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Geng DY, Chen QS, Chen WX, Zhou LS, Han XS, Xie QH, Guo GH, Chen XF, Chen JS, Zhong XP. Molecular targets and mechanisms of different aberrant alternative splicing in metastatic liver cancer. World J Clin Oncol 2024; 15:531-539. [PMID: 38689626 PMCID: PMC11056863 DOI: 10.5306/wjco.v15.i4.531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/29/2024] [Accepted: 03/07/2024] [Indexed: 04/22/2024] Open
Abstract
Metastasis remains a major challenge in the successful management of malignant diseases. The liver is a major site of metastatic disease and a leading cause of death from gastrointestinal malignancies such as colon, stomach, and pancreatic cancers, as well as melanoma, breast cancer, and sarcoma. As an important factor that influences the development of metastatic liver cancer, alternative splicing drives the diversity of RNA transcripts and protein subtypes, which may provide potential to broaden the target space. In particular, the dysfunction of splicing factors and abnormal expression of splicing variants are associated with the occurrence, progression, aggressiveness, and drug resistance of cancers caused by the selective splicing of specific genes. This review is the first to provide a detailed summary of the normal splicing process and alterations that occur during metastatic liver cancer. It will cover the role of alternative splicing in the mechanisms of metastatic liver cancer by examining splicing factor changes, abnormal splicing, and the contribution of hypoxia to these changes during metastasis.
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Affiliation(s)
- De-Yi Geng
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515000, Guangdong Province, China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center of Shantou University Medical College, Shantou 515000, Guangdong Province, China
| | - Qing-Shan Chen
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515000, Guangdong Province, China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center of Shantou University Medical College, Shantou 515000, Guangdong Province, China
| | - Wan-Xian Chen
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515000, Guangdong Province, China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center of Shantou University Medical College, Shantou 515000, Guangdong Province, China
| | - Lin-Sa Zhou
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515000, Guangdong Province, China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center of Shantou University Medical College, Shantou 515000, Guangdong Province, China
| | - Xiao-Sha Han
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515000, Guangdong Province, China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center of Shantou University Medical College, Shantou 515000, Guangdong Province, China
| | - Qi-Hu Xie
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515000, Guangdong Province, China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center of Shantou University Medical College, Shantou 515000, Guangdong Province, China
| | - Geng-Hong Guo
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515000, Guangdong Province, China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center of Shantou University Medical College, Shantou 515000, Guangdong Province, China
| | - Xue-Fen Chen
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515000, Guangdong Province, China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center of Shantou University Medical College, Shantou 515000, Guangdong Province, China
| | - Jia-Sheng Chen
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515000, Guangdong Province, China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center of Shantou University Medical College, Shantou 515000, Guangdong Province, China
| | - Xiao-Ping Zhong
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515000, Guangdong Province, China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center of Shantou University Medical College, Shantou 515000, Guangdong Province, China
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2
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Zhang Z, Dong L, Tao H, Dong Y, Xiang W, Tao F, Zhao Y. RNA-binding proteins potentially regulate the alternative splicing of apoptotic genes during knee osteoarthritis progression. BMC Genomics 2024; 25:293. [PMID: 38504181 PMCID: PMC10949708 DOI: 10.1186/s12864-024-10181-w] [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: 01/19/2024] [Accepted: 03/04/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND Alternative splicing (AS) is a principal mode of genetic regulation and one of the most widely used mechanisms to generate structurally and functionally distinct mRNA and protein variants. Dysregulation of AS may result in aberrant transcription and protein products, leading to the emergence of human diseases. Although considered important for regulating gene expression, genome-wide AS dysregulation, underlying mechanisms, and clinical relevance in knee osteoarthritis (OA) remain unelucidated. Therefore, in this study, we elucidated and validated AS events and their regulatory mechanisms during OA progression. RESULTS In this study, we identified differentially expressed genes between human OA and healthy meniscus samples. Among them, the OA-associated genes were primarily enriched in biological pathways such as extracellular matrix organization and ossification. The predominant OA-associated regulated AS (RAS) events were found to be involved in apoptosis during OA development. The expression of the apoptosis-related gene BCL2L13, XAF1, and NF2 were significantly different between OA and healthy meniscus samples. The construction of a covariation network of RNA-binding proteins (RBPs) and RAS genes revealed that differentially expressed RBP genes LAMA2 and CUL4B may regulate the apoptotic genes XAF1 and BCL2L13 to undergo AS events during OA progression. Finally, RT-qPCR revealed that CUL4B expression was significantly higher in OA meniscus samples than in normal controls and that the AS ratio of XAF1 was significantly different between control and OA samples; these findings were consistent with their expected expression and regulatory relationships. CONCLUSIONS Differentially expressed RBPs may regulate the AS of apoptotic genes during knee OA progression. XAF1 and its regulator, CUL4B, may serve as novel biomarkers and potential therapeutic targets for this disease.
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Affiliation(s)
- Zheng Zhang
- Department of Orthopedics, Renmin Hospital of Wuhan University, 238, Jiefang Road, Wuchang District, 430060, Wuhan, Hubei, China.
| | - Limei Dong
- School of Basic Medical Sciences, Wuhan University, 430071, Wuhan, Hubei, China
| | - Hai Tao
- Department of Orthopedics, Renmin Hospital of Wuhan University, 238, Jiefang Road, Wuchang District, 430060, Wuhan, Hubei, China
| | - Yusong Dong
- School of Basic Medical Sciences, Wuhan University, 430071, Wuhan, Hubei, China
| | - Wei Xiang
- Department of Orthopedics, Renmin Hospital of Wuhan University, 238, Jiefang Road, Wuchang District, 430060, Wuhan, Hubei, China
| | - Fenghua Tao
- Department of Orthopedics, Renmin Hospital of Wuhan University, 238, Jiefang Road, Wuchang District, 430060, Wuhan, Hubei, China
| | - Yingchun Zhao
- Department of Orthopedics, Renmin Hospital of Wuhan University, 238, Jiefang Road, Wuchang District, 430060, Wuhan, Hubei, China
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Malakar P, Shukla S, Mondal M, Kar RK, Siddiqui JA. The nexus of long noncoding RNAs, splicing factors, alternative splicing and their modulations. RNA Biol 2024; 21:1-20. [PMID: 38017665 PMCID: PMC10761143 DOI: 10.1080/15476286.2023.2286099] [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] [Accepted: 11/14/2023] [Indexed: 11/30/2023] Open
Abstract
The process of alternative splicing (AS) is widely deregulated in a variety of cancers. Splicing is dependent upon splicing factors. Recently, several long noncoding RNAs (lncRNAs) have been shown to regulate AS by directly/indirectly interacting with splicing factors. This review focuses on the regulation of AS by lncRNAs through their interaction with splicing factors. AS mis-regulation caused by either mutation in splicing factors or deregulated expression of splicing factors and lncRNAs has been shown to be involved in cancer development and progression, making aberrant splicing, splicing factors and lncRNA suitable targets for cancer therapy. This review also addresses some of the current approaches used to target AS, splicing factors and lncRNAs. Finally, we discuss research challenges, some of the unanswered questions in the field and provide recommendations to advance understanding of the nexus of lncRNAs, AS and splicing factors in cancer.
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Affiliation(s)
- Pushkar Malakar
- Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India
| | - Sudhanshu Shukla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, Karnataka, India
| | - Meghna Mondal
- Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India
| | - Rajesh Kumar Kar
- Department of Neurosurgery, School of Medicine, Yale University, New Haven, CT, USA
| | - Jawed Akhtar Siddiqui
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
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4
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Pascal C, Zonszain J, Hameiri O, Gargi-Levi C, Lev-Maor G, Tammer L, Levy T, Tarabeih A, Roy VR, Ben-Salmon S, Elbaz L, Eid M, Hakim T, Abu Rabe'a S, Shalev N, Jordan A, Meshorer E, Ast G. Human histone H1 variants impact splicing outcome by controlling RNA polymerase II elongation. Mol Cell 2023; 83:3801-3817.e8. [PMID: 37922872 DOI: 10.1016/j.molcel.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 08/17/2023] [Accepted: 10/05/2023] [Indexed: 11/07/2023]
Abstract
Histones shape chromatin structure and the epigenetic landscape. H1, the most diverse histone in the human genome, has 11 variants. Due to the high structural similarity between the H1s, their unique functions in transferring information from the chromatin to mRNA-processing machineries have remained elusive. Here, we generated human cell lines lacking up to five H1 subtypes, allowing us to characterize the genomic binding profiles of six H1 variants. Most H1s bind to specific sites, and binding depends on multiple factors, including GC content. The highly expressed H1.2 has a high affinity for exons, whereas H1.3 binds intronic sequences. H1s are major splicing regulators, especially of exon skipping and intron retention events, through their effects on the elongation of RNA polymerase II (RNAPII). Thus, H1 variants determine splicing fate by modulating RNAPII elongation.
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Affiliation(s)
- Corina Pascal
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jonathan Zonszain
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ofir Hameiri
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Chen Gargi-Levi
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Galit Lev-Maor
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Luna Tammer
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tamar Levy
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Anan Tarabeih
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Vanessa Rachel Roy
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Stav Ben-Salmon
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Liraz Elbaz
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Mireille Eid
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tamar Hakim
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Salima Abu Rabe'a
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Nana Shalev
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Albert Jordan
- Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), Carrer de Baldiri Reixac, 15, 08028 Barcelona, Spain
| | - Eran Meshorer
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Jerusalem 91904, Israel; Edmond and Lily Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Gil Ast
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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Yan Y, Ren Y, Bao Y, Wang Y. RNA splicing alterations in lung cancer pathogenesis and therapy. CANCER PATHOGENESIS AND THERAPY 2023; 1:272-283. [PMID: 38327600 PMCID: PMC10846331 DOI: 10.1016/j.cpt.2023.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/25/2023] [Accepted: 04/29/2023] [Indexed: 02/09/2024]
Abstract
RNA splicing alterations are widespread and play critical roles in cancer pathogenesis and therapy. Lung cancer is highly heterogeneous and causes the most cancer-related deaths worldwide. Large-scale multi-omics studies have not only characterized the mutational landscapes but also discovered a plethora of transcriptional and post-transcriptional changes in lung cancer. Such resources have greatly facilitated the development of new diagnostic markers and therapeutic options over the past two decades. Intriguingly, altered RNA splicing has emerged as an important molecular feature and therapeutic target of lung cancer. In this review, we provide a brief overview of splicing dysregulation in lung cancer and summarize the recent progress on key splicing events and splicing factors that contribute to lung cancer pathogenesis. Moreover, we describe the general strategies targeting splicing alterations in lung cancer and highlight the potential of combining splicing modulation with currently approved therapies to combat this deadly disease. This review provides new mechanistic and therapeutic insights into splicing dysregulation in cancer.
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Affiliation(s)
- Yueren Yan
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Yunpeng Ren
- Department of Cellular and Genetic Medicine, Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yufang Bao
- Department of Cellular and Genetic Medicine, Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yongbo Wang
- Department of Cellular and Genetic Medicine, Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
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Haddad-Mashadrizeh A, Mirahmadi M, Taghavizadeh Yazdi ME, Gholampour-Faroji N, Bahrami A, Zomorodipour A, Moghadam Matin M, Qayoomian M, Saebnia N. Introns and Their Therapeutic Applications in Biomedical Researches. IRANIAN JOURNAL OF BIOTECHNOLOGY 2023; 21:e3316. [PMID: 38269198 PMCID: PMC10804063 DOI: 10.30498/ijb.2023.334488.3316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 03/23/2023] [Indexed: 01/26/2024]
Abstract
Context Although for a long time, it was thought that intervening sequences (introns) were junk DNA without any function, their critical roles and the underlying molecular mechanisms in genome regulation have only recently come to light. Introns not only carry information for splicing, but they also play many supportive roles in gene regulation at different levels. They are supposed to function as useful tools in various biological processes, particularly in the diagnosis and treatment of diseases. Introns can contribute to numerous biological processes, including gene silencing, gene imprinting, transcription, mRNA metabolism, mRNA nuclear export, mRNA localization, mRNA surveillance, RNA editing, NMD, translation, protein stability, ribosome biogenesis, cell growth, embryonic development, apoptosis, molecular evolution, genome expansion, and proteome diversity through various mechanisms. Evidence Acquisition In order to fulfill the objectives of this study, the following databases were searched: Medline, Scopus, Web of Science, EBSCO, Open Access Journals, and Google Scholar. Only articles published in English were included. Results & Conclusions The intervening sequences of eukaryotic genes have critical functions in genome regulation, as well as in molecular evolution. Here, we summarize recent advances in our understanding of how introns influence genome regulation, as well as their effects on molecular evolution. Moreover, therapeutic strategies based on intron sequences are discussed. According to the obtained results, a thorough understanding of intron functional mechanisms could lead to new opportunities in disease diagnosis and therapies, as well as in biotechnology applications.
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Affiliation(s)
- Aliakbar Haddad-Mashadrizeh
- Industrial Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mahdi Mirahmadi
- Stem Cell and Regenerative Medicine Research Group, Iranian Academic Center for Education, Culture and Research (ACECR), Khorasan Razavi Branch, Mashhad, Iran
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Nazanin Gholampour-Faroji
- Industrial Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Ahmadreza Bahrami
- Industrial Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Maryam Moghadam Matin
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohsen Qayoomian
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Neda Saebnia
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
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Ura H, Togi S, Niida Y. Target-capture full-length double-stranded cDNA long-read sequencing through Nanopore revealed novel intron retention in patient with tuberous sclerosis complex. Front Genet 2023; 14:1256064. [PMID: 37829285 PMCID: PMC10565506 DOI: 10.3389/fgene.2023.1256064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/11/2023] [Indexed: 10/14/2023] Open
Abstract
Tuberous sclerosis complex (TSC) is a relatively common autosomal dominant disorder characterized by multiple dysplastic organ lesions and neuropsychiatric symptoms caused by loss-of-function mutation of either TSC1 or TSC2. The genetic diagnosis of inherited diseases, including TSC, in the clinical field is widespread using next-generation sequencing. The mutations in protein-coding exon tend to be verified because mutations directly cause abnormal protein. However, it is relatively difficult to verify mutations in the intron region because it is required to investigate whether the intron mutations affect the abnormal splicing of transcripts. In this study, we developed a target-capture full-length double-stranded cDNA sequencing method using Nanopore long-read sequencer (Nanopore long-read target sequencing). This method revealed the occurrence of intron mutation in the TSC2 gene and found that the intron mutation produces novel intron retention splicing transcripts that generate truncated proteins. The protein-coding transcripts were decreased due to the expression of the novel intron retention transcripts, which caused TSC in patients with the intron mutation. Our results indicate that Nanopore long-read target sequencing is useful for the detection of mutations and confers information on the full-length alternative splicing of transcripts for genetic diagnosis.
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Affiliation(s)
- Hiroki Ura
- Center for Clinical Genomics, Kanazawa Medical University Hospital, Uchinada, Ishikawa, Japan
- Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Uchinada, Ishikawa, Japan
| | - Sumihito Togi
- Center for Clinical Genomics, Kanazawa Medical University Hospital, Uchinada, Ishikawa, Japan
- Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Uchinada, Ishikawa, Japan
| | - Yo Niida
- Center for Clinical Genomics, Kanazawa Medical University Hospital, Uchinada, Ishikawa, Japan
- Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Uchinada, Ishikawa, Japan
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Chen X, Liu X, Li QH, Lu BF, Xie BM, Ji YM, Zhao Y. A patient-derived organoid-based study identified an ASO targeting SNORD14E for endometrial cancer through reducing aberrant FOXM1 Expression and β-catenin nuclear accumulation. J Exp Clin Cancer Res 2023; 42:230. [PMID: 37667311 PMCID: PMC10478245 DOI: 10.1186/s13046-023-02801-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 08/16/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Most of the endometrial cancer (EC) patients are diagnosis in early stage with a good prognosis while the patients with locally advanced recurrent or metastatic result in a poor prognosis. Adjuvant therapy could benefit the prognosis of patients with high-risk factors. Unfortunately, the molecular classification of great prognostic value has not yet reached an agreement and need to be further refined. The present study aims to identify new targets that have prognostic value in EC based on the method of EC patient-derived organ-like organs (PDOs), and further investigate their efficacy and mechanism. METHODS The Cancer Genome Atlas (TCGA) database was used to determine SNORD14E expression. The effects of SNORD14E were investigated using CCK8, Transwell, wound-healing assays, and a xenograft model experiment; apoptosis was measured by flow cytometry. Antisense oligonucleotide (ASO) targeting SNORD14E was designed and patient-derived organoids (PDO) models in EC patients was established. A xenograft mouse and PDO model were employed to evaluate the effects of ASO targeting SNORD14E. RNA-seq, Nm-seq, and RNA immunoprecipitation (RIP) experiments were employed to confirm the alternative splicing (AS) and modification induced by SNORD14E. A minigene reporter gene assay was conducted to confirm AS and splicing factors on a variable exon. Actinomycin-d (Act-D) and Reverse Transcription at Low deoxy-ribonucleoside triphosphate concentrations followed by PCR (RTL-P) were utilized to confirm the effects of 2'-O methylation modification on FOXM1. RESULTS We found that SNORD14E was overexpressed in EC tissues and patients with high expressed SNORD14E were distributed in the TCGA biomolecular classification subgroups without difference. Further, SNORD14E could reduce disease-free survival (DFS) and recurrence free survival (RFS) of EC patients. SNORD14E promoted proliferation, migration, and invasion and inhibited the apoptosis of EC cells in vitro. ASOs targeting SNORD14E inhibited cell proliferation, migration, invasion while promoted cell apoptosis. ASOs targeting SNORD14E inhibited tumor growth in the xenograft mouse model. TCGA-UCEC database showed that the proportion of patients with high expression of SNORD14E in middle-high risk and high-risk patients recommended by EMSO-ESGO-ESTRO guidelines for adjuvant therapy is more than 50%. Next, we enrolled 8 cases of high-risk and high-risk EC patients according to EMSO-ESGO-ESTRO guidelines and successfully constructed EC-PDOs. ASOs targeting SNORD14E inhibited the EC-PDO growth. Mechanistically, SNORD14E could recognize the mRNA of FOXM1 and recruit SRSF1 to promote the shearing of the variable exon VIIa of FOXM1, resulting in the overexpression of the FOXM1 malignant subtypes FOXM1b and FOXM1c. In addition, SNORD14E modified FOXM1 mRNA with 2`-O-methylation, which prolonged the half-life of FOXM1 mRNA. The nucleus accumulation of β-catenin caused by aberrant FOXM1 expression led to EC progression. CONCLUSIONS ASO targeting SNORD14E can be an effective treatment for EC.
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Affiliation(s)
- Xi Chen
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong Province, PR China
| | - Xin Liu
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong Province, PR China
| | - Qian-Hui Li
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong Province, PR China
| | - Bing-Feng Lu
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong Province, PR China
| | - Bu-Min Xie
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong Province, PR China
| | - Yu-Meng Ji
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong Province, PR China
| | - Yang Zhao
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office, Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, No.63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong Province, PR China.
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Kolathur KK, Mallya S, Barve S, Bojja SL, Wagle MM. Moonlighting functions of the ubiquitin-like protein, Hub1/UBL-5. Int J Biochem Cell Biol 2023; 162:106445. [PMID: 37453225 DOI: 10.1016/j.biocel.2023.106445] [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: 03/31/2023] [Revised: 06/28/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023]
Abstract
The faithful splicing of pre-mRNA is critical for accurate gene expression. Dysregulation of pre-mRNA splicing has been associated with several human diseases including cancer. The ubiquitin-like protein Hub1/UBL5 binds to the substrates non-covalently and promotes pre-mRNA splicing. Additionally, UBL5 promotes the common fragile sites stability and the Fanconi anemia pathway of DNA damage repair. These functions strongly suggests that UBL5 could potentially be implicated in cancer. Therefore, we analyzed the UBL5 expression in TCGA tumor sample datasets and observed the differences between tumor and normal tissues among different tumor subtypes. We have noticed the alteration frequency of UBL5 in TCGA tumor samples. Altogether, this review summarizes the UBL5 functions and discusses its putative role in tumorigenesis.
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Affiliation(s)
- Kiran Kumar Kolathur
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences (MCOPS), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka 576104, India.
| | - Sandeep Mallya
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Shivmani Barve
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences (MCOPS), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka 576104, India
| | - Sree Lalitha Bojja
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences (MCOPS), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka 576104, India
| | - Manoj M Wagle
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
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10
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Li Y, Dou Y, Da Veiga Leprevost F, Geffen Y, Calinawan AP, Aguet F, Akiyama Y, Anand S, Birger C, Cao S, Chaudhary R, Chilappagari P, Cieslik M, Colaprico A, Zhou DC, Day C, Domagalski MJ, Esai Selvan M, Fenyö D, Foltz SM, Francis A, Gonzalez-Robles T, Gümüş ZH, Heiman D, Holck M, Hong R, Hu Y, Jaehnig EJ, Ji J, Jiang W, Katsnelson L, Ketchum KA, Klein RJ, Lei JT, Liang WW, Liao Y, Lindgren CM, Ma W, Ma L, MacCoss MJ, Martins Rodrigues F, McKerrow W, Nguyen N, Oldroyd R, Pilozzi A, Pugliese P, Reva B, Rudnick P, Ruggles KV, Rykunov D, Savage SR, Schnaubelt M, Schraink T, Shi Z, Singhal D, Song X, Storrs E, Terekhanova NV, Thangudu RR, Thiagarajan M, Wang LB, Wang JM, Wang Y, Wen B, Wu Y, Wyczalkowski MA, Xin Y, Yao L, Yi X, Zhang H, Zhang Q, Zuhl M, Getz G, Ding L, Nesvizhskii AI, Wang P, Robles AI, Zhang B, Payne SH. Proteogenomic data and resources for pan-cancer analysis. Cancer Cell 2023; 41:1397-1406. [PMID: 37582339 PMCID: PMC10506762 DOI: 10.1016/j.ccell.2023.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/15/2022] [Accepted: 06/27/2023] [Indexed: 08/17/2023]
Abstract
The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) investigates tumors from a proteogenomic perspective, creating rich multi-omics datasets connecting genomic aberrations to cancer phenotypes. To facilitate pan-cancer investigations, we have generated harmonized genomic, transcriptomic, proteomic, and clinical data for >1000 tumors in 10 cohorts to create a cohesive and powerful dataset for scientific discovery. We outline efforts by the CPTAC pan-cancer working group in data harmonization, data dissemination, and computational resources for aiding biological discoveries. We also discuss challenges for multi-omics data integration and analysis, specifically the unique challenges of working with both nucleotide sequencing and mass spectrometry proteomics data.
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Affiliation(s)
- Yize Li
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Yongchao Dou
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Yifat Geffen
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Anna P Calinawan
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - François Aguet
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Yo Akiyama
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Shankara Anand
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Chet Birger
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Song Cao
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | | | | | - Marcin Cieslik
- Department of Computational Medicine & Bioinformatics, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Antonio Colaprico
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Daniel Cui Zhou
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Corbin Day
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | | | - Myvizhi Esai Selvan
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - David Fenyö
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Steven M Foltz
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | | | - Tania Gonzalez-Robles
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Zeynep H Gümüş
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - David Heiman
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | | | - Runyu Hong
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Yingwei Hu
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Eric J Jaehnig
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jiayi Ji
- Tisch Cancer Institute and Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Wen Jiang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lizabeth Katsnelson
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | | | - Robert J Klein
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jonathan T Lei
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wen-Wei Liang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Yuxing Liao
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Caleb M Lindgren
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Weiping Ma
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lei Ma
- ICF, Rockville, MD 20850, USA
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Fernanda Martins Rodrigues
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Wilson McKerrow
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | | | - Robert Oldroyd
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | | | - Pietro Pugliese
- Department of Sciences and Technologies, University of Sannio, Benevento 82100, Italy
| | - Boris Reva
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Paul Rudnick
- Spectragen Informatics, Bainbridge Island, WA 98110, USA
| | - Kelly V Ruggles
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Dmitry Rykunov
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sara R Savage
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael Schnaubelt
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Tobias Schraink
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Zhiao Shi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Xiaoyu Song
- Tisch Cancer Institute and Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Erik Storrs
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Nadezhda V Terekhanova
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | | | | | - Liang-Bo Wang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Joshua M Wang
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Ying Wang
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Bo Wen
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yige Wu
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Matthew A Wyczalkowski
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Yi Xin
- ICF, Rockville, MD 20850, USA
| | - Lijun Yao
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Xinpei Yi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Qing Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | | | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA; Cancer Center and Department of Pathology, Mass. General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | | | - Pei Wang
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA.
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, UT 84602, USA.
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11
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Li X, Li J, Zheng Y, Lee SJ, Zhou J, Giobbie-Hurder A, Butterfield LH, Dranoff G, Hodi FS. Granulocyte-Macrophage Colony-Stimulating Factor Influence on Soluble and Membrane-Bound ICOS in Combination with Immune Checkpoint Blockade. Cancer Immunol Res 2023; 11:1100-1113. [PMID: 37262321 PMCID: PMC10398357 DOI: 10.1158/2326-6066.cir-22-0702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 01/03/2023] [Accepted: 05/23/2023] [Indexed: 06/03/2023]
Abstract
With the successful development of immune checkpoint blockade, there remains the continued need to improve efficacy and decrease toxicities. The addition of granulocyte-macrophage colony-stimulating factor (GM-CSF) to ipilimumab has previously demonstrated both an improvement in efficacy and decrease in the incidence of high-grade adverse events. ICOS+CD4+ or ICOS+CD8+ peripheral blood T cells are significantly greater in the patients treated with ipilimumab plus GM-CSF than in the patients treated with ipilimumab alone. To better understand the effects of GM-CSF on inducible T-cell costimulator (ICOS) and clinical outcomes, the relative roles of identified soluble ICOS and membrane-bound ICOS were evaluated. The ICOS splice variant was secreted and found to have immunologic suppressive effects. Changes in soluble ICOS splice variant levels in treated patients correlated with clinical outcomes. GM-CSF enhanced membrane-bound ICOS in an IL12-dependent manner but did not increase soluble ICOS levels. Whereas soluble ICOS plays a role in immune suppression, GM-CSF efficacy involves increasing membrane-bound ICOS and induction of dendritic cell development. Thus, soluble ICOS splice variants may be used as a biomarker for GM-CSF and immune checkpoint blockade-based therapies.
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Affiliation(s)
- Xiaoyu Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Melanoma Division, Dana-Farber Cancer Institute, Boston, Massachusetts
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jingjing Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Melanoma Division, Dana-Farber Cancer Institute, Boston, Massachusetts
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Yue Zheng
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Sandra J. Lee
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jun Zhou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Melanoma Division, Dana-Farber Cancer Institute, Boston, Massachusetts
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Anita Giobbie-Hurder
- Melanoma Division, Dana-Farber Cancer Institute, Boston, Massachusetts
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Lisa H. Butterfield
- Parker Institute for Cancer Immunotherapy and University of California San Francisco, San Francisco, California
| | - Glenn Dranoff
- Immuno-Oncology, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - F. Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Melanoma Division, Dana-Farber Cancer Institute, Boston, Massachusetts
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
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12
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Zhang B, Li H, Kong L, Yang N, Yang S, Qi L, Liu T, Wang X, Qin W. Tandem enrichment of serum exosomes and exosomal RNA with titanium dioxide. J Chromatogr A 2023; 1693:463882. [PMID: 36857982 DOI: 10.1016/j.chroma.2023.463882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 02/25/2023]
Abstract
Exosomes have great potential as biomarker carriers for disease diagnosis and prognosis. In recent years, exosomal RNA (exoRNA) has become a promising candidate for the early diagnosis and prognosis of cancers, and its pathophysiological roles in various diseases have been revealed. For example, exosome-derived mRNAs, miRNAs, circRNAs, and lncRNAs function as signalling molecules to regulate tumour growth, angiogenesis, invasion, metastasis, and the response to chemotherapy. However, the isolation of exosomes and exoRNA with high quality and purity remains challenging due to the relatively small size of exosomes and the limited amount of RNA in exosomes. In this work, we developed a novel tandem enrichment method to isolate exoRNA from serum based on the specific interaction between titanium dioxide (TiO2) and the phosphate groups on the lipid bilayer of exosomes and of the exoRNA. TiO2-based RNA isolation was first demonstrated and optimized in HeLa cells. A total of 130.9 ± 8.34 µg of RNA was rapidly enriched from approximately 5 × 106 HeLa cells within 10 min. This was a 41.5% higher yield than that using a commercial Ultrapure RNA Kit. TiO2-based tandem enrichment of exoRNA was then performed using human serum, obtaining 64.53±3.41 ng of exoRNA from 500 µL of human serum within 30 min. A total of 2,137,902 reads, including seven types of exoRNAs, were identified from the exosomes. This method is compatible with various downstream RNA processing techniques and does not use toxic or irritating reagents, such as phenol or chloroform, providing a simple, economical, rapid, and safe approach for exoRNA extraction from biological samples.
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Affiliation(s)
- Baoying Zhang
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, PR China; National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, PR China
| | - Hang Li
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, PR China
| | - Linlin Kong
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, PR China
| | - Ningli Yang
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, PR China
| | - Shengjie Yang
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, PR China
| | - Lu Qi
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, PR China
| | - Tong Liu
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, PR China.
| | - Xinghe Wang
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, PR China.
| | - Weijie Qin
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, PR China.
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13
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Cotto KC, Feng YY, Ramu A, Richters M, Freshour SL, Skidmore ZL, Xia H, McMichael JF, Kunisaki J, Campbell KM, Chen THP, Rozycki EB, Adkins D, Devarakonda S, Sankararaman S, Lin Y, Chapman WC, Maher CA, Arora V, Dunn GP, Uppaluri R, Govindan R, Griffith OL, Griffith M. Integrated analysis of genomic and transcriptomic data for the discovery of splice-associated variants in cancer. Nat Commun 2023; 14:1589. [PMID: 36949070 PMCID: PMC10033906 DOI: 10.1038/s41467-023-37266-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/08/2023] [Indexed: 03/24/2023] Open
Abstract
Somatic mutations within non-coding regions and even exons may have unidentified regulatory consequences that are often overlooked in analysis workflows. Here we present RegTools ( www.regtools.org ), a computationally efficient, free, and open-source software package designed to integrate somatic variants from genomic data with splice junctions from bulk or single cell transcriptomic data to identify variants that may cause aberrant splicing. We apply RegTools to over 9000 tumor samples with both tumor DNA and RNA sequence data. RegTools discovers 235,778 events where a splice-associated variant significantly increases the splicing of a particular junction, across 158,200 unique variants and 131,212 unique junctions. To characterize these somatic variants and their associated splice isoforms, we annotate them with the Variant Effect Predictor, SpliceAI, and Genotype-Tissue Expression junction counts and compare our results to other tools that integrate genomic and transcriptomic data. While many events are corroborated by the aforementioned tools, the flexibility of RegTools also allows us to identify splice-associated variants in known cancer drivers, such as TP53, CDKN2A, and B2M, and other genes.
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Affiliation(s)
- Kelsy C Cotto
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Yang-Yang Feng
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Avinash Ramu
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Megan Richters
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Sharon L Freshour
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Zachary L Skidmore
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Huiming Xia
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Joshua F McMichael
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Jason Kunisaki
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Katie M Campbell
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Timothy Hung-Po Chen
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Emily B Rozycki
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Douglas Adkins
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Siddhartha Devarakonda
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Sumithra Sankararaman
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Yiing Lin
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - William C Chapman
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Christopher A Maher
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Vivek Arora
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Gavin P Dunn
- Department of Neurosurgery, Mass General Hospital, Boston, MA, USA
- Center for Brain Tumor Immunology and Immunotherapy, Mass General Hospital, Boston, MA, USA
| | - Ravindra Uppaluri
- Department of Surgery, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ramaswamy Govindan
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Obi L Griffith
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
| | - Malachi Griffith
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
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14
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Qazi S, Uckun FM. CD22 Exon 12 Deletion as an Independent Predictor of Poor Treatment Outcomes in B-ALL. Cancers (Basel) 2023; 15:1599. [PMID: 36900389 PMCID: PMC10000517 DOI: 10.3390/cancers15051599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/21/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023] Open
Abstract
We previously reported a splicing defect (CD22ΔE12) associated with the deletion of exon 12 of the inhibitory co-receptor CD22 (Siglec-2) in leukemia cells from patients with CD19+ B-precursor acute lymphoblastic leukemia (B-ALL). CD22ΔE12 causes a truncating frameshift mutation and yields a dysfunctional CD22 protein that lacks most of the cytoplasmic domain required for its inhibitory function, and it is associated with aggressive in vivo growth of human B-ALL cells in mouse xenograft models. Although CD22ΔE12 with selective reduction of CD22 exon 12 (CD22E12) levels was detected in a high percentage of newly diagnosed as well as relapsed B-ALL patients, its clinical significance remains unknown. We hypothesized that B-ALL patients with very low levels of wildtype CD22 would exhibit a more aggressive disease with a worse prognosis because the missing inhibitory function of the truncated CD22 molecules could not be adequately compensated by competing wildtype CD22. Here, we demonstrate that newly diagnosed B-ALL patients with very low levels of residual wildtype CD22 ("CD22E12low"), as measured by RNAseq-based CD22E12 mRNA levels, have significantly worse leukemia-free survival (LFS) as well as overall survival (OS) than other B-ALL patients. CD22E12low status was identified as a poor prognostic indicator in both univariate and multivariate Cox proportional hazards models. CD22E12low status at presentation shows clinical potential as a poor prognostic biomarker that may guide the early allocation of risk-adjusted, patient-tailored treatment regimens and refine risk classification in high-risk B-ALL.
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Affiliation(s)
- Sanjive Qazi
- Ares Pharmaceuticals, Saint Paul, MN 55110, USA
- Division of Hematology-Oncology, Department of Pediatrics and Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine (USC KSOM), Los Angeles, CA 90027, USA
| | - Fatih M. Uckun
- Ares Pharmaceuticals, Saint Paul, MN 55110, USA
- Division of Hematology-Oncology, Department of Pediatrics and Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine (USC KSOM), Los Angeles, CA 90027, USA
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15
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Shaglouf LHF, Ranjpour M, Wajid S, Tandon R, Vasudevan KR, Jain SK. Elevated expression of ISY1, APOA-1, SYNE1, MTG1, and MMP10 at HCC initiation: HCC specific protein network involving interactions of key regulators of lipid metabolism, EGFR signaling, MAPK, and splicing pathways. PROTOPLASMA 2023; 260:651-662. [PMID: 35962262 DOI: 10.1007/s00709-022-01796-5] [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: 02/26/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
Identification of molecular regulators of hepatocellular carcinoma (HCC) initiation and progression is not well understood. We chemically induced HCC in male Wistar rats by administration of diethyl nitrosamine (DEN) and 2-acetylaminofluorene (2-AFF). Using 2D-electrophoresis and MALDI-TOF-MS/MS analyses, we characterized differentially expressed proteins in liver tissues at early stage of HCC progression. Using RT-PCR analysis, we quantified the mRNA expression of the characterized proteins and validated the transcript expression with tumor tissues of clinically confirmed HCC patients. Using bioinformatic tools, we analyzed a network among the introduced proteins that identified their interacting partners and analyzed the molecular mechanisms associated with signaling pathways during HCC progression. We characterized a protein, namely, pre-mRNA splicing factor 1 homolog (ISY1), which is upregulated at both transcriptome and proteome levels at HCC initiation, progression, and tumor stages. We analyzed the interacting partners of ISY1, namely, APOA-1, SYNE1, MMP10, and MTG1. Real-time PCR analysis confirmed elevated expression of APOA-1 mRNA at HCC initiation, progression, and tumor stages in animals undergoing tumorigenesis. The mRNA expression of the interacting partners was validated with tumor tissues of clinically confirmed liver cancer patients; the analysis revealed significant elevation in expression of transcripts. The transcriptome and proteome analyses complement each other and dysregulation in mRNA and protein expression of these regulators may play critical role in HCC initiation and progression.
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Affiliation(s)
- Laila H Faraj Shaglouf
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, 110062, India
| | - Maryam Ranjpour
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, 110062, India.
| | - Saima Wajid
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, 110062, India
| | - Rakesh Tandon
- Institute of Gastroenterology, PSRI Hospital, New Delhi, India
| | | | - Swatantra Kumar Jain
- Department of Medical Biochemistry, HIMSR, Jamia Hamdard, New Delhi, 110062, India
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16
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Hall RC, Vaidya AM, Schiemann WP, Pan Q, Lu ZR. RNA-Seq Analysis of Extradomain A and Extradomain B Fibronectin as Extracellular Matrix Markers for Cancer. Cells 2023; 12:cells12050685. [PMID: 36899821 PMCID: PMC10000746 DOI: 10.3390/cells12050685] [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: 12/30/2022] [Revised: 02/09/2023] [Accepted: 02/17/2023] [Indexed: 02/25/2023] Open
Abstract
Alternatively spliced forms of fibronectin, called oncofetal fibronectin, are aberrantly expressed in cancer, with little to no expression in normal tissue, making them attractive biomarkers to exploit for tumor-targeted therapeutics and diagnostics. While prior studies have explored oncofetal fibronectin expression in limited cancer types and limited sample sizes, no studies have performed a large-scale pan-cancer analysis in the context of clinical diagnostics and prognostics to posit the utility of these biomarkers across multiple cancer types. In this study, RNA-Seq data sourced from the UCSC Toil Recompute project were extracted and analyzed to determine the correlation between the expression of oncofetal fibronectin, including extradomain A and extradomain B fibronectin, and patient diagnosis and prognosis. We determined that oncofetal fibronectin is significantly overexpressed in most cancer types relative to corresponding normal tissues. In addition, strong correlations exist between increasing oncofetal fibronectin expression levels and tumor stage, lymph node activity, and histological grade at the time of diagnosis. Furthermore, oncofetal fibronectin expression is shown to be significantly associated with overall patient survival within a 10-year window. Thus, the results presented in this study suggest oncofetal fibronectin as a commonly upregulated biomarker in cancer with the potential to be used for tumor-selective diagnosis and treatment applications.
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Affiliation(s)
- Ryan C. Hall
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Amita M. Vaidya
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA
| | - William P. Schiemann
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Quintin Pan
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
- University Hospitals Seidman Cancer Center, Cleveland, OH 44106, USA
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University Hospitals, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Zheng-Rong Lu
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
- Correspondence: ; Tel.: +1-216-368-0187; Fax: +1-216-368-4969
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17
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Liu E, Becker N, Sudha P, Dong C, Liu Y, Keats J, Morgan G, Walker BA. Alternative splicing in multiple myeloma is associated with the non-homologous end joining pathway. Blood Cancer J 2023; 13:16. [PMID: 36670103 PMCID: PMC9859791 DOI: 10.1038/s41408-023-00783-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 12/27/2022] [Accepted: 01/05/2023] [Indexed: 01/21/2023] Open
Abstract
Alternative splicing plays a pivotal role in tumorigenesis and proliferation. However, its pattern and pathogenic role has not been systematically analyzed in multiple myeloma or its subtypes. Alternative splicing profiles for 598 newly diagnosed myeloma patients with comprehensive genomic annotation identified primary translocations, 1q amplification, and DIS3 events to have more differentially spliced events than those without. Splicing levels were correlated with expression of splicing factors. Moreover, the non-homologous end joining pathway was an independent factor that was highly associated with splicing frequency as well as an increased number of structural variants. We therefore identify an axis of high-risk disease encompassing expression of the non-homologous end joining pathway, increase structural variants, and increased alternative splicing that are linked together. This indicates a joint pathogenic role for DNA damage response and alternative RNA processing in myeloma.
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Affiliation(s)
- Enze Liu
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Nathan Becker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Parvathi Sudha
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Chuanpeng Dong
- Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, IN, USA
- Department of Genetics, School of Medicine, Yale University, New Haven, CT, USA
| | - Yunlong Liu
- Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Jonathan Keats
- Translational Genomics Research Institute (TGen), Integrated Cancer Genomics Division, Phoenix, AZ, USA
| | - Gareth Morgan
- NYU Langone Medical Center, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Brian A Walker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA.
- Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, IN, USA.
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18
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Dai Z, Sun Y, Maihemuti M, Jiang R. Genome-wide identification of alternative splicing and splicing regulated in immune infiltration in osteosarcoma patients. Front Genet 2023; 14:1051192. [PMID: 37139238 PMCID: PMC10149916 DOI: 10.3389/fgene.2023.1051192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 04/03/2023] [Indexed: 05/05/2023] Open
Abstract
Background: Osteosarcoma typically occurs in adolescents, and the survival rate of patients with metastatic and recurrent osteosarcoma remains low. Abnormal regulation of alternative splicing is associated with the development of osteosarcoma. However, there is no genome-wide analysis of the function and regulatory mechanisms of aberrant alternative splicing associated with osteosarcoma. Methods: Published transcriptome data on osteosarcoma (GSE126209) derived from osteosarcoma patient tissue were downloaded. Gene expression profiling by high-throughput sequencing was performed on 9 normal samples and 10 tumor samples for genome-wide identification of osteosarcoma-related alternative splicing events. The potential function of osteosarcoma-associated alternative splicing events was examined by immune infiltration and correlation analysis. Regulation of aberrantly expressed RNA-binding proteins (RBPs) related to alternative splicing in osteosarcoma was clarified by co-expression analysis. Results: A total of 63 alternative splicing events, which are highly credible and dominant, were identified. GO enrichment analysis indicated that alternative splicing may be closely related to the immune response process. Immune infiltration analysis showed significant changes in the percentages of CD8 T cells, resting memory CD4 T cells, activated memory CD4 T cells, monocytes, resting dendritic cells, and activated mast cells in tumors compared to normal tissues, indicating the involvement of these immune cell types in the occurrence of osteosarcoma. Moreover, the analysis identified alternative splicing events that were co-altered with resting memory CD4 T cells, resting dendritic cells, and activated mast cells, events that may be associated with regulation of the osteosarcoma immune microenvironment. In addition, a co-regulatory network (RBP-RAS-immune) of osteosarcoma-associated RBPs with aberrant alternative splicing and altered immune cells was established. These RBPs include NOP58, FAM120C, DYNC1H1, TRAP1, and LMNA, which may serve as molecular targets for osteosarcoma immune regulation. Conclusion: These findings allow us to further understand the causes of osteosarcoma development and provide a new research direction for osteosarcoma immunotherapy or targeted therapy.
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Gupta J, Kareem Al-Hetty HRA, Aswood MS, Turki Jalil A, Azeez MD, Aminov Z, Alsaikhan F, Ramírez-Coronel AA, Ramaiah P, Farhood B. The key role of microRNA-766 in the cancer development. Front Oncol 2023; 13:1173827. [PMID: 37205191 PMCID: PMC10185842 DOI: 10.3389/fonc.2023.1173827] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 04/18/2023] [Indexed: 05/21/2023] Open
Abstract
Cancer is caused by defects in coding and non-coding RNAs. In addition, duplicated biological pathways diminish the efficacy of mono target cancer drugs. MicroRNAs (miRNAs) are short, endogenous, non-coding RNAs that regulate many target genes and play a crucial role in physiological processes such as cell division, differentiation, cell cycle, proliferation, and apoptosis, which are frequently disrupted in diseases such as cancer. MiR-766, one of the most adaptable and highly conserved microRNAs, is notably overexpressed in several diseases, including malignant tumors. Variations in miR-766 expression are linked to various pathological and physiological processes. Additionally, miR-766 promotes therapeutic resistance pathways in various types of tumors. Here, we present and discuss evidence implicating miR-766 in the development of cancer and treatment resistance. In addition, we discuss the potential applications of miR-766 as a therapeutic cancer target, diagnostic biomarker, and prognostic indicator. This may shed light on the development of novel therapeutic strategies for cancer therapy.
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Affiliation(s)
- Jitendra Gupta
- Institute of Pharmaceutical Research, GLA University, Mathura, India
| | - Hussein Riyadh Abdul Kareem Al-Hetty
- Department of Nursing, Al-Maarif University College, Ramadi, Anbar, Iraq
- *Correspondence: Hussein Riyadh Abdul Kareem Al-Hetty, ; Abduladheem Turki Jalil, ; Bagher Farhood, ,
| | - Murtadha Sh. Aswood
- Department of Physics, College of Education, University of Al-Qadisiyah, Al-Diwaniyah, Iraq
| | - Abduladheem Turki Jalil
- Medical Laboratories Techniques Department, Al-Mustaqbal University College, Babylon, Hilla, Iraq
- *Correspondence: Hussein Riyadh Abdul Kareem Al-Hetty, ; Abduladheem Turki Jalil, ; Bagher Farhood, ,
| | | | - Zafar Aminov
- Department of Public Health and Healthcare management, Samarkand State Medical University, Samarkand, Uzbekistan
- Department of Scientific Affairs, Tashkent State Dental Institute, Tashkent, Uzbekistan
| | - Fahad Alsaikhan
- College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkharj, Saudi Arabia
| | - Andrés Alexis Ramírez-Coronel
- Azogues Campus Nursing Career, Health and Behavior Research Group (HBR), Psychometry and Ethology Laboratory, Catholic University of Cuenca, Cuenca, Ecuador
- Epidemiology and Biostatistics Research Group, CES University, Medellín, Colombia
- Educational Statistics Research Group (GIEE), National University of Education, Azogues, Ecuador
| | | | - Bagher Farhood
- Department of Medical Physics and Radiology, Faculty of Paramedical Sciences, Kashan University of Medical Sciences, Kashan, Iran
- *Correspondence: Hussein Riyadh Abdul Kareem Al-Hetty, ; Abduladheem Turki Jalil, ; Bagher Farhood, ,
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20
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Petrovsky DV, Rudnev VR, Nikolsky KS, Kulikova LI, Malsagova KM, Kopylov AT, Kaysheva AL. PSSNet-An Accurate Super-Secondary Structure for Protein Segmentation. Int J Mol Sci 2022; 23:ijms232314813. [PMID: 36499138 PMCID: PMC9740782 DOI: 10.3390/ijms232314813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/18/2022] [Accepted: 11/24/2022] [Indexed: 12/03/2022] Open
Abstract
A super-secondary structure (SSS) is a spatially unique ensemble of secondary structural elements that determine the three-dimensional shape of a protein and its function, rendering SSSs attractive as folding cores. Understanding known types of SSSs is important for developing a deeper understanding of the mechanisms of protein folding. Here, we propose a universal PSSNet machine-learning method for SSS recognition and segmentation. For various types of SSS segmentation, this method uses key characteristics of SSS geometry, including the lengths of secondary structural elements and the distances between them, torsion angles, spatial positions of Cα atoms, and primary sequences. Using four types of SSSs (βαβ-unit, α-hairpin, β-hairpin, αα-corner), we showed that extensive SSS sets could be reliably selected from the Protein Data Bank and AlphaFold 2.0 database of protein structures.
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21
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Chen Y, Jiang N, Chen M, Sui B, Liu X. Identification of tumor antigens and immune subtypes in head and neck squamous cell carcinoma for mRNA vaccine development. Front Cell Dev Biol 2022; 10:1064754. [PMID: 36467412 PMCID: PMC9714632 DOI: 10.3389/fcell.2022.1064754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 11/03/2022] [Indexed: 08/08/2023] Open
Abstract
The mRNA vaccines have been considered effective for combating cancer. However, the core components of the mRNA vaccines against head and neck squamous cell carcinoma (HNSCC) and the effects remain unclear. Our study aims to identify effective antigens in HNSCC to develop mRNA vaccines for corresponding potential patients. Here, we analyzed alternative splicing and mutation of genes in TCGA-HNSCC samples and identified seven potential tumor antigens, including SREBF1, LUC7L3, LAMA5, PCGF3, HNRNPH1, KLC4, and OFD1, which were associated with nonsense-mediated mRNA decay factor expression, overall survival prognosis and the infiltration of antigen-presenting cells. Furthermore, to select suitable patients for vaccination, immune subtypes related to HNSCC were identified by consensus clustering analysis, and visualization of the HNSCC immune landscape was performed by graph-learning-based dimensionality reduction. To address the heterogeneity of the population that is suitable for vaccination, plot cell trajectory and WGCNA were also utilized. HNSCC patients were classified into three prognostically relevant immune subtypes (Cluster 1, Cluster 2, and Cluster 3) possessing different molecular and cellular characteristics, immune modulators, and mutation statuses. Cluster 1 had an immune-activated phenotype and was associated with better survival, while Cluster 2 and Cluster 3 were immunologically cold and linked to increased tumor mutation burden. Therefore, HNSCC patients with immune subtypes Cluster 2 and Cluster 3 are potentially suitable for mRNA vaccination. Moreover, the prognostic module hub genes screened seven genes, including IGKC, IGHV3-15, IGLV1-40, IGLV1-51, IGLC3, IGLC2, and CD79A, which could be potential biomarkers to predict prognosis and identify suitable patients for mRNA vaccines. Our findings provide a theoretical basis for further research and the development of anti-HNSCC mRNA vaccines and the selection of suitable patients for vaccination.
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Affiliation(s)
- Yan Chen
- Department of Periodontology, Shanghai Stomatological Hospital & School of Stomatology, Fudan University; Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases, Fudan University, Shanghai, China
| | - Ning Jiang
- Department of Oral and Craniomaxillofacial Science, Shanghai Key Laboratory of Stomatology, College of Stomatology, Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Meihua Chen
- Department of Periodontology, Shanghai Stomatological Hospital & School of Stomatology, Fudan University; Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases, Fudan University, Shanghai, China
| | - Baiyan Sui
- Department of Dental Materials, Shanghai Key Laboratory of Stomatology, Shanghai Biomaterials Research & Testing Center, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases, Shanghai, China
| | - Xin Liu
- Department of Dental Materials, Shanghai Key Laboratory of Stomatology, Shanghai Biomaterials Research & Testing Center, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases, Shanghai, China
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22
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Zanelli M, Parente P, Sanguedolce F, Zizzo M, Palicelli A, Bisagni A, Carosi I, Trombetta D, Mastracci L, Ricci L, Pancetti S, Martino G, Broggi G, Caltabiano R, Cavazza A, Ascani S. Intravascular NK/T-Cell Lymphoma: What We Know about This Diagnostically Challenging, Aggressive Disease. Cancers (Basel) 2022; 14:5458. [PMID: 36358876 PMCID: PMC9658079 DOI: 10.3390/cancers14215458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/02/2022] [Accepted: 11/05/2022] [Indexed: 08/27/2023] Open
Abstract
Intravascular lymphoma is a form of lymphoid malignancy characterized by neoplastic cells growing almost exclusively within the lumina of small- to medium-sized blood vessels. Most cases are of B-cell origin with rare cases of natural killer or T-cell lineage. Extranodal sites are affected, mainly the skin and central nervous system, although any organ may be involved. Intravascular NK/T-cell lymphoma deserves special attention because of its clinicopathologic features and the need for adequate immunophenotyping combined with clonality test for a proper diagnosis. Moreover, intravascular NK/T-cell lymphoma is strongly linked to Epstein-Barr virus (EBV), which is considered to play a role in tumorigenesis and to be responsible for the aggressive behavior of the disease. In this paper, we review the current knowledge on this rare lymphoma and, in particular, the most recent advances about its molecular landscape. The main distinguishing features with other EBV-related entities, such as extranodal NK/T-cell lymphoma, EBV-positive primary nodal T/NK-cell lymphoma, and aggressive NK-cell leukemia, are discussed to help pathologists obtain the correct diagnosis and consequently develop an adequate and prompt therapy response.
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Affiliation(s)
- Magda Zanelli
- Pathology Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Paola Parente
- Pathology Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy
| | | | - Maurizio Zizzo
- Surgical Oncology Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Andrea Palicelli
- Pathology Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Alessandra Bisagni
- Pathology Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Illuminato Carosi
- Pathology Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy
| | - Domenico Trombetta
- Laboratory Oncology, Fondazione IRCCS Casa Sollievo della Sofferenza San Giovanni Rotondo, 71013 San Giovanni Rotondo, Italy
| | - Luca Mastracci
- Anatomic Pathology, Ospedale Policlinico San Martino IRCCS Genova, 16132 Genova, Italy
| | - Linda Ricci
- Pathology Unit, Azienda Ospedaliera Santa Maria di Terni, University of Perugia, 05100 Terni, Italy
| | - Saverio Pancetti
- Pathology Unit, Humanitas University, Pieve Emanuele, 20072 Milan, Italy
- Pathology Unit, Humanitas Research Hospital-IRCCS, Rozzano, 20089 Milan, Italy
| | - Giovanni Martino
- Pathology Unit, Azienda Ospedaliera Santa Maria di Terni, University of Perugia, 05100 Terni, Italy
| | - Giuseppe Broggi
- Department of Medical and Surgical Sciences and Advanced Technologies “G.F. Ingrassia” Anatomic Pathology, University of Catania, 95123 Catania, Italy
| | - Rosario Caltabiano
- Department of Medical and Surgical Sciences and Advanced Technologies “G.F. Ingrassia” Anatomic Pathology, University of Catania, 95123 Catania, Italy
| | - Alberto Cavazza
- Pathology Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Stefano Ascani
- Pathology Unit, Azienda Ospedaliera Santa Maria di Terni, University of Perugia, 05100 Terni, Italy
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23
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Zhou J, Chen W, He Q, Chen D, Li C, Jiang C, Ding Z, Qian Q. SERBP1 affects the apoptotic level by regulating the expression and alternative splicing of cellular and metabolic process genes in HeLa cells. PeerJ 2022; 10:e14084. [PMID: 36213507 PMCID: PMC9536300 DOI: 10.7717/peerj.14084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/29/2022] [Indexed: 01/20/2023] Open
Abstract
Background RNA-binding proteins (RBPs) have important roles in orchestrating posttranscriptional regulation and modulating many tumorigenesis events. SERBP1 has been recognized as an important regulator in multiple cancers, while it remains unclear whether SERBP1-regulated gene expression at the transcriptome-wide level is significantly correlated with tumorigenesis. Methods We overexpressed SERBP1 in HeLa cells and explored whether SERBP1 overexpression (SERBP1-OE) affects the proliferation and apoptosis of HeLa cells. We analyzed the transcriptome-wide gene expression changes and alternative splicing changes mediated by SERBP1-OE using the transcriptome sequencing method (RNA-seq). RT-qPCR was conducted to assay SERBP1-regulated alternative splicing. Results SERBP1-OE induced the apoptosis of HeLa cells. The downregulated genes were strongly enriched in the cell proliferation and apoptosis pathways according to the GO analysis, including FOS, FOSB, PAK6 and RAB26. The genes undergoing at least one SERBP1-regulated alternative splicing event were enriched in transcriptional regulation, suggesting a mechanism of the regulation of gene expression, and in pyruvate and fatty acid metabolic processes critical for tumorigenesis events. The SERBP1-regulated alternative splicing of ME3, LPIN3, CROT, PDP1, SLC27A1 and ALKBH7 was validated by RT-qPCR analysis. Conclusions We for the first time demonstrated the cellular function and molecular targets of SERBP1 in HeLa cells at transcriptional and post-transcriptional levels. The SERBP1-regulated gene expression and alternative splicing networks revealed by this study provide important information for exploring the functional roles and regulatory mechanisms of SERBP1 in cancer development and progression.
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Affiliation(s)
- Junjie Zhou
- Department of Colorectal and Anal Surgery, Zhongnan Hospital, Wuhan University, Wu Han, Hubei, China
| | - Wenhao Chen
- Department of Colorectal and Anal Surgery, Zhongnan Hospital, Wuhan University, Wu Han, Hubei, China
| | - Qianwen He
- Department of Anesthesiology, Zhongnan Hospital, Wuhan University, Wu Han, Hubei, China
| | - Dong Chen
- Center for Genome Analysis, Wuhan Ruixing Biotechnology Co., Ltd., Wu Han, Hubei, China
| | - Chunguang Li
- Department of Colorectal and Anal Surgery, Zhongnan Hospital, Wuhan University, Wu Han, Hubei, China
| | - Congqing Jiang
- Department of Colorectal and Anal Surgery, Zhongnan Hospital, Wuhan University, Wu Han, Hubei, China
| | - Zhao Ding
- Department of Colorectal and Anal Surgery, Zhongnan Hospital, Wuhan University, Wu Han, Hubei, China
| | - Qun Qian
- Department of Colorectal and Anal Surgery, Zhongnan Hospital, Wuhan University, Wu Han, Hubei, China
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24
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Kiyose H, Nakagawa H, Ono A, Aikata H, Ueno M, Hayami S, Yamaue H, Chayama K, Shimada M, Wong JH, Fujimoto A. Comprehensive analysis of full-length transcripts reveals novel splicing abnormalities and oncogenic transcripts in liver cancer. PLoS Genet 2022; 18:e1010342. [PMID: 35926060 PMCID: PMC9380957 DOI: 10.1371/journal.pgen.1010342] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/16/2022] [Accepted: 07/14/2022] [Indexed: 12/24/2022] Open
Abstract
Genes generate transcripts of various functions by alternative splicing. However, in most transcriptome studies, short-reads sequencing technologies (next-generation sequencers) have been used, leaving full-length transcripts unobserved directly. Although long-reads sequencing technologies would enable the sequencing of full-length transcripts, the data analysis is difficult. In this study, we developed an analysis pipeline named SPLICE and analyzed cDNA sequences from 42 pairs of hepatocellular carcinoma (HCC) and matched non-cancerous livers with an Oxford Nanopore sequencer. Our analysis detected 46,663 transcripts from the protein-coding genes in the HCCs and the matched non-cancerous livers, of which 5,366 (11.5%) were novel. A comparison of expression levels identified 9,933 differentially expressed transcripts (DETs) in 4,744 genes. Interestingly, 746 genes with DETs, including the LINE1-MET transcript, were not found by a gene-level analysis. We also found that fusion transcripts of transposable elements and hepatitis B virus (HBV) were overexpressed in HCCs. In vitro experiments on DETs showed that LINE1-MET and HBV-human transposable elements promoted cell growth. Furthermore, fusion gene detection showed novel recurrent fusion events that were not detected in the short-reads. These results suggest the efficiency of full-length transcriptome studies and the importance of splicing variants in carcinogenesis. Genes generate transcripts of various functions by alternative splicing. However, in most transcriptome studies, short-reads sequencing technologies (next-generation sequencers) have been used, leaving full-length transcripts unobserved directly. In this study, we developed an analysis pipeline named SPLICE for long-read transcriptome sequencing and analyzed cDNA sequences from 42 pairs of hepatocellular carcinoma (HCC), and matched non-cancerous livers with an Oxford Nanopore sequencer. Our analysis detected 5,366 novel transcripts and 9,933 differentially expressed transcripts in 4,744 genes between HCCs and non-cancerous livers. An analysis of hepatitis B virus (HBV) transcripts showed that fusion transcripts of the HBV gene and human transposable elements were overexpressed in HBV-infected HCCs. We also identified fusion genes that were not found in the short-reads. These results suggest that long-reads sequencing technologies provide a fuller understanding of cancer transcripts and that our method contributes to the analysis of transcriptome sequences by such technologies.
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Affiliation(s)
- Hiroki Kiyose
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Atsushi Ono
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hiroshi Aikata
- Department of Gastroenterology and Metabolism, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Masaki Ueno
- Department of Surgery II, Wakayama Medical University, Wakayama, Japan
| | - Shinya Hayami
- Department of Surgery II, Wakayama Medical University, Wakayama, Japan
| | - Hiroki Yamaue
- Department of Surgery II, Wakayama Medical University, Wakayama, Japan
| | - Kazuaki Chayama
- Collaborative Research Laboratory of Medical Innovation, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- Research Center for Hepatology and Gastroenterology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Mihoko Shimada
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jing Hao Wong
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Akihiro Fujimoto
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- * E-mail:
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Fatima S, Gupta S, Khan AB, Rehman SU, Jairajpuri MA. Identification and validation of two alternatively spliced novel isoforms of human alpha-1-antichymotrypsin. Biochem Biophys Res Commun 2022; 628:25-31. [DOI: 10.1016/j.bbrc.2022.08.061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 11/02/2022]
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Tan Y, Zhao L, Yang YG, Liu W. The Role of Osteopontin in Tumor Progression Through Tumor-Associated Macrophages. Front Oncol 2022; 12:953283. [PMID: 35898884 PMCID: PMC9309262 DOI: 10.3389/fonc.2022.953283] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/15/2022] [Indexed: 11/18/2022] Open
Abstract
Osteopontin (OPN) is a multifunctional phosphorylated protein. It is widely involved in solid tumor progression, such as intensification of macrophage recruitment, inhibition of T-cell activity, aggravation of tumor interstitial fibrosis, promotion of tumor metastasis, chemotherapy resistance, and angiogenesis. Most of these pathologies are affected by tumor-associated macrophages (TAMs), an important component of the tumor microenvironment (TME). TAMs have been extensively characterized, including their subsets, phenotypes, activation status, and functions, and are considered a promising therapeutic target for cancer treatment. This review focuses on the interaction between OPN and TAMs in mediating tumor progression. We discuss the strategies for targeting OPN and TAMs to treat cancer and factors that may affect the therapeutic outcomes of blocking OPN or depleting TAMs. We also discuss the role of cancer cell- vs. TAM-derived OPN in tumorigenesis, the mechanisms of how OPN affects TAM recruitment and polarization, and why OPN could mediate anti-tumor and pro-tumor effects, as well as previously reported discrepancies.
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Affiliation(s)
- Yuying Tan
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
- National–Local Joint Engineering Laboratory of Animal Models for Human Diseases, Jilin University, Changchun, China
| | - Lei Zhao
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
- National–Local Joint Engineering Laboratory of Animal Models for Human Diseases, Jilin University, Changchun, China
| | - Yong-Guang Yang
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
- National–Local Joint Engineering Laboratory of Animal Models for Human Diseases, Jilin University, Changchun, China
- International Center of Future Science, Jilin University, Changchun, China
- *Correspondence: Yong-Guang Yang, ; Wentao Liu,
| | - Wentao Liu
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
- National–Local Joint Engineering Laboratory of Animal Models for Human Diseases, Jilin University, Changchun, China
- *Correspondence: Yong-Guang Yang, ; Wentao Liu,
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27
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Sun D, Zhang A, Gao B, Zou L, Huang H, Zhao X, Xu D. Identification of Alternative Splicing-Related Genes CYB561 and FOLH1 in the Tumor-Immune Microenvironment for Endometrial Cancer Based on TCGA Data Analysis. Front Genet 2022; 13:770569. [PMID: 35836577 PMCID: PMC9274141 DOI: 10.3389/fgene.2022.770569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 06/13/2022] [Indexed: 12/24/2022] Open
Abstract
Background: Advanced and recurrent endometrial cancer EC remains controversial. Immunotherapy will play a landmark role in cancer treatment, and alternative splicing (AS) of messenger RNA (mRNA) may offer the potential of a broadened target space.Methods: We downloaded the clinical information and mRNA expression profiles from The Cancer Genome Atlas (TCGA) database. Hub genes were extracted from 11 AS-related genes to analyze the correlation between clinical parameters and the tumor-immune microenvironment. We also analyzed the correlations between the copy numbers, gene expressions of hub genes, and immune cells. The correlation between the risk score and the six most important checkpoint genes was also investigated. The ESTIMATE algorithm was finally performed on each EC sample based on the high- and low-risk groups.Results: The risk score was a reliable and stable independent risk predictor in the Uterine Corpus Endometrial Carcinoma (UCEC) cohort. CYB561|42921|AP and FOLH1|15817|ES were extracted. The expression of CYB561 and FOLH1 decreased gradually with the increased grade and International Federation of Gynecology and Obstetrics (FIGO) stage (p < 0.05). Gene copy number changes in CYB561 and FOLH1 led to the deletion number of myeloid DC cells and T cell CD8+. Low expression of both CYB561 and FOLH1 was associated with poor prognosis (p < 0.001). The checkpoint genes, CTLA-4 and PDCD1, exhibited a negative correlation with the risk score of AS in UCEC.Conclusion: AS-related gene signatures were related to the immune-tumor microenvironment and prognosis. These outcomes were significant for studying EC’s immune-related mechanisms and exploring novel prognostic predictors and precise therapy methods.
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Affiliation(s)
| | | | | | | | | | | | - Dabao Xu
- *Correspondence: Xingping Zhao, ; Dabao Xu,
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Poly(A) capture full length cDNA sequencing improves the accuracy and detection ability of transcript quantification and alternative splicing events. Sci Rep 2022; 12:10599. [PMID: 35732903 PMCID: PMC9217819 DOI: 10.1038/s41598-022-14902-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/14/2022] [Indexed: 11/08/2022] Open
Abstract
The full-length double-strand cDNA sequencing, one of the RNA-Seq methods, is a powerful method used to investigate the transcriptome status of a gene of interest, such as its transcription level and alternative splicing variants. Furthermore, full-length double-strand cDNA sequencing has the advantage that it can create a library from a small amount of sample and the library can be applied to long-read sequencers in addition to short-read sequencers. Nevertheless, one of our previous studies indicated that the full-length double-strand cDNA sequencing yields non-specific genomic DNA amplification, affecting transcriptome analysis, such as transcript quantification and alternative splicing analysis. In this study, it was confirmed that it is possible to produce the RNA-Seq library from only genomic DNA and that the full-length double-strand cDNA sequencing of genomic DNA yielded non-specific genomic DNA amplification. To avoid non-specific genomic DNA amplification, two methods were examined, which are the DNase I-treated full-length double-strand cDNA sequencing and poly(A) capture full-length double-strand cDNA sequencing. Contrary to expectations, the non-specific genomic DNA amplification was increased and the number of the detected expressing genes was reduced in DNase I-treated full-length double-strand cDNA sequencing. On the other hand, in the poly(A) capture full-length double-strand cDNA sequencing, the non-specific genomic DNA amplification was significantly reduced, accordingly the accuracy and the number of detected expressing genes and splicing events were increased. The expression pattern and percentage spliced in index of splicing events were highly correlated. Our results indicate that the poly(A) capture full-length double-strand cDNA sequencing improves transcript quantification accuracy and the detection ability of alternative splicing events. It is also expected to contribute to the determination of the significance of DNA variants to splicing events.
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29
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Zhao Y, Sun H, Zhao Y, Liu Q, Liu Y, Hou Y, Jin W. NSrp70 suppresses metastasis in triple-negative breast cancer by modulating Numb/TβR1/EMT axis. Oncogene 2022; 41:3409-3422. [PMID: 35568738 DOI: 10.1038/s41388-022-02349-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 04/12/2022] [Accepted: 05/06/2022] [Indexed: 11/09/2022]
Abstract
Alternative splicing of mRNA precursors allows cancer cells to create different protein isoforms that promote growth and survival. Compared to normal cells, cancer cells frequently exhibit a higher diversity of their transcriptomes. A comprehensive understanding of splicing regulation is required to correct the splicing alterations for the future precision oncology. A quantitative proteomic screen was performed to identify the regulators associated the metastasis in triple-negative breast cancer. Multiple in vitro and in vivo functional analyses were used to study the effects of NSrp70 on breast cancer metastasis. Next, transcriptomic sequencing (RNA-seq) and alternative splicing bioinformatics analysis was applied to screen the potential targets of NSrp70. Moreover, in vitro splicing assays, RNA pull-down, and RNA immunoprecipitation assay were used to confirm the specific binding between NSrp70 and downstream target genes. Furthermore, the prognostic value of NSrp70 was analyzed in a cohort of patients by performing IHC. We uncovered NSrp70 as a novel suppressor of breast cancer metastasis. We discovered that NSrp70 inhibited the skipped exon alternative splicing of NUMB, promoted the degradation of transforming growth factor receptor 1 through lysosome pathway, and regulated TGFβ/SMAD-mediated epithelial-mesenchymal transition phenotype in breast cancer cells. Furthermore, high NSrp70 expression correlated with a better prognosis in breast cancer patients. Our findings revealed that splicing regulator NSrp70 serves as a metastasis suppressor.
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Affiliation(s)
- Yang Zhao
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Hefen Sun
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Yuanyuan Zhao
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Qiqi Liu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yang Liu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Yifeng Hou
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Wei Jin
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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Kwiatkowski M, Hotze M, Schumacher J, Asif AR, Pittol JMR, Brenig B, Ramljak S, Zischler H, Herlyn H. Protein speciation is likely to increase the chance of proteins to be determined in 2‐DE/MS. Electrophoresis 2022; 43:1203-1214. [DOI: 10.1002/elps.202000393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 11/30/2021] [Accepted: 02/02/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Marcel Kwiatkowski
- Department of Biochemistry and Center for Molecular Biosciences Innsbruck University of Innsbruck Innsbruck Austria
| | - Madlen Hotze
- Department of Biochemistry and Center for Molecular Biosciences Innsbruck University of Innsbruck Innsbruck Austria
| | | | - Abdul R. Asif
- Department of Clinical Chemistry/UMG‐Laboratories University Medical Center Göttingen Germany
| | - Jose Miguel Ramos Pittol
- Department of Biochemistry and Center for Molecular Biosciences Innsbruck University of Innsbruck Innsbruck Austria
| | - Bertram Brenig
- Department of Molecular Biology of Livestock Institute of Veterinary Medicine University of Göttingen Göttingen Germany
| | | | - Hans Zischler
- Institute of Organismic and Molecular Evolution, Anthropology University of Mainz Mainz Germany
| | - Holger Herlyn
- Institute of Organismic and Molecular Evolution, Anthropology University of Mainz Mainz Germany
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31
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Malhan D, Basti A, Relógio A. Transcriptome analysis of clock disrupted cancer cells reveals differential alternative splicing of cancer hallmarks genes. NPJ Syst Biol Appl 2022; 8:17. [PMID: 35552415 PMCID: PMC9098426 DOI: 10.1038/s41540-022-00225-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/04/2022] [Indexed: 12/13/2022] Open
Abstract
Emerging evidence points towards a regulatory role of the circadian clock in alternative splicing (AS). Whether alterations in core-clock components may contribute to differential AS events is largely unknown. To address this, we carried out a computational analysis on recently generated time-series RNA-seq datasets from three core-clock knockout (KO) genes (ARNTL, NR1D1, PER2) and WT of a colorectal cancer (CRC) cell line, and time-series RNA-seq datasets for additional CRC and Hodgkin’s lymphoma (HL) cells, murine WT, Arntl KO, and Nr1d1/2 KO, and murine SCN WT tissue. The deletion of individual core-clock genes resulted in the loss of circadian expression in crucial spliceosome components such as SF3A1 (in ARNTLKO), SNW1 (in NR1D1KO), and HNRNPC (in PER2KO), which led to a differential pattern of KO-specific AS events. All HCT116KO cells showed a rhythmicity loss of a crucial spliceosome gene U2AF1, which was also not rhythmic in higher progression stage CRC and HL cancer cells. AS analysis revealed an increase in alternative first exon events specific to PER2 and NR1D1 KO in HCT116 cells, and a KO-specific change in expression and rhythmicity pattern of AS transcripts related to cancer hallmarks genes including FGFR2 in HCT116_ARNTLKO, CD44 in HCT116_NR1D1KO, and MET in HCT116_PER2KO. KO-specific changes in rhythmic properties of known spliced variants of these genes (e.g. FGFR2 IIIb/FGFR2 IIIc) correlated with epithelial-mesenchymal-transition signalling. Altogether, our bioinformatic analysis highlights a role for the circadian clock in the regulation of AS, and reveals a potential impact of clock disruption in aberrant splicing in cancer hallmark genes.
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Affiliation(s)
- Deeksha Malhan
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany.,Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany.,Institute for Systems Medicine, Faculty of Human Medicine, MSH Medical School Hamburg, Hamburg, 20457, Germany
| | - Alireza Basti
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany.,Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany.,Institute for Systems Medicine, Faculty of Human Medicine, MSH Medical School Hamburg, Hamburg, 20457, Germany
| | - Angela Relógio
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany. .,Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany. .,Institute for Systems Medicine, Faculty of Human Medicine, MSH Medical School Hamburg, Hamburg, 20457, Germany.
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32
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Ura H, Togi S, Niida Y. A comparison of mRNA sequencing (RNA-Seq) library preparation methods for transcriptome analysis. BMC Genomics 2022; 23:303. [PMID: 35418012 PMCID: PMC9008973 DOI: 10.1186/s12864-022-08543-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 04/08/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND mRNA sequencing is a powerful technique, which is used to investigate the transcriptome status of a gene of interest, such as its transcription level and splicing variants. Presently, several RNA sequencing (RNA-Seq) methods have been developed; however, the relative advantage of each method has remained unknown. Here we used three commercially available RNA-Seq library preparation kits; the traditional method (TruSeq), in addition to full-length double-stranded cDNA methods (SMARTer and TeloPrime) to investigate the advantages and disadvantages of these three approaches in transcriptome analysis. RESULTS We observed that the number of expressed genes detected from the TeloPrime sequencing method was fewer than that obtained using the TruSeq and SMARTer. We also observed that the expression patterns between TruSeq and SMARTer correlated strongly. Alternatively, SMARTer and TeloPrime methods underestimated the expression of relatively long transcripts. Moreover, genes having low expression levels were undetected stochastically regardless of any three methods used. Furthermore, although TeloPrime detected a significantly higher proportion at the transcription start site (TSS), its coverage of the gene body was not uniform. SMARTer is proposed to be yielded for nonspecific genomic DNA amplification. In contrast, the detected splicing event number was highest in the TruSeq. The percent spliced in index (PSI) of the three methods was highly correlated. CONCLUSIONS TruSeq detected transcripts and splicing events better than the other methods and measured expression levels of genes, in addition to splicing events accurately. However, although detected transcripts and splicing events in TeloPrime were fewer, the coverage at TSS was highest. Additionally, SMARTer was better than TeloPrime with regards to the detected number of transcripts and splicing events among the understudied full-length double-stranded cDNA methods. In conclusion, for short-read sequencing, TruSeq has relative advantages for use in transcriptome analysis.
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Affiliation(s)
- Hiroki Ura
- Center for Clinical Genomics, Kanazawa Medical University Hospital, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa, 920-0923, Japan. .,Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa, 920-0923, Japan.
| | - Sumihito Togi
- Center for Clinical Genomics, Kanazawa Medical University Hospital, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa, 920-0923, Japan.,Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa, 920-0923, Japan
| | - Yo Niida
- Center for Clinical Genomics, Kanazawa Medical University Hospital, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa, 920-0923, Japan.,Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa, 920-0923, Japan
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The aberrant upregulation of exon 10-inclusive SREK1 through SRSF10 acts as an oncogenic driver in human hepatocellular carcinoma. Nat Commun 2022; 13:1363. [PMID: 35296659 PMCID: PMC8927159 DOI: 10.1038/s41467-022-29016-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 02/23/2022] [Indexed: 12/13/2022] Open
Abstract
Deregulation of alternative splicing is implicated as a relevant source of molecular heterogeneity in cancer. However, the targets and intrinsic mechanisms of splicing in hepatocarcinogenesis are largely unknown. Here, we report a functional impact of a Splicing Regulatory Glutamine/Lysine-Rich Protein 1 (SREK1) variant and its regulator, Serine/arginine-rich splicing factor 10 (SRSF10). HCC patients with poor prognosis express higher levels of exon 10-inclusive SREK1 (SREK1L). SREK1L can sustain BLOC1S5-TXNDC5 (B-T) expression, a targeted gene of nonsense-mediated mRNA decay through inhibiting exon-exon junction complex binding with B-T to exert its oncogenic role. B-T plays its competing endogenous RNA role by inhibiting miR-30c-5p and miR-30e-5p, and further promoting the expression of downstream oncogenic targets SRSF10 and TXNDC5. Interestingly, SRSF10 can act as a splicing regulator for SREK1L to promote hepatocarcinogenesis via the formation of a SRSF10-associated complex. In summary, we demonstrate a SRSF10/SREK1L/B-T signalling loop to accelerate the hepatocarcinogenesis. Alternative splicing is dysregulated in hepatocellular carcinoma. Here, the authors investigate the role of the splice variant of Splicing Regulatory Glutamic Acid and Lysine Rich Protein 1 (SREK1) and its upstream regulator, Serine/arginine-rich splicing factor 10 (SRSF10) in sustaining the oncogenic signal.
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34
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Lepucki A, Orlińska K, Mielczarek-Palacz A, Kabut J, Olczyk P, Komosińska-Vassev K. The Role of Extracellular Matrix Proteins in Breast Cancer. J Clin Med 2022; 11:jcm11051250. [PMID: 35268340 PMCID: PMC8911242 DOI: 10.3390/jcm11051250] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 01/16/2022] [Accepted: 02/22/2022] [Indexed: 12/12/2022] Open
Abstract
The extracellular matrix is a structure composed of many molecules, including fibrillar (types I, II, III, V, XI, XXIV, XXVII) and non-fibrillar collagens (mainly basement membrane collagens: types IV, VIII, X), non-collagenous glycoproteins (elastin, laminin, fibronectin, thrombospondin, tenascin, osteopontin, osteonectin, entactin, periostin) embedded in a gel of negatively charged water-retaining glycosaminoglycans (GAGs) such as non-sulfated hyaluronic acid (HA) and sulfated GAGs which are linked to a core protein to form proteoglycans (PGs). This highly dynamic molecular network provides critical biochemical and biomechanical cues that mediate the cell–cell and cell–matrix interactions, influence cell growth, migration and differentiation and serve as a reservoir of cytokines and growth factors’ action. The breakdown of normal ECM and its replacement with tumor ECM modulate the tumor microenvironment (TME) composition and is an essential part of tumorigenesis and metastasis, acting as key driver for malignant progression. Abnormal ECM also deregulate behavior of stromal cells as well as facilitating tumor-associated angiogenesis and inflammation. Thus, the tumor matrix modulates each of the classically defined hallmarks of cancer promoting the growth, survival and invasion of the cancer. Moreover, various ECM-derived components modulate the immune response affecting T cells, tumor-associated macrophages (TAM), dendritic cells and cancer-associated fibroblasts (CAF). This review article considers the role that extracellular matrix play in breast cancer. Determining the detailed connections between the ECM and cellular processes has helped to identify novel disease markers and therapeutic targets.
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Affiliation(s)
- Arkadiusz Lepucki
- Department of Community Pharmacy, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 41-200 Sosnowiec, Poland; (A.L.); (K.O.)
| | - Kinga Orlińska
- Department of Community Pharmacy, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 41-200 Sosnowiec, Poland; (A.L.); (K.O.)
| | - Aleksandra Mielczarek-Palacz
- Department of Immunology and Serology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 41-200 Sosnowiec, Poland; (A.M.-P.); (J.K.)
| | - Jacek Kabut
- Department of Immunology and Serology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 41-200 Sosnowiec, Poland; (A.M.-P.); (J.K.)
| | - Pawel Olczyk
- Department of Community Pharmacy, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 41-200 Sosnowiec, Poland; (A.L.); (K.O.)
- Correspondence:
| | - Katarzyna Komosińska-Vassev
- Department of Clinical Chemistry and Laboratory Diagnostics, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 41-200 Sosnowiec, Poland;
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35
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USP15 and USP4 facilitate lung cancer cell proliferation by regulating the alternative splicing of SRSF1. Cell Death Dis 2022; 8:24. [PMID: 35027535 PMCID: PMC8758713 DOI: 10.1038/s41420-022-00820-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/07/2021] [Accepted: 12/22/2021] [Indexed: 01/14/2023]
Abstract
The deubiquitinating enzyme USP15 is implicated in several human cancers by regulating different cellular processes, including splicing regulation. However, the underlying molecular mechanisms of its functional relevance and the successive roles in enhanced tumorigenesis remain ambiguous. Here, we found that USP15 and its close paralog USP4 are overexpressed and facilitate lung cancer cell proliferation by regulating the alternative splicing of SRSF1. Depletion of USP15 and USP4 impair SRSF1 splicing characterized by the replacement of exon 4 with non-coding intron sequences retained at its C-terminus, resulting in an alternative isoform SRSF1-3. We observed an increased endogenous expression of SRSF1 in lung cancer cells as well, and its overexpression significantly enhanced cancer cell phenotype and rescued the depletion effect of USP15 and USP4. However, the alternatively spliced isoform SRSF1-3 was deficient in such aspects for its premature degradation through nonsense-mediated mRNA decay. The increased USP15 expression contributes to the lung adenocarcinoma (LUAD) development and shows significantly lower disease-specific survival of patients with USP15 alteration. In short, we identified USP15 and USP4 as key regulators of SRSF1 alternative splicing with altered functions, which may represent the novel prognostic biomarker as well as a potential target for LUAD.
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36
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Zheng X, Zhang D, Xu M, Zeng W, Zhou R, Zhang Y, Tang C, Chen L, Chen L, Lin JW. Short-read and long-read RNA sequencing of mouse hematopoietic stem cells at bulk and single-cell levels. Sci Data 2021; 8:309. [PMID: 34845251 PMCID: PMC8630105 DOI: 10.1038/s41597-021-01078-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/27/2021] [Indexed: 02/05/2023] Open
Abstract
Hematopoietic stem cells (HSCs) lie at the top of the differentiation hierarchy. Although HSC and their immediate downstream, multipotent progenitors (MPP) have full multilineage differentiation capacity, only long-term (LT-) HSC has the capacity of long-term self-renewal. The heterogeneity within the HSC population is gradually acknowledged with the development of single-cell RNA sequencing and lineage tracing technologies. Transcriptional and post-transcriptional regulations play important roles in controlling the differentiation and self-renewal capacity within HSC population. Here we report a dataset comprising short- and long-read RNA sequencing for mouse long- and short-term HSC and MPP at bulk and single-cell levels. We demonstrate that integrating short- and long-read sequencing can facilitate the identification and quantification of known and unannotated isoforms. Thus, this dataset provides a groundwork for comprehensive and comparative studies on transcriptional diversity and heterogeneity within different HSC cell types.
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Affiliation(s)
- Xiuran Zheng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Dan Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Mengying Xu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Wanqin Zeng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Ran Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Yiming Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Chao Tang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Li Chen
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Lu Chen
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China.
| | - Jing-Wen Lin
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China.
- Biosafety Laboratory of West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
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Li H, Jin XK, Zhou KM, Zhao H, Zhao YH, Wang Q, Li WW. Down Syndrome Cell Adhesion Molecule Triggers Membrane-to-Nucleus Signaling-Regulated Hemocyte Proliferation against Bacterial Infection in Invertebrates. THE JOURNAL OF IMMUNOLOGY 2021; 207:2265-2277. [PMID: 34580107 DOI: 10.4049/jimmunol.2100575] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/27/2021] [Indexed: 11/19/2022]
Abstract
Down syndrome cell adhesion molecule (Dscam) generates tens of thousands of isoforms by alternative splicing, thereby providing crucial functions during immune responses. In this study, a novel Dscam signaling pathway was investigated in crab, which remains poorly characterized in invertebrates. Bacterial infection induced the cytoplasmic cleavage of Dscam intracellular domains (ICDs) by γ-secretase, and then the released ICDs carrying specific alternatively spliced exons could directly interact with IPO5 to facilitate nuclear translocation. Nuclear imported ICDs thus promoted hemocyte proliferation and protect the host from bacterial infection. Protein-interaction studies revealed that the ectodomain of Dscam bound to a disintegrin and metalloprotease domain 10 (ADAM10) rather than ADAM17. Inhibition or overexpression of ADAM10 impaired or accelerated Dscam shedding activity post-bacterial stimulation, respectively. Moreover, the shedding signal then mediated Dscam with an intact cytoplasmic domain to promote the cleavage of ICDs by γ-secretase. Furthermore, the transcription of ADAM10 was regulated by Dscam-induced canonical signaling, but not nuclear imported ICDs, to serve as a feedback regulation between two different Dscam pathways. Thus, membrane-to-nuclear signaling of Dscam regulated hemocyte proliferation in response to bacterial infection.
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Affiliation(s)
- Hao Li
- Laboratory of Invertebrate Immunological Defense & Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China; and
| | - Xing-Kun Jin
- Department of Marine Biology, College of Oceanography, Hohai University, Nanjing, China
| | - Kai-Min Zhou
- Laboratory of Invertebrate Immunological Defense & Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China; and
| | - Hui Zhao
- Laboratory of Invertebrate Immunological Defense & Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China; and
| | - Yue-Hong Zhao
- Laboratory of Invertebrate Immunological Defense & Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China; and
| | - Qun Wang
- Laboratory of Invertebrate Immunological Defense & Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China; and
| | - Wei-Wei Li
- Laboratory of Invertebrate Immunological Defense & Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China; and
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38
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Zhao Z, Xu Q, Wei R, Huang L, Wang W, Wei G, Ni T. Comprehensive characterization of somatic variants associated with intronic polyadenylation in human cancers. Nucleic Acids Res 2021; 49:10369-10381. [PMID: 34508351 PMCID: PMC8501991 DOI: 10.1093/nar/gkab772] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 08/16/2021] [Accepted: 08/26/2021] [Indexed: 11/29/2022] Open
Abstract
Somatic single nucleotide variants (SNVs) in cancer genome affect gene expression through various mechanisms depending on their genomic location. While somatic SNVs near canonical splice sites have been reported to cause abnormal splicing of cancer-related genes, whether these SNVs can affect gene expression through other mechanisms remains an open question. Here, we analyzed RNA sequencing and exome data from 4,998 cancer patients covering ten cancer types and identified 152 somatic SNVs near splice sites that were associated with abnormal intronic polyadenylation (IPA). IPA-associated somatic variants favored the localization near the donor splice sites compared to the acceptor splice sites. A proportion of SNV-associated IPA events overlapped with premature cleavage and polyadenylation events triggered by U1 small nuclear ribonucleoproteins (snRNP) inhibition. GC content, intron length and polyadenylation signal were three genomic features that differentiated between SNV-associated IPA and intron retention. Notably, IPA-associated SNVs were enriched in tumor suppressor genes (TSGs), including the well-known TSGs such as PTEN and CDH1 with recurrent SNV-associated IPA events. Minigene assay confirmed that SNVs from PTEN, CDH1, VEGFA, GRHL2, CUL3 and WWC2 could lead to IPA. This work reveals that IPA acts as a novel mechanism explaining the functional consequence of somatic SNVs in human cancer.
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Affiliation(s)
- Zhaozhao Zhao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai 200438, P.R. China
| | - Qiushi Xu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai 200438, P.R. China
| | - Ran Wei
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai 200438, P.R. China.,Department of Pathology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Leihuan Huang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai 200438, P.R. China
| | - Weixu Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai 200438, P.R. China
| | - Gang Wei
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai 200438, P.R. China.,MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China
| | - Ting Ni
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai 200438, P.R. China.,Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China
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39
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Yang TH, Chiang YH, Shiue SC, Lin PH, Yang YC, Tu KC, Tseng YY, Tseng JT, Wu WS. Cancer DEIso: An integrative analysis platform for investigating differentially expressed gene-level and isoform-level human cancer markers. Comput Struct Biotechnol J 2021; 19:5149-5159. [PMID: 34589189 PMCID: PMC8463781 DOI: 10.1016/j.csbj.2021.09.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 09/06/2021] [Accepted: 09/06/2021] [Indexed: 12/19/2022] Open
Abstract
Transcript isoforms regulated by alternative splicing can substantially impact carcinogenesis, leading to a need to obtain clues for both gene differential expression and malfunctions of isoform distributions in cancer studies. The Cancer Genome Atlas (TCGA) project was launched in 2008 to collect cancer-related genome mutation raw data from the population. While many repositories tried to add insights into the raw data in TCGA, no existing database provides both comprehensive gene-level and isoform-level cancer stage marker investigation and survival analysis. We constructed Cancer DEIso to facilitate in-depth analyses for both gene-level and isoform-level human cancer studies. Patient RNA-seq data, sample sheets, patient clinical data, and human genome datasets were collected and processed in Cancer DEIso. And four functions to search differentially expressed genes/isoforms between cancer stages were implemented: (i) Search potential gene/isoform markers for a specified cancer type and its two stages; (ii) Search potentially induced cancer types and stages for a gene/isoform; (iii) Expression survival analysis on a given gene/isoform for some cancer; (iv) Gene/isoform stage expression comparison visualization. As an example, we demonstrate that Cancer DEIso can indicate potential colorectal cancer isoform diagnostic markers that are not easily detected when only gene-level expressions are considered. Cancer DEIso is available at http://cosbi4.ee.ncku.edu.tw/DEIso/.
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Affiliation(s)
- Tzu-Hsien Yang
- Department of Information Management, National University of Kaohsiung, Kaohsiung University Rd, 811 Kaohsiung, Taiwan
| | - Yu-Hsuan Chiang
- Department of Electrical Engineering, National Cheng Kung University, University Road, 701 Tainan, Taiwan
| | - Sheng-Cian Shiue
- Department of Electrical Engineering, National Cheng Kung University, University Road, 701 Tainan, Taiwan
| | - Po-Heng Lin
- Department of Electrical Engineering, National Cheng Kung University, University Road, 701 Tainan, Taiwan
| | - Ya-Chiao Yang
- Department of Information Management, National University of Kaohsiung, Kaohsiung University Rd, 811 Kaohsiung, Taiwan
| | - Kai-Chi Tu
- Department of Information Management, National University of Kaohsiung, Kaohsiung University Rd, 811 Kaohsiung, Taiwan
| | - Yan-Yuan Tseng
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, MI, USA
| | - Joseph T. Tseng
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, University Road, 701 Tainan, Taiwan
- Corresponding authors.
| | - Wei-Sheng Wu
- Department of Electrical Engineering, National Cheng Kung University, University Road, 701 Tainan, Taiwan
- Corresponding authors.
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40
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A pan-cancer analysis of alternative splicing of splicing factors in 6904 patients. Oncogene 2021; 40:5441-5450. [PMID: 34285345 DOI: 10.1038/s41388-021-01947-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 07/01/2021] [Accepted: 07/08/2021] [Indexed: 02/07/2023]
Abstract
Great progress has been made in the investigation on mutation and expression of splicing factor. However, little is known on the role of alternative splicing of splicing factors across cancers. Here, we reported a pan-cancer analysis of alternative splicing of splicing factors spanning 6904 patients across 16 cancer types, and identified 167 splicing factors with implications regulating cancer-specific splicing patterns through alternative splicing. Furthermore, we found that abnormal splicing events of splicing factors could serve as potential common regulators for alternative splicing in different cancers. In addition, we developed a splicing-derived neoepitopes database (ASPNs), which provided the corresponding putative alternative splicing-derived neoepitopes of 16 cancer types. Our results suggested that alternative splicing of splicing factors involved in the pre-RNA splicing process was common across cancer types and may represent an underestimated hallmark of tumorigenesis.
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41
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Peng Q, Wang L, Wang J, Liu C, Zheng X, Zhang X, Wei L, Li Z, Wu Y, Wen Y, Cao P, Liao Q, Yan Q, Ma J. Epstein-Barr virus EBNA2 phase separation regulates cancer-associated alternative RNA splicing patterns. Clin Transl Med 2021; 11:e504. [PMID: 34459139 PMCID: PMC8351520 DOI: 10.1002/ctm2.504] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 07/06/2021] [Accepted: 07/11/2021] [Indexed: 12/21/2022] Open
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, China.,Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Lujuan Wang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Jia Wang
- Department of Immunology, Department of Pathology, Heping Hospital, Changzhi Medical College, Changzhi, China
| | - Can Liu
- Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Xiang Zheng
- Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China.,Department of Pathology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Xiaoyue Zhang
- Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Lingyu Wei
- Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China.,Department of Immunology, Department of Pathology, Heping Hospital, Changzhi Medical College, Changzhi, China
| | - Zhengshuo Li
- Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Yangge Wu
- Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Yuqing Wen
- Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Pengfei Cao
- Department of Clinical Laboratory, Department of Hematology, Xiangya Hospital, 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, China
| | - Qun Yan
- Department of Clinical Laboratory, Department of Hematology, Xiangya Hospital, Central South University, Changsha, 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, China.,Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
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42
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Zaitceva V, Kopeina GS, Zhivotovsky B. Anastasis: Return Journey from Cell Death. Cancers (Basel) 2021; 13:3671. [PMID: 34359573 PMCID: PMC8345212 DOI: 10.3390/cancers13153671] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/16/2021] [Accepted: 07/17/2021] [Indexed: 12/12/2022] Open
Abstract
For over 20 years, it has been a dogma that once the integrity of mitochondria is disrupted and proapoptotic proteins that are normally located in the intermembrane space of mitochondria appeared in the cytoplasm, the process of cell death becomes inevitable. However, it has been recently shown that upon removal of the death signal, even at the stage of disturbance in the mitochondria, cells can recover and continue to grow. This phenomenon was named anastasis. Here, we will critically discuss the present knowledge concerning the mechanisms of cell death reversal, or development of anastasis, methods for its detection, and what role signaling from different intracellular compartments plays in anastasis stimulation.
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Affiliation(s)
- Victoria Zaitceva
- Faculty of Medicine, MV Lomonosov Moscow State University, 119991 Moscow, Russia; (V.Z.); (G.S.K.)
| | - Gelina S. Kopeina
- Faculty of Medicine, MV Lomonosov Moscow State University, 119991 Moscow, Russia; (V.Z.); (G.S.K.)
| | - Boris Zhivotovsky
- Faculty of Medicine, MV Lomonosov Moscow State University, 119991 Moscow, Russia; (V.Z.); (G.S.K.)
- Division of Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Box 210, 17177 Stockholm, Sweden
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43
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Cheng C, Liu L, Bao Y, Yi J, Quan W, Xue Y, Sun L, Zhang Y. SUVA: splicing site usage variation analysis from RNA-seq data reveals highly conserved complex splicing biomarkers in liver cancer. RNA Biol 2021; 18:157-171. [PMID: 34152934 DOI: 10.1080/15476286.2021.1940037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Most of the current alternative splicing (AS) analysis tools are powerless to analyse complex splicing. To address this, we developed SUVA (Splice sites Usage Variation Analysis) that decomposes complex splicing events into five types of splice junction pairs. By analysing real and simulated data, SUVA showed higher sensitivity and accuracy in detecting AS events than the compared methods. Notably, SUVA detected extensive complex AS events and screened out 69 highly conserved and dominant AS events associated with cancer. The cancer-associated complex AS events in FN1 and the co-regulated RNA-binding proteins were significantly correlated with patient survival.
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Affiliation(s)
- Chao Cheng
- ABLife BioBigData Institute, Wuhan, Hubei China.,Center for Genome Analysis, ABLife Inc., Wuhan, Hubei China
| | - Lei Liu
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun China
| | - Yongli Bao
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun China
| | - Jingwen Yi
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun China
| | - Weili Quan
- ABLife BioBigData Institute, Wuhan, Hubei China
| | - Yaqiang Xue
- ABLife BioBigData Institute, Wuhan, Hubei China
| | - Luguo Sun
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun China
| | - Yi Zhang
- ABLife BioBigData Institute, Wuhan, Hubei China.,Center for Genome Analysis, ABLife Inc., Wuhan, Hubei China
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44
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Otani Y, Fujita KI, Kameyama T, Mayeda A. The Exon Junction Complex Core Represses Cancer-Specific Mature mRNA Re-splicing: A Potential Key Role in Terminating Splicing. Int J Mol Sci 2021; 22:ijms22126519. [PMID: 34204574 PMCID: PMC8234774 DOI: 10.3390/ijms22126519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/08/2021] [Indexed: 02/08/2023] Open
Abstract
Using TSG101 pre-mRNA, we previously discovered cancer-specific re-splicing of mature mRNA that generates aberrant transcripts/proteins. The fact that mRNA is aberrantly re-spliced in various cancer cells implies there must be an important mechanism to prevent deleterious re-splicing on the spliced mRNA in normal cells. We thus postulated that mRNA re-splicing is controlled by specific repressors, and we searched for repressor candidates by siRNA-based screening for mRNA re-splicing activity. We found that knock-down of EIF4A3, which is a core component of the exon junction complex (EJC), significantly promoted mRNA re-splicing. Remarkably, we could recapitulate cancer-specific mRNA re-splicing in normal cells by knock-down of any of the core EJC proteins, EIF4A3, MAGOH, or RBM8A (Y14), implicating the EJC core as the repressor of mRNA re-splicing often observed in cancer cells. We propose that the EJC core is a critical mRNA quality control factor to prevent over-splicing of mature mRNA.
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Affiliation(s)
- Yuta Otani
- Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Aichi, Japan; (Y.O.); (K.-i.F.)
- Laboratories of Discovery Research, Nippon Shinyaku Co., Ltd., Kyoto 601-8550, Kyoto, Japan
| | - Ken-ichi Fujita
- Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Aichi, Japan; (Y.O.); (K.-i.F.)
| | - Toshiki Kameyama
- Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Aichi, Japan; (Y.O.); (K.-i.F.)
- Department of Physiology, School of Medicine, Fujita Health University, Toyoake 470-1192, Aichi, Japan
- Correspondence: (T.K.); (A.M.)
| | - Akila Mayeda
- Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Aichi, Japan; (Y.O.); (K.-i.F.)
- Correspondence: (T.K.); (A.M.)
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45
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Zhang J, Goel A, Zhu L. Identification of Novel Alternative Splicing Events Associated With Tumorigenesis, Protein Modification, and Immune Microenvironment in Early-Onset Gastric Cancer. Front Oncol 2021; 11:640272. [PMID: 34168979 PMCID: PMC8217769 DOI: 10.3389/fonc.2021.640272] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 05/10/2021] [Indexed: 01/22/2023] Open
Abstract
Background Alternative splicing (AS), e.g. the tandem alternative polyadenylation (TAPA), has emerged as major post-transcriptional modification events in human disease. However, the roles of the AS and TAPA in early-onset gastric cancer (EOGC) have not been revealed. Methods The global AS profiles of 80 EOGC patients were analyzed. The EOGC-specific AS events (ESASs) were identified in both the EOGC and adjacent non-tumor tissues. The functional enrichment analysis, Splicing network, Alternative Polyadenylation (APA) core factor network, and cell abundancy analysis were performed. Furthermore, the landscapes of the AS events in the varied subtypes of the EOGC patients were evaluated. Results Overall, 66,075 AS events and 267 ESASs were identified in the EOGC. Furthermore, 4809 genes and 6152 gene isoforms were found to be aberrantly expressed in the EOGC. The Gene Ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway analyses showed that the significant pathway alterations might exist in these AS events, genes, and gene isoforms. Moreover, the Protein-protein interaction (PPI) network analysis revealed that the UBC, NEK2, EPHB2, and DCTN1 genes were the hub genes in the AS events in the EOGC. The immune cell infiltration analysis indicated a correlation between the AS events and the cancer immune microenvironment. The distribution of the AS events in varied EOGC subtypes, protein phosphorylation and glycosylation was uneven. Conclusion The study highlighted the vital roles of the AS in the EOGC, including modulating the specific protein modification and reshaping the cancer immune microenvironment, and yielded new insights into the diagnosis of the EOGC as well as cancer treatment.
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Affiliation(s)
- Jian Zhang
- Department of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, TX, United States
| | - Ajay Goel
- Beckman Research Institute, City of Hope Comprehensive Cancer Center, Biomedical Research Center, Monrovia, CA, United States
| | - Lin Zhu
- Department of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, TX, United States
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46
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The landscape and driver potential of site-specific hotspots across cancer genomes. NPJ Genom Med 2021; 6:33. [PMID: 33986299 PMCID: PMC8119706 DOI: 10.1038/s41525-021-00197-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/15/2021] [Indexed: 11/09/2022] Open
Abstract
Large sets of whole cancer genomes make it possible to study mutation hotspots genome-wide. Here we detect, categorize, and characterize site-specific hotspots using 2279 whole cancer genomes from the Pan-Cancer Analysis of Whole Genomes project and provide a resource of annotated hotspots genome-wide. We investigate the excess of hotspots in both protein-coding and gene regulatory regions and develop measures of positive selection and functional impact for individual hotspots. Using cancer allele fractions, expression aberrations, mutational signatures, and a variety of genomic features, such as potential gain or loss of transcription factor binding sites, we annotate and prioritize all highly mutated hotspots. Genome-wide we find more high-frequency SNV and indel hotspots than expected given mutational background models. Protein-coding regions are generally enriched for SNV hotspots compared to other regions. Gene regulatory hotspots show enrichment of potential same-patient second-hit missense mutations, consistent with enrichment of hotspot driver mutations compared to singletons. For protein-coding regions, splice-sites, promoters, and enhancers, we see an excess of hotspots associated with cancer genes. Interestingly, missense hotspot mutations in tumor suppressors are associated with elevated expression, suggesting localized amino-acid changes with functional impact. For individual non-coding hotspots, only a small number show clear signs of positive selection, including known sites in the TERT promoter and the 5' UTR of TP53. Most of the new candidates have few mutations and limited driver evidence. However, a hotspot in an enhancer of the oncogene POU2AF1, which may create a transcription factor binding site, presents multiple lines of driver-consistent evidence.
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47
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Tripathi A, Kashyap A, Tripathi G, Yadav J, Bibban R, Aggarwal N, Thakur K, Chhokar A, Jadli M, Sah AK, Verma Y, Zayed H, Husain A, Bharti AC, Kashyap MK. Tumor reversion: a dream or a reality. Biomark Res 2021; 9:31. [PMID: 33958005 PMCID: PMC8101112 DOI: 10.1186/s40364-021-00280-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/30/2021] [Indexed: 02/07/2023] Open
Abstract
Reversion of tumor to a normal differentiated cell once considered a dream is now at the brink of becoming a reality. Different layers of molecules/events such as microRNAs, transcription factors, alternative RNA splicing, post-transcriptional, post-translational modifications, availability of proteomics, genomics editing tools, and chemical biology approaches gave hope to manipulation of cancer cells reversion to a normal cell phenotype as evidences are subtle but definitive. Regardless of the advancement, there is a long way to go, as customized techniques are required to be fine-tuned with precision to attain more insights into tumor reversion. Tumor regression models using available genome-editing methods, followed by in vitro and in vivo proteomics profiling techniques show early evidence. This review summarizes tumor reversion developments, present issues, and unaddressed challenges that remained in the uncharted territory to modulate cellular machinery for tumor reversion towards therapeutic purposes successfully. Ongoing research reaffirms the potential promises of understanding the mechanism of tumor reversion and required refinement that is warranted in vitro and in vivo models of tumor reversion, and the potential translation of these into cancer therapy. Furthermore, therapeutic compounds were reported to induce phenotypic changes in cancer cells into normal cells, which will contribute in understanding the mechanism of tumor reversion. Altogether, the efforts collectively suggest that tumor reversion will likely reveal a new wave of therapeutic discoveries that will significantly impact clinical practice in cancer therapy.
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Affiliation(s)
- Avantika Tripathi
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon, Haryana, Manesar (Gurugram), -122413, India
| | - Anjali Kashyap
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, India
| | - Greesham Tripathi
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon, Haryana, Manesar (Gurugram), -122413, India
| | - Joni Yadav
- Department of Zoology, Molecular Oncology Laboratory, University of Delhi (North Campus), New Delhi, 110007, India
| | - Rakhi Bibban
- Department of Zoology, Molecular Oncology Laboratory, University of Delhi (North Campus), New Delhi, 110007, India
| | - Nikita Aggarwal
- Department of Zoology, Molecular Oncology Laboratory, University of Delhi (North Campus), New Delhi, 110007, India
| | - Kulbhushan Thakur
- Department of Zoology, Molecular Oncology Laboratory, University of Delhi (North Campus), New Delhi, 110007, India
| | - Arun Chhokar
- Department of Zoology, Molecular Oncology Laboratory, University of Delhi (North Campus), New Delhi, 110007, India
| | - Mohit Jadli
- Department of Zoology, Molecular Oncology Laboratory, University of Delhi (North Campus), New Delhi, 110007, India
| | - Ashok Kumar Sah
- Department of Medical Laboratory Technology, Amity Medical School, Amity University Haryana, Panchgaon, Haryana, Manesar (Gurugram), India
- Department of Pathology and Laboratory Medicine, Medanta-The Medicity, Haryana, Gurugram, India
| | - Yeshvandra Verma
- Department of Toxicology, C C S University, Meerut, UP, 250004, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Amjad Husain
- Centre for Science & Society, Indian Institute of Science Education and Research (IISER), Bhopal, India
- Innovation and Incubation Centre for Entrepreneurship (IICE), Indian Institute of Science Education and Research (IISER), Bhopal, India
| | - Alok Chandra Bharti
- Department of Zoology, Molecular Oncology Laboratory, University of Delhi (North Campus), New Delhi, 110007, India.
| | - Manoj Kumar Kashyap
- Amity Stem Cell Institute, Amity Medical School, Amity University Haryana, Panchgaon, Haryana, Manesar (Gurugram), -122413, India.
- Department of Zoology, Molecular Oncology Laboratory, University of Delhi (North Campus), New Delhi, 110007, India.
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48
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Lim CC, Chan SK, Lim YY, Ishikawa Y, Choong YS, Nagaoka Y, Lim TS. Development and structural characterisation of human scFv targeting MDM2 spliced variant MDM2 15kDa. Mol Immunol 2021; 135:191-203. [PMID: 33930714 DOI: 10.1016/j.molimm.2021.04.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/09/2021] [Accepted: 04/18/2021] [Indexed: 01/10/2023]
Abstract
The murine double minute 2 (MDM2) protein is a major negative regulator of the tumour suppressor protein p53. Under normal conditions, MDM2 constantly binds to p53 transactivation domain and/or ubiquinates p53 via its role as E3 ubiquitin ligase to promote p53 degradation as well as nuclear export to maintain p53 levels in cells. Meanwhile, amplification of MDM2 and appearance of MDM2 spliced variants occur in many tumours and normal tissues making it a prognostic indicator for human cancers. The mutation or deletion of p53 protein in half of human cancers inactivates its tumour suppressor activity. However, cancers with wild type p53 have its function effectively inhibited through direct interaction with MDM2 oncoprotein. Here, we described the construction of a MDM2 spliced variant (rMDM215kDa) consisting of SWIB/MDM2 domain and its central region for antibody generation. Biopanning with a human naïve scFv library generated four scFv clones specific to rMDM215kDa. Additionally, the selected scFv clones were able to bind to the recombinant full length MDM2 (rMDM2-FL). Computational prediction showed that the selected scFv clones potentially bind to exon 7-8 of MDM2 while leaving the MDM2/SWIB domain free for p53 interaction. The developed antibodies exhibit good specificity can be further investigated for downstream biomedical and research applications.
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Affiliation(s)
- Chia Chiu Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Soo Khim Chan
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Yee Ying Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Yuya Ishikawa
- Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, 3-3-35 Yamate-cho Suita, Osaka, 564-8680, Japan
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Yasuo Nagaoka
- Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, 3-3-35 Yamate-cho Suita, Osaka, 564-8680, Japan
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Penang, Malaysia; Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800, Penang, Malaysia.
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49
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Shuai T, Khan MR, Zhang XD, Li J, Thorne RF, Wu M, Shao F. lncRNA TRMP-S directs dual mechanisms to regulate p27-mediated cellular senescence. MOLECULAR THERAPY-NUCLEIC ACIDS 2021; 24:971-985. [PMID: 34094715 PMCID: PMC8141606 DOI: 10.1016/j.omtn.2021.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/05/2021] [Indexed: 01/10/2023]
Abstract
Long noncoding RNAs (lncRNAs) undergo extensive alternative splicing, but little is known about isoform functions. A prior investigation of lncRNA RP11-369C8.1 reported that its splice variant TRMP suppressed p27 translation through PTBP1. Here we characterize a second major splice variant, TRMP-S (short variant), whose enforced loss promotes cancer cell-cycle arrest and p27-dependent entry into cellular senescence. Remarkably, despite sharing a single common exon with TRMP, TRMP-S restrains p27 expression through distinct mechanisms. First, TRMP-S stabilizes UHRF1 protein levels, an epigenetic inhibitor of p27, by promoting interactions between UHRF1 and its deubiquitinating enzyme USP7. Alternatively, binding interactions between TRMP-S and FUBP3 prevent p53 mRNA interactions with RPL26 ribosomal protein, the latter essential for promoting p53 translation with ensuing suppression of p53 translation limiting p27 expression. Significantly, as TRMP-S is itself transactivated by p53, this identifies negative feedback regulation between p53 and TRMP-S. Different splicing variants of the RP11-369C8.1 gene thereby exert distinct roles that converge on the homeostatic control of p27 expression, providing an important precedent for understanding the actions of alternatively spliced lncRNAs.
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Affiliation(s)
- Tian Shuai
- Translational Research Institute, Henan Provincial People's Hospital, School of Clinical Medicine, Henan University, Zhengzhou 450003, China
| | - Muhammad Riaz Khan
- Translational Research Institute, Henan Provincial People's Hospital, School of Clinical Medicine, Henan University, Zhengzhou 450003, China
| | - Xu Dong Zhang
- Translational Research Institute, Henan Provincial People's Hospital, School of Clinical Medicine, Henan University, Zhengzhou 450003, China.,School of Biomedical Sciences & Pharmacy, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - Jingmin Li
- Translational Research Institute, Henan Provincial People's Hospital, School of Clinical Medicine, Henan University, Zhengzhou 450003, China
| | - Rick Francis Thorne
- Translational Research Institute, Henan Provincial People's Hospital, School of Clinical Medicine, Henan University, Zhengzhou 450003, China.,School of Environmental & Life Sciences, The University of Newcastle, Callaghan, NSW 2258, Australia
| | - Mian Wu
- Translational Research Institute, Henan Provincial People's Hospital, School of Clinical Medicine, Henan University, Zhengzhou 450003, China.,CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Centre for Excellence in Molecular Cell Science, the First Affiliated Hospital of University of Science and Technology of China, Hefei 230027, China
| | - Fengmin Shao
- Translational Research Institute, Henan Provincial People's Hospital, School of Clinical Medicine, Henan University, Zhengzhou 450003, China
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50
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Development of alternative splicing signature in lung squamous cell carcinoma. Med Oncol 2021; 38:49. [PMID: 33772655 PMCID: PMC8004499 DOI: 10.1007/s12032-021-01490-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/01/2021] [Indexed: 12/21/2022]
Abstract
Increasing evidence demonstrated that alternative splicing (AS) plays a vital role in tumorigenesis and clinical outcome of patient. However, systematical analysis of AS in lung squamous cell carcinoma (LUSC) is lacking and greatly necessary. Thus, this study was to systematically estimate the function of AS events served as prognostic indicators in LUSC. Among 31,345 mRNA AS events in 9633 genes, we detected 1996 AS in 1409 genes which have significant connection with overall survival (OS) of LUSC patients. Then, prognostic model based on seven types of AS events was established and we further constructed a combined prognostic model. The Kaplan–Meier curve results suggested that seven types of AS signatures and the combined prognostic model could exhibit robust performance in predicting prognosis. Patients in the high-risk group had significantly shorter OS than those in the low-risk group. The ROC showed all prognostic models had high accuracy and powerful predictive performance with different AUC ranging from 0.837 to 0.978. Moreover, the combined prognostic model had highest performance in risk stratification and predictive accuracy than single prognostic models and had higher accuracy than other mRNA model. Finally, a significant correlation network between survival-related AS genes and prognostic splicing factors (SFs) was established. In conclusion, our study provided several potential prognostic AS models and constructed splicing network between AS and SFs in LUSC, which could be used as potential indicators and treatment targets for LUSC patients.
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