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Huang KB, Gui CP, Xu YZ, Li XS, Zhao HW, Cao JZ, Chen YH, Pan YH, Liao B, Cao Y, Zhang XK, Han H, Zhou FJ, Liu RY, Chen WF, Jiang ZY, Feng ZH, Jiang FN, Yu YF, Xiong SW, Han GP, Tang Q, Ouyang K, Qu GM, Wu JT, Cao M, Dong BJ, Huang YR, Zhang J, Li CX, Li PX, Chen W, Zhong WD, Guo JP, Liu ZP, Hsieh JT, Xie D, Cai MY, Xue W, Wei JH, Luo JH. A multi-classifier system integrated by clinico-histology-genomic analysis for predicting recurrence of papillary renal cell carcinoma. Nat Commun 2024; 15:6215. [PMID: 39043664 PMCID: PMC11266571 DOI: 10.1038/s41467-024-50369-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 07/02/2024] [Indexed: 07/25/2024] Open
Abstract
Integrating genomics and histology for cancer prognosis demonstrates promise. Here, we develop a multi-classifier system integrating a lncRNA-based classifier, a deep learning whole-slide-image-based classifier, and a clinicopathological classifier to accurately predict post-surgery localized (stage I-III) papillary renal cell carcinoma (pRCC) recurrence. The multi-classifier system demonstrates significantly higher predictive accuracy for recurrence-free survival (RFS) compared to the three single classifiers alone in the training set and in both validation sets (C-index 0.831-0.858 vs. 0.642-0.777, p < 0.05). The RFS in our multi-classifier-defined high-risk stage I/II and grade 1/2 groups is significantly worse than in the low-risk stage III and grade 3/4 groups (p < 0.05). Our multi-classifier system is a practical and reliable predictor for recurrence of localized pRCC after surgery that can be used with the current staging system to more accurately predict disease course and inform strategies for individualized adjuvant therapy.
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Affiliation(s)
- Kang-Bo Huang
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Urology, Sun Yat-sen University Cancer center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer center, Guangzhou, China
| | - Cheng-Peng Gui
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yun-Ze Xu
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xue-Song Li
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing, China
| | - Hong-Wei Zhao
- Department of Urology, Affiliated Yantai Yuhuangding Hospital, Qingdao University, Yantai, China
| | - Jia-Zheng Cao
- Department of Urology, Jiangmen Hospital, Sun Yat-sen University, Jiangmen, China
| | - Yu-Hang Chen
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yi-Hui Pan
- Department of Urology, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Bing Liao
- Department of Pathology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yun Cao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer center, Guangzhou, China
- Department of Pathology, Sun Yat-sen University Cancer center, Guangzhou, China
| | - Xin-Ke Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer center, Guangzhou, China
- Department of Pathology, Sun Yat-sen University Cancer center, Guangzhou, China
| | - Hui Han
- Department of Urology, Sun Yat-sen University Cancer center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer center, Guangzhou, China
| | - Fang-Jian Zhou
- Department of Urology, Sun Yat-sen University Cancer center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer center, Guangzhou, 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, China
| | - Wen-Fang Chen
- Department of Pathology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ze-Ying Jiang
- Department of Pathology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zi-Hao Feng
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Fu-Neng Jiang
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Yan-Fei Yu
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing, China
| | - Sheng-Wei Xiong
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing, China
| | - Guan-Peng Han
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing, China
| | - Qi Tang
- Department of Urology, Peking University First Hospital, Institute of Urology, Peking University, National Urological Cancer Center, Beijing, China
| | - Kui Ouyang
- Department of Urology, Affiliated Yantai Yuhuangding Hospital, Qingdao University, Yantai, China
| | - Gui-Mei Qu
- Department of Pathology, Affiliated Yantai Yuhuangding Hospital, Qingdao University, Yantai, China
| | - Ji-Tao Wu
- Department of Urology, Affiliated Yantai Yuhuangding Hospital, Qingdao University, Yantai, China
| | - Ming Cao
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Bai-Jun Dong
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yi-Ran Huang
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jin Zhang
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Cai-Xia Li
- School of Mathematics and Computational Science, Sun Yat-sen University, Guangzhou, China
| | - Pei-Xing Li
- School of Mathematics and Computational Science, Sun Yat-sen University, Guangzhou, China
| | - Wei Chen
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wei-De Zhong
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Jian-Ping Guo
- Institute of Precision Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhi-Ping Liu
- Department of Internal Medicine and Department of Molecular Biology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Jer-Tsong Hsieh
- Department of Urology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Dan Xie
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer center, Guangzhou, China
- Department of Pathology, Sun Yat-sen University Cancer center, Guangzhou, China
| | - Mu-Yan Cai
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer center, Guangzhou, China
- Department of Pathology, Sun Yat-sen University Cancer center, Guangzhou, China
| | - Wei Xue
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Jin-Huan Wei
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
| | - Jun-Hang Luo
- Department of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
- Institute of Precision Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
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2
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Zhao SG, Bootsma M, Zhou S, Shrestha R, Moreno-Rodriguez T, Lundberg A, Pan C, Arlidge C, Hawley JR, Foye A, Weinstein AS, Sjöström M, Zhang M, Li H, Chesner LN, Rydzewski NR, Helzer KT, Shi Y, Lynch M, Dehm SM, Lang JM, Alumkal JJ, He HH, Wyatt AW, Aggarwal R, Zwart W, Small EJ, Quigley DA, Lupien M, Feng FY. Integrated analyses highlight interactions between the three-dimensional genome and DNA, RNA and epigenomic alterations in metastatic prostate cancer. Nat Genet 2024:10.1038/s41588-024-01826-3. [PMID: 39020220 DOI: 10.1038/s41588-024-01826-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/10/2024] [Indexed: 07/19/2024]
Abstract
The impact of variations in the three-dimensional structure of the genome has been recognized, but solid cancer tissue studies are limited. Here, we performed integrated deep Hi-C sequencing with matched whole-genome sequencing, whole-genome bisulfite sequencing, 5-hydroxymethylcytosine (5hmC) sequencing and RNA sequencing across a cohort of 80 biopsy samples from patients with metastatic castration-resistant prostate cancer. Dramatic differences were present in gene expression, 5-methylcytosine/5hmC methylation and in structural variation versus mutation rate between A and B (open and closed) chromatin compartments. A subset of tumors exhibited depleted regional chromatin contacts at the AR locus, linked to extrachromosomal circular DNA (ecDNA) and worse response to AR signaling inhibitors. We also identified topological subtypes associated with stark differences in methylation structure, gene expression and prognosis. Our data suggested that DNA interactions may predispose to structural variant formation, exemplified by the recurrent TMPRSS2-ERG fusion. This comprehensive integrated sequencing effort represents a unique clinical tumor resource.
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Affiliation(s)
- Shuang G Zhao
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI, USA
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
- William S. Middleton Memorial Veterans Hospital, Madison, Madison, WI, USA
| | - Matthew Bootsma
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI, USA
| | - Stanley Zhou
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Raunak Shrestha
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Thaidy Moreno-Rodriguez
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Arian Lundberg
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Chu Pan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Christopher Arlidge
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - James R Hawley
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Alana S Weinstein
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Martin Sjöström
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Meng Zhang
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Haolong Li
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Lisa N Chesner
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Nicholas R Rydzewski
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI, USA
- Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kyle T Helzer
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI, USA
| | - Yue Shi
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI, USA
| | - Molly Lynch
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Scott M Dehm
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Department of Urology, University of Minnesota, Minneapolis, MN, USA
| | - Joshua M Lang
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Joshi J Alumkal
- Department of Internal Medicine, Division of Hematology-Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Hansen H He
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Alexander W Wyatt
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Wilbert Zwart
- Netherlands Cancer Institute, Oncode Institute, Amsterdam, the Netherlands
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Felix Y Feng
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
- Department of Urology, University of California San Francisco, San Francisco, CA, USA.
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3
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Kulac I, Roudier MP, Haffner MC. Molecular Pathology of Prostate Cancer. Clin Lab Med 2024; 44:161-180. [PMID: 38821639 DOI: 10.1016/j.cll.2023.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2024]
Abstract
Molecular profiling studies have shed new light on the complex biology of prostate cancer. Genomic studies have highlighted that structural rearrangements are among the most common recurrent alterations. In addition, both germline and somatic mutations in DNA repair genes are enriched in patients with advanced disease. Primary prostate cancer has long been known to be multifocal, but recent studies demonstrate that a large fraction of prostate cancer shows evidence of multiclonality, suggesting that genetically distinct, independently arising tumor clones coexist. Metastatic prostate cancer shows a high level of morphologic and molecular diversity, which is associated with resistance to systemic therapies. The resulting high level of intratumoral heterogeneity has important implications for diagnosis and poses major challenges for the implementation of molecular studies. Here we provide a concise review of the molecular pathology of prostate cancer, highlight clinically relevant alterations, and discuss opportunities for molecular testing.
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Affiliation(s)
- Ibrahim Kulac
- Department of Pathology, Koç University School of Medicine, Davutpasa Caddesi No:4, Istanbul 34010, Turkey
| | - Martine P Roudier
- Department of Urology, University of Washington, Northeast Pacific Street, Seattle, WA 98195, USA
| | - Michael C Haffner
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue, Seattle, WA 98109, USA; Division of Clinical Research, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue, Seattle, WA 98109, USA; Department of Pathology, University of Washington, Seattle, WA, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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4
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Tosoian JJ, Zhang Y, Xiao L, Xie C, Samora NL, Niknafs YS, Chopra Z, Siddiqui J, Zheng H, Herron G, Vaishampayan N, Robinson HS, Arivoli K, Trock BJ, Ross AE, Morgan TM, Palapattu GS, Salami SS, Kunju LP, Tomlins SA, Sokoll LJ, Chan DW, Srivastava S, Feng Z, Sanda MG, Zheng Y, Wei JT, Chinnaiyan AM. Development and Validation of an 18-Gene Urine Test for High-Grade Prostate Cancer. JAMA Oncol 2024; 10:726-736. [PMID: 38635241 PMCID: PMC11190811 DOI: 10.1001/jamaoncol.2024.0455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/06/2023] [Indexed: 04/19/2024]
Abstract
Importance Benefits of prostate cancer (PCa) screening with prostate-specific antigen (PSA) alone are largely offset by excess negative biopsies and overdetection of indolent cancers resulting from the poor specificity of PSA for high-grade PCa (ie, grade group [GG] 2 or greater). Objective To develop a multiplex urinary panel for high-grade PCa and validate its external performance relative to current guideline-endorsed biomarkers. Design, Setting, and Participants RNA sequencing analysis of 58 724 genes identified 54 markers of PCa, including 17 markers uniquely overexpressed by high-grade cancers. Gene expression and clinical factors were modeled in a new urinary test for high-grade PCa (MyProstateScore 2.0 [MPS2]). Optimal models were developed in parallel without prostate volume (MPS2) and with prostate volume (MPS2+). The locked models underwent blinded external validation in a prospective National Cancer Institute trial cohort. Data were collected from January 2008 to December 2020, and data were analyzed from November 2022 to November 2023. Exposure Protocolized blood and urine collection and transrectal ultrasound-guided systematic prostate biopsy. Main Outcomes and Measures Multiple biomarker tests were assessed in the validation cohort, including serum PSA alone, the Prostate Cancer Prevention Trial risk calculator, and the Prostate Health Index (PHI) as well as derived multiplex 2-gene and 3-gene models, the original 2-gene MPS test, and the 18-gene MPS2 models. Under a testing approach with 95% sensitivity for PCa of GG 2 or greater, measures of diagnostic accuracy and clinical consequences of testing were calculated. Cancers of GG 3 or greater were assessed secondarily. Results Of 761 men included in the development cohort, the median (IQR) age was 63 (58-68) years, and the median (IQR) PSA level was 5.6 (4.6-7.2) ng/mL; of 743 men included in the validation cohort, the median (IQR) age was 62 (57-68) years, and the median (IQR) PSA level was 5.6 (4.1-8.0) ng/mL. In the validation cohort, 151 (20.3%) had high-grade PCa on biopsy. Area under the receiver operating characteristic curve values were 0.60 using PSA alone, 0.66 using the risk calculator, 0.77 using PHI, 0.76 using the derived multiplex 2-gene model, 0.72 using the derived multiplex 3-gene model, and 0.74 using the original MPS model compared with 0.81 using the MPS2 model and 0.82 using the MPS2+ model. At 95% sensitivity, the MPS2 model would have reduced unnecessary biopsies performed in the initial biopsy population (range for other tests, 15% to 30%; range for MPS2, 35% to 42%) and repeat biopsy population (range for other tests, 9% to 21%; range for MPS2, 46% to 51%). Across pertinent subgroups, the MPS2 models had negative predictive values of 95% to 99% for cancers of GG 2 or greater and of 99% for cancers of GG 3 or greater. Conclusions and Relevance In this study, a new 18-gene PCa test had higher diagnostic accuracy for high-grade PCa relative to existing biomarker tests. Clinically, use of this test would have meaningfully reduced unnecessary biopsies performed while maintaining highly sensitive detection of high-grade cancers. These data support use of this new PCa biomarker test in patients with elevated PSA levels to reduce the potential harms of PCa screening while preserving its long-term benefits.
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Affiliation(s)
- Jeffrey J. Tosoian
- Department of Urology, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Yuping Zhang
- Department of Pathology, University of Michigan, Ann Arbor
| | - Lanbo Xiao
- Department of Pathology, University of Michigan, Ann Arbor
| | - Cassie Xie
- Department of Biostatistics, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Nathan L. Samora
- Department of Urology, Vanderbilt University Medical Center, Nashville, Tennessee
| | | | - Zoey Chopra
- Department of Pathology, University of Michigan, Ann Arbor
| | - Javed Siddiqui
- Department of Pathology, University of Michigan, Ann Arbor
| | - Heng Zheng
- Department of Pathology, University of Michigan, Ann Arbor
| | - Grace Herron
- Department of Pathology, University of Michigan, Ann Arbor
| | | | - Hunter S. Robinson
- Department of Urology, Vanderbilt University Medical Center, Nashville, Tennessee
| | | | - Bruce J. Trock
- Departments of Pathology and Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ashley E. Ross
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Todd M. Morgan
- Department of Urology, University of Michigan, Ann Arbor
| | | | | | | | - Scott A. Tomlins
- Department of Urology, University of Michigan, Ann Arbor
- Strata Oncology, Ann Arbor, Michigan
| | - Lori J. Sokoll
- Departments of Pathology and Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Daniel W. Chan
- Departments of Pathology and Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sudhir Srivastava
- Division of Cancer Prevention, National Institutes of Health, Bethesda, Maryland
| | - Ziding Feng
- Department of Biostatistics, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | - Yingye Zheng
- Department of Biostatistics, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - John T. Wei
- Department of Urology, University of Michigan, Ann Arbor
| | - Arul M. Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor
- Department of Urology, University of Michigan, Ann Arbor
- Howard Hughes Medical Institute, Chevy Chase, Maryland
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5
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Lu B, Liu Y, Yao Y, Yang T, Zhang H, Yang X, Huang R, Zhou W, Pan X, Cui X. Advances in sequencing and omics studies in prostate cancer: unveiling molecular pathogenesis and clinical applications. Front Oncol 2024; 14:1355551. [PMID: 38800374 PMCID: PMC11116611 DOI: 10.3389/fonc.2024.1355551] [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: 12/14/2023] [Accepted: 04/16/2024] [Indexed: 05/29/2024] Open
Abstract
Background Prostate cancer (PCa) is one of the most threatening health problems for the elderly males. However, our understanding of the disease has been limited by the research technology for a long time. Recently, the maturity of sequencing technology and omics studies has been accelerating the studies of PCa, establishing themselves as an essential impetus in this field. Methods We assessed Web of Science (WoS) database for publications of sequencing and omics studies in PCa on July 3rd, 2023. Bibliometrix was used to conduct ulterior bibliometric analysis of countries/affiliations, authors, sources, publications, and keywords. Subsequently, purposeful large amounts of literature reading were proceeded to analyze research hotspots in this field. Results 3325 publications were included in the study. Research associated with sequencing and omics studies in PCa had shown an obvious increase recently. The USA and China were the most productive countries, and harbored close collaboration. CHINNAIYAN AM was identified as the most influential author, and CANCER RESEARCH exhibited huge impact in this field. Highly cited publications and their co-citation relationships were used to filtrate literatures for subsequent literature reading. Based on keyword analysis and large amounts of literature reading, 'the molecular pathogenesis of PCa' and 'the clinical application of sequencing and omics studies in PCa' were summarized as two research hotspots in the field. Conclusion Sequencing technology had a deep impact on the studies of PCa. Sequencing and omics studies in PCa helped researchers reveal the molecular pathogenesis, and provided new possibilities for the clinical practice of PCa.
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Affiliation(s)
- Bingnan Lu
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yifan Liu
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuntao Yao
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tianyue Yang
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haoyu Zhang
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xinyue Yang
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Runzhi Huang
- Department of Burn Surgery, The First Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Wang Zhou
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiuwu Pan
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xingang Cui
- Department of Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
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6
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Tosoian JJ, Penson DF, Chinnaiyan AM. A Pragmatic Approach to Prostate Cancer Screening. JAMA 2024; 331:1448-1450. [PMID: 38581253 DOI: 10.1001/jama.2024.4089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/08/2024]
Affiliation(s)
- Jeffrey J Tosoian
- Department of Urology, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - David F Penson
- Department of Urology, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor
- Department of Urology, University of Michigan, Ann Arbor
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor
- Rogel Cancer Center, University of Michigan, Ann Arbor
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7
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Paul AK, Melson JW, Hirani S, Muthusamy S. Systemic therapy landscape of advanced prostate cancer. Adv Cancer Res 2024; 161:367-402. [PMID: 39032954 DOI: 10.1016/bs.acr.2024.04.004] [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] [Indexed: 07/23/2024]
Abstract
Prostate cancer is the most commonly diagnosed cancer in American men and 2nd leading cause of cancer-related deaths in the United States. Androgen deprivation therapy (ADT) is the backbone of treatment for advanced prostate cancer. Over the past several decades a number of new therapeutics, such as novel androgen receptor pathway inhibitors, targeted agents and radionuclide therapies, have been introduced for the treatment of prostate cancers. These agents have been demonstrated to improve clinical outcomes of prostate cancer patients in randomized clinical trials. In addition, new therapeutic strategies, such as early intensification of ADT, novel treatment combinations, and treatment sequencing, are expected to improve outcomes further. In this clinical review, we discuss the changing treatment landscape for advanced prostate cancer with a focus on new therapeutics.
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Affiliation(s)
- Asit K Paul
- Department of Internal Medicine, Division of Hematology, Oncology and Palliative Care, Virginia Commonwealth University, Richmond, VA, United States; VCU Massey Comprehensive Cancer Center, Richmond, VA, United States.
| | - John W Melson
- Department of Internal Medicine, Division of Hematology, Oncology and Palliative Care, Virginia Commonwealth University, Richmond, VA, United States; VCU Massey Comprehensive Cancer Center, Richmond, VA, United States
| | - Samina Hirani
- Department of Internal Medicine, Division of Hematology, Oncology and Palliative Care, Virginia Commonwealth University, Richmond, VA, United States
| | - Selvaraj Muthusamy
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, United States
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8
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Gao J, Shi W, Wang J, Guan C, Dong Q, Sheng J, Zou X, Xu Z, Ge Y, Yang C, Li J, Bao H, Zhong X, Cui Y. Research progress and applications of epigenetic biomarkers in cancer. Front Pharmacol 2024; 15:1308309. [PMID: 38681199 PMCID: PMC11048075 DOI: 10.3389/fphar.2024.1308309] [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: 10/06/2023] [Accepted: 03/25/2024] [Indexed: 05/01/2024] Open
Abstract
Epigenetic changes are heritable changes in gene expression without changes in the nucleotide sequence of genes. Epigenetic changes play an important role in the development of cancer and in the process of malignancy metastasis. Previous studies have shown that abnormal epigenetic changes can be used as biomarkers for disease status and disease prediction. The reversibility and controllability of epigenetic modification changes also provide new strategies for early disease prevention and treatment. In addition, corresponding drug development has also reached the clinical stage. In this paper, we will discuss the recent progress and application status of tumor epigenetic biomarkers from three perspectives: DNA methylation, non-coding RNA, and histone modification, in order to provide new opportunities for additional tumor research and applications.
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Affiliation(s)
- Jianjun Gao
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Wujiang Shi
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jiangang Wang
- Department of General Surgery, Tangdu Hospital, Air Force Medical University, Xi’an, China
| | - Canghai Guan
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Qingfu Dong
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jialin Sheng
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xinlei Zou
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhaoqiang Xu
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yifei Ge
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Chengru Yang
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jiehan Li
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Haolin Bao
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiangyu Zhong
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yunfu Cui
- Department of Hepatopancreatobiliary Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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9
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Liu Y, Hatano K, Nonomura N. Liquid Biomarkers in Prostate Cancer Diagnosis: Current Status and Emerging Prospects. World J Mens Health 2024; 42:42.e45. [PMID: 38772530 DOI: 10.5534/wjmh.230386] [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: 12/31/2023] [Revised: 01/12/2024] [Accepted: 01/22/2024] [Indexed: 05/23/2024] Open
Abstract
Prostate cancer (PCa) is a major health concern that necessitates appropriate diagnostic approaches for timely intervention. This review critically evaluates the role of liquid biopsy techniques, focusing on blood- and urine-based biomarkers, in overcoming the limitations of conventional diagnostic methods. The 4Kscore test and Prostate Health Index have demonstrated efficacy in distinguishing PCa from benign conditions. Urinary biomarker tests such as PCa antigen 3, MyProstateScore, SelectMDx, and ExoDx Prostate IntelliScore test have revolutionized risk stratification and minimized unnecessary biopsies. Emerging biomarkers, including non-coding RNAs, circulating tumor DNA, and prostate-specific antigen (PSA) glycosylation, offer valuable insights into PCa biology, enabling personalized treatment strategies. Advancements in non-invasive liquid biomarkers for PCa diagnosis may facilitate the stratification of patients and avoid unnecessary biopsies, particularly when PSA is in the gray area of 4 to 10 ng/mL.
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Affiliation(s)
- Yutong Liu
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Koji Hatano
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan.
| | - Norio Nonomura
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
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10
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Osiecki R, Kozikowski M, Białek Ł, Pyzlak M, Dobruch J. The presence of cribriform pattern in prostate biopsy and radical prostatectomy is associated with negative postoperative pathological features. Cent European J Urol 2024; 77:22-29. [PMID: 38645812 PMCID: PMC11032032 DOI: 10.5173/ceju.2023.215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/20/2023] [Accepted: 12/03/2023] [Indexed: 04/23/2024] Open
Abstract
Introduction Prostate cancer is the second most common male cancer worldwide. Its rising incidence and high overtreatment rate drive the search for new prognostic factors. Histopathological variants, such as cribriform pattern (CP), are associated with poorer oncologic outcome. The aim of this study was to assess the correlation between CP in prostate biopsy and radical prostatectomy (RP) and postoperative pathological features. Material and methods In this retrospective, single-centre study we analysed the reviewed medical records of 100 men who underwent minimally invasive RP in the years 2017-2019. RP histopathological examination was performed by a single expert pathologist, and preoperative biopsies were assessed by various professionals from different referral centres. Results 48% of men underwent endoscopic RP with limited lymphadenectomy, whereas 52% underwent laparoscopic RP with extended lymphadenectomy. CP in biopsy was present in 6 patients: 3 in each of both groups (6.3% and 5.8%, respectively). Lymph node metastases were present in 50% and 10% of patients with and without CP in biopsy, respectively (p = 0.028). Postoperative histopathological examination revealed CP in 65%. CP in RP was associated with higher International Society of Urological Pathology (ISUP) (p < 0.001), extraprostatic extension (EPE) (p = 0.001), seminal vesicle invasion (SVI) (p = 0.001), and positive surgical margin (PSM) (p = 0.004). Thirteen (20%) of the patients with CP in the RP specimen had lymph node metastasis, and none of the patients without CP in the RP specimen had regional LN metastasis. Conclusions The presence of CP in a biopsy specimen and RP is associated with negative postoperative features. Therefore, efforts should be made to increase CP reporting in biopsies because its identification could trigger a more radical surgical approach with extended lymphadenectomy.
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Affiliation(s)
- Rafal Osiecki
- Department of Urology, Independent Public Hospital them. prof. W. Orlowski, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Mieszko Kozikowski
- Department of Urology, Polish Centre of Advanced Urology, St. Anne's Hospital EMC, Piaseczno, Poland
- QUADIA MRI Centre, Piaseczno, Poland
| | - Łukasz Białek
- Department of Urology, Independent Public Hospital them. prof. W. Orlowski, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Michał Pyzlak
- Department of Pathology, Institute of Mother and Child, Warsaw, Poland
- Centre for Diagnostic Pathology, Warsaw, Poland
| | - Jakub Dobruch
- Department of Urology, Independent Public Hospital them. prof. W. Orlowski, Centre of Postgraduate Medical Education, Warsaw, Poland
- Department of Urology, Polish Centre of Advanced Urology, St. Anne's Hospital EMC, Piaseczno, Poland
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11
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Zhu S, Xu N, Zeng H. Molecular complexity of intraductal carcinoma of the prostate. Cancer Med 2024; 13:e6939. [PMID: 38379333 PMCID: PMC10879723 DOI: 10.1002/cam4.6939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 11/21/2023] [Accepted: 12/04/2023] [Indexed: 02/22/2024] Open
Abstract
Intraductal carcinoma of the prostate (IDC-P) is an aggressive subtype of prostate cancer characterized by the growth of tumor cells within the prostate ducts. It is often found alongside invasive carcinoma and is associated with poor prognosis. Understanding the molecular mechanisms driving IDC-P is crucial for improved diagnosis, prognosis, and treatment strategies. This review summarizes the molecular characteristics of IDC-P and their prognostic indications, comparing them to conventional prostate acinar adenocarcinoma, to gain insights into its unique behavior and identify potential therapeutic targets.
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Affiliation(s)
- Sha Zhu
- Department of Urology, Institute of Urology, West China HospitalSichuan UniversityChengduChina
| | - Nanwei Xu
- Department of Urology, Institute of Urology, West China HospitalSichuan UniversityChengduChina
| | - Hao Zeng
- Department of Urology, Institute of Urology, West China HospitalSichuan UniversityChengduChina
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12
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Solati A, Thvimi S, Khatami SH, Shabaninejad Z, Malekzadegan Y, Alizadeh M, Mousavi P, Taheri-Anganeh M, Razmjoue D, Bahmyari S, Ghasemnejad-Berenji H, Vafadar A, Soltani Fard E, Ghasemi H, Movahedpour A. Non-coding RNAs in gynecologic cancer. Clin Chim Acta 2023; 551:117618. [PMID: 38375624 DOI: 10.1016/j.cca.2023.117618] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 02/21/2024]
Abstract
The term "gynecologic cancer" pertains to neoplasms impacting the reproductive tissues and organs of women encompassing the endometrium, vagina, cervix, uterus, vulva, and ovaries. The progression of gynecologic cancer is linked to various molecular mechanisms. Historically, cancer research primarily focused on protein-coding genes. However, recent years have unveiled the involvement of non-coding RNAs (ncRNAs), including microRNAs, long non-coding RNAs (LncRNAs), and circular RNAs, in modulating cellular functions within gynecological cancer. Substantial evidence suggests that ncRNAs may wield a dual role in gynecological cancer, acting as either oncogenic or tumor-suppressive agents. Numerous clinical trials are presently investigating the roles of ncRNAs as biomarkers and therapeutic agents. These endeavors may introduce a fresh perspective on the diagnosis and treatment of gynecological cancer. In this overview, we highlight some of the ncRNAs associated with gynecological cancers.
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Affiliation(s)
- Arezoo Solati
- Department of Reproductive Biology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sina Thvimi
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Seyyed Hossein Khatami
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Shabaninejad
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | | | - Mehdi Alizadeh
- Molecular Medicine Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Pegah Mousavi
- Molecular Medicine Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Mortaza Taheri-Anganeh
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Research Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Damoun Razmjoue
- Medicinal Plants Research Center, Yasuj University of Medical Sciences, Yasuj, Iran; Department of Pharmacognosy, Faculty of Pharmacy, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Sedigheh Bahmyari
- Department of Reproductive Biology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hojat Ghasemnejad-Berenji
- Reproductive Health Research Center, Clinical Research Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Asma Vafadar
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Elahe Soltani Fard
- Department of Molecular Medicine, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
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13
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Tao W, Wang BY, Luo L, Li Q, Meng ZA, Xia TL, Deng WM, Yang M, Zhou J, Zhang X, Gao X, Li LY, He YD. A urine extracellular vesicle lncRNA classifier for high-grade prostate cancer and increased risk of progression: A multi-center study. Cell Rep Med 2023; 4:101240. [PMID: 37852185 PMCID: PMC10591064 DOI: 10.1016/j.xcrm.2023.101240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 07/03/2023] [Accepted: 09/21/2023] [Indexed: 10/20/2023]
Abstract
To construct a urine extracellular vesicle long non-coding RNA (lncRNA) classifier that can detect high-grade prostate cancer (PCa) of grade group 2 or greater and estimate the risk of progression during active surveillance, we identify high-grade PCa-specific lncRNAs by combined analyses of cohorts from TAHSY, TCGA, and the GEO database. We develop and validate a 3-lncRNA diagnostic model (Clnc, being made of AC015987.1, CTD-2589M5.4, RP11-363E6.3) that can detect high-grade PCa. Clnc shows higher accuracy than prostate cancer antigen 3 (PCA3), multiparametric magnetic resonance imaging (mpMRI), and two risk calculators (Prostate Cancer Prevention Trial [PCPT]-RC 2.0 and European Randomized Study of Screening for Prostate Cancer [ERSPC]-RC) in the training cohort (n = 350), two independent cohorts (n = 232; n = 251), and TCGA cohort (n = 499). In the prospective active surveillance cohort (n = 182), Clnc at diagnosis remains a powerful independent predictor for overall active surveillance progression. Thus, Clnc is a potential biomarker for high-grade PCa and can also serve as a biomarker for improved selection of candidates for active surveillance.
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Affiliation(s)
- Wen Tao
- Department of Urology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Bang-Yu Wang
- Department of Anesthesiology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200080, China
| | - Liang Luo
- Department of Urology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Qing Li
- Food and Nutritional Sciences Programme, School of Life Sciences, The Chinese University of Hong Kong, Shatin 999077, Hong Kong
| | - Zhan-Ao Meng
- Department of Radiology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Tao-Lin Xia
- Department of Urology, Foshan First Municipal People's Hospital, Sun Yat-sen University, Foshan 528000, China
| | - Wei-Ming Deng
- Department of Urology, The First Affiliated Hospital, University of South China, Hengyang 421000, China
| | - Ming Yang
- Department of Urology, Foshan Municipal Chinese Medicine Hospital, Foshan 528000, China
| | - Jing Zhou
- Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Xin Zhang
- Department of Pathology, Foshan First Municipal People's Hospital, Sun Yat-sen University, Foshan 528000, China
| | - Xin Gao
- Department of Urology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China.
| | - Liao-Yuan Li
- Department of Urology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China.
| | - Ya-Di He
- Health Management Center, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China.
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14
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Li Y, Fang Z, Ge S, Li J, Qu L, Shi X, Zhang W, Sun Y, Ren S, Wang L. Long non-coding RNA ENST00000503625 is a potential prognostic biomarker and metastasis suppressor gene in prostate cancer. J Cancer Res Clin Oncol 2023; 149:7305-7317. [PMID: 36920562 DOI: 10.1007/s00432-023-04676-4] [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: 11/06/2022] [Accepted: 03/04/2023] [Indexed: 03/16/2023]
Abstract
BACKGROUND Dysregulation of Long Non-coding RNAs (lncRNAs) emerges to be a hallmark of cancers. Metastatic prostate cancer and localized disease that recurs after treatment are clinical challenges, it remains unclear how lncRNA plays a role in those processes. METHODS From previous RNA-Seq data on 65 prostate cancer and adjacent normal tissues. We identified a novel lncRNA ENST00000503625 down-regulated in prostate cancer and correlated with tumor progression characteristics. Public datasets were examined for associations between ENST00000503625 expression and clinical parameters and prognoses. Subsequently, we constructed and externally validated a nomogram for predicting biochemical recurrence (BCR). Finally, in vitro experiments were carried out to determine how ENST00000503625 functions biologically in prostate cancer. RESULTS Low ENST00000503625 in tumor was associated with poor clinical features and prognoses. TCGA pan-cancer analysis found that ENST00000503625 was deregulated in a variety of tumors and correlated with overall survival, disease-specific survival, and progression-free survival. The nomogram for predicting BCR was constructed using TCGA data, which exhibited excellent accuracy in external validation with Chinese Prostate Cancer Genome and Epigenome Atlas data. Gene Ontology and KEGG pathway analysis found that genes related to ENST00000503625 were enriched in multiple tumor progression related pathways. When ENST00000503625 was knocked down in vitro, the epithelial-mesenchymal transition was induced, by which cancer cells migrated and invaded more readily. CONCLUSION Our data suggested that ENST00000503625 may serve as a potential prognostic marker or a therapeutic target for prostate cancer metastases.
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Affiliation(s)
- Yaoming Li
- Department of Urology, Institute of Surgery Research, Daping Hospital/Army Medical Center, Army Medical University, Chongqing, 400042, China
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
| | - Ziyu Fang
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
| | - Silun Ge
- Department of Urology, Jinling Hospital, Nanjing Medical University, Nanjing, 201101, China
| | - Jingyi Li
- Department of Urology, Institute of Surgery Research, Daping Hospital/Army Medical Center, Army Medical University, Chongqing, 400042, China
| | - Le Qu
- Department of Urology, Jinling Hospital, Nanjing Medical University, Nanjing, 201101, China
| | - Xiaolei Shi
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
| | - Wei Zhang
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
| | - Yinghao Sun
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, 200433, China
| | - Shancheng Ren
- Department of Urology, Changzheng Hospital, Naval Medical University, Shanghai, 200003, China.
| | - Luofu Wang
- Department of Urology, Institute of Surgery Research, Daping Hospital/Army Medical Center, Army Medical University, Chongqing, 400042, China.
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15
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Shukla N, Kour B, Sharma D, Vijayvargiya M, Sadasukhi TC, Medicherla KM, Malik B, Bissa B, Vuree S, Lohiya NK, Suravajhala P. Towards Understanding the Key Signature Pathways Associated from Differentially Expressed Gene Analysis in an Indian Prostate Cancer Cohort. Diseases 2023; 11:diseases11020072. [PMID: 37218885 DOI: 10.3390/diseases11020072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/13/2023] [Accepted: 04/18/2023] [Indexed: 05/24/2023] Open
Abstract
Prostate cancer (PCa) is one of the most prevalent cancers among men in India. Although studies on PCa have dealt with genetics, genomics, and the environmental influence in the causality of PCa, not many studies employing the Next Generation Sequencing (NGS) approaches of PCa have been carried out. In our previous study, we identified some causal genes and mutations specific to Indian PCa using Whole Exome Sequencing (WES). In the recent past, with the help of different cancer consortiums such as The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC), along with differentially expressed genes (DEGs), many cancer-associated novel non-coding RNAs have been identified as biomarkers. In this work, we attempt to identify differentially expressed genes (DEGs) including long non-coding RNAs (lncRNAs) associated with signature pathways from an Indian PCa cohort using the RNA-sequencing (RNA-seq) approach. From a cohort of 60, we screened six patients who underwent prostatectomy; we performed whole transcriptome shotgun sequencing (WTSS)/RNA-sequencing to decipher the DEGs. We further normalized the read counts using fragments per kilobase of transcript per million mapped reads (FPKM) and analyzed the DEGs using a cohort of downstream regulatory tools, viz., GeneMANIA, Stringdb, Cytoscape-Cytohubba, and cbioportal, to map the inherent signatures associated with PCa. By comparing the RNA-seq data obtained from the pairs of normal and PCa tissue samples using our benchmarked in-house cuffdiff pipeline, we observed some important genes specific to PCa, such as STEAP2, APP, PMEPA1, PABPC1, NFE2L2, and HN1L, and some other important genes known to be involved in different cancer pathways, such as COL6A1, DOK5, STX6, BCAS1, BACE1, BACE2, LMOD1, SNX9, CTNND1, etc. We also identified a few novel lncRNAs such as LINC01440, SOX2OT, ENSG00000232855, ENSG00000287903, and ENST00000647843.1 that need to be characterized further. In comparison with publicly available datasets, we have identified characteristic DEGs and novel lncRNAs implicated in signature PCa pathways in an Indian PCa cohort which perhaps have not been reported. This has set a precedent for us to validate candidates further experimentally, and we firmly believe this will pave a way toward the discovery of biomarkers and the development of novel therapies.
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Affiliation(s)
- Nidhi Shukla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302001, India
- Department of Chemistry, School of Basic Sciences, Manipal University Jaipur, Jaipur 303007, India
| | - Bhumandeep Kour
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144001, India
| | - Devendra Sharma
- Department of Urology, Rukmani Birla Hospital, Jaipur 302018, India
| | - Maneesh Vijayvargiya
- Department of Pathology, Mahatma Gandhi University of Medical Sciences and Technology, Jaipur 302022, India
| | - T C Sadasukhi
- Department of Urology, Mahatma Gandhi University of Medical Sciences and Technology, Jaipur 302022, India
| | - Krishna Mohan Medicherla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research (BISR), Statue Circle, Jaipur 302001, India
- Department of Bioengineering, Birla Institute of Technology, Mesra Jaipur Campus, 27-Malaviya Industrial Area, Jaipur 302017, India
| | - Babita Malik
- Department of Chemistry, School of Basic Sciences, Manipal University Jaipur, Jaipur 303007, India
| | - Bhawana Bissa
- Department of Biochemistry, Central University of Rajasthan, Ajmer 305817, India
| | - Sugunakar Vuree
- Bioclues.org, Hyderabad 500072, India
- MNR Foundation for Research & Innovation, MNR University, Sangareddy 502294, India
| | - Nirmal Kumar Lohiya
- Department of Zoology, Center for Advanced Studies, University of Rajasthan, Jaipur 302004, India
| | - Prashanth Suravajhala
- Bioclues.org, Hyderabad 500072, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India
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16
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Zhao X, Ye J, Lin X, Xue H, Zou X, Liu G, Deng M, Sun B, Guo Y, Liu D, Li Y. Identification of Key Functional Genes and LncRNAs Influencing Muscle Growth and Development in Leizhou Black Goats. Genes (Basel) 2023; 14:genes14040881. [PMID: 37107639 PMCID: PMC10138011 DOI: 10.3390/genes14040881] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/31/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Meat yield and quality are important economic traits of livestock. Herein, longissimus dorsi (LD) muscles of Leizhou black goats aged 0, 3, and 6 months were used to identify differentially expressed messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs) by high-throughput RNA sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were used to analyze differentially expressed genes. Expression levels of regulator of calcineurin 1 (RCAN1) and olfactory receptor 2AP1 (OR2AP1) were significantly different in LD muscles of goats aged 0, 3, and 6 months, indicating potentially important roles in postnatal muscle development. Differentially expressed lncRNAs and mRNAs were mainly enriched in biological processes and pathways related to cellular energy metabolism, consistent with previous studies. Three lncRNAs, TCONS_00074191, TCONS_00074190, and TCONS_00078361, may play a cis-acting role with methyltransferase-like 11B (METTL11B) genes and participate in the methylation of goat muscle proteins. Some of the identified genes may provide valuable resources for future studies on postnatal meat development in goat muscles.
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Affiliation(s)
- Xiuhui Zhao
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
| | - Junning Ye
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
| | - Xunkai Lin
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Huiwen Xue
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xian Zou
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Guangbin Liu
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
| | - Ming Deng
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
| | - Baoli Sun
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
| | - Yongqing Guo
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
| | - Dewu Liu
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
| | - Yaokun Li
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou 510642, China
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17
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The diagnostic role and mechanistic functions of exosomal lncRNAs in prostate cancer. Clin Transl Oncol 2023; 25:592-600. [PMID: 36266385 DOI: 10.1007/s12094-022-02982-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 10/10/2022] [Indexed: 10/24/2022]
Abstract
Exosomes are small membrane-enclosed vesicles that are released by most living cells and harbor a diverse array of proteins, nucleic acids, and lipid cargos. These exosomes offer valuable biomarkers that may offer insights regarding as a range of physiological and pathological processes, including immune responses, cancer development, pregnancy, and diseases of the central nervous system. With the development of high-throughput technologies, the vital functions of long non-coding RNAs (lncRNAs) have been gradually entered people's vision and become new research hotspots. Nowadays, lncRNAs can play important roles in cancer progression by combining with miRNAs, activating molecular targets and other ways, and are also related to the diagnosis, treatment and prognosis for cancer, such as prostate cancer. Current review focused on the summary of diagnostic roles and mechanistic functions about exosomal lncRNAs in prostate cancer.
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18
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Maroni P, Gomarasca M, Lombardi G. Long non-coding RNAs in bone metastasis: progresses and perspectives as potential diagnostic and prognostic biomarkers. Front Endocrinol (Lausanne) 2023; 14:1156494. [PMID: 37143733 PMCID: PMC10153099 DOI: 10.3389/fendo.2023.1156494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/27/2023] [Indexed: 05/06/2023] Open
Abstract
In a precision medicine perspective, among the biomarkers potentially useful for early diagnosis of cancers, as well as to define their prognosis and eventually to identify novel and more effective therapeutic targets, there are the long non-coding RNAs (lncRNAs). The term lncRNA identifies a class of non-coding RNA molecules involved in the regulation of gene expression that intervene at the transcriptional, post-transcriptional, and epigenetic level. Metastasis is a natural evolution of some malignant tumours, frequently encountered in patients with advanced cancers. Onset and development of metastasis represents a detrimental event that worsen the patient's prognosis by profoundly influencing the quality of life and is responsible for the ominous progression of the disease. Due to the peculiar environment and the biomechanical properties, bone is a preferential site for the secondary growth of breast, prostate and lung cancers. Unfortunately, only palliative and pain therapies are currently available for patients with bone metastases, while no effective and definitive treatments are available. The understanding of pathophysiological basis of bone metastasis formation and progression, as well as the improvement in the clinical management of the patient, are central but challenging topics in basic research and clinical practice. The identification of new molecular species that may have a role as early hallmarks of the metastatic process could open the door to the definition of new, and more effective, therapeutic and diagnostic approaches. Non-coding RNAs species and, particularly, lncRNAs are promising compounds in this setting, and their study may bring to the identification of relevant processes. In this review, we highlight the role of lncRNAs as emerging molecules in mediating the formation and development of bone metastases, as possible biomarkers for cancer diagnosis and prognosis, and as therapeutic targets to counteract cancer spread.
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Affiliation(s)
- Paola Maroni
- Laboratory of Experimental Biochemistry and Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milano, Italy
| | - Marta Gomarasca
- Laboratory of Experimental Biochemistry and Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milano, Italy
- *Correspondence: Marta Gomarasca,
| | - Giovanni Lombardi
- Laboratory of Experimental Biochemistry and Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milano, Italy
- Department of Athletics, Strength and Conditioning, Poznań University of Physical Education, Poznań, Poland
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19
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Rezaee M, Mohammadi F, Keshavarzmotamed A, Yahyazadeh S, Vakili O, Milasi YE, Veisi V, Dehmordi RM, Asadi S, Ghorbanhosseini SS, Rostami M, Alimohammadi M, Azadi A, Moussavi N, Asemi Z, Aminianfar A, Mirzaei H, Mafi A. The landscape of exosomal non-coding RNAs in breast cancer drug resistance, focusing on underlying molecular mechanisms. Front Pharmacol 2023; 14:1152672. [PMID: 37153758 PMCID: PMC10154547 DOI: 10.3389/fphar.2023.1152672] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 03/29/2023] [Indexed: 05/10/2023] Open
Abstract
Breast cancer (BC) is the most common malignancy among women worldwide. Like many other cancers, BC therapy is challenging and sometimes frustrating. In spite of the various therapeutic modalities applied to treat the cancer, drug resistance, also known as, chemoresistance, is very common in almost all BCs. Undesirably, a breast tumor might be resistant to different curative approaches (e.g., chemo- and immunotherapy) at the same period of time. Exosomes, as double membrane-bound extracellular vesicles 1) secreted from different cell species, can considerably transfer cell products and components through the bloodstream. In this context, non-coding RNAs (ncRNAs), including miRNAs, long ncRNAs (lncRNAs), and circular RNAs (circRNAs), are a chief group of exosomal constituents with amazing abilities to regulate the underlying pathogenic mechanisms of BC, such as cell proliferation, angiogenesis, invasion, metastasis, migration, and particularly drug resistance. Thereby, exosomal ncRNAs can be considered potential mediators of BC progression and drug resistance. Moreover, as the corresponding exosomal ncRNAs circulate in the bloodstream and are found in different body fluids, they can serve as foremost prognostic/diagnostic biomarkers. The current study aims to comprehensively review the most recent findings on BC-related molecular mechanisms and signaling pathways affected by exosomal miRNAs, lncRNAs, and circRNAs, with a focus on drug resistance. Also, the potential of the same exosomal ncRNAs in the diagnosis and prognosis of BC will be discussed in detail.
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Affiliation(s)
- Malihe Rezaee
- Department of Pharmacology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Tehran Heart Center, Cardiovascular Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Mohammadi
- Afzalipour Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | | | - Sheida Yahyazadeh
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Omid Vakili
- Autophagy Research Center, Department of Clinical Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Yaser Eshaghi Milasi
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Vida Veisi
- School of Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Rohollah Mousavi Dehmordi
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
- Department of Clinical Biochemistry, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Sepideh Asadi
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Seyedeh Sara Ghorbanhosseini
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mehdi Rostami
- Department of Clinical Biochemistry, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mina Alimohammadi
- Student Research Committee, Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- *Correspondence: Mina Alimohammadi, ; Abbas Azadi, ; Hamed Mirzaei, ; Alireza Mafi,
| | - Abbas Azadi
- Department of Internal Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
- *Correspondence: Mina Alimohammadi, ; Abbas Azadi, ; Hamed Mirzaei, ; Alireza Mafi,
| | - Nushin Moussavi
- Department of Surgery, Kashan University of Medical Sciences, Kashan, Iran
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran
| | - Azadeh Aminianfar
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran
- *Correspondence: Mina Alimohammadi, ; Abbas Azadi, ; Hamed Mirzaei, ; Alireza Mafi,
| | - Alireza Mafi
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
- Nutrition and Food Security Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
- *Correspondence: Mina Alimohammadi, ; Abbas Azadi, ; Hamed Mirzaei, ; Alireza Mafi,
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20
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Liu M, Chen MY, Huang JM, Liu Q, Wang L, Liu R, Yang N, Huang WH, Zhang W. LncRNA weighted gene co-expression network analysis reveals novel biomarkers related to prostate cancer metastasis. BMC Med Genomics 2022; 15:256. [PMID: 36514044 PMCID: PMC9745985 DOI: 10.1186/s12920-022-01410-w] [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: 06/26/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Most prostate cancer patients die from metastasis and lack accurate efficacious biomarkers to monitor the disease behavior, optimize treatment and assess prognosis. Herein, we aimed to identify meaningful lncRNA biomarkers associated with prostate cancer metastatic progression. METHODS By repurposing microarray probes, 11,624 lncRNAs in prostate cancer were obtained from Gene Expression Omnibus database (GSE46691, N = 545; GSE29079, N = 235; GSE94767, N = 130). Weighted gene co-expression network analysis was applied to determine the co-expression lncRNA network pertinent to metastasis. Hub lncRNAs were screened. RNA-seq and clinical data from the Cancer Genome Atlas prostate cancer (TCGA-PRAD) cohort (N = 531) were analyzed. Transwell assay and bioinformatic analysis were performed for mechanism research. RESULTS The high expression levels of nine hub lncRNAs (FTX, AC005261.1, NORAD, LINC01578, AC004542.2, ZFAS1, EBLN3P, THUMPD3-AS1, GAS5) were significantly associated with Gleason score and increased probability of metastatic progression. Among these lncRNAs, ZFAS1 had the consistent trends of expression in all of the analysis from different cohorts, and the Kaplan-Meier survival analyses showed higher expression of ZFAS1 was associated with shorter relapse free survival. In-vitro studies confirmed that downregulation of ZFAS1 decreased prostate cancer cell migration. CONCLUSION We offered some new insights into discovering lncRNA markers correlated with metastatic progression of prostate cancer using the WGCNA. Some may serve as potential prognostic biomarkers and therapeutic targets for advanced metastatic prostate cancer.
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Affiliation(s)
- Miao Liu
- grid.216417.70000 0001 0379 7164Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, 410008 Changsha, People’s Republic of China ,grid.216417.70000 0001 0379 7164Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, 110 Xiangya Road, 410078 Changsha, People’s Republic of China ,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Hunan 410008 Changsha, People’s Republic of China
| | - Man-Yun Chen
- grid.216417.70000 0001 0379 7164Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, 410008 Changsha, People’s Republic of China ,grid.216417.70000 0001 0379 7164Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, 110 Xiangya Road, 410078 Changsha, People’s Republic of China ,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Hunan 410008 Changsha, People’s Republic of China
| | - Jia-Meng Huang
- grid.216417.70000 0001 0379 7164Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, 410008 Changsha, People’s Republic of China ,grid.216417.70000 0001 0379 7164Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, 110 Xiangya Road, 410078 Changsha, People’s Republic of China ,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Hunan 410008 Changsha, People’s Republic of China
| | - Qian Liu
- grid.216417.70000 0001 0379 7164Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, 410008 Changsha, People’s Republic of China ,grid.216417.70000 0001 0379 7164Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, 110 Xiangya Road, 410078 Changsha, People’s Republic of China ,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Hunan 410008 Changsha, People’s Republic of China
| | - Lin Wang
- grid.216417.70000 0001 0379 7164Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, 410008 Changsha, People’s Republic of China ,grid.216417.70000 0001 0379 7164Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, 110 Xiangya Road, 410078 Changsha, People’s Republic of China ,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Hunan 410008 Changsha, People’s Republic of China
| | - Rong Liu
- grid.216417.70000 0001 0379 7164Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, 410008 Changsha, People’s Republic of China ,grid.216417.70000 0001 0379 7164Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, 110 Xiangya Road, 410078 Changsha, People’s Republic of China ,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Hunan 410008 Changsha, People’s Republic of China
| | - Nian Yang
- grid.216417.70000 0001 0379 7164Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, 410008 Changsha, People’s Republic of China ,grid.216417.70000 0001 0379 7164Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, 110 Xiangya Road, 410078 Changsha, People’s Republic of China ,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Hunan 410008 Changsha, People’s Republic of China
| | - Wei-Hua Huang
- grid.216417.70000 0001 0379 7164Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, 410008 Changsha, People’s Republic of China ,grid.216417.70000 0001 0379 7164Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, 110 Xiangya Road, 410078 Changsha, People’s Republic of China ,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Hunan 410008 Changsha, People’s Republic of China
| | - Wei Zhang
- grid.216417.70000 0001 0379 7164Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, 410008 Changsha, People’s Republic of China ,grid.216417.70000 0001 0379 7164Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, 110 Xiangya Road, 410078 Changsha, People’s Republic of China ,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Hunan 410008 Changsha, People’s Republic of China
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21
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Eickelschulte S, Riediger AL, Angeles AK, Janke F, Duensing S, Sültmann H, Görtz M. Biomarkers for the Detection and Risk Stratification of Aggressive Prostate Cancer. Cancers (Basel) 2022; 14:cancers14246094. [PMID: 36551580 PMCID: PMC9777028 DOI: 10.3390/cancers14246094] [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: 11/17/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Current strategies for the clinical management of prostate cancer are inadequate for a precise risk stratification between indolent and aggressive tumors. Recently developed tissue-based molecular biomarkers have refined the risk assessment of the disease. The characterization of tissue biopsy components and subsequent identification of relevant tissue-based molecular alterations have the potential to improve the clinical decision making and patient outcomes. However, tissue biopsies are invasive and spatially restricted due to tumor heterogeneity. Therefore, there is an urgent need for complementary diagnostic and prognostic options. Liquid biopsy approaches are minimally invasive with potential utility for the early detection, risk stratification, and monitoring of tumors. In this review, we focus on tissue and liquid biopsy biomarkers for early diagnosis and risk stratification of prostate cancer, including modifications on the genomic, epigenomic, transcriptomic, and proteomic levels. High-risk molecular alterations combined with orthogonal clinical parameters can improve the identification of aggressive tumors and increase patient survival.
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Affiliation(s)
- Samaneh Eickelschulte
- Junior Clinical Cooperation Unit, Multiparametric Methods for Early Detection of Prostate Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Urology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Anja Lisa Riediger
- Junior Clinical Cooperation Unit, Multiparametric Methods for Early Detection of Prostate Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Urology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Arlou Kristina Angeles
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Florian Janke
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Stefan Duensing
- Molecular Urooncology, Department of Urology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Holger Sültmann
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Magdalena Görtz
- Junior Clinical Cooperation Unit, Multiparametric Methods for Early Detection of Prostate Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Urology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Correspondence: ; Tel.: +49-6221-42-2603
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22
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Wong HY, Sheng Q, Hesterberg AB, Croessmann S, Rios BL, Giri K, Jackson J, Miranda AX, Watkins E, Schaffer KR, Donahue M, Winkler E, Penson DF, Smith JA, Herrell SD, Luckenbaugh AN, Barocas DA, Kim YJ, Graves D, Giannico GA, Rathmell JC, Park BH, Gordetsky JB, Hurley PJ. Single cell analysis of cribriform prostate cancer reveals cell intrinsic and tumor microenvironmental pathways of aggressive disease. Nat Commun 2022; 13:6036. [PMID: 36229464 PMCID: PMC9562361 DOI: 10.1038/s41467-022-33780-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 10/03/2022] [Indexed: 12/03/2022] Open
Abstract
Cribriform prostate cancer, found in both invasive cribriform carcinoma (ICC) and intraductal carcinoma (IDC), is an aggressive histological subtype that is associated with progression to lethal disease. To delineate the molecular and cellular underpinnings of ICC/IDC aggressiveness, this study examines paired ICC/IDC and benign prostate surgical samples by single-cell RNA-sequencing, TCR sequencing, and histology. ICC/IDC cancer cells express genes associated with metastasis and targets with potential for therapeutic intervention. Pathway analyses and ligand/receptor status model cellular interactions among ICC/IDC and the tumor microenvironment (TME) including JAG1/NOTCH. The ICC/IDC TME is hallmarked by increased angiogenesis and immunosuppressive fibroblasts (CTHRC1+ASPN+FAP+ENG+) along with fewer T cells, elevated T cell dysfunction, and increased C1QB+TREM2+APOE+-M2 macrophages. These findings support that cancer cell intrinsic pathways and a complex immunosuppressive TME contribute to the aggressive phenotype of ICC/IDC. These data highlight potential therapeutic opportunities to restore immune signaling in patients with ICC/IDC that may afford better outcomes.
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Affiliation(s)
- Hong Yuen Wong
- grid.412807.80000 0004 1936 9916Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA
| | - Quanhu Sheng
- grid.412807.80000 0004 1936 9916Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN USA
| | - Amanda B. Hesterberg
- grid.412807.80000 0004 1936 9916Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA
| | - Sarah Croessmann
- grid.412807.80000 0004 1936 9916Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA
| | - Brenda L. Rios
- grid.412807.80000 0004 1936 9916Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA
| | - Khem Giri
- grid.412807.80000 0004 1936 9916Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA
| | - Jorgen Jackson
- grid.412807.80000 0004 1936 9916Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA
| | - Adam X. Miranda
- grid.412807.80000 0004 1936 9916Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA
| | - Evan Watkins
- grid.412807.80000 0004 1936 9916Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA
| | - Kerry R. Schaffer
- grid.412807.80000 0004 1936 9916Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Vanderbilt-Ingram Cancer Center, Nashville, TN USA
| | - Meredith Donahue
- grid.412807.80000 0004 1936 9916Department of Urology, Vanderbilt University Medical Center, Nashville, TN USA
| | - Elizabeth Winkler
- grid.412807.80000 0004 1936 9916Department of Urology, Vanderbilt University Medical Center, Nashville, TN USA
| | - David F. Penson
- grid.412807.80000 0004 1936 9916Vanderbilt-Ingram Cancer Center, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Department of Urology, Vanderbilt University Medical Center, Nashville, TN USA
| | - Joseph A. Smith
- grid.412807.80000 0004 1936 9916Department of Urology, Vanderbilt University Medical Center, Nashville, TN USA
| | - S. Duke Herrell
- grid.412807.80000 0004 1936 9916Department of Urology, Vanderbilt University Medical Center, Nashville, TN USA
| | - Amy N. Luckenbaugh
- grid.412807.80000 0004 1936 9916Department of Urology, Vanderbilt University Medical Center, Nashville, TN USA
| | - Daniel A. Barocas
- grid.412807.80000 0004 1936 9916Department of Urology, Vanderbilt University Medical Center, Nashville, TN USA
| | - Young J. Kim
- grid.412807.80000 0004 1936 9916Vanderbilt-Ingram Cancer Center, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Department of Otolaryngology-Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, TN USA ,grid.418961.30000 0004 0472 2713Regeneron Pharmaceuticals, Tarrytown, New York, USA
| | - Diana Graves
- grid.412807.80000 0004 1936 9916Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN USA
| | - Giovanna A. Giannico
- grid.412807.80000 0004 1936 9916Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN USA
| | - Jeffrey C. Rathmell
- grid.412807.80000 0004 1936 9916Vanderbilt-Ingram Cancer Center, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN USA ,Vanderbilt Center for Immunobiology, Nashville, TN USA
| | - Ben H. Park
- grid.412807.80000 0004 1936 9916Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Vanderbilt-Ingram Cancer Center, Nashville, TN USA
| | - Jennifer B. Gordetsky
- grid.412807.80000 0004 1936 9916Vanderbilt-Ingram Cancer Center, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN USA
| | - Paula J. Hurley
- grid.412807.80000 0004 1936 9916Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Vanderbilt-Ingram Cancer Center, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Department of Urology, Vanderbilt University Medical Center, Nashville, TN USA
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23
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Guo S, Chen J, Yi X, Lu Z, Guo W. Identification and validation of ferroptosis-related lncRNA signature as a prognostic model for skin cutaneous melanoma. Front Immunol 2022; 13:985051. [PMID: 36248853 PMCID: PMC9556814 DOI: 10.3389/fimmu.2022.985051] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 09/07/2022] [Indexed: 11/15/2022] Open
Abstract
Background Melanoma is a type of skin cancer, which originates from the malignant transformation of epidermal melanocytes, with extremely high lethality. Ferroptosis has been documented to be highly related to cancer pathogenesis and the effect of immunotherapy. In addition, the dysregulation of lncRNAs is greatly implicated in melanoma progression and ferroptosis regulation. However, the significance of ferroptosis-related lncRNA in melanoma treatment and the prognosis of melanoma patients remains elusive. Methods Via Least Absolute Shrinkage Selection Operator (LASSO) regression analysis in the TCGA SKCM database, a cutaneous melanoma risk model was established based on differentially-expressed ferroptosis-related lncRNAs (DEfrlncRNAs). The nomogram, receiver operating characteristic (ROC) curves, and calibration plots were conducted to examine the predictive performance of this model. Sequentially, we continued to analyze the differences between the high- and low-risk groups, in terms of clinical characteristics, immune cell infiltration, immune-related functions, and chemotherapy drug sensitivity. Moreover, the expressions of DEfrlncRNAs, PD-L1, and CD8 were also examined by qRT-PCR and immunohistochemical staining in melanoma tissues to further confirm the potential clinical implication of DEfrlncRNAs in melanoma immunotherapy. Results 16 DEfrlncRNAs were identified, and a representative risk score for patient survival was constructed based on these 16 genes. The risk score was found to be an independent prognostic factor for the survival of melanoma patients. In addition, the low-risk group of patients had higher immune cell infiltration in the melanoma lesions, higher sensitivity to chemotherapeutic agents, and a better survival prognosis. Besides, the high expression of the identified 5 DEfrlncRNA in the low-risk group might suggest a higher possibility to benefit from immune checkpoint blockade therapy in the treatment of melanoma. Conclusion The DEfrlncRNA risk prediction model related to ferroptosis genes can independently predict the prognosis of patients with melanoma and provide a basis for evaluating the response of clinical treatment in melanoma.
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Affiliation(s)
- Sen Guo
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Jianru Chen
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Xiuli Yi
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Zifan Lu
- Department of Biopharmaceuticals, School of Pharmacy, Fourth Military Medical University, Xi’an, China
- *Correspondence: Weinan Guo, ; Zifan Lu,
| | - Weinan Guo
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi’an, China
- *Correspondence: Weinan Guo, ; Zifan Lu,
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24
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Diao X, Guo C, Li S. Construction of a Novel Prognostic Signature in Lung Adenocarcinoma Based on Necroptosis-Related lncRNAs. Front Genet 2022; 13:833362. [PMID: 35938013 PMCID: PMC9354127 DOI: 10.3389/fgene.2022.833362] [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: 12/11/2021] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Long non-coding RNAs (lncRNAs) are drawing increasing attention as promising predictors of prognosis for lung adenocarcinoma (LUAD) patients. Necroptosis, a novel regulated mechanism of necrotic cell death, plays an important role in the biological process of cancer. The aim of this study was to identify the necroptosis-related lncRNAs (NRLRs) in a LUAD cohort and establish a necroptosis-related lncRNA signature (NRLSig) to stratify LUAD patients.Methods: NRLRs were identified in LUAD patients from The Cancer Genome Atlas (TCGA) database using Pearson correlation analysis between necroptosis-related genes and lncRNAs. Then the NRLSig was identified using univariate Cox regression analysis and LASSO regression analysis. Assessments of the signature were performed based on survival analysis, receiver operating characteristic (ROC) curve analysis and clustering analysis. Next, a nomogram containing the NRLSig and clinical information was developed through univariate and multivariate Cox regression analysis. Further, functional enrichment analysis of the selected lncRNAs in NRLSig and the association between NRLSig and the immune infiltration were also evaluated.Results: A 4-lncRNA signature, incorporating LINC00941, AP001453.2, AC026368.1, and AC236972.3, was identified to predict overall survival (OS) and stratify LUAD patients into different groups. Survival analysis, ROC curve analysis and clustering analysis showed good performance in the prognostic prediction of the lncRNA signature. Then, a nomogram containing the NRLSig was developed and showed satisfactory predictive accuracy, calibration and clinical usefulness. The co-expressed genes of selected NRLRs were enriched in several biological functions and signaling pathways. Finally, differences in the abundance of immune cells were investigated among the high-risk group and low-risk group divided by the NRLSig.Conclusion: The proposed NRLSig may provide promising therapeutic targets or prognostic predictors for LUAD patients.
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Zhang M, Zheng S, Liang JQ. Transcriptional and reverse transcriptional regulation of host genes by human endogenous retroviruses in cancers. Front Microbiol 2022; 13:946296. [PMID: 35928153 PMCID: PMC9343867 DOI: 10.3389/fmicb.2022.946296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/29/2022] [Indexed: 11/16/2022] Open
Abstract
Human endogenous retroviruses (HERVs) originated from ancient retroviral infections of germline cells millions of years ago and have evolved as part of the host genome. HERVs not only retain the capacity as retroelements but also regulate host genes. The expansion of HERVs involves transcription by RNA polymerase II, reverse transcription, and re-integration into the host genome. Fast progress in deep sequencing and functional analysis has revealed the importance of domesticated copies of HERVs, including their regulatory sequences, transcripts, and proteins in normal cells. However, evidence also suggests the involvement of HERVs in the development and progression of many types of cancer. Here we summarize the current state of knowledge about the expression of HERVs, transcriptional regulation of host genes by HERVs, and the functions of HERVs in reverse transcription and gene editing with their reverse transcriptase.
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Affiliation(s)
- Mengwen Zhang
- The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
- Ministry of Education Key Laboratory of Cancer Prevention and Intervention, Second Affiliated Hospital, Cancer Institute, Zhejiang University School of Medicine, Hangzhou, China
| | - Shu Zheng
- The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
- Ministry of Education Key Laboratory of Cancer Prevention and Intervention, Second Affiliated Hospital, Cancer Institute, Zhejiang University School of Medicine, Hangzhou, China
- *Correspondence: Shu Zheng,
| | - Jessie Qiaoyi Liang
- Department of Medicine and Therapeutics, Faculty of Medicine, Center for Gut Microbiota Research, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Jessie Qiaoyi Liang,
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CircSCAF8 promotes growth and metastasis of prostate cancer through the circSCAF8-miR-140-3p/miR-335-LIF pathway. Cell Death Dis 2022; 13:517. [PMID: 35654787 PMCID: PMC9163066 DOI: 10.1038/s41419-022-04913-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 04/23/2022] [Accepted: 05/04/2022] [Indexed: 02/07/2023]
Abstract
Circular RNAs (circRNAs) have been increasingly linked to cancer progression. However, the detailed biological functions of circRNAs in prostate cancer (PCa) remain unclear. Using high-throughput circRNA sequencing, we previously identified 18 urine extracellular vesicle circRNAs that were increased in patients with PCa compared with those with benign prostatic hyperplasia. Spearman correlation analysis of the expression levels of the 18 circRNAs between the tumor tissue and matched urine extracellular vesicles in 30 PCa patients showed that circSCAF8 had the highest R2 (R2 = 0.635, P < 0.001). The Cox proportional hazards regression model was used to estimate the effect of circSCAF8 on progression-free survival. The in vitro and in vivo functional experiments were implemented to investigate the effects of circSCAF8 on the phenotype of PCa. We found that the knockdown of circSCAF8 in PCa cells suppressed the proliferation, migration, and invasion ability, while overexpression of circSCAF8 had the opposite effects. Similar results were observed in vivo. In a cohort of 85 patients who had undergone radical prostatectomy, circSCAF8 expression in PCa tissues was a powerful predictor of progression-free survival (HR = 2.14, P = 0.022). Mechanistically, circSCAF8 can function by binding to both miR-140-3p and miR-335 to regulate LIF expression and activate the LIF-STAT3 pathway that leads to the growth and metastasis of PCa. Collectively, our findings demonstrate that circSCAF8 contributes to PCa progression through the circSCAF8-miR-140-3p/miR-335-LIF pathway.
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A lncRNA signature associated with tumor immune heterogeneity predicts distant metastasis in locoregionally advanced nasopharyngeal carcinoma. Nat Commun 2022; 13:2996. [PMID: 35637194 PMCID: PMC9151760 DOI: 10.1038/s41467-022-30709-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 05/12/2022] [Indexed: 12/24/2022] Open
Abstract
Increasing evidence has revealed the roles of long noncoding RNAs (lncRNAs) as tumor biomarkers. Here, we introduce an immune-associated nine-lncRNA signature for predicting distant metastasis in locoregionally advanced nasopharyngeal carcinoma (LA-NPC). The nine lncRNAs are identified through microarray profiling, followed by RT–qPCR validation and selection using a machine learning method in the training cohort (n = 177). This nine-lncRNA signature classifies patients into high and low risk groups, which have significantly different distant metastasis-free survival. Validations in the Guangzhou internal (n = 177) and Guilin external (n = 150) cohorts yield similar results, confirming that the signature is an independent risk factor for distant metastasis and outperforms anatomy-based metrics in identifying patients with high metastatic risk. Integrative analyses show that this nine-lncRNA signature correlates with immune activity and lymphocyte infiltration, which is validated by digital pathology. Our results suggest that the immune-associated nine-lncRNA signature can serve as a promising biomarker for metastasis prediction in LA-NPC. Long noncoding RNAs (lncRNAs) can be used for the development of prognostic signatures to predict tumour metastasis. Here the authors identify an immune-associated nine-lncRNA signature for predicting metastasis in a multicentre cohort of locoregionally advanced nasopharyngeal cancer patients.
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28
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The promising role of new molecular biomarkers in prostate cancer: from coding and non-coding genes to artificial intelligence approaches. Prostate Cancer Prostatic Dis 2022; 25:431-443. [PMID: 35422101 PMCID: PMC9385485 DOI: 10.1038/s41391-022-00537-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/24/2022] [Accepted: 03/30/2022] [Indexed: 12/15/2022]
Abstract
Background Risk stratification or progression in prostate cancer is performed with the support of clinical-pathological data such as the sum of the Gleason score and serum levels PSA. For several decades, methods aimed at the early detection of prostate cancer have included the determination of PSA serum levels. The aim of this systematic review is to provide an overview about recent advances in the discovery of new molecular biomarkers through transcriptomics, genomics and artificial intelligence that are expected to improve clinical management of the prostate cancer patient. Methods An exhaustive search was conducted by Pubmed, Google Scholar and Connected Papers using keywords relating to the genetics, genomics and artificial intelligence in prostate cancer, it includes “biomarkers”, “non-coding RNAs”, “lncRNAs”, “microRNAs”, “repetitive sequence”, “prognosis”, “prediction”, “whole-genome sequencing”, “RNA-Seq”, “transcriptome”, “machine learning”, and “deep learning”. Results New advances, including the search for changes in novel biomarkers such as mRNAs, microRNAs, lncRNAs, and repetitive sequences, are expected to contribute to an earlier and accurate diagnosis for each patient in the context of precision medicine, thus improving the prognosis and quality of life of patients. We analyze several aspects that are relevant for prostate cancer including its new molecular markers associated with diagnosis, prognosis, and prediction to therapy and how bioinformatic approaches such as machine learning and deep learning can contribute to clinic. Furthermore, we also include current techniques that will allow an earlier diagnosis, such as Spatial Transcriptomics, Exome Sequencing, and Whole-Genome Sequencing. Conclusion Transcriptomic and genomic analysis have contributed to generate knowledge in the field of prostate carcinogenesis, new information about coding and non-coding genes as biomarkers has emerged. Synergies created by the implementation of artificial intelligence to analyze and understand sequencing data have allowed the development of clinical strategies that facilitate decision-making and improve personalized management in prostate cancer.
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29
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Li Y, Pan B, Guo X, Meng X, Tian X. Prognostic Value of Long Noncoding RNA SNHG11 in Patients with Prostate Cancer. Horm Metab Res 2022; 54:187-193. [PMID: 35276744 DOI: 10.1055/a-1745-8952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The present study was aimed to explore the prognostic value of long noncoding RNA SNHG11 in prostate cancer, study its expression, and assess its effect on tumor progression. One hundred and twenty prostate cancer patients and 45 cases of benign prostate hyperplasia (BPH) patients were collected. RT-qPCR was used to test the expression of SNHG11 in prostate cancer and BPH tissues, as well as in cell lines. Kaplan-Meier survival analysis and Cox regression assays were introduced to evaluate the prognostic meaning of SNHG11 in prostate cancer. The CCK-8 assays were performed to explore the effect of SNHG11 on prostate cancer cell proliferation, and a Transwell assay was conducted to access the influence of SNHG11 on prostate cancer cell migration and invasion. SNHG11 expression level was upregulated both in prostate cancer tissues and cell lines. Overexpression of SNHG11 was significantly associated with Gleason score, clinical T stage, surgical margin status, and lymph node metastasis. Patients with high SNHG11 expression levels led to a shorter overall survival time and biochemical recurrence-free survival when compared with those of low expression levels. Multivariate Cox regression results suggested that SNHG11 has the potential to act as a prognostic marker for prostate cancer patients. Knockdown of SNHG11 suppressed 22RV1 cell proliferation, migration, and invasion. In conclusion, SNHG11 is upregulated in prostate cancer patients and predicts an unfavorable prognosis for prostate cancer patients. Its knockdown can weaken prostate cancer cell metastasis and growth in vitro.
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Affiliation(s)
- Ying Li
- Department of Urology Surgery, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Bin Pan
- Department of Urology Surgery, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Xiuqin Guo
- Department of Supply Room, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Xiaomin Meng
- Department of Urology Surgery, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Xiaojing Tian
- Department of Thoracic Surgery, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
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Zhu YS, Zhu J. Molecular and cellular functions of long non-coding RNAs in prostate and breast cancer. Adv Clin Chem 2022; 106:91-179. [PMID: 35152976 DOI: 10.1016/bs.acc.2021.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Long noncoding RNAs (lncRNAs) are defined as noncoding RNA transcripts with a length greater than 200 nucleotides. Research over the last decade has made great strides in our understanding of lncRNAs, especially in the biology of their role in cancer. In this article, we will briefly discuss the biogenesis and characteristics of lncRNAs, then review their molecular and cellular functions in cancer by using prostate and breast cancer as examples. LncRNAs are abundant, diverse, and evolutionarily, less conserved than protein-coding genes. They are often expressed in a tumor and cell-specific manner. As a key epigenetic factor, lncRNAs can use a wide variety of molecular mechanisms to regulate gene expression at each step of the genetic information flow pathway. LncRNAs display widespread effects on cell behavior, tumor growth, and metastasis. They act intracellularly and extracellularly in an autocrine, paracrine and endocrine fashion. Increased understanding of lncRNA's role in cancer has facilitated the development of novel biomarkers for cancer diagnosis, led to greater understanding of cancer prognosis, enabled better prediction of therapeutic responses, and promoted identification of potential targets for cancer therapy.
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Affiliation(s)
- Yuan-Shan Zhu
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Clinical and Translational Science Center, Weill Cornell Medicine, New York, NY, United States.
| | - Jifeng Zhu
- Clinical and Translational Science Center, Weill Cornell Medicine, New York, NY, United States
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31
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Pradhan RK, Ramakrishna W. Transposons: Unexpected players in cancer. Gene 2022; 808:145975. [PMID: 34592349 DOI: 10.1016/j.gene.2021.145975] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/19/2021] [Accepted: 09/24/2021] [Indexed: 12/21/2022]
Abstract
Transposons are repetitive DNA sequences encompassing about half of the human genome. They play a vital role in genome stability maintenance and contribute to genomic diversity and evolution. Their activity is regulated by various mechanisms considering the deleterious effects of these mobile elements. Various genetic risk factors and environmental stress conditions affect the regulatory pathways causing alteration of transposon expression. Our knowledge of the biological role of transposons is limited especially in various types of cancers. Retrotransposons of different types (LTR-retrotransposons, LINEs and SINEs) regulate a plethora of genes that have a role in cell reprogramming, tumor suppression, cell cycle, apoptosis, cell adhesion and migration, and DNA repair. The regulatory mechanisms of transposons, their deregulation and different mechanisms underlying transposon-mediated carcinogenesis in humans focusing on the three most prevalent types, lung, breast and colorectal cancers, were reviewed. The modes of regulation employed include alternative splicing, deletion, insertion, duplication in genes and promoters resulting in upregulation, downregulation or silencing of genes.
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32
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Hickman AR, Hang Y, Pauly R, Feltus FA. Identification of condition-specific biomarker systems in uterine cancer. G3 GENES|GENOMES|GENETICS 2022; 12:6427626. [PMID: 34791179 PMCID: PMC8727964 DOI: 10.1093/g3journal/jkab392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/30/2021] [Indexed: 11/23/2022]
Abstract
Uterine cancer is the fourth most common cancer among women, projected to affect 66,000 US women in 2021. Uterine cancer often arises in the inner lining of the uterus, known as the endometrium, but can present as several different types of cancer, including endometrioid cancer, serous adenocarcinoma, and uterine carcinosarcoma. Previous studies have analyzed the genetic changes between normal and cancerous uterine tissue to identify specific genes of interest, including TP53 and PTEN. Here we used Gaussian Mixture Models to build condition-specific gene coexpression networks for endometrial cancer, uterine carcinosarcoma, and normal uterine tissue. We then incorporated uterine regulatory edges and investigated potential coregulation relationships. These networks were further validated using differential expression analysis, functional enrichment, and a statistical analysis comparing the expression of transcription factors and their target genes across cancerous and normal uterine samples. These networks allow for a more comprehensive look into the biological networks and pathways affected in uterine cancer compared with previous singular gene analyses. We hope this study can be incorporated into existing knowledge surrounding the genetics of uterine cancer and soon become clinical biomarkers as a tool for better prognosis and treatment.
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Affiliation(s)
- Allison R Hickman
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Yuqing Hang
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Rini Pauly
- Biomedical Data Science and Informatics Program, Clemson University, Clemson, SC 29634, USA
| | - Frank A Feltus
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
- Biomedical Data Science and Informatics Program, Clemson University, Clemson, SC 29634, USA
- College of Science, Center for Human Genetics, Clemson University, Clemson, SC 29634, USA
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33
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Mugoni V, Ciani Y, Nardella C, Demichelis F. Circulating RNAs in prostate cancer patients. Cancer Lett 2022; 524:57-69. [PMID: 34656688 DOI: 10.1016/j.canlet.2021.10.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 10/06/2021] [Accepted: 10/09/2021] [Indexed: 12/12/2022]
Abstract
Growing bodies of evidence have demonstrated that the identification of prostate cancer (PCa) biomarkers in the patients' blood and urine may remarkably improve PCa diagnosis and progression monitoring. Among diverse cancer-derived circulating materials, extracellular RNA molecules (exRNAs) represent a compelling component to investigate cancer-related alterations. Once outside the intracellular environment, exRNAs circulate in biofluids either in association with protein complexes or encapsulated inside extracellular vesicles (EVs). Notably, EV-associated RNAs (EV-RNAs) were used for the development of several assays (such as the FDA-approved Progensa Prostate Cancer Antigen 3 (PCA3 test) aiming at improving early PCa detection. EV-RNAs encompass a mixture of species, including small non-coding RNAs (e.g. miRNA and circRNA), lncRNAs and mRNAs. Several methods have been proposed to isolate EVs and relevant RNAs, and to perform RNA-Seq studies to identify potential cancer biomarkers. However, EVs in the circulation of a cancer patient include a multitude of diverse populations that are released by both cancer and normal cells from different tissues, thereby leading to a heterogeneous EV-RNA-associated transcriptional signal. Decrypting the complexity of such a composite signal is nowadays the major challenge faced in the identification of specific tumor-associated RNAs. Multiple deconvolution algorithms have been proposed so far to infer the enrichment of cancer-specific signals from gene expression data. However, novel strategies for EVs sorting and sequencing of RNA associated to single EVs populations will remarkably facilitate the identification of cancer-related molecules. Altogether, the studies summarized here demonstrate the high potential of using EV-RNA biomarkers in PCa and highlight the urgent need of improving technologies and computational approaches to characterize specific EVs populations and their relevant RNA cargo.
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Affiliation(s)
- Vera Mugoni
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Yari Ciani
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Caterina Nardella
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Francesca Demichelis
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy.
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Bae J, Yang SH, Kim A, Kim HG. RNA-based biomarkers for the diagnosis, prognosis, and therapeutic response monitoring of prostate cancer. Urol Oncol 2021; 40:105.e1-105.e10. [PMID: 34952790 DOI: 10.1016/j.urolonc.2021.11.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/22/2021] [Accepted: 11/11/2021] [Indexed: 10/19/2022]
Abstract
Prostate cancer (CaP) is the most common malignant neoplasm of the urinary tract. The current recommendations for CaP diagnosis rely on the prostate-specific antigen levels and a digital rectal examination for anatomical abnormalities. However, these diagnostic tools are not highly sensitive. In particular, prostate-specific antigen has a low positive predictive value (approximately 30%). Thus, there is a need to develop biomarkers to improve the early clinical detection of CaP. Several novel technologies enable the identification of biomarkers from diverse sources, including the urine, serum, and prostate tissues. Furthermore, advances in genomic techniques have enabled the analysis of novel biomarkers, such as deoxyribonucleic acids (DNAs), ribonucleic acids (RNAs), proteins, and circulating tumor cells. Previous studies have demonstrated that RNAs are potential diagnostic biomarkers for various cancers using high-throughput sequencing analysis. The sensitivity and specificity of RNA biomarkers are higher than those of protein biomarkers. Polymerase chain reaction enables the amplification of trace levels of RNAs with high sensitivity and specificity. RNA biomarkers provide dynamic insights into cellular states and regulatory processes when compared with DNA biomarkers. Additionally, multiple copies of various RNAs in a cell provide more information than DNA. The levels of specific RNAs in CaP tissues are upregulated when compared with those in non-cancerous tissues. Additionally, RNAs can be easily isolated from various body fluids. Thus, RNAs are potential non-invasive biomarkers for CaP. Moreover, the analysis of RNA levels adjusted for each stage of CaP enables the determination of prognostic individualized therapy for aggressive or progressive CaP. This review focused on the diagnostic and prognostic values of RNAs for CaP.
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Affiliation(s)
- Juhyeon Bae
- Department of Medical Biotechnology, College of Life Science and Biotechnology, Dongguk University, Seoul, Republic of Korea
| | - Seung-Hoon Yang
- Department of Medical Biotechnology, College of Life Science and Biotechnology, Dongguk University, Seoul, Republic of Korea
| | - Aram Kim
- Department of Urology, KonKuk University Medical Center, KonKuk University School of Medicine, Seoul, Republic of Korea
| | - Hyeong Gon Kim
- Department of Urology, KonKuk University Medical Center, KonKuk University School of Medicine, Seoul, Republic of Korea.
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35
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Eksi SE, Chitsazan A, Sayar Z, Thomas GV, Fields AJ, Kopp RP, Spellman PT, Adey AC. Epigenetic loss of heterogeneity from low to high grade localized prostate tumours. Nat Commun 2021; 12:7292. [PMID: 34911933 PMCID: PMC8674326 DOI: 10.1038/s41467-021-27615-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 11/30/2021] [Indexed: 12/13/2022] Open
Abstract
Identifying precise molecular subtypes attributable to specific stages of localized prostate cancer has proven difficult due to high levels of heterogeneity. Bulk assays represent a population-average, which mask the heterogeneity that exists at the single-cell level. In this work, we sequence the accessible chromatin regions of 14,424 single-cells from 18 flash-frozen prostate tumours. We observe shared chromatin features among low-grade prostate cancer cells are lost in high-grade tumours. Despite this loss, high-grade tumours exhibit an enrichment for FOXA1, HOXB13 and CDX2 transcription factor binding sites, indicating a shared trans-regulatory programme. We identify two unique genes encoding neuronal adhesion molecules that are highly accessible in high-grade prostate tumours. We show NRXN1 and NLGN1 expression in epithelial, endothelial, immune and neuronal cells in prostate cancer using cyclic immunofluorescence. Our results provide a deeper understanding of the active gene regulatory networks in primary prostate tumours, critical for molecular stratification of the disease.
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Affiliation(s)
- Sebnem Ece Eksi
- Cancer Early Detection Advanced Research (CEDAR), Knight Cancer Institute, OHSU, Portland, OR, 97239, USA.
- Department of Biomedical Engineering, School of Medicine, OHSU, Portland, OR, 97209, USA.
| | - Alex Chitsazan
- Cancer Early Detection Advanced Research (CEDAR), Knight Cancer Institute, OHSU, Portland, OR, 97239, USA
| | - Zeynep Sayar
- Cancer Early Detection Advanced Research (CEDAR), Knight Cancer Institute, OHSU, Portland, OR, 97239, USA
- Department of Biomedical Engineering, School of Medicine, OHSU, Portland, OR, 97209, USA
| | - George V Thomas
- Cancer Early Detection Advanced Research (CEDAR), Knight Cancer Institute, OHSU, Portland, OR, 97239, USA
- Department of Pathology & Laboratory Medicine, School of Medicine, OHSU, Portland, OR, 97239, USA
| | - Andrew J Fields
- Department of Molecular and Medical Genetics, School of Medicine, OHSU, Portland, OR, 97239, USA
| | - Ryan P Kopp
- Department of Urology, School of Medicine, OHSU, Portland, OR, 97239, USA
| | - Paul T Spellman
- Cancer Early Detection Advanced Research (CEDAR), Knight Cancer Institute, OHSU, Portland, OR, 97239, USA
- Department of Molecular and Medical Genetics, School of Medicine, OHSU, Portland, OR, 97239, USA
| | - Andrew C Adey
- Cancer Early Detection Advanced Research (CEDAR), Knight Cancer Institute, OHSU, Portland, OR, 97239, USA.
- Department of Molecular and Medical Genetics, School of Medicine, OHSU, Portland, OR, 97239, USA.
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36
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Deng T, Xiao Y, Dai Y, Xie L, Li X. Roles of Key Epigenetic Regulators in the Gene Transcription and Progression of Prostate Cancer. Front Mol Biosci 2021; 8:743376. [PMID: 34977151 PMCID: PMC8714908 DOI: 10.3389/fmolb.2021.743376] [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: 07/18/2021] [Accepted: 11/25/2021] [Indexed: 12/24/2022] Open
Abstract
Prostate cancer (PCa) is a top-incidence malignancy, and the second most common cause of death amongst American men and the fifth leading cause of cancer death in men around the world. Androgen receptor (AR), the key transcription factor, is critical for the progression of PCa by regulating a series of target genes by androgen stimulation. A number of co-regulators of AR, including co-activators or co-repressors, have been implicated in AR-mediated gene transcription and PCa progression. Epigenetic regulators, by modifying chromatin integrity and accessibility for transcription regulation without altering DNA sequences, influence the transcriptional activity of AR and further regulate the gene expression of AR target genes in determining cell fate, PCa progression and therapeutic response. In this review, we summarized the structural interaction of AR and epigenetic regulators including histone or DNA methylation, histone acetylation or non-coding RNA, and functional synergy in PCa progression. Importantly, epigenetic regulators have been validated as diagnostic markers and therapeutic targets. A series of epigenetic target drugs have been developed, and have demonstrated the potential to treat PCa alone or in combination with antiandrogens.
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Affiliation(s)
- Tanggang Deng
- Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
- NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, Guangdong Pharmaceutical University, Guangzhou, China
| | - Yugang Xiao
- Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
- NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, Guangdong Pharmaceutical University, Guangzhou, China
- School of Clinical Pharmacy, Guangdong Pharmaceutical University, Guangzhou, China
| | - Yi Dai
- Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
- NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, Guangdong Pharmaceutical University, Guangzhou, China
- School of Clinical Pharmacy, Guangdong Pharmaceutical University, Guangzhou, China
| | - Lin Xie
- Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
- NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, Guangdong Pharmaceutical University, Guangzhou, China
| | - Xiong Li
- Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
- NMPA Key Laboratory for Technology Research and Evaluation of Pharmacovigilance, Guangdong Pharmaceutical University, Guangzhou, China
- School of Clinical Pharmacy, Guangdong Pharmaceutical University, Guangzhou, China
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37
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Park EG, Pyo SJ, Cui Y, Yoon SH, Nam JW. Tumor immune microenvironment lncRNAs. Brief Bioinform 2021; 23:6458113. [PMID: 34891154 PMCID: PMC8769899 DOI: 10.1093/bib/bbab504] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/15/2021] [Accepted: 11/02/2021] [Indexed: 01/17/2023] Open
Abstract
Long non-coding ribonucleic acids (RNAs) (lncRNAs) are key players in tumorigenesis and immune responses. The nature of their cell type-specific gene expression and other functional evidence support the idea that lncRNAs have distinct cellular functions in the tumor immune microenvironment (TIME). To date, the majority of lncRNA studies have heavily relied on bulk RNA-sequencing data in which various cell types contribute to an averaged signal, limiting the discovery of cell type-specific lncRNA functions. Single-cell RNA-sequencing (scRNA-seq) is a potential solution for tackling this limitation despite the lack of annotations for low abundance yet cell type-specific lncRNAs. Hence, updated annotations and further understanding of the cellular expression of lncRNAs will be necessary for characterizing cell type-specific functions of lncRNA genes in the TIME. In this review, we discuss lncRNAs that are specifically expressed in tumor and immune cells, summarize the regulatory functions of the lncRNAs at the cell type level and highlight how a scRNA-seq approach can help to study the cell type-specific functions of TIME lncRNAs.
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Affiliation(s)
- Eun-Gyeong Park
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Sung-Jin Pyo
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Youxi Cui
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Sang-Ho Yoon
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Jin-Wu Nam
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea.,Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 04763, Republic of Korea.,Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
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PCAT6 May Be a Whistler and Checkpoint Target for Precision Therapy in Human Cancers. Cancers (Basel) 2021; 13:cancers13236101. [PMID: 34885209 PMCID: PMC8656686 DOI: 10.3390/cancers13236101] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/21/2021] [Accepted: 11/29/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Prostate cancer-associated transcript 6 (PCAT6), as a newly discovered carcinogenic long non-coding RNA (lncRNA), is abnormally expressed in multiple diseases. With the accumulation of studies on PCAT6, we have a deeper understanding of its biological functions and mechanisms. Therefore, in this review, the various molecular mechanisms by which PCAT6 promotes multiple tumorigenesis and progression are summarized and discussed. Furthermore, its potential diagnostic, prognostic, and immunotherapeutic values are also clarified. Abstract LncRNAs are involved in the occurrence and progressions of multiple cancers. Emerging evidence has shown that PCAT6, a newly discovered carcinogenic lncRNA, is abnormally elevated in various human malignant tumors. Until now, PCAT6 has been found to sponge various miRNAs to activate the signaling pathways, which further affects tumor cell proliferation, migration, invasion, cycle, apoptosis, radioresistance, and chemoresistance. Moreover, PCAT6 has been shown to exert biological functions beyond ceRNAs. In this review, we summarize the biological characteristics of PCAT6 in a variety of human malignancies and describe the biological mechanisms by which PCAT6 can facilitate tumor progression. Finally, we discuss its diagnostic and prognostic values and clinical applications in various human malignancies.
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Morgan R, da Silveira WA, Kelly RC, Overton I, Allott EH, Hardiman G. Long non-coding RNAs and their potential impact on diagnosis, prognosis, and therapy in prostate cancer: racial, ethnic, and geographical considerations. Expert Rev Mol Diagn 2021; 21:1257-1271. [PMID: 34666586 DOI: 10.1080/14737159.2021.1996227] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
INTRODUCTION Advances in high-throughput sequencing have greatly advanced our understanding of long non-coding RNAs (lncRNAs) in a relatively short period of time. This has expanded our knowledge of cancer, particularly how lncRNAs drive many important cancer phenotypes via their regulation of gene expression. AREAS COVERED Men of African descent are disproportionately affected by PC in terms of incidence, morbidity, and mortality. LncRNAs could serve as biomarkers to differentiate low-risk from high-risk diseases. Additionally, they may represent therapeutic targets for advanced and castrate-resistant cancer. We review current research surrounding lncRNAs and their association with PC. We discuss how lncRNAs can provide new insights and diagnostic biomarkers for African American men. Finally, we review advances in computational approaches that predict the regulatory effects of lncRNAs in cancer. EXPERT OPINION PC diagnostic biomarkers that offer high specificity and sensitivity are urgently needed. PC specific lncRNAs are compelling as diagnostic biomarkers owing to their high tissue and tumor specificity and presence in bodily fluids. Recent studies indicate that PCA3 clinical utility might be restricted to men of European descent. Further work is required to develop lncRNA biomarkers tailored for men of African descent.
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Affiliation(s)
- Rebecca Morgan
- Faculty of Medicine, Health and Life Sciences, School of Biological Sciences, Queen's University Belfast, Belfast, UK.,Institute for Global Food Security (IGFS), Queen's University Belfast, Belfast, UK
| | - Willian Abraham da Silveira
- Faculty of Medicine, Health and Life Sciences, School of Biological Sciences, Queen's University Belfast, Belfast, UK.,Institute for Global Food Security (IGFS), Queen's University Belfast, Belfast, UK
| | - Ryan Christopher Kelly
- Faculty of Medicine, Health and Life Sciences, Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Ian Overton
- Faculty of Medicine, Health and Life Sciences, Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Emma H Allott
- Institute for Global Food Security (IGFS), Queen's University Belfast, Belfast, UK.,Faculty of Medicine, Health and Life Sciences, Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK.,Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
| | - Gary Hardiman
- Faculty of Medicine, Health and Life Sciences, School of Biological Sciences, Queen's University Belfast, Belfast, UK.,Institute for Global Food Security (IGFS), Queen's University Belfast, Belfast, UK.,Department of Medicine, Medical University of South Carolina (MUSC), Charleston, South Carolina
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Peng N, Zhang Z, Wang Y, Yang M, Fan J, Wang Q, Deng L, Chen D, Cai Y, Li Q, Wang X, Li W. Down-regulated LINC00115 inhibits prostate cancer cell proliferation and invasion via targeting miR-212-5p/FZD5/Wnt/β-catenin axis. J Cell Mol Med 2021; 25:10627-10637. [PMID: 34697900 PMCID: PMC8581327 DOI: 10.1111/jcmm.17000] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 01/21/2023] Open
Abstract
Prostate cancer is the second most frequent malignancy in men worldwide, and its incidence is increasing. Therefore, it is urgently required to clarify the underlying mechanisms of prostate cancer. Although the long non‐coding RNA LINC00115 was identified as an oncogene in several cancers, the expression and function of LINC00115 in prostate cancer have not been explored. Our results showed that LINC00115 was significantly up‐regulated in prostate cancer tissues, which was significantly associated with a poor prognosis for prostate cancer patients. Functional studies showed that knockdown LINC00115 inhibited cell proliferation and invasion. In addition, LINC00115 served as a competing endogenous RNA (ceRNA) through sponging miR‐212‐5p to release Frizzled Family Receptor 5 (FZD5) expression. The expression of miR‐212‐5p was noticeably low in tumour tissues, and FZD5 expression level was down‐regulated with the knockdown of LINC00115. Knockdown LINC00115 inhibited the Wnt/β‑catenin signalling pathway by inhibiting the expression of FZD5. Rescue experiments further showed that LINC00115 inhibits prostate cancer cell proliferation and invasion via targeting miR‐212‐5p/ FZD5/ Wnt/β‐catenin axis. The present study provided clues that LINC00115 may be a promising novel therapeutic target for prostate cancer patients.
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Affiliation(s)
- Naixiong Peng
- Department of Urology, Shenzhen Longhua District Central Hospital, The Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
| | - Zejian Zhang
- Department of Urology, Shenzhen Longhua District Central Hospital, The Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
| | - Yaomin Wang
- Wake Forest University, Winston-Salem, NC, USA
| | - Minlong Yang
- Department of Urology, Shenzhen Longhua District Central Hospital, The Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
| | - Jiqing Fan
- Department of Urology, Shenzhen Longhua District Central Hospital, The Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
| | - Qinjun Wang
- Department of Urology, Shenzhen Longhua District Central Hospital, The Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
| | - Ling Deng
- Department of Urology, Shenzhen Longhua District Central Hospital, The Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
| | - Dong Chen
- Department of Urology, Shenzhen Longhua District Central Hospital, The Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
| | - Yuefeng Cai
- Department of Urology, Shenzhen Longhua District Central Hospital, The Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
| | - Qihui Li
- Department of Urology, Shenzhen Longhua District Central Hospital, The Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
| | - Xisheng Wang
- Department of Urology, Shenzhen Longhua District Central Hospital, The Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
| | - Wei Li
- Department of Urology, Shenzhen Longhua District Central Hospital, The Affiliated Central Hospital of Shenzhen Longhua District, Guangdong Medical University, Shenzhen, China
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Barik GK, Sahay O, Behera A, Naik D, Kalita B. Keep your eyes peeled for long noncoding RNAs: Explaining their boundless role in cancer metastasis, drug resistance, and clinical application. Biochim Biophys Acta Rev Cancer 2021; 1876:188612. [PMID: 34391844 DOI: 10.1016/j.bbcan.2021.188612] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/07/2021] [Accepted: 08/08/2021] [Indexed: 12/12/2022]
Abstract
Cancer metastasis and drug resistance are two major obstacles in the treatment of cancer and therefore, the leading cause of cancer-associated mortalities worldwide. Hence, an in-depth understanding of these processes and identification of the underlying key players could help design a better therapeutic regimen to treat cancer. Earlier thought to be merely transcriptional junk and having passive or secondary function, recent advances in the genomic research have unravelled that long noncoding RNAs (lncRNAs) play pivotal roles in diverse physiological as well as pathological processes including cancer metastasis and drug resistance. LncRNAs can regulate various steps of the complex metastatic cascade such as epithelial-mesenchymal transition (EMT), invasion, migration and metastatic colonization, and also affect the sensitivity of cancer cells to various chemotherapeutic drugs. A substantial body of literature for more than a decade of research evince that lncRNAs can regulate gene expression at different levels such as epigenetic, transcriptional, posttranscriptional, translational and posttranslational levels, depending on their subcellular localization and through their ability to interact with DNA, RNA and proteins. In this review, we mainly focus on how lncRNAs affect cancer metastasis by modulating expression of key metastasis-associated genes at various levels of gene regulation. We also discuss how lncRNAs confer cancer cells either sensitivity or resistance to various chemo-therapeutic drugs via different mechanisms. Finally, we highlight the immense potential of lncRNAs as prognostic and diagnostic biomarkers as well as therapeutic targets in cancer.
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Affiliation(s)
- Ganesh Kumar Barik
- Cancer Biology Division, National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Osheen Sahay
- Proteomics Laboratory, National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Abhayananda Behera
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Debasmita Naik
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Bhargab Kalita
- Proteomics Laboratory, National Centre for Cell Science, Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India.
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Abstract
Metastasis is a major contributor to cancer-associated deaths. It is characterized by a multistep process that occurs through the acquisition of molecular and phenotypic changes enabling cancer cells from a primary tumour to disseminate and colonize at distant organ sites. Over the past decade, the discovery and characterization of long noncoding RNAs (lncRNAs) have revealed the diversity of their regulatory roles, including key contributions throughout the metastatic cascade. Here, we review how lncRNAs promote metastasis by functioning in discrete pro-metastatic steps including the epithelial-mesenchymal transition, invasion and migration and organotrophic colonization, and by influencing the metastatic tumour microenvironment, often by interacting within ribonucleoprotein complexes or directly with other nucleic acid entities. We discuss well-characterized lncRNAs with in vivo phenotypes and highlight mechanistic commonalities such as convergence with the TGFβ-ZEB1/ZEB2 axis or the nuclear factor-κB pathway, in addition to lncRNAs with controversial mechanisms and the influence of methodologies on mechanistic interpretation. Furthermore, some lncRNAs can help identify tumours with increased metastatic risk and spur novel therapeutic strategies, with several lncRNAs having shown potential as novel targets for antisense oligonucleotide therapy in animal models. In addition to well-characterized examples of lncRNAs functioning in metastasis, we discuss controversies and ongoing challenges in lncRNA biology. Finally, we present areas for future study for this rapidly evolving field.
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Affiliation(s)
- S John Liu
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA
| | - Ha X Dang
- Department of Internal Medicine, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Daniel A Lim
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA
- San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Felix Y Feng
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Christopher A Maher
- Department of Internal Medicine, Washington University in St Louis, St Louis, MO, USA.
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA.
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St Louis, St Louis, MO, USA.
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Song HK, Kim SY. The Role of Sex-specific Long Non-coding RNAs in Cancer Prevention and Therapy. J Cancer Prev 2021; 26:98-109. [PMID: 34258248 PMCID: PMC8249206 DOI: 10.15430/jcp.2021.26.2.98] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/11/2021] [Accepted: 05/21/2021] [Indexed: 12/15/2022] Open
Abstract
The functions of a large number of non-coding genes in human DNA have yet to be accurately identified. Long non-coding RNA (lncRNA) measuring 10 kb or less in length regulates transcription or post-transcriptional events. The lncRNAs have attracted increased attention of researchers in recent years. In this review, we summarize the recently published lncRNAs which are known to influence cancer development and progression. We also discuss recent studies investigating tumor-specific lncRNA expression. These lncRNAs provide very useful information that allows prediction of the degree of malignancy and a survival rate in cancer patients as clinically relevant biomarkers. Because symptoms and progression of cancer differ from onset to death between males and females, it is important to consider the gender of the patient when diagnosing cancer and predicting the progression. Considering the importance of gender difference, we also examine the influence of sex hormones involved in the expression and regulation of lncRNAs as biomarkers. Many of the lncRNAs examined in this review have been studied in cancers occurring in the female or male reproductive organs, but the association between lncRNAs and sex hormones has also been reported in common organs such as the lung, renal and colon. Although lncRNAs have not yet been widely used as definitive cancer indicators, recent studies have demonstrated the potential role of lncRNAs as biomarkers and therapeutic targets reflecting sex-specificity in a number of different cancers.
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Affiliation(s)
- Hye Kyung Song
- Department of Chemistry, College of Science and Technology, Duksung Women's University, Seoul, Korea
| | - Sun Young Kim
- Department of Chemistry, College of Science and Technology, Duksung Women's University, Seoul, Korea
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Prostate Cancer Biomarkers: From diagnosis to prognosis and precision-guided therapeutics. Pharmacol Ther 2021; 228:107932. [PMID: 34174272 DOI: 10.1016/j.pharmthera.2021.107932] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 12/23/2022]
Abstract
Prostate cancer (PCa) is one of the most commonly diagnosed malignancies and among the leading causes of cancer-related death worldwide. It is a highly heterogeneous disease, ranging from remarkably slow progression or inertia to highly aggressive and fatal disease. As therapeutic decision-making, clinical trial design and outcome highly depend on the appropriate stratification of patients to risk groups, it is imperative to differentiate between benign versus more aggressive states. The incorporation of clinically valuable prognostic and predictive biomarkers is also potentially amenable in this process, in the timely prevention of metastatic disease and in the decision for therapy selection. This review summarizes the progress that has so far been made in the identification of the genomic events that can be used for the classification, prediction and prognostication of PCa, and as major targets for clinical intervention. We include an extensive list of emerging biomarkers for which there is enough preclinical evidence to suggest that they may constitute crucial targets for achieving significant advances in the management of the disease. Finally, we highlight the main challenges that are associated with the identification of clinically significant PCa biomarkers and recommend possible ways to overcome such limitations.
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46
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Lu L, Liu LP, Zhao QQ, Gui R, Zhao QY. Identification of a Ferroptosis-Related LncRNA Signature as a Novel Prognosis Model for Lung Adenocarcinoma. Front Oncol 2021; 11:675545. [PMID: 34249715 PMCID: PMC8260838 DOI: 10.3389/fonc.2021.675545] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/08/2021] [Indexed: 12/16/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is a highly heterogeneous malignancy, which makes prognosis prediction of LUAD very challenging. Ferroptosis is an iron-dependent cell death mechanism that is important in the survival of tumor cells. Long non-coding RNAs (lncRNAs) are considered to be key regulators of LUAD development and are involved in ferroptosis of tumor cells, and ferroptosis-related lncRNAs have gradually emerged as new targets for LUAD treatment and prognosis. It is essential to determine the prognostic value of ferroptosis-related lncRNAs in LUAD. In this study, we obtained RNA sequencing (RNA-seq) data and corresponding clinical information of LUAD patients from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database and ferroptosis-related lncRNAs by co-expression analysis. The best predictors associated with LUAD prognosis, including C5orf64, LINC01800, LINC00968, LINC01352, PGM5-AS1, LINC02097, DEPDC1-AS1, WWC2-AS2, SATB2-AS1, LINC00628, LINC01537, LMO7DN, were identified by Least Absolute Shrinkage and Selection Operator (LASSO) Cox regression analysis, and the LUAD risk prediction model was successfully constructed. Kaplan-Meier analysis, receiver operating characteristic (ROC) time curve analysis and univariate and multivariate Cox regression analysis and further demonstrated that the model has excellent robustness and predictive ability. Further, based on the risk prediction model, functional enrichment analysis revealed that 12 prognostic indicators involved a variety of cellular functions and signaling pathways, and the immune status was different in the high-risk and low-risk groups. In conclusion, a risk model of 12 ferroptosis related lncRNAs has important prognostic value for LUAD and may be ferroptosis-related therapeutic targets in the clinic.
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Affiliation(s)
- Lu Lu
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Le-Ping Liu
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Qiang-Qiang Zhao
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Rong Gui
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Qin-Yu Zhao
- Department of Blood Transfusion, The Third Xiangya Hospital of Central South University, Changsha, China
- College of Engineering and Computer Science, Australian National University, Canberra, ACT, Australia
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Boerrigter E, Benoist GE, van Oort IM, Verhaegh GW, van Hooij O, Groen L, Smit F, Oving IM, de Mol P, Smilde TJ, Somford DM, Mehra N, Schalken JA, van Erp NP. Liquid biopsy reveals KLK3 mRNA as a prognostic marker for progression free survival in patients with metastatic castration-resistant prostate cancer undergoing first-line abiraterone acetate and prednisone treatment. Mol Oncol 2021; 15:2453-2465. [PMID: 33650292 PMCID: PMC8410566 DOI: 10.1002/1878-0261.12933] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/12/2021] [Accepted: 02/26/2021] [Indexed: 12/22/2022] Open
Abstract
Circulating RNAs extracted from liquid biopsies represent a promising source of cancer‐ and therapy‐related biomarkers. We screened whole blood from patients with metastatic castration‐resistant prostate cancer (mCRPC) following their first‐line treatment with abiraterone acetate and prednisone (AA‐P) to identify circulating RNAs that may correlate with progression‐free survival (PFS). In a prospective multicenter observational study, 53 patients with mCRPC were included after they started first‐line AA‐P treatment. Blood was drawn at baseline, 1, 3, and 6 months after treatment initiation. The levels of predefined circulating RNAs earlier identified as being upregulated in patients with mCRPC (e.g., microRNAs, long noncoding RNAs, and mRNAs), were analyzed. Uni‐ and multivariable Cox regression and Kaplan–Meier analyses were used to analyze the prognostic value of the various circulating RNAs for PFS along treatment. Detectable levels of kallikrein‐related peptidase 3 (KLK3) mRNA at baseline were demonstrated to be an independent prognostic marker for PFS (201 vs 501 days, P = 0.00054). Three months after AA‐P treatment initiation, KLK3 could not be detected in the blood of responding patients, but was still detectable in 56% of the patients with early progression. Our study confirmed that KLK3 mRNA detection in whole blood is an independent prognostic marker in mCRPC patients receiving AA‐P treatment. Furthermore, the levels of circulating KLK3 mRNA in patients receiving AA‐P treatment might reflect treatment response or early signs of progression.
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Affiliation(s)
- Emmy Boerrigter
- Department of PharmacyRadboud University Medical CenterRadboud Institute for Health SciencesNijmegenthe Netherlands
| | - Guillemette E. Benoist
- Department of PharmacyRadboud University Medical CenterRadboud Institute for Health SciencesNijmegenthe Netherlands
| | - Inge M. van Oort
- Department of UrologyRadboud University Medical CenterRadboud Institute for Molecular Life SciencesNijmegenthe Netherlands
| | - Gerald W. Verhaegh
- Department of UrologyRadboud University Medical CenterRadboud Institute for Molecular Life SciencesNijmegenthe Netherlands
| | - Onno van Hooij
- Department of UrologyRadboud University Medical CenterRadboud Institute for Molecular Life SciencesNijmegenthe Netherlands
| | - Levi Groen
- Department of UrologyRadboud University Medical CenterRadboud Institute for Molecular Life SciencesNijmegenthe Netherlands
| | | | - Irma M. Oving
- Department of Medical OncologyZiekenhuisgroep TwenteAlmelothe Netherlands
| | - Pieter de Mol
- Department of Medical OncologyGelderse Vallei HospitalEdethe Netherlands
| | - Tineke J. Smilde
- Department of Medical OncologyJeroen Bosch Hospital‘s Hertogenboschthe Netherlands
| | | | - Niven Mehra
- Deparment of Medical OncologyRadboud University Medical CenterNijmegenthe Netherlands
| | - Jack A. Schalken
- Department of UrologyRadboud University Medical CenterRadboud Institute for Molecular Life SciencesNijmegenthe Netherlands
| | - Nielka P. van Erp
- Department of PharmacyRadboud University Medical CenterRadboud Institute for Health SciencesNijmegenthe Netherlands
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Hesterberg AB, Gordetsky JB, Hurley PJ. Cribriform Prostate Cancer: Clinical Pathologic and Molecular Considerations. Urology 2021; 155:47-54. [PMID: 34058243 DOI: 10.1016/j.urology.2021.05.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 05/11/2021] [Indexed: 02/07/2023]
Abstract
Intraductal cribriform (IDC) and invasive cribriform morphologies are associated with worse prostate cancer outcomes. Limited retrospective studies have associated IDC and cribriform morphology with germline mutations in DNA repair genes, particularly BRCA2. These findings, which prompted the National Comprehensive Cancer Network (NCCN) Guidelines for Prostate Cancer and Genetic/Familial High- Risk Assessment to consider germline testing for individuals with IDC/cribriform histology, have been questioned in a recent prospective study. A deepened understanding of the molecular mechanisms driving disease aggressiveness in cribriform morphology is critical to provide more clarity in clinical decision making. This review summarizes the current understanding of IDC and cribriform prostate cancer, with an emphasis on clinical outcomes and molecular alterations.
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Affiliation(s)
| | - Jennifer B Gordetsky
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN; Department of Urology, Vanderbilt University Medical Center, Nashville, TN
| | - Paula J Hurley
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN; Department of Urology, Vanderbilt University Medical Center, Nashville, TN; Vanderbilt-Ingram Cancer Center, Nashville, TN.
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Current Trends in Prevalence and Role of Long Noncoding RNA and Gene Fusion in Prostate Cancer: An Overview. ANNALS OF THE NATIONAL ACADEMY OF MEDICAL SCIENCES (INDIA) 2021. [DOI: 10.1055/s-0041-1729780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Abstract
Objectives The aim of this study is to analyze the current scenario in the diagnostic modalities for prostate cancer.
Materials and Methods We searched PubMed, Google Scholar, and ResearchGate for relevant data. Articles published in the last 10 years were taken into consideration. The role of long noncoding RNA and gene fusion products in the context of prostate cancer was reviewed, which included their roles in diagnosis, prognosis, and assessment of response to therapy.
Results Several long noncoding RNAs (lncRNA) have been isolated and have been shown to be useful in diagnosing and prognosticating prostate cancer. We have also looked into the role of TMPRSS2:ERG gene fusion in prostate carcinoma diagnosis. These molecular parameters have been looked into due to the fact that the current parameters in use such as prostate-specific antigen have several drawbacks that limit their potential.
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de Sá Pereira BM, Montalvão de Azevedo R, da Silva Guerra JV, Faria PA, Soares-Lima SC, De Camargo B, Maschietto M. Non-coding RNAs in Wilms' tumor: biological function, mechanism, and clinical implications. J Mol Med (Berl) 2021; 99:1043-1055. [PMID: 33950291 DOI: 10.1007/s00109-021-02075-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 03/04/2021] [Accepted: 04/06/2021] [Indexed: 10/21/2022]
Abstract
Non-coding RNAs are involved with maintenance and regulation of physiological mechanisms and are involved in pathological processes, such as cancer. Among the small ncRNAs, miRNAs are the most explored in tumorigenesis, metastasis development, and resistance to chemotherapy. These small molecules of ~ 22 nucleotides are modulated during early renal development, involved in the regulation of gene expression and Wilms' tumor progression. Wilms' tumors are embryonic tumors with few mutations and complex epigenetic dysregulation. In recent years, the small ncRNAs have been explored as potentially related both in physiological development and in the tumorigenesis of several types of cancer. Besides, genes regulated by miRNAs are related to biological pathways as PI3K, Wnt, TGF-β, and Hippo signaling pathways, among others, which may be involved with the underlying mechanisms of resistance to chemotherapy, and in this way, it has emerged as potential targets for cancer therapies, including for Wilms' tumors.
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Affiliation(s)
| | - Rafaela Montalvão de Azevedo
- Brazilian National Cancer Institute (INCa), Rio de Janeiro, RJ, Brazil.,Current institution: Molecular Bases of Genetic Risk and Genetic Testing Unit, Research Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - João Victor da Silva Guerra
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil.,Postgraduate Program in Pharmaceutical Sciences, Faculty of Pharmaceutic Sciences, University of Campinas, Campinas, SP, Brazil
| | - Paulo A Faria
- Brazilian National Cancer Institute (INCa), Rio de Janeiro, RJ, Brazil
| | | | | | - Mariana Maschietto
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil. .,Current: Research Institute, Boldrini Children's Hospital, Rua Dr. Gabriel Porto, 1270 - Cidade Universitária, Campinas, SP, 13083-210, Brazil.
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