou, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan Province 646000, China; Nucleic Acid Medicine of Luzhou Key Laboratory, Southwest Medical University, Luzhou, Sichuan Province 646000, China.
| |
Collapse
|
2
|
Emilius L, Bremm F, Binder AK, Schaft N, Dörrie J. Tumor Antigens beyond the Human Exome. Int J Mol Sci 2024; 25:4673. [PMID: 38731892 PMCID: PMC11083240 DOI: 10.3390/ijms25094673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
With the advent of immunotherapeutics, a new era in the combat against cancer has begun. Particularly promising are neo-epitope-targeted therapies as the expression of neo-antigens is tumor-specific. In turn, this allows the selective targeting and killing of cancer cells whilst healthy cells remain largely unaffected. So far, many advances have been made in the development of treatment options which are tailored to the individual neo-epitope repertoire. The next big step is the achievement of efficacious "off-the-shelf" immunotherapies. For this, shared neo-epitopes propose an optimal target. Given the tremendous potential, a thorough understanding of the underlying mechanisms which lead to the formation of neo-antigens is of fundamental importance. Here, we review the various processes which result in the formation of neo-epitopes. Broadly, the origin of neo-epitopes can be categorized into three groups: canonical, noncanonical, and viral neo-epitopes. For the canonical neo-antigens that arise in direct consequence of somatic mutations, we summarize past and recent findings. Beyond that, our main focus is put on the discussion of noncanonical and viral neo-epitopes as we believe that targeting those provides an encouraging perspective to shape the future of cancer immunotherapeutics.
Collapse
Affiliation(s)
- Lisabeth Emilius
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (L.E.); (F.B.); (A.K.B.); (J.D.)
- Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
- Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
| | - Franziska Bremm
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (L.E.); (F.B.); (A.K.B.); (J.D.)
- Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
- Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
| | - Amanda Katharina Binder
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (L.E.); (F.B.); (A.K.B.); (J.D.)
- Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
- Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
| | - Niels Schaft
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (L.E.); (F.B.); (A.K.B.); (J.D.)
- Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
- Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
| | - Jan Dörrie
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; (L.E.); (F.B.); (A.K.B.); (J.D.)
- Comprehensive Cancer Center Erlangen European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
- Bavarian Cancer Research Center (BZKF), 91054 Erlangen, Germany
| |
Collapse
|
3
|
Neoantigens: promising targets for cancer therapy. Signal Transduct Target Ther 2023; 8:9. [PMID: 36604431 PMCID: PMC9816309 DOI: 10.1038/s41392-022-01270-x] [Citation(s) in RCA: 173] [Impact Index Per Article: 173.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/14/2022] [Accepted: 11/27/2022] [Indexed: 01/07/2023] Open
Abstract
Recent advances in neoantigen research have accelerated the development and regulatory approval of tumor immunotherapies, including cancer vaccines, adoptive cell therapy and antibody-based therapies, especially for solid tumors. Neoantigens are newly formed antigens generated by tumor cells as a result of various tumor-specific alterations, such as genomic mutation, dysregulated RNA splicing, disordered post-translational modification, and integrated viral open reading frames. Neoantigens are recognized as non-self and trigger an immune response that is not subject to central and peripheral tolerance. The quick identification and prediction of tumor-specific neoantigens have been made possible by the advanced development of next-generation sequencing and bioinformatic technologies. Compared to tumor-associated antigens, the highly immunogenic and tumor-specific neoantigens provide emerging targets for personalized cancer immunotherapies, and serve as prospective predictors for tumor survival prognosis and immune checkpoint blockade responses. The development of cancer therapies will be aided by understanding the mechanism underlying neoantigen-induced anti-tumor immune response and by streamlining the process of neoantigen-based immunotherapies. This review provides an overview on the identification and characterization of neoantigens and outlines the clinical applications of prospective immunotherapeutic strategies based on neoantigens. We also explore their current status, inherent challenges, and clinical translation potential.
Collapse
|
4
|
Siebert AE, Corll J, Paige Gronevelt J, Levine L, Hobbs LM, Kenney C, Powell CLE, Battistuzzi FU, Davenport R, Mark Settles A, Brad Barbazuk W, Westrick RJ, Madlambayan GJ, Lal S. Genetic analysis of human RNA binding motif protein 48 (RBM48) reveals an essential role in U12-type intron splicing. Genetics 2022; 222:iyac129. [PMID: 36040194 PMCID: PMC9526058 DOI: 10.1093/genetics/iyac129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
U12-type or minor introns are found in most multicellular eukaryotes and constitute ∼0.5% of all introns in species with a minor spliceosome. Although the biological significance for the evolutionary conservation of U12-type introns is debated, mutations disrupting U12 splicing cause developmental defects in both plants and animals. In human hematopoietic stem cells, U12 splicing defects disrupt proper differentiation of myeloid lineages and are associated with myelodysplastic syndrome, predisposing individuals to acute myeloid leukemia. Mutants in the maize ortholog of RNA binding motif protein 48 (RBM48) have aberrant U12-type intron splicing. Human RBM48 was recently purified biochemically as part of the minor spliceosome and shown to recognize the 5' end of the U6atac snRNA. In this report, we use CRISPR/Cas9-mediated ablation of RBM48 in human K-562 cells to show the genetic function of RBM48. RNA-seq analysis comparing wild-type and mutant K-562 genotypes found that 48% of minor intron-containing genes have significant U12-type intron retention in RBM48 mutants. Comparing these results to maize rbm48 mutants defined a subset of minor intron-containing genes disrupted in both species. Mutations in the majority of these orthologous minor intron-containing genes have been reported to cause developmental defects in both plants and animals. Our results provide genetic evidence that the primary defect of human RBM48 mutants is aberrant U12-type intron splicing, while a comparison of human and maize RNA-seq data identifies candidate genes likely to mediate mutant phenotypes of U12-type splicing defects.
Collapse
Affiliation(s)
- Amy E Siebert
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Jacob Corll
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - J Paige Gronevelt
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Laurel Levine
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Linzi M Hobbs
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Catalina Kenney
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Christopher L E Powell
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Fabia U Battistuzzi
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Ruth Davenport
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - A Mark Settles
- Horticultural Sciences Department and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA
| | - W Brad Barbazuk
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Randal J Westrick
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Gerard J Madlambayan
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Shailesh Lal
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| |
Collapse
|
5
|
De Kesel J, Fijalkowski I, Taylor J, Ntziachristos P. Splicing dysregulation in human hematologic malignancies: beyond splicing mutations. Trends Immunol 2022; 43:674-686. [PMID: 35850914 DOI: 10.1016/j.it.2022.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/09/2022] [Accepted: 06/14/2022] [Indexed: 11/16/2022]
Abstract
Splicing is a fundamental process in pre-mRNA maturation. Whereas alternative splicing (AS) enriches the diversity of the proteome, its aberrant regulation can drive oncogenesis. So far, most attention has been given to spliceosome mutations (SMs) in the context of splicing dysregulation in hematologic diseases. However, in recent years, post-translational modifications (PTMs) and transcriptional alterations of splicing factors (SFs), just as epigenetic signatures, have all been shown to contribute to global splicing dysregulation as well. In addition, the contribution of aberrant splicing to the neoantigen repertoire of cancers has been recognized. With the pressing need for novel therapeutics to combat blood cancers, this article provides an overview of emerging mechanisms that contribute to aberrant splicing, as well as their clinical potential.
Collapse
Affiliation(s)
- Jonas De Kesel
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent, Ghent, Belgium; Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Igor Fijalkowski
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent, Ghent, Belgium; Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Justin Taylor
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Panagiotis Ntziachristos
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent, Ghent, Belgium; Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.
| |
Collapse
|
6
|
Noy-Lotan S, Krasnov T, Dgany O, Jeison M, Yanir AD, Gilad O, Toledano H, Barzilai-Birenboim S, Yacobovich J, Izraeli S, Tamary H, Steinberg-Shemer O. Incorporation of somatic panels for the detection of haematopoietic transformation in children and young adults with leukaemia predisposition syndromes and with acquired cytopenias. Br J Haematol 2020; 193:570-580. [PMID: 33368157 DOI: 10.1111/bjh.17285] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/25/2020] [Indexed: 12/16/2022]
Abstract
Detection of somatic mutations may help verify the diagnosis of myelodysplastic syndrome (MDS) in patients with persistent cytopenias or with MDS-predisposition syndromes, prior to the development of overt leukemia. However, the spectrum and consequences of acquired changes in paediatric patients have not been fully evaluated, and especially not in the context of an underlying syndrome. We incorporated a targeted next-generation-sequencing panel of 54 genes for the detection of somatic mutations in paediatric and young adult patients with inherited or acquired cytopenias. Sixty-five patients were included in this study, of whom 17 (26%) had somatic mutations. We detected somatic mutations in 20% of individuals with inherited MDS-predisposition syndromes, including in patients with severe congenital neutropenia and Fanconi anaemia, and with germline mutations in SAMD9L. Thirty-eight per cent of children with acquired cytopenias and suspected MDS had somatic changes, most commonly in genes related to signal transduction and transcription. Molecularly abnormal clones often preceded cytogenetic changes. Thus, routine performance of somatic panels can establish the diagnosis of MDS and determine the optimal timing of haematopoietic stem cell transplantation, prior to the development of leukaemia. In addition, performing somatic panels in patients with inherited MDS-predisposition syndromes may reveal their unique spectrum of acquired mutations.
Collapse
Affiliation(s)
- Sharon Noy-Lotan
- Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Tanya Krasnov
- Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Orly Dgany
- Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Marta Jeison
- Department of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Asaf D Yanir
- Department of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Oded Gilad
- Department of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Helen Toledano
- Department of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shlomit Barzilai-Birenboim
- Department of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Joanne Yacobovich
- Department of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shai Izraeli
- Department of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hannah Tamary
- Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Petach Tikva, Israel.,Department of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Orna Steinberg-Shemer
- Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Petach Tikva, Israel.,Department of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
7
|
Zhang N, Zhang P, Chen Y, Lou S, Zeng H, Deng J. Clusterization in acute myeloid leukemia based on prognostic alternative splicing signature to reveal the clinical characteristics in the bone marrow microenvironment. Cell Biosci 2020; 10:118. [PMID: 33062256 PMCID: PMC7552347 DOI: 10.1186/s13578-020-00481-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/06/2020] [Indexed: 12/29/2022] Open
Abstract
Background Alternative splicing (AS), a crucial post-transcriptional regulatory mechanism in expanding the coding capacities of genomes and increasing the diversity of proteins, still faces various challenges in the splicing regulation mechanism of acute myeloid leukemia (AML) and microenvironmental changes. Results A total of 27,833 AS events were detected in 8337 genes in 178 AML patients, with exon skip being the predominant type. Approximately 11% of the AS events were significantly related to prognosis, and the prediction models based on various events demonstrated high classification efficiencies. Splicing factors correlation networks further altered the diversity of AS events through epigenetic regulation and clarified the potential mechanism of the splicing pathway. Unsupervised cluster analysis revealed significant correlations between AS and immune features, molecular mutations, immune checkpoints and clinical outcome. The results suggested that AS clusters could be used to identify patient subgroups with different survival outcomes in AML, among which C1 was both associated with good outcome in overall survival. Interestingly, C1 was associated with lower immune scores compared with C2 and C3, and favorable-risk cytogenetics was rarely distributed in C2, but much more common in C1. Conclusions This study revealed a comprehensive landscape of AS events, and provides new insight into molecular targeted therapy and immunotherapy strategy for AML.
Collapse
Affiliation(s)
- Nan Zhang
- Department of Hematology, The Second Affiliated Hospital of Chongqing Medical University, 76 Linjiang Road, Chongqing, 400010 People's Republic of China
| | - Ping Zhang
- Hematology Laboratory, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010 China
| | - Ying Chen
- Department of Hematology, The Second Affiliated Hospital of Chongqing Medical University, 76 Linjiang Road, Chongqing, 400010 People's Republic of China
| | - Shifeng Lou
- Department of Hematology, The Second Affiliated Hospital of Chongqing Medical University, 76 Linjiang Road, Chongqing, 400010 People's Republic of China
| | - Hanqing Zeng
- Department of Hematology, The Second Affiliated Hospital of Chongqing Medical University, 76 Linjiang Road, Chongqing, 400010 People's Republic of China
| | - Jianchuan Deng
- Department of Hematology, The Second Affiliated Hospital of Chongqing Medical University, 76 Linjiang Road, Chongqing, 400010 People's Republic of China
| |
Collapse
|
8
|
Novel quinolin-4(1H)-one derivatives as multi-effective aldose reductase inhibitors for treatment of diabetic complications: Synthesis, biological evaluation, and molecular modeling studies. Bioorg Med Chem Lett 2020; 30:127101. [PMID: 32192796 DOI: 10.1016/j.bmcl.2020.127101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 03/04/2020] [Accepted: 03/07/2020] [Indexed: 10/24/2022]
|
9
|
Ren X, Jiang Q, Li L. Survival-associated alternative splicing signatures in soft tissue sarcomas. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:149. [PMID: 32309298 PMCID: PMC7154430 DOI: 10.21037/atm.2020.01.113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Xianghai Ren
- Department of Pediatric Surgery, Capital Institute of Pediatrics, Beijing 100020, China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Qi Jiang
- Department of Pathology and Pathophysiology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Long Li
- Department of Pediatric Surgery, Capital Institute of Pediatrics, Beijing 100020, China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
| |
Collapse
|
10
|
Smith CC, Selitsky SR, Chai S, Armistead PM, Vincent BG, Serody JS. Alternative tumour-specific antigens. Nat Rev Cancer 2019; 19:465-478. [PMID: 31278396 PMCID: PMC6874891 DOI: 10.1038/s41568-019-0162-4] [Citation(s) in RCA: 203] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/29/2019] [Indexed: 12/20/2022]
Abstract
The study of tumour-specific antigens (TSAs) as targets for antitumour therapies has accelerated within the past decade. The most commonly studied class of TSAs are those derived from non-synonymous single-nucleotide variants (SNVs), or SNV neoantigens. However, to increase the repertoire of available therapeutic TSA targets, 'alternative TSAs', defined here as high-specificity tumour antigens arising from non-SNV genomic sources, have recently been evaluated. Among these alternative TSAs are antigens derived from mutational frameshifts, splice variants, gene fusions, endogenous retroelements and other processes. Unlike the patient-specific nature of SNV neoantigens, some alternative TSAs may have the advantage of being widely shared by multiple tumours, allowing for universal, off-the-shelf therapies. In this Opinion article, we will outline the biology, available computational tools, preclinical and/or clinical studies and relevant cancers for each alternative TSA class, as well as discuss both current challenges preventing the therapeutic application of alternative TSAs and potential solutions to aid in their clinical translation.
Collapse
Affiliation(s)
- Christof C Smith
- Department of Microbiology and Immunology, UNC School of Medicine, Marsico Hall, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sara R Selitsky
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Bioinformatics Core, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Marsico Hall, Chapel Hill, NC, USA
| | - Shengjie Chai
- Department of Microbiology and Immunology, UNC School of Medicine, Marsico Hall, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Paul M Armistead
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Hematology/Oncology, Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Benjamin G Vincent
- Department of Microbiology and Immunology, UNC School of Medicine, Marsico Hall, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Division of Hematology/Oncology, Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Program in Computational Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Jonathan S Serody
- Department of Microbiology and Immunology, UNC School of Medicine, Marsico Hall, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Division of Hematology/Oncology, Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Program in Computational Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| |
Collapse
|
11
|
Interaction paths promote module integration and network-level robustness of spliceosome to cascading effects. Sci Rep 2018; 8:17441. [PMID: 30487551 PMCID: PMC6261937 DOI: 10.1038/s41598-018-35160-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 10/26/2018] [Indexed: 11/22/2022] Open
Abstract
The functionality of distinct types of protein networks depends on the patterns of protein-protein interactions. A problem to solve is understanding the fragility of protein networks to predict system malfunctioning due to mutations and other errors. Spectral graph theory provides tools to understand the structural and dynamical properties of a system based on the mathematical properties of matrices associated with the networks. We combined two of such tools to explore the fragility to cascading effects of the network describing protein interactions within a key macromolecular complex, the spliceosome. Using S. cerevisiae as a model system we show that the spliceosome network has more indirect paths connecting proteins than random networks. Such multiplicity of paths may promote routes to cascading effects to propagate across the network. However, the modular network structure concentrates paths within modules, thus constraining the propagation of such cascading effects, as indicated by analytical results from the spectral graph theory and by numerical simulations of a minimal mathematical model parameterized with the spliceosome network. We hypothesize that the concentration of paths within modules favors robustness of the spliceosome against failure, but may lead to a higher vulnerability of functional subunits, which may affect the temporal assembly of the spliceosome. Our results illustrate the utility of spectral graph theory for identifying fragile spots in biological systems and predicting their implications.
Collapse
|
12
|
Abstract
During erythropoiesis, hematopoietic stem and progenitor cells transition to erythroblasts en route to terminal differentiation into enucleated red blood cells. Transcriptome-wide changes underlie distinct morphological and functional characteristics at each cell division during this process. Many studies of gene expression have historically been carried out in erythroblasts, and the biogenesis of β-globin mRNA—the most highly expressed transcript in erythroblasts—was the focus of many seminal studies on the mechanisms of pre-mRNA splicing. We now understand that pre-mRNA splicing plays an important role in shaping the transcriptome of developing erythroblasts. Recent advances have provided insight into the role of alternative splicing and intron retention as important regulatory mechanisms of erythropoiesis. However, dysregulation of splicing during erythropoiesis is also a cause of several hematological diseases, including β-thalassemia and myelodysplastic syndromes. With a growing understanding of the role that splicing plays in these diseases, we are well poised to develop gene-editing treatments. In this review, we focus on changes in the developing erythroblast transcriptome caused by alternative splicing, the molecular basis of splicing-related blood diseases, and therapeutic advances in disease treatment using CRISPR/Cas9 gene editing.
Collapse
Affiliation(s)
- Kirsten A Reimer
- Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, 06520, USA
| | - Karla M Neugebauer
- Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, 06520, USA
| |
Collapse
|
13
|
Hallmarks of cancer- focus on RNA metabolism and regulatory noncoding RNAs. Cancer Lett 2018; 420:208-209. [PMID: 29409790 DOI: 10.1016/j.canlet.2018.01.063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 01/23/2018] [Indexed: 11/22/2022]
|