1
|
Yao X, Zhou H, Duan C, Wu X, Li B, Liu H, Zhang Y. Comprehensive characteristics of pathological subtypes in testicular germ cell tumor: Gene expression, mutation and alternative splicing. Front Immunol 2023; 13:1096494. [PMID: 36713456 PMCID: PMC9883017 DOI: 10.3389/fimmu.2022.1096494] [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: 11/12/2022] [Accepted: 12/23/2022] [Indexed: 01/15/2023] Open
Abstract
Background Testicular germ cell tumor (TGCT) is the most common tumor in young men, but molecular signatures, especially the alternative splicing (AS) between its subtypes have not yet been explored. Methods To investigate the differences between TGCT subtypes, we comprehensively analyzed the data of gene expression, alternative splicing (AS), and somatic mutation in TGCT patients from the TCGA database. The gene ontology (GO) enrichment analyses were used to explore the function of differentially expressed genes and spliced genes respectively, and Spearman correlation analysis was performed to explore the correlation between differential genes and AS events. In addition, the possible patterns in which AS regulates gene expression were elaborated by the ensemble database transcript atlas. And, we identified important transcription factors that regulate gene expression and AS and functionally validated them in TGCT cell lines. Results We found significant differences between expression and AS in embryonal carcinoma and seminoma, while mixed cell tumors were in between. GO enrichment analyses revealed that both differentially expressed and spliced genes were enriched in transcriptional regulatory pathways, and obvious correlation between expression and AS events was determined. By analyzing the transcript map and the sites where splicing occurs, we have demonstrated that AS regulates gene expression in a variety of ways. We further identified two pivot AS-related molecules (SOX2 and HDAC9) involved in AS regulation, which were validated in embryonal carcinoma and seminoma cell lines. Differences in somatic mutations between subtypes are also of concern, with our results suggesting that mutations in some genes (B3GNT8, CAPN7, FAT4, GRK1, TACC2, and TRAM1L1) occur only in embryonal carcinoma, while mutations in KIT, KARS, and NRAS are observed only in seminoma. Conclusions In conclusion, our analysis revealed the differences in gene expression, AS and somatic mutation among TGCT subtypes, providing a molecular basis for clinical diagnosis and precise therapy of TGCT patients.
Collapse
Affiliation(s)
- Xiangyang Yao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hui Zhou
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chen Duan
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoliang Wu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bo Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Haoran Liu
- Stanford Bio-X, Stanford University, Stanford, CA, United States
| | - Yangjun Zhang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China,Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China,Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China,*Correspondence: Yangjun Zhang,
| |
Collapse
|
2
|
Gadelha RB, Machado CB, Pessoa FMCDP, Pantoja LDC, Barreto IV, Ribeiro RM, de Moraes Filho MO, de Moraes MEA, Khayat AS, Moreira-Nunes CA. The Role of WRAP53 in Cell Homeostasis and Carcinogenesis Onset. Curr Issues Mol Biol 2022; 44:5498-5515. [PMID: 36354684 PMCID: PMC9688736 DOI: 10.3390/cimb44110372] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/30/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2023] Open
Abstract
The WD repeat containing antisense to TP53 (WRAP53) gene codifies an antisense transcript for tumor protein p53 (TP53), stabilization (WRAP53α), and a functional protein (WRAP53β, WDR79, or TCAB1). The WRAP53β protein functions as a scaffolding protein that is important for telomerase localization, telomere assembly, Cajal body integrity, and DNA double-strand break repair. WRAP53β is one of many proteins known for containing WD40 domains, which are responsible for mediating a variety of cell interactions. Currently, WRAP53 overexpression is considered a biomarker for a diverse subset of cancer types, and in this study, we describe what is known about WRAP53β's multiple interactions in cell protein trafficking, Cajal body formation, and DNA double-strand break repair and its current perspectives as a biomarker for cancer.
Collapse
Affiliation(s)
- Renan Brito Gadelha
- Pharmacogenetics Laboratory, Department of Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
| | - Caio Bezerra Machado
- Pharmacogenetics Laboratory, Department of Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
| | - Flávia Melo Cunha de Pinho Pessoa
- Pharmacogenetics Laboratory, Department of Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
| | - Laudreísa da Costa Pantoja
- Department of Pediatrics, Octávio Lobo Children’s Hospital, Belém 60430-275, PA, Brazil
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil
| | - Igor Valentim Barreto
- Pharmacogenetics Laboratory, Department of Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
| | | | - Manoel Odorico de Moraes Filho
- Pharmacogenetics Laboratory, Department of Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
| | - Maria Elisabete Amaral de Moraes
- Pharmacogenetics Laboratory, Department of Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
| | - André Salim Khayat
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil
| | - Caroline Aquino Moreira-Nunes
- Pharmacogenetics Laboratory, Department of Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil
- Northeast Biotechnology Network (RENORBIO), Itaperi Campus, Ceará State University, Fortaleza 60740-903, CE, Brazil
| |
Collapse
|
3
|
Medvedev KE, Savelyeva AV, Chen KS, Bagrodia A, Jia L, Grishin NV. Integrated Molecular Analysis Reveals 2 Distinct Subtypes of Pure Seminoma of the Testis. Cancer Inform 2022; 21:11769351221132634. [PMID: 36330202 PMCID: PMC9623390 DOI: 10.1177/11769351221132634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/24/2022] [Indexed: 11/07/2022] Open
Abstract
Objective: Testicular germ cell tumors (TGCT) are the most common solid malignancy in
adolescent and young men, with a rising incidence over the past 20 years.
Overall, TGCTs are second in terms of the average life years lost per person
dying of cancer, and clinical therapeutics without adverse long-term side
effects are lacking. Platinum-based regimens for TGCTs have heterogeneous
outcomes even within the same histotype that frequently leads to under- and
over-treatment. Understanding of molecular differences that lead to diverse
outcomes of TGCT patients may improve current treatment approaches. Seminoma
is the most common subtype of TGCTs, which can either be pure or present in
combination with other histotypes. Methods: Here we conducted a computational study of 64 pure seminoma samples from The
Cancer Genome Atlas, applied consensus clustering approach to their
transcriptomic data and revealed 2 clinically relevant seminoma subtypes:
seminoma subtype 1 and 2. Results: Our analysis identified significant differences in pluripotency stage,
activity of double stranded DNA breaks repair mechanisms, rates of loss of
heterozygosity, and expression of lncRNA responsible for cisplatin
resistance between the subtypes. Seminoma subtype 1 is characterized by
higher pluripotency state, while subtype 2 showed attributes of reprograming
into non-seminomatous TGCT. The seminoma subtypes we identified may provide
a molecular underpinning for variable responses to chemotherapy and
radiation. Conclusion: Translating our findings into clinical care may help improve risk
stratification of seminoma, decrease overtreatment rates, and increase
long-term quality of life for TGCT survivors.
Collapse
Affiliation(s)
- Kirill E Medvedev
- Department of Biophysics, University of
Texas Southwestern Medical Center, Dallas, TX, USA,Kirill E Medvedev, Department of
Biophysics, University of Texas Southwestern Medical Center, 5323 Harry Hines
Blvd, Dallas, TX 75390, USA.
| | - Anna V Savelyeva
- Department of Urology, University of
Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kenneth S Chen
- Department of Pediatrics, University of
Texas Southwestern Medical Center, Dallas, TX, USA,Children’s Medical Center Research
Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Aditya Bagrodia
- Department of Urology, University of
Texas Southwestern Medical Center, Dallas, TX, USA,Department of Urology, University of
California San Diego Health, La Jolla, CA, USA
| | - Liwei Jia
- Department of Pathology, University of
Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nick V Grishin
- Department of Biophysics, University of
Texas Southwestern Medical Center, Dallas, TX, USA,Department of Biochemistry, University
of Texas Southwestern Medical Center, Dallas, TX, USA
| |
Collapse
|
4
|
Thool M, Sundaravadivelu PK, Sudhagar S, Thummer RP. A Comprehensive Review on the Role of ZSCAN4 in Embryonic Development, Stem Cells, and Cancer. Stem Cell Rev Rep 2022; 18:2740-2756. [PMID: 35739386 DOI: 10.1007/s12015-022-10412-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2022] [Indexed: 10/17/2022]
Abstract
ZSCAN4 is a transcription factor that plays a pivotal role during early embryonic development. It is a unique gene expressed specifically during the first tide of de novo transcription during the zygotic genome activation. Moreover, it is reported to regulate telomere length in embryonic stem cells and induced pluripotent stem cells. Interestingly, ZSCAN4 is expressed in approximately 5% of the embryonic stem cells in culture at any given time, which points to the fact that it has a tight regulatory system. Furthermore, ZSCAN4, if included in the reprogramming cocktail along with core reprogramming factors, increases the reprogramming efficiency and results in better quality, genetically stable induced pluripotent stem cells. Also, it is reported to have a role in promoting cancer stem cell phenotype and can prospectively be used as a marker for the same. In this review, the multifaceted role of ZSCAN4 in embryonic development, embryonic stem cells, induced pluripotent stem cells, cancer, and germ cells are discussed comprehensively.
Collapse
Affiliation(s)
- Madhuri Thool
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, 781039, Guwahati, Assam, India.,Department of Biotechnology, National Institute of Pharmaceutical Education and Research Guwahati, Changsari, 781101, Guwahati, Assam, India
| | - Pradeep Kumar Sundaravadivelu
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, 781039, Guwahati, Assam, India
| | - S Sudhagar
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research Guwahati, Changsari, 781101, Guwahati, Assam, India
| | - Rajkumar P Thummer
- Laboratory for Stem Cell Engineering and Regenerative Medicine, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, 781039, Guwahati, Assam, India.
| |
Collapse
|
5
|
Suzuki A, Yoshioka H, Liu T, Gull A, Singh N, Le T, Zhao Z, Iwata J. Crucial Roles of microRNA-16-5p and microRNA-27b-3p in Ameloblast Differentiation Through Regulation of Genes Associated With Amelogenesis Imperfecta. Front Genet 2022; 13:788259. [PMID: 35401675 PMCID: PMC8990915 DOI: 10.3389/fgene.2022.788259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
Amelogenesis imperfecta is a congenital disorder within a heterogeneous group of conditions characterized by enamel hypoplasia. Patients suffer from early tooth loss, social embarrassment, eating difficulties, and pain due to an abnormally thin, soft, fragile, and discolored enamel with poor aesthetics and functionality. The etiology of amelogenesis imperfecta is complicated by genetic interactions. To identify mouse amelogenesis imperfecta-related genes (mAIGenes) and their respective phenotypes, we conducted a systematic literature review and database search and found and curated 70 mAIGenes across all of the databases. Our pathway enrichment analysis indicated that these genes were enriched in tooth development-associated pathways, forming four distinct groups. To explore how these genes are regulated and affect the phenotype, we predicted microRNA (miRNA)-gene interaction pairs using our bioinformatics pipeline. Our miRNA regulatory network analysis pinpointed that miR-16-5p, miR-27b-3p, and miR-23a/b-3p were hub miRNAs. The function of these hub miRNAs was evaluated through ameloblast differentiation assays with/without the candidate miRNA mimics using cultured mouse ameloblast cells. Our results revealed that overexpression of miR-16-5p and miR-27b-3p, but not miR-23a/b-3p, significantly inhibited ameloblast differentiation through regulation of mAIGenes. Thus, our study shows that miR-16-5p and miR-27b-3p are candidate pathogenic miRNAs for amelogenesis imperfecta.
Collapse
Affiliation(s)
- Akiko Suzuki
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, United States
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Hiroki Yoshioka
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, United States
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Teng Liu
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Aania Gull
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, United States
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Naina Singh
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Thanh Le
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, United States
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
| | - Junichi Iwata
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, United States
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, United States
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
| |
Collapse
|
6
|
Spinelli C, Cito G, Morelli G, Ghionzoli M, Bertocchini A, Sanna B, Galli L, Antonuzzo A, Morganti R, Strambi S. Testicular germ cells tumors in adolescents and young adults: Management and outcomes from a single-center experience. Arch Ital Urol Androl 2021; 93:301-306. [PMID: 34839629 DOI: 10.4081/aiua.2021.3.301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/07/2021] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVE To investigate and compare the effectiveness of active surveillance versus post-surgical active treatment, in patients with testicular germ cells tumor (TGCT). MATERIALS AND METHODS We retrospectively analyzed 52 patients who underwent surgery for TGCT from January 2009 to December 2014. All the patients were divided into two age groups: the Group A included children-adolescents from 18 months to 21 years old, while the Group B comprised young adults from 22 to 39 years old. Clinical, histopathological, therapeutic and follow-up data were collected. RESULTS Overall, 22 patients (42,3%) were enrolled in the Group A and 30 patients (57.7%) were categorized in the Group B. Inguinal orchiectomy was performed in all patients. Retroperitoneal lymphadenectomy was performed in 4 patients (7.7%). Post-surgical management differed based on clinical stage, resulting in active surveillance or adjuvant therapy. After an average 7 years follow-up period (range: 3.5-9.0 years), the overall survival rate is 100%. The relapse risk is significantly higher for the patients in the Group B, displaying a recurrence free-survival rate of 72% versus 95% (Group A); 11 relapses (21.1%) were recorded 2 years after surgery. Of these, 3 recurrences (12.0%) occurred in patients undergoing an active surveillance approach, while 8 (29.6%) in patients subjected to an active treatment. CONCLUSIONS The excellent prognosis in both age groups confirms the high curability of this neoplasia. The active surveillance could represent an optimal option for low recurrence risk tumors. However, post-surgical treatments should be taken into consideration for TGCT with high risk factors, including tumor size, lymphovascular and rete testis invasion.
Collapse
Affiliation(s)
- Claudio Spinelli
- Division of Pediatric, Adolescents and Young Adults Surgery, Department of Surgical Pathology, Medical, Molecular and Critical Area, University of Pisa.
| | - Gianmartin Cito
- Department of Urology and Andrology Surgery, Careggi Hospital, University of Florence.
| | - Girolamo Morelli
- Department of Urology and Andrology Surgery, University of Pisa.
| | - Marco Ghionzoli
- Division of Pediatric, Adolescents and Young Adults Surgery, Department of Surgical Pathology, Medical, Molecular and Critical Area, University of Pisa.
| | - Alessia Bertocchini
- Division of Pediatric, Adolescents and Young Adults Surgery, Department of Surgical Pathology, Medical, Molecular and Critical Area, University of Pisa.
| | - Beatrice Sanna
- Division of Pediatric, Adolescents and Young Adults Surgery, Department of Surgical Pathology, Medical, Molecular and Critical Area, University of Pisa.
| | - Luca Galli
- Medical Oncology II, University of Pisa, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa.
| | - Andrea Antonuzzo
- Medical Oncology I, National Health Service Department of Translational Medicine Research and New Technologies in Medicine and Surgery, University of Pisa.
| | - Riccardo Morganti
- Section of Statistics, Department of Clinical and Experimental Medicine, University of Pisa.
| | - Silvia Strambi
- Division of Pediatric, Adolescents and Young Adults Surgery, Department of Surgical Pathology, Medical, Molecular and Critical Area, University of Pisa.
| |
Collapse
|
7
|
Subasri M, Shooshtari P, Watson AJ, Betts DH. Analysis of TERT Isoforms across TCGA, GTEx and CCLE Datasets. Cancers (Basel) 2021; 13:cancers13081853. [PMID: 33924498 PMCID: PMC8070023 DOI: 10.3390/cancers13081853] [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: 03/01/2021] [Revised: 04/01/2021] [Accepted: 04/08/2021] [Indexed: 12/14/2022] Open
Abstract
Reactivation of the multi-subunit ribonucleoprotein telomerase is the primary telomere maintenance mechanism in cancer, but it is rate-limited by the enzymatic component, telomerase reverse transcriptase (TERT). While regulatory in nature, TERT alternative splice variant/isoform regulation and functions are not fully elucidated and are further complicated by their highly diverse expression and nature. Our primary objective was to characterize TERT isoform expression across 7887 neoplastic and 2099 normal tissue samples using The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression Project (GTEx), respectively. We confirmed the global overexpression and splicing shift towards full-length TERT in neoplastic tissue. Stratifying by tissue type we found uncharacteristic TERT expression in normal brain tissue subtypes. Stratifying by tumor-specific subtypes, we detailed TERT expression differences potentially regulated by subtype-specific molecular characteristics. Focusing on β-deletion splicing regulation, we found the NOVA1 trans-acting factor to mediate alternative splicing in a cancer-dependent manner. Of relevance to future tissue-specific studies, we clustered cancer cell lines with tumors from related origin based on TERT isoform expression patterns. Taken together, our work has reinforced the need for tissue and tumour-specific TERT investigations, provided avenues to do so, and brought to light the current technical limitations of bioinformatic analyses of TERT isoform expression.
Collapse
Affiliation(s)
- Mathushan Subasri
- Department of Physiology and Pharmacology, The University of Western Ontario, London, ON N6A 5C1, Canada; (M.S.); (A.J.W.)
| | - Parisa Shooshtari
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada;
- Department of Pathology and Laboratory Medicine, The University of Western Ontario, London, ON N6A 5C1, Canada
- Department of Computer Science, The University of Western Ontario, London, ON N6A 5C1, Canada
- The Children’s Health Research Institute—Lawson Health Research Institute, London, ON N6C 2R5, Canada
| | - Andrew J. Watson
- Department of Physiology and Pharmacology, The University of Western Ontario, London, ON N6A 5C1, Canada; (M.S.); (A.J.W.)
- The Children’s Health Research Institute—Lawson Health Research Institute, London, ON N6C 2R5, Canada
- Department of Obstetrics and Gynaecology, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Dean H. Betts
- Department of Physiology and Pharmacology, The University of Western Ontario, London, ON N6A 5C1, Canada; (M.S.); (A.J.W.)
- The Children’s Health Research Institute—Lawson Health Research Institute, London, ON N6C 2R5, Canada
- Department of Obstetrics and Gynaecology, The University of Western Ontario, London, ON N6A 5C1, Canada
- Correspondence: ; Tel.: +1-519-661-2111 (ext. 83786)
| |
Collapse
|
8
|
Song Y, Qi X, Kang J, Wang X, Ou N, Zhu J, Wang S, Liu X. Identification of new biomarkers in immune microenvironment of testicular germ cell tumour. Andrologia 2021; 53:e13986. [PMID: 33544925 DOI: 10.1111/and.13986] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 12/24/2020] [Accepted: 01/06/2021] [Indexed: 12/24/2022] Open
Abstract
To seek novel prognostic biomarkers for testicular germ cell tumour (TGCT) and investigate the tumour immune microenvironment, we identified critical differentially expressed genes (DEGs) by overlapping GSE1818 dataset from Gene Expression Omnibus (GEO). Protein-protein interaction (PPI) network was used to investigate key modules and hub genes. Functional enrichment analysis was performed to investigate the underlying molecular functions of the DEGs in TGCT development and progression. The following survival analysis based on The Cancer Genome Atlas (TCGA) TGCT dataset indicated that AKAP4, SPA17 and TNP1 are correlated with TGCT prognosis. Immunohistochemistry and quantitative real-time polymerase chain reaction verified the down-regulation of the 3 hub genes in TGCT. Gene set enrichment analysis was conducted to further explore the role of the 3 hub genes in TGCT respectively. In addition, TGCT samples had high infiltration of CD8+ T cells, M0 and M1 macrophage cells, and resting myeloid dendritic cells in immune microenvironment. We also constructed the microRNA-gene regulatory networks to identify the key upstream microRNAs in TGCT. In conclusion, our findings indicated that AKAP4, SPA17 and TNP1 are promising biomarkers of TGCT. AKAP4 and TNP1 might regulate immune cells infiltration in immune microenvironment.
Collapse
Affiliation(s)
- Yuxuan Song
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Xiangjie Qi
- Department of Urology, Linzi District People's Hospital, Zibo, China
| | - Jiaqi Kang
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Xiao Wang
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Ningjing Ou
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Jun Zhu
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Shangren Wang
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Xiaoqiang Liu
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| |
Collapse
|
9
|
Qiu S, An Z, Tan R, He PA, Jing J, Li H, Wu S, Xu Y. Understanding the unimodal distributions of cancer occurrence rates: it takes two factors for a cancer to occur. Brief Bioinform 2020; 22:6055138. [PMID: 33377150 PMCID: PMC8294564 DOI: 10.1093/bib/bbaa349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/19/2020] [Accepted: 11/01/2020] [Indexed: 12/25/2022] Open
Abstract
Data from the SEER reports reveal that the occurrence rate of a cancer type generally follows a unimodal distribution over age, peaking at an age that is cancer-type specific and ranges from 30+ through 70+. Previous studies attribute such bell-shaped distributions to the reduced proliferative potential in senior years but fail to explain why some cancers have their occurrence peak at 30+ or 40+. We present a computational model to offer a new explanation to such distributions. The model uses two factors to explain the observed age-dependent cancer occurrence rates: cancer risk of an organ and the availability level of the growth signals in circulation needed by a cancer type, with the former increasing and the latter decreasing with age. Regression analyses were conducted of known occurrence rates against such factors for triple negative breast cancer, testicular cancer and cervical cancer; and all achieved highly tight fitting results, which were also consistent with clinical, gene-expression and cancer-drug data. These reveal a fundamentally important relationship: while cancer is driven by endogenous stressors, it requires sufficient levels of exogenous growth signals to happen, hence suggesting the realistic possibility for treating cancer via cleaning out the growth signals in circulation needed by a cancer.
Collapse
Affiliation(s)
- Shuang Qiu
- Cancer Systems Biology Center, China-Japan Union Hospital of Jilin University
| | - Zheng An
- Cancer Systems Biology Center, China-Japan Union Hospital of Jilin University
| | - Renbo Tan
- Cancer Systems Biology Center, China-Japan Union Hospital of Jilin University
| | | | - Jingjing Jing
- China Medical University and Jilin University First Hospital
| | - Hongxia Li
- China Medical University and Jilin University First Hospital
| | | | - Ying Xu
- University of Georgia and Jilin University
| |
Collapse
|
10
|
Mallik S, Qin G, Jia P, Zhao Z. Molecular signatures identified by integrating gene expression and methylation in non-seminoma and seminoma of testicular germ cell tumours. Epigenetics 2020; 16:162-176. [PMID: 32615059 DOI: 10.1080/15592294.2020.1790108] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Testicular germ cell tumours (TGCTs) are the most common cancer in young male adults (aged 15 to 40). Unlike most other cancer types, identification of molecular signatures in TGCT has rarely reported. In this study, we developed a novel integrative analysis framework to identify co-methylated and co-expressed genes [mRNAs and microRNAs (miRNAs)] modules in two TGCT subtypes: non-seminoma (NSE) and seminoma (SE). We first integrated DNA methylation and mRNA/miRNA expression data and then used a statistical method, CoMEx (Combined score of DNA Methylation and Expression), to assess differentially expressed and methylated (DEM) genes/miRNAs. Next, we identified co-methylation and co-expression modules by applying WGCNA (Weighted Gene Correlation Network Analysis) tool to these DEM genes/miRNAs. The module with the highest average Pearson's Correlation Coefficient (PCC) after considering all pair-wise molecules (genes/miRNAs) included 91 molecules. By integrating both transcription factor and miRNA regulations, we constructed subtype-specific regulatory networks for NSE and SE. We identified four hub miRNAs (miR-182-5p, miR-520b, miR-520c-3p, and miR-7-5p), two hub TFs (MYC and SP1), and two genes (RECK and TERT) in the NSE-specific regulatory network, and two hub miRNAs (miR-182-5p and miR-338-3p), five hub TFs (ETS1, HIF1A, HNF1A, MYC, and SP1), and three hub genes (CDH1, CXCR4, and SNAI1) in the SE-specific regulatory network. miRNA (miR-182-5p) and two TFs (MYC and SP1) were common hubs of NSE and SE. We further examined pathways enriched in these subtype-specific networks. Our study provides a comprehensive view of the molecular signatures and co-regulation in two TGCT subtypes.
Collapse
Affiliation(s)
- Saurav Mallik
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston , Houston, TX, USA
| | - Guimin Qin
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston , Houston, TX, USA
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston , Houston, TX, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston , Houston, TX, USA.,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston , Houston, TX, USA.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences , Houston, TX, USA.,Department of Biomedical Informatics, Vanderbilt University Medical Center , Nashville, TN, USA
| |
Collapse
|
11
|
Loveday C, Litchfield K, Proszek PZ, Cornish AJ, Santo F, Levy M, Macintyre G, Holryod A, Broderick P, Dudakia D, Benton B, Bakir MA, Hiley C, Grist E, Swanton C, Huddart R, Powles T, Chowdhury S, Shipley J, O'Connor S, Brenton JD, Reid A, de Castro DG, Houlston RS, Turnbull C. Genomic landscape of platinum resistant and sensitive testicular cancers. Nat Commun 2020; 11:2189. [PMID: 32366847 PMCID: PMC7198558 DOI: 10.1038/s41467-020-15768-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 03/23/2020] [Indexed: 12/11/2022] Open
Abstract
While most testicular germ cell tumours (TGCTs) exhibit exquisite sensitivity to platinum chemotherapy, ~10% are platinum resistant. To gain insight into the underlying mechanisms, we undertake whole exome sequencing and copy number analysis in 40 tumours from 26 cases with platinum-resistant TGCT, and combine this with published genomic data on an additional 624 TGCTs. We integrate analyses for driver mutations, mutational burden, global, arm-level and focal copy number (CN) events, and SNV and CN signatures. Albeit preliminary and observational in nature, these analyses provide support for a possible mechanistic link between early driver mutations in RAS and KIT and the widespread copy number events by which TGCT is characterised.
Collapse
Affiliation(s)
- Chey Loveday
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, UK
| | - Kevin Litchfield
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Paula Z Proszek
- The Centre for Molecular Pathology, The Royal Marsden NHS Trust, Sutton, London, UK
| | - Alex J Cornish
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, UK
| | - Flavia Santo
- The Centre for Molecular Pathology, The Royal Marsden NHS Trust, Sutton, London, UK
| | - Max Levy
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, UK
| | - Geoff Macintyre
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Amy Holryod
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, UK
| | - Peter Broderick
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, UK
| | - Darshna Dudakia
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, UK
| | - Barbara Benton
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, UK
| | - Maise Al Bakir
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Crispin Hiley
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Emily Grist
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
- Translational Cancer Therapeutics Laboratory, UCL Cancer Institute, London, UK
| | - Robert Huddart
- Academic Radiotherapy Unit, Institute of Cancer Research, London, UK
| | - Tom Powles
- Barts Cancer Institute, Queen Mary University, London, UK
| | - Simon Chowdhury
- Department of Oncology, Guys and St Thomas' NHS Foundation Trust, London, UK
| | - Janet Shipley
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Simon O'Connor
- The Centre for Molecular Pathology, The Royal Marsden NHS Trust, Sutton, London, UK
- Addenbrooke's Hospital, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - James D Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Alison Reid
- Academic Uro-oncology Unit, The Royal Marsden NHS Foundation Trust, Sutton, London, UK
| | | | - Richard S Houlston
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Clare Turnbull
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, UK.
- William Harvey Research Institute, Queen Mary University, London, UK.
- Guys and St Thomas' NHS Foundation Trust, Great Maze Pond, London, UK.
- Public Health England, National Cancer Registration and Analysis Service, London, UK.
| |
Collapse
|
12
|
Qin G, Mallik S, Mitra R, Li A, Jia P, Eischen CM, Zhao Z. MicroRNA and transcription factor co-regulatory networks and subtype classification of seminoma and non-seminoma in testicular germ cell tumors. Sci Rep 2020; 10:852. [PMID: 31965022 PMCID: PMC6972857 DOI: 10.1038/s41598-020-57834-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 12/24/2019] [Indexed: 12/11/2022] Open
Abstract
Recent studies have revealed that feed-forward loops (FFLs) as regulatory motifs have synergistic roles in cellular systems and their disruption may cause diseases including cancer. FFLs may include two regulators such as transcription factors (TFs) and microRNAs (miRNAs). In this study, we extensively investigated TF and miRNA regulation pairs, their FFLs, and TF-miRNA mediated regulatory networks in two major types of testicular germ cell tumors (TGCT): seminoma (SE) and non-seminoma (NSE). Specifically, we identified differentially expressed mRNA genes and miRNAs in 103 tumors using the transcriptomic data from The Cancer Genome Atlas. Next, we determined significantly correlated TF-gene/miRNA and miRNA-gene/TF pairs with regulation direction. Subsequently, we determined 288 and 664 dysregulated TF-miRNA-gene FFLs in SE and NSE, respectively. By constructing dysregulated FFL networks, we found that many hub nodes (12 out of 30 for SE and 8 out of 32 for NSE) in the top ranked FFLs could predict subtype-classification (Random Forest classifier, average accuracy ≥90%). These hub molecules were validated by an independent dataset. Our network analysis pinpointed several SE-specific dysregulated miRNAs (miR-200c-3p, miR-25-3p, and miR-302a-3p) and genes (EPHA2, JUN, KLF4, PLXDC2, RND3, SPI1, and TIMP3) and NSE-specific dysregulated miRNAs (miR-367-3p, miR-519d-3p, and miR-96-5p) and genes (NR2F1 and NR2F2). This study is the first systematic investigation of TF and miRNA regulation and their co-regulation in two major TGCT subtypes.
Collapse
Affiliation(s)
- Guimin Qin
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA.,School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi, China
| | - Saurav Mallik
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ramkrishna Mitra
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Aimin Li
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA.,School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, Shaanxi, China
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Christine M Eischen
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA. .,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA.
| |
Collapse
|
13
|
Bergstrand S, O'Brien EM, Farnebo M. The Cajal Body Protein WRAP53β Prepares the Scene for Repair of DNA Double-Strand Breaks by Regulating Local Ubiquitination. Front Mol Biosci 2019; 6:51. [PMID: 31334247 PMCID: PMC6624377 DOI: 10.3389/fmolb.2019.00051] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 06/20/2019] [Indexed: 12/27/2022] Open
Abstract
Proper repair of DNA double-strand breaks is critical for maintaining genome integrity and avoiding disease. Modification of damaged chromatin has profound consequences for the initial signaling and regulation of repair. One such modification involves ubiquitination by E3 ligases RNF8 and RNF168 within minutes after DNA double-strand break formation, altering chromatin structure and recruiting factors such as 53BP1 and BRCA1 for repair via non-homologous end-joining (NHEJ) and homologous recombination (HR), respectively. The WD40 protein WRAP53β plays an essential role in localizing RNF8 to DNA breaks by scaffolding its interaction with the upstream factor MDC1. Loss of WRAP53β impairs ubiquitination at DNA lesions and reduces downstream repair by both NHEJ and HR. Intriguingly, WRAP53β depletion attenuates repair of DNA double-strand breaks more than depletion of RNF8, indicating functions other than RNF8-mediated ubiquitination. WRAP53β plays key roles with respect to the nuclear organelles Cajal bodies, including organizing the genome to promote associated transcription and collecting factors involved in maturation of the spliceosome and telomere elongation within these organelles. It is possible that similar functions may aid also in DNA repair. Here we describe the involvement of WRAP53β in Cajal bodies and DNA double-strand break repair in detail and explore whether and how these processes may be linked. We also discuss the possibility that the overexpression of WRAP53β detected in several cancer types may reflect its normal participation in the DNA damage response rather than oncogenic properties.
Collapse
Affiliation(s)
- Sofie Bergstrand
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Eleanor M O'Brien
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Marianne Farnebo
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.,Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
14
|
Dai Y, Pei G, Zhao Z, Jia P. A Convergent Study of Genetic Variants Associated With Crohn's Disease: Evidence From GWAS, Gene Expression, Methylation, eQTL and TWAS. Front Genet 2019; 10:318. [PMID: 31024628 PMCID: PMC6467075 DOI: 10.3389/fgene.2019.00318] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 03/21/2019] [Indexed: 12/12/2022] Open
Abstract
Crohn’s Disease (CD) is one of the predominant forms of inflammatory bowel disease (IBD). A combination of genetic and non-genetic risk factors have been reported to contribute to the development of CD. Many high-throughput omics studies have been conducted to identify disease associated risk variants that might contribute to CD, such as genome-wide association studies (GWAS) and next generation sequencing studies. A pressing need remains to prioritize and characterize candidate genes that underlie the etiology of CD. In this study, we collected a comprehensive multi-dimensional data from GWAS, gene expression, and methylation studies and generated transcriptome-wide association study (TWAS) data to further interpret the GWAS association results. We applied our previously developed method called mega-analysis of Odds Ratio (MegaOR) to prioritize CD candidate genes (CDgenes). As a result, we identified consensus sets of CDgenes (62–235 genes) based on the evidence matrix. We demonstrated that these CDgenes were significantly more frequently interact with each other than randomly expected. Functional annotation of these genes highlighted critical immune-related processes such as immune response, MHC class II receptor activity, and immunological disorders. In particular, the constitutive photomorphogenesis 9 (COP9) signalosome related genes were found to be significantly enriched in CDgenes, implying a potential role of COP9 signalosome involved in the pathogenesis of CD. Finally, we found some of the CDgenes shared biological functions with known drug targets of CD, such as the regulation of inflammatory response and the leukocyte adhesion to vascular endothelial cell. In summary, we identified highly confident CDgenes from multi-dimensional evidence, providing insights for the understanding of CD etiology.
Collapse
Affiliation(s)
- Yulin Dai
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Guangsheng Pei
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States.,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States.,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
| |
Collapse
|