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Xu S, Shi C, Zhou R, Han Y, Li N, Qu C, Xia R, Zhang C, Hu Y, Tian Z, Liu S, Wang L, Li J, Zhang Z. Mapping the landscape of HPV integration and characterising virus and host genome interactions in HPV-positive oropharyngeal squamous cell carcinoma. Clin Transl Med 2024; 14:e1556. [PMID: 38279874 PMCID: PMC10819103 DOI: 10.1002/ctm2.1556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 01/03/2024] [Accepted: 01/09/2024] [Indexed: 01/29/2024] Open
Abstract
BACKGROUND Human papillomavirus (HPV) integration into the host genome is an important factor in HPV(+)OPSCC carcinogenesis, in conjunction with HPV oncoproteins E6/E7. However, a well-studied investigation about virus-host interaction still needs to be completed. Our objective is to characterise HPV integration to investigate potential mechanisms of tumourigenesis independent of E6/E7 oncoproteins. MATERIALS AND METHODS High-throughput viral integration detection was performed on 109 HPV(+)OPSCC tumours with relevant clinicopathological information. Of these tumours, 38 tumours underwent targeted gene sequencing, 29 underwent whole exome sequencing and 26 underwent RNA sequencing. RESULTS HPV integration was detected in 94% of tumours (with a mean integration count of 337). Tumours occurring at the tonsil/oropharyngeal wall that exhibit higher PD-L1 expression demonstrated increased integration sites (p = .024). HPV exhibited a propensity for integration at genomic sites located within specific fragile sites (FRA19A) or genes associated with functional roles such as cell proliferation and differentiation (PTEN, AR), immune evasion (CD274) and glycoprotein biosynthesis process (FUT8). The viral oncogenes E2, E4, E6 and E7 tended to remain intact. HPV fragments displayed enrichment within host copy number variation (CNV) regions. However, insertions into genes related to altered homologous recombination repair were infrequent. Genes with integration had distinct expression levels. Fifty-nine genes whose expression level was affected by viral integration were identified, for example, EPHB1, which was reported to be involved in cellular protein metabolic process. CONCLUSIONS HPV can promote oncogenesis through recurrent integration into functional host genome regions, leading to subsequent genomic aberrations and gene expression disruption. This study characterises viral integrations and virus-host interactions, enhancing our understanding of HPV-related carcinogenesis mechanisms.
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Affiliation(s)
- Shengming Xu
- Department of Oral and Maxillofacial‐Head Neck OncologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
| | - Chaoji Shi
- Department of Oral and Maxillofacial‐Head Neck OncologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
| | - Rong Zhou
- Department of Oral and Maxillofacial‐Head Neck OncologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
| | - Yong Han
- Department of Oral and Maxillofacial‐Head Neck OncologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
| | - NianNian Li
- Department of BioinfomaticsSequantaShanghaiChina
| | - Chuxiang Qu
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Ronghui Xia
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Chunye Zhang
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Yuhua Hu
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Zhen Tian
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Shuli Liu
- Department of Oral and Maxillofacial‐Head Neck OncologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
| | - Lizhen Wang
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Jiang Li
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Zhiyuan Zhang
- Department of Oral and Maxillofacial‐Head Neck OncologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
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Wei L, Huang K, Han H, Liu RY. Human Papillomavirus Infection in Penile Cancer: Multidimensional Mechanisms and Vaccine Strategies. Int J Mol Sci 2023; 24:16808. [PMID: 38069131 PMCID: PMC10706305 DOI: 10.3390/ijms242316808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/19/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Penile cancer (PC) is a rare male malignant tumor, with early lymph node metastasis and poor prognosis. Human papillomavirus (HPV) plays a key role in the carcinogenesis of PC. This review aims to summarize the association between HPV infection and PC in terms of virus-host genome integration patterns (the disrupted regions in the HPV and PC genome), genetic alterations, and epigenetic regulation (methylation and microRNA modification) occurring in HPV and PC DNA, as well as tumor immune microenvironment reprogramming. In addition, the potential of HPV vaccination strategies for PC prevention and treatment is discussed. Understanding of the HPV-related multidimensional mechanisms and the application of HPV vaccines will promote rational and novel management of PC.
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Affiliation(s)
- Lichao Wei
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; (L.W.); (K.H.)
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Kangbo Huang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; (L.W.); (K.H.)
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Hui Han
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; (L.W.); (K.H.)
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Ran-yi Liu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; (L.W.); (K.H.)
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Kolb S, Hoffmann I, Monjé N, Dragomir MP, Jank P, Bischoff P, Keunecke C, Pohl J, Kunze CA, Marchenko S, Schmitt WD, Kulbe H, Sers C, Sehouli J, Braicu EI, Denkert C, Darb-Esfahani S, Horst D, Sinn BV, Taube ET. LRP1B-a prognostic marker in tubo-ovarian high-grade serous carcinoma. Hum Pathol 2023; 141:158-168. [PMID: 37742945 DOI: 10.1016/j.humpath.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/14/2023] [Accepted: 09/18/2023] [Indexed: 09/26/2023]
Abstract
Low-density lipoprotein (LDL) receptor-related protein 1B (LRP1B) is a member of the LDL receptor family and has often been discussed as a tumor suppressor gene, as its down-regulation is correlated with a poor prognosis in multiple carcinoma entities. Due to the high metastasis rate into the fatty peritoneal cavity and current research findings showing a dysregulation of lipid metabolism in tubo-ovarian high-grade serous carcinoma (HGSC), we questioned the prognostic impact of the LRP1B protein expression. We examined a well-characterized large cohort of 571 patients with primary HGSC and analyzed the LRP1B protein expression via immunohistochemical staining (both in tumor and stroma cells separately), performed precise bioimage analysis with QuPath, and calculated the prognostic impact using SPSS. Our results demonstrate that LRP1B functions as a significant prognostic marker for overall survival (OS) and progression-free survival (PFS) in HGSC on the protein level. High cytoplasmic expression of LRP1B in tumor, stroma, and combined tumor and stroma cells has a significantly positive association with a mean prolongation of the OS by 42 months (P = .005), 29 months (P = .005), and 25 months (P = .001), respectively. Additionally, the mean PFS was 18 months longer in tumor (P = .002), 19 months in stroma (P = .004), and 19 months in both cell types combined (P = .01). Our results remained significant in multivariate analysis. We envision LRP1B as a potential prognostic tool that could help us understand the functional role of lipid metabolism in advanced HGSC, especially regarding liposomal medications.
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Affiliation(s)
- Svenja Kolb
- Department of Gynecology, Vivantes Netzwerk für Gesundheit GmbH Berlin, Vivantes Hospital Neukölln, 12351, Berlin, Germany
| | - Inga Hoffmann
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, 10117, Berlin, Germany
| | - Nanna Monjé
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, 10117, Berlin, Germany
| | - Mihnea P Dragomir
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, 10117, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Paul Jank
- Institute of Pathology, Philipps-University Marburg and University Hospital Marburg, 35043 Marburg, Germany
| | - Philip Bischoff
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, 10117, Berlin, Germany
| | - Carlotta Keunecke
- Department of Gynecology, European Competence Center for Ovarian Cancer, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Jonathan Pohl
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, 10117, Berlin, Germany
| | - Catarina Alisa Kunze
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, 10117, Berlin, Germany
| | - Sofya Marchenko
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, 10117, Berlin, Germany
| | - Wolfgang D Schmitt
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, 10117, Berlin, Germany
| | - Hagen Kulbe
- Department of Gynecology, European Competence Center for Ovarian Cancer, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; Tumorbank Ovarian Cancer Network, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Christine Sers
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, 10117, Berlin, Germany
| | - Jalid Sehouli
- Department of Gynecology, European Competence Center for Ovarian Cancer, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; Tumorbank Ovarian Cancer Network, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Elena Ioana Braicu
- Department of Gynecology, European Competence Center for Ovarian Cancer, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; Tumorbank Ovarian Cancer Network, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Carsten Denkert
- Institute of Pathology, Philipps-University Marburg and University Hospital Marburg, 35043 Marburg, Germany
| | - Silvia Darb-Esfahani
- MVZ Pathologie Spandau, 13589 Berlin, Spandau, Germany; MVZ Pathologie Berlin-Buch, 13125 Berlin, Germany
| | - David Horst
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, 10117, Berlin, Germany
| | - Bruno V Sinn
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, 10117, Berlin, Germany
| | - Eliane T Taube
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, 10117, Berlin, Germany.
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Shaikh MH, Dawson A, Prokopec SD, Barrett JW, Y F Zeng P, Khan MI, Ryan SEB, Cecchini M, Palma DA, Mymryk JS, Boutros PC, Nichols AC. Loss of LRP1B expression drives acquired chemo and radio-resistance in HPV-positive head and neck cancer. Oral Oncol 2023; 146:106580. [PMID: 37778229 DOI: 10.1016/j.oraloncology.2023.106580] [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: 05/19/2023] [Revised: 09/01/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023]
Abstract
OBJECTIVES Although human papillomavirus positive (HPV+) oropharyngeal squamous cell carcinoma (OPSCC) patients typically experience excellent survival, 15-20 % of patients recur after treatment with chemotherapy and radiation. Therefore, there is a need for biomarkers of treatment failure to guide treatment intensity. MATERIALS AND METHODS Whole genome sequencing was carried out on HPV+OPSCC patients who were primarily treated with concurrent chemotherapy (cisplatin) and radiation. We then explored whether the loss of LRP1Bwas sufficient to drive an aggressive phenotype, and promote a resistance to cisplatin and radiation therapy both in vitro using HPV+ cell lines (93VU147T, UMSCC47, UWO37 and UWO23) and in vivo. RESULTS Through integrative genomic analysis of three HPV+OPSCC tumour datasets, we identified that deletion of LRP1B was enriched in samples that recurred following chemo-radiation. Knockdown using siRNA in four HPV+ cell lines (UWO23, UWO37, UMSCC47 and 93VU147T) resulted in increased proliferation of all cases. CRISPR/Cas9 deletion of LRP1B in the same cell line panel demonstrated increased proliferation, clonogenic growth and migration, as well as resistance to both cisplatin and radiation in LRP1B deleted cells compared to their respective non-targeting control cells. Cell line derived xenograft studies indicated that the LRP1B knockout tumours were more resistant to cisplatin and radiation therapy compared to their controls invivo. CONCLUSION Taken together, our work implicates LRP1B deletion as a potential biomarker for identifying treatment resistant HPV+ OPSCC cases.
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Affiliation(s)
- Mushfiq H Shaikh
- Department of Otolaryngology-Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Alice Dawson
- Department of Otolaryngology-Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada; Department of Pathology and Laboratory Medicine, University of Western Ontario, London, Ontario, Canada
| | | | - John W Barrett
- Department of Otolaryngology-Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada; Department of Oncology, University of Western Ontario, London, Ontario, Canada
| | - Peter Y F Zeng
- Department of Otolaryngology-Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Mohammed I Khan
- Department of Otolaryngology-Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Sarah E B Ryan
- Department of Otolaryngology-Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada; Department of Pathology and Laboratory Medicine, University of Western Ontario, London, Ontario, Canada
| | - Matthew Cecchini
- Department of Pathology and Laboratory Medicine, University of Western Ontario, London, Ontario, Canada
| | - David A Palma
- Department of Otolaryngology-Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada; Department of Oncology, University of Western Ontario, London, Ontario, Canada
| | - Joe S Mymryk
- Department of Otolaryngology-Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada; Department of Oncology, University of Western Ontario, London, Ontario, Canada; Department of Microbiology & Immunology, University of Western Ontario, London, Ontario, Canada
| | - Paul C Boutros
- Department of Human Genetics, University of California, Los Angeles, CA, USA; Department of Urology, University of California, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA; Institute for Precision Health, University of California, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, CA, USA
| | - Anthony C Nichols
- Department of Otolaryngology-Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada; Department of Oncology, University of Western Ontario, London, Ontario, Canada.
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Chen G, Zhu W, Liu Y, Zhang L, Xie L, Song X, Song X. The clonal heterogeneity of colon cancer with liver metastases. J Gastroenterol 2023; 58:642-655. [PMID: 37042990 PMCID: PMC10307713 DOI: 10.1007/s00535-023-01989-6] [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: 09/10/2022] [Accepted: 03/29/2023] [Indexed: 04/13/2023]
Abstract
BACKGROUND Colon cancer with liver metastases (CCLM) characterized by genetic heterogeneity is an evolutionary process leading to variations in response to selective pressure, but the underlying evolutionary models still remains unclear. METHODS Total of 30 samples, including primary tumor and two to four matched liver metastases from 8 treatment-naïve patients with CCLM were collected, and subjected to whole-exome DNA sequencing. PyClone was used to calculate intra and inter-tumor heterogeneity, LICHeE was used to reconstruct the cancer phylogeny trees and investigate the subclonal composition. RESULTS The genetic differences were observed between primary and metastatic lesions, as well as among multiple metastases in all patients. The natural history models of colorectal cancer in each case were identified, including parallel, linear, and branching evolution. Liver metastases could originate from primary lesions or other metastases. Pathway and process enrichment analysis also showed obvious heterogeneity and enhancement of several molecular functions. CONCLUSIONS Our data reveal the genetic and heterogeneity between primary and metastatic lesions, as well as among multiple metastases and provide genomic evidence for clonal heterogeneity for CCLM.
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Affiliation(s)
- Guanxuan Chen
- Department of Intensive Care Unit, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
| | - Wanqi Zhu
- Department of Research and Education, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
| | - Yang Liu
- Shanghai OrigiMed Co., Ltd, Shanghai, People's Republic of China
| | - Liwen Zhang
- Shanghai OrigiMed Co., Ltd, Shanghai, People's Republic of China
| | - Li Xie
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
- Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
| | - Xingguo Song
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China.
| | - Xianrang Song
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China.
- Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China.
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Wang CX, Yan J, Lin S, Ding Y, Qin YR. Mutant-allele dispersion correlates with prognosis risk in patients with advanced non-small cell lung cancer. J Cancer Res Clin Oncol 2023:10.1007/s00432-023-04801-3. [PMID: 37093348 DOI: 10.1007/s00432-023-04801-3] [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: 11/29/2022] [Accepted: 04/17/2023] [Indexed: 04/25/2023]
Abstract
BACKGROUND Intra-tumor heterogeneity (ITH) contributes to lung cancer progression and resistance to therapy. To evaluate ITH and determine whether it may be employed as a predictive biomarker of prognosis in patients with advanced non-small cell lung cancer (NSCLC), we used a novel algorithm called mutant-allele dispersion (MAD). METHODS In the study, 103 patients with advanced NSCLC were enrolled. Using a panel of 425 cancer-related genes, next-generation sequencing (NGS) was performed on tumor specimens that had been collected. From NGS data, we derived MAD values, and we next looked into their relationships with clinical variables and different mutation subtypes. RESULTS The median MAD among 103 NSCLC patients was 0.73. EGFR mutation, tyrosine kinase inhibitor (TKI) therapy, radiotherapy, and chemotherapy cycles were all substantially correlated with the MAD score. In patients with lung adenocarcinoma (LUAD), correlation analysis revealed that the MAD score was substantially linked with Notch pathway mutation (P = 0.021). A significant relationship between high MAD and shorter progression-free survival (PFS) was found (HR = 2.004, 95%CI 1.269-3.163, P = 0.003). In patients with advanced NSCLC, histological type (P = 0.004), SMARCA4 mutation (P = 0.038), and LRP1B mutation (P = 0.006) were all independently associated with prognosis. The disease control rate was considerably greater in the low MAD group compared to the high MAD group in 19 LUAD patients receiving immunotherapy (92.9% vs. 40%, P = 0.037). TKI-PFS was longer in 37 patients with low MAD who received first-line TKI therapy (P = 0.014). CONCLUSION Our findings suggested that MAD is a practical and simple algorithm for assessing ITH, and populations with high MAD values are more likely to have EGFR mutations. MAD can be used as a potential biomarker to predict not only the prognosis of NSCLC but also the efficacy of immunotherapy and TKI therapy in patients with advanced NSCLC.
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Affiliation(s)
- Chen-Xu Wang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Jie Yan
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Shan Lin
- Department of Oncology, Zhongshan Hospital Affiliated to Xiamen University, Xiamen, 361004, Fujian, China
| | - Yi Ding
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Yan-Ru Qin
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
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Duan XP, Liu K, Jiao XD, Qin BD, Li B, He X, Ling Y, Wu Y, Chen SQ, Zang YS. Prognostic value of tumor mutation burden in patients with advanced gastric cancer receiving first-line chemotherapy. Front Oncol 2023; 12:1007146. [PMID: 36686739 PMCID: PMC9847361 DOI: 10.3389/fonc.2022.1007146] [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: 07/30/2022] [Accepted: 12/05/2022] [Indexed: 01/06/2023] Open
Abstract
Background Tumor mutation burden (TMB) is a promising biomarker positively associated with the benefit of immunotherapy and that might predict the outcome of chemotherapy. We described the prognostic value of TMB in advanced gastric cancer and explored the underlying mechanism. Methods We enrolled 155 TMB-evaluated advanced gastric cancer patients and analyzed the relationship between clinicopathological characteristics and both overall survival (OS) and progression-free survival (PFS) among 40 patients treated with first-line chemotherapy. We further verified the distribution of TMB and analyzed the potential mechanism underlying the prognosis based on The Cancer Genome Atlas (TCGA) database. Results Among the 155 patients, 29 (18.7%) were TMB-high (TMB ≥ 10), roughly the same as the proportion in the TCGA data. Of the 40 patients receiving first-line chemotherapy, the median OS (7.9 vs. 12.1 months; HR 3.18; p = 0.0056) and PFS (4.4 vs. 6.2 months; HR 2.94; p = 0.0099) of the tissue-tested TMB (tTMB)-high patients were inferior to those of the tTMB-low patients. Similarly, unfavorable median OS (9.9 vs. 12.1 months; HR 2.11; p = 0.028) and PFS (5.3 vs. 6.5 months; HR 2.49; p = 0.0054) were shown in the blood-tested TMB (bTMB)-high than in the bTMB-low patients. The Cox analysis demonstrated that both tTMB-high and bTMB-high were significant independent predictors of dreadful OS and PFS. The differentially expressed genes (DEGs) according to TMB status were most significantly enriched in the downregulated metabolic pathway among the TMB-high patients. Conclusions TMB-high advanced gastric cancer patients accounted for around one-sixth and had a poorer prognosis than TMB-low patients when treated with first-line chemotherapy. The potential mechanism might be the downregulated metabolic activity in TMB-high patients.
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Affiliation(s)
- Xiao-Peng Duan
- Department of Medical Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Ke Liu
- Department of Medical Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Xiao-Dong Jiao
- Department of Medical Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Bao-Dong Qin
- Department of Medical Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Bing Li
- Burning Rock Biotech, Shanghai, China
| | - Xi He
- Department of Medical Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Yan Ling
- Department of Medical Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Ying Wu
- Department of Medical Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Shi-Qi Chen
- Department of Medical Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Yuan-Sheng Zang
- Department of Medical Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China,*Correspondence: Yuan-Sheng Zang,
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8
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Wei Y, Yu R, Cheng S, Zhou P, Mo S, He C, Deng C, Wu P, Liu H, Cao C. Single-cell profiling of mouse and primate ovaries identifies high levels of EGFR for stromal cells in ovarian aging. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 31:1-12. [PMID: 36570672 PMCID: PMC9761475 DOI: 10.1016/j.omtn.2022.11.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/22/2022] [Indexed: 11/26/2022]
Abstract
Increased ovarian fibrosis and an expanded stromal cell compartment are the main characteristics of aging ovaries. However, the molecular mechanisms and the key factor of stromal cells underlying ovarian aging remain unclear. Here, we explored single-cell transcriptomic data of ovaries from the adult mouse (4,363 cells), young (1,122 cells), and aged (1,479 cells) non-human primates (NHPs) to identify expression patterns of stromal cells between young and old ovaries. An increased number of stromal cells (p = 0.0386) was observed in aged ovaries of NHPs, with enrichment processes related to the collagen-containing extracellular matrix. In addition, differentially expressed genes of stromal cells between young and old ovaries were regulated by ESR1 (p = 7.94E-08) and AR (p = 1.99E-05). Among them, EGFR was identified as the common target and was highly expressed (p = 7.69E-39) in old ovaries. In human ovaries, the correlated genes of EGFR were associated with the process of the cell-substrate junction. Silencing of EGFR in human ovarian stromal cells led to the reduction of cell-substrate junction via regulating phosphorylation modification of the AKT-mTOR signaling pathway and stromal cell marker genes. Overall, we identified high levels of EGFR for stromal cells in ovarian aging, which provides insight into the cell type-specific molecular mechanisms underlying ovarian aging at single-cell resolution.
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Affiliation(s)
- Ye Wei
- Department of Gynecology and Obstetrics, Key Laboratory of the Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ruidi Yu
- Department of Gynecology and Obstetrics, Key Laboratory of the Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Sheng Cheng
- Department of Gynecology and Obstetrics, Key Laboratory of the Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Ping Zhou
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Shaomei Mo
- Department of Gastrointestinal Surgery, Reproductive Research Institute, Peking University Shenzhen Hospital, Guangdong 518036, China,The Fifth Clinical College, Anhui Medical University, Hefei 230000, China
| | - Chao He
- Department of Gynecology and Obstetrics, Key Laboratory of the Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Chang Deng
- Department of Gynecology and Obstetrics, Key Laboratory of the Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Peng Wu
- Department of Gynecology and Obstetrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China,Corresponding author Peng Wu, Department of Gynecology and Obstetrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - He Liu
- Department of Gastrointestinal Surgery, Reproductive Research Institute, Peking University Shenzhen Hospital, Guangdong 518036, China,Corresponding author He Liu, Department of Gastrointestinal Surgery, Reproductive Research Institute, Peking University Shenzhen Hospital, Guangdong 518036, China.
| | - Canhui Cao
- Department of Gynecology and Obstetrics, Key Laboratory of the Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China,Department of Gastrointestinal Surgery, Reproductive Research Institute, Peking University Shenzhen Hospital, Guangdong 518036, China,Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China,Corresponding author Canhui Cao, Department of Gynecology and Obstetrics, Key Laboratory of the Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China.
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9
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Liu Z, Cai C, Ma X, Liu J, Chen L, Lui VWY, Cooper GF, Lu X. A Novel Bayesian Framework Infers Driver Activation States and Reveals Pathway-Oriented Molecular Subtypes in Head and Neck Cancer. Cancers (Basel) 2022; 14:cancers14194825. [PMID: 36230748 PMCID: PMC9563147 DOI: 10.3390/cancers14194825] [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: 09/02/2022] [Revised: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 02/08/2023] Open
Abstract
Head and neck squamous cell cancer (HNSCC) is an aggressive cancer resulting from heterogeneous causes. To reveal the underlying drivers and signaling mechanisms of different HNSCC tumors, we developed a novel Bayesian framework to identify drivers of individual tumors and infer the states of driver proteins in cellular signaling system in HNSCC tumors. First, we systematically identify causal relationships between somatic genome alterations (SGAs) and differentially expressed genes (DEGs) for each TCGA HNSCC tumor using the tumor-specific causal inference (TCI) model. Then, we generalize the most statistically significant driver SGAs and their regulated DEGs in TCGA HNSCC cohort. Finally, we develop machine learning models that combine genomic and transcriptomic data to infer the protein functional activation states of driver SGAs in tumors, which enable us to represent a tumor in the space of cellular signaling systems. We discovered four mechanism-oriented subtypes of HNSCC, which show distinguished patterns of activation state of HNSCC driver proteins, and importantly, this subtyping is orthogonal to previously reported transcriptomic-based molecular subtyping of HNSCC. Further, our analysis revealed driver proteins that are likely involved in oncogenic processes induced by HPV infection, even though they are not perturbed by genomic alterations in HPV+ tumors.
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Affiliation(s)
- Zhengping Liu
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh 15206, PA, USA
- School of Medicine, Tsinghua University, Beijing 100190, China
| | - Chunhui Cai
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh 15206, PA, USA
- Correspondence:
| | - Xiaojun Ma
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh 15206, PA, USA
| | - Jinling Liu
- Department of Engineering Management and Systems Engineering, Missouri University of Science and Technology, Rolla, MO 65409, USA
- Department of Biological Sciences, Missouri University of Science and Technology, Rolla, MO 65409, USA
| | - Lujia Chen
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh 15206, PA, USA
| | - Vivian Wai Yan Lui
- Georgia Cancer Center, and Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Gregory F. Cooper
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh 15206, PA, USA
- UPMC Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA 15232, USA
| | - Xinghua Lu
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh 15206, PA, USA
- UPMC Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA 15232, USA
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10
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Zou S, Ye M, Zhang JA, Ji H, Chen Y, Zhu X. Establishment and genetically characterization of patient-derived xenograft models of cervical cancer. BMC Med Genomics 2022; 15:191. [PMID: 36076209 PMCID: PMC9461207 DOI: 10.1186/s12920-022-01342-5] [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: 03/28/2022] [Accepted: 08/29/2022] [Indexed: 11/30/2022] Open
Abstract
Purpose Patient-derived xenograft (PDX) models were established to reproduce the clinical situation of original cancers and have increasingly been applied to preclinical cancer research. Our study was designed to establish and genetically characterize cervical cancer PDX models. Methods A total of 91 fresh fragments obtained from 22 surgically resected cervical cancer tissues were subcutaneously engrafted into female NOD-SCID mice. Hematoxylin and eosin (H&E) staining was performed to assess whether the established PDX models conserved the histological features of original patient cervical cancer tissues. Moreover, a Venn diagram was applied to display the overlap of all mutations detected in whole-genome sequencing (WGS) data from patient original cervical cancer (F0) and F2-, F3-PDX models. The whole exome sequencing (WES) and the “maftools” package were applied to determine the somatic mutations among primary cervical cancers and the established PDX models. Results Our study successfully developed a panel of cervical cancer PDX models and the latency time of cervical cancer PDX model establishment was variable with a progressive decrease as the passage number increased, with a mean time to initial growth of 94.71 days in F1 engraftment to 40.65 days in F3 engraftment. Moreover, the cervical cancer PDX models preserved the histological features of their original cervical cancer. WGS revealed that the genome of original cervical cancer was preserved with high fidelity in cervical cancer PDX models throughout the xenografting and passaging process. Furthermore, WES demonstrated that the cervical cancer PDX models maintained the majority somatic mutations of original cervical cancer, of which the KMT2D, LRP1B, NAV3, TP53, FAT1, MKI67 and PKHD1L1 genes were identified as the most frequently mutated genes. Conclusions The cervical cancer PDX models preserved the histologic and genetic characteristics of their original cervical cancer, which helped to gain a deeper insight into the genetic alterations and lay a foundation for further investigation of the molecular targeted therapy of cervical cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01342-5.
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Affiliation(s)
- Shuangwei Zou
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, No. 109 Xueyuan Xi Road, Wenzhou, 325027, Zhejiang, China
| | - Miaomiao Ye
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, No. 109 Xueyuan Xi Road, Wenzhou, 325027, Zhejiang, China
| | - Jian-An Zhang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, No. 109 Xueyuan Xi Road, Wenzhou, 325027, Zhejiang, China
| | - Huihui Ji
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, No. 109 Xueyuan Xi Road, Wenzhou, 325027, Zhejiang, China
| | - Yijie Chen
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, No. 109 Xueyuan Xi Road, Wenzhou, 325027, Zhejiang, China
| | - Xueqiong Zhu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, No. 109 Xueyuan Xi Road, Wenzhou, 325027, Zhejiang, China.
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11
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Chen H, Zhao L, Liu J, Zhou H, Wang X, Fang X, Xia X. Bioinformatic Analyzes of the Association Between Upregulated Expression of JUN Gene via APOBEC-Induced FLG Gene Mutation and Prognosis of Cervical Cancer. Front Med (Lausanne) 2022; 9:815450. [PMID: 35510248 PMCID: PMC9058067 DOI: 10.3389/fmed.2022.815450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/15/2022] [Indexed: 02/01/2023] Open
Abstract
Globally, cervical cancer (CC) is the most common malignant tumor of the female reproductive system and its incidence is only second after breast cancer. Although screening and advanced treatment strategies have improved the rates of survival, some patients with CC still die due to metastasis and drug resistance. It is considered that cancer is driven by somatic mutations, such as single nucleotide, small insertions/deletions, copy number, and structural variations, as well as epigenetic changes. Previous studies have shown that cervical intraepithelial neoplasia is associated with copy number variants (CNVs) and/or mutations in cancer-related genes. Further, CC is also related to genetic mutations. The present study analyzed the data on somatic mutations of cervical squamous cell carcinoma (CESC) in the Cancer Genome Atlas database. It was evident that the Apolipoprotein B mRNA editing enzyme-catalyzed polypeptide-like (APOBEC)-related mutation of the FLG gene can upregulate the expression of the JUN gene and ultimately lead to poor prognosis for patients with CC. Therefore, the findings of the current study provide a new direction for future treatment of CC.
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Affiliation(s)
- Huan Chen
- Department of Obstetrics and Gynecology, The Second XIANGYA Hospital of Central South University, Changsha, China
| | - Liyun Zhao
- Department of Obstetrics and Gynecology, The Second XIANGYA Hospital of Central South University, Changsha, China
| | - Jiaqiang Liu
- Laboratory Medicine Center, Zhu Zhou Hospital Affiliated to Xiangya School of Medicine, Central South University (CSU), Zhuzhou, China
| | - Housheng Zhou
- Department of Obstetrics and Gynecology, Zhu Zhou Hospital Affiliated to Xiangya School of Medicine, CSU, Zhuzhou, China
| | - Xi Wang
- Department of Obstetrics and Gynecology, The Second XIANGYA Hospital of Central South University, Changsha, China
| | - Xiaoling Fang
- Department of Obstetrics and Gynecology, The Second XIANGYA Hospital of Central South University, Changsha, China
| | - Xiaomeng Xia
- Department of Obstetrics and Gynecology, The Second XIANGYA Hospital of Central South University, Changsha, China
- *Correspondence: Xiaomeng Xia
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12
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Wang X, Xu C, Sun H. DNA Damage Repair-Related Genes Signature for Immune Infiltration and Outcome in Cervical Cancer. Front Genet 2022; 13:733164. [PMID: 35309134 PMCID: PMC8927729 DOI: 10.3389/fgene.2022.733164] [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: 06/29/2021] [Accepted: 02/08/2022] [Indexed: 12/11/2022] Open
Abstract
Background: The mechanism of DNA damage repair plays an important role in many solid tumors represented by cervical cancer. Purpose: The purpose of this study was to explore the effect of DNA damage repair-related genes on immune function of patients with cervical cancer, and to establish and evaluate a prognosis model based on DNA damage repair-related genes. Methods: In the study, we analyzed the genes related to DNA damage and repair, and obtained two subtypes (F1 and F2). We selected two groups of samples for different selection, and studied which pathways were enriched expression. For different subtypes, the immune score was explored to explain immune infiltration. We got the key genes through screening, and established the prognosis model through the key genes. These 11 key genes were correlated with the expression of common Clusters of Differentiation (CD) genes in order to explore the effects of these genes on immunity. Results: Through the Least absolute shrinkage and selection operator (LASSO) method, we screened 11 genes from 232 candidate genes as the key genes for the prognosis score. Through the Kaplan-Meier method, four genes (HAP1, MCM5, RNASEH2A, CETN2) with significant prognostic significance were screened into the final model, forming a Nomogram with C-index of 0.716 (0.649–1.0). Conclusion: In cervical cancer, DNA damage repair related genes and immune cell infection characteristics have certain association, and DNA damage repair related genes and immune cell infection characteristics can effectively predict the prognosis.
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Affiliation(s)
- Xinghao Wang
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Chen Xu
- Department of Surgical Oncology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Hongzan Sun
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, China
- *Correspondence: Hongzan Sun,
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13
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Cao C, Yu R, Gong W, Liu D, Zhang X, Fang Y, Xia Y, Zhang W, Gao Q. Genomic mutation features identify distinct BRCA-associated mutation characteristics in endometrioid carcinoma and endometrioid ovarian carcinoma. Aging (Albany NY) 2021; 13:24686-24709. [PMID: 34837690 PMCID: PMC8660599 DOI: 10.18632/aging.203710] [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: 06/11/2021] [Accepted: 10/25/2021] [Indexed: 01/19/2023]
Abstract
Although endometrioid carcinoma (EC) and endometrioid ovarian carcinoma (EnOC) display similar pathological features, their molecular characteristics remain to be determined. Somatic mutation data from 2777 EC, 423 EnOC, and 57 endometriosis patients from the Catalogue of Somatic Mutations in Cancer (COSMIC) dataset were analyzed and showed similar profiles with different mutation frequencies among them. By using 275 overlapping mutated genes, EC was clustered into two groups with different disease outcomes and different clinical characteristics. Although BRCA-associated mutation characteristics were identified in both EC and EnOC, the mutation frequencies of BRCA1 (P=0.0146), BRCA2 (P=0.0321), ATR (P=3.25E-11), RAD51 (P=3.95E-08), RAD1 (P=0.0003), TP53 (P=6.11E-33), and BRIP1 (P=2.90E-09) were higher in EnOC. Further analysis showed that EnOC cell lines with BRCA-associated mutation characteristics were more sensitive to poly ADP-ribose polymerase (PARP) inhibitors than EC cell lines, including olaparib, talazoparib, rucaparib, and veliparib. Moreover, based on BRCA-associated mutational and transcriptomic profiles, EC with BRCA-associated mutational burdens shows lower levels of immune cell infiltration, higher expression of immunosuppressive checkpoint molecules and worse prognosis than EC without BRCA mutation. Our study comprehensively analyzed the genome mutation features of EC and EnOC and provide insights into the molecular characteristics of EC and EnOC.
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Affiliation(s)
- Canhui Cao
- Cancer Biology Research Center, Key Laboratory of the Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ruidi Yu
- Cancer Biology Research Center, Key Laboratory of the Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wenjian Gong
- Cancer Biology Research Center, Key Laboratory of the Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Dan Liu
- Cancer Biology Research Center, Key Laboratory of the Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaoxue Zhang
- Cancer Biology Research Center, Key Laboratory of the Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yong Fang
- Cancer Biology Research Center, Key Laboratory of the Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yu Xia
- Cancer Biology Research Center, Key Laboratory of the Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wei Zhang
- Cancer Biology Research Center, Key Laboratory of the Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qinglei Gao
- Cancer Biology Research Center, Key Laboratory of the Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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14
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Zhang P, Li S, Zhang T, Cui F, Shi JH, Zhao F, Sheng X. Characterization of Molecular Subtypes in Head and Neck Squamous Cell Carcinoma With Distinct Prognosis and Treatment Responsiveness. Front Cell Dev Biol 2021; 9:711348. [PMID: 34595167 PMCID: PMC8476885 DOI: 10.3389/fcell.2021.711348] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/10/2021] [Indexed: 12/20/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is one of the most aggressive malignancies with complex phenotypic, etiological, biological, and clinical heterogeneities. Previous studies have proposed different clinically relevant subtypes of HNSCC, but little is known about its corresponding prognosis or suitable treatment strategy. Here, we identified 101 core genes from three prognostic pathways, including mTORC1 signaling, unfold protein response, and UV response UP, in 124 pairs of tumor and matched normal tissues of HNSCC. Moreover, we identified three robust subtypes associated with distinct molecular characteristics and clinical outcomes using consensus clustering based on the gene expression profiles of 944 HNSCC patients from four independent datasets. We then integrated the genomic information of The Cancer Genome Atlas (TCGA) HNSCC cohort to comprehensively evaluate the molecular features of different subtypes and screen for potentially effective therapeutic agents. Cluster 1 had more arrested oncogenic signaling, the highest immune cell infiltration, the highest immunotherapy and chemotherapeutic responsiveness, and the best prognosis. By contrast, Cluster 3 showed more activated oncogenic signaling, the lowest immune cell infiltration, the lowest immunotherapy and chemotherapy responsiveness, and the worst prognosis. Our findings corroborate the molecular diversity of HNSCC tumors and provide a novel classification strategy that may guide for prognosis and treatment allocation.
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Affiliation(s)
- Pei Zhang
- Department of Stomatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shue Li
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration, Wuhan, China
| | - Tingting Zhang
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, State Key Laboratory of Environmental Health (Incubation), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fengzhen Cui
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, State Key Laboratory of Environmental Health (Incubation), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ji-Hua Shi
- Department of Hepatobiliary and Pancreatic Surgery, Henan Key Laboratory of Digestive Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Faming Zhao
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, State Key Laboratory of Environmental Health (Incubation), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xia Sheng
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, State Key Laboratory of Environmental Health (Incubation), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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