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Andersen K, Salachan PV, Borre M, Ulhøi B, Stougaard M, Sørensen KD, Steiniche T. Highly sensitive deep panel sequencing of 27 HPV genotypes in prostate cancer biopsies results in very low detection rates and indicates that HPV is not a major etiological driver of this malignancy. Infect Agent Cancer 2024; 19:57. [PMID: 39543738 PMCID: PMC11566718 DOI: 10.1186/s13027-024-00619-x] [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: 08/15/2024] [Accepted: 10/28/2024] [Indexed: 11/17/2024] Open
Abstract
BACKGROUND Human papillomavirus (HPV) has been proposed to contribute to the carcinogenesis of prostate cancer. However, previous studies have yielded conflicting results. This study aims to add useful information to the ongoing discussion concerning the association between HPV infection and prostate cancer. METHODS We used two high-throughput next-generation sequencing (NGS) approaches to detect HPV RNA in malignant and adjacent normal (AN) prostate tissue (cohorts 1 and 2) and HPV DNA from carcinogenic and probably/possibly carcinogenic-classified HPV types (cohort 3) in malignant prostate, AN prostate, and benign prostatic hyperplasia (BPH) tissues. RESULTS In total, 0% (cohort 1: 0/83, cohort 2: 0/16) of the malignant prostate tissue samples and 0% (cohort 1: 0/23, cohort 2: 0/8) of the AN prostate tissue samples were positive for HPV RNA. A total of 8.3% (1/12) of the BPH samples, 0% (0/28) of the AN samples, and 0.8% (1/132) of the malignant prostate samples were positive for HPV16 DNA. However, the normalized read count of the HPV16-positive malignant sample was close to the cut-off. In addition, no other carcinogenic-classified HPV types were detected in any of the BPH, AN, or malignant prostate tissue samples. CONCLUSION Our study does not support HPV infection as a major contributor to the etiology of prostate cancer.
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Affiliation(s)
- Karoline Andersen
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, Aarhus N, 8200, Denmark.
- Department of Pathology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, Aarhus N, 8200, Denmark.
| | - Paul Vinu Salachan
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, Aarhus N, 8200, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Brendstrupgaardsvej 21A, Aarhus N, 8200, Denmark
| | - Michael Borre
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, Aarhus N, 8200, Denmark
- Department of Urology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, Aarhus N, 8200, Denmark
| | - Benedicte Ulhøi
- Department of Pathology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, Aarhus N, 8200, Denmark
| | - Magnus Stougaard
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, Aarhus N, 8200, Denmark
- Department of Clinical Genetics, Aarhus University Hospital, Brendstrupgaardsvej 21C, Aarhus N, 8200, Denmark
| | - Karina Dalsgaard Sørensen
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, Aarhus N, 8200, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Brendstrupgaardsvej 21A, Aarhus N, 8200, Denmark
| | - Torben Steiniche
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, Aarhus N, 8200, Denmark
- Department of Pathology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, Aarhus N, 8200, Denmark
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2
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Shrestha R, Chesner LN, Zhang M, Zhou S, Foye A, Lundberg A, Weinstein AS, Sjöström M, Zhu X, Moreno-Rodriguez T, Li H, Alumkal JJ, Aggarwal R, Small EJ, Lupien M, Quigley DA, Feng FY. An Atlas of Accessible Chromatin in Advanced Prostate Cancer Reveals the Epigenetic Evolution during Tumor Progression. Cancer Res 2024; 84:3086-3100. [PMID: 38990734 DOI: 10.1158/0008-5472.can-24-0890] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/16/2024] [Accepted: 07/03/2024] [Indexed: 07/13/2024]
Abstract
Metastatic castration-resistant prostate cancer (mCRPC) is a lethal disease that resists therapy targeting androgen signaling, the primary driver of prostate cancer. mCRPC resists androgen receptor (AR) inhibitors by amplifying AR signaling or by evolving into therapy-resistant subtypes that do not depend on AR. Elucidation of the epigenetic underpinnings of these subtypes could provide important insights into the drivers of therapy resistance. In this study, we produced chromatin accessibility maps linked to the binding of lineage-specific transcription factors (TF) by performing assay for transposase-accessible chromatin sequencing on 70 mCRPC tissue biopsies integrated with transcriptome and whole-genome sequencing. mCRPC had a distinct global chromatin accessibility profile linked to AR function. Analysis of TF occupancy across accessible chromatin revealed 203 TFs associated with mCRPC subtypes. Notably, ZNF263 was identified as a putative prostate cancer TF with a significant impact on gene activity in the double-negative subtype (AR- neuroendocrine-), potentially activating MYC targets. Overall, this analysis of chromatin accessibility in mCRPC provides valuable insights into epigenetic changes that occur during progression to mCRPC. Significance: Integration of a large cohort of transcriptome, whole-genome, and ATAC sequencing characterizes the chromatin accessibility changes in advanced prostate cancer and identifies therapy-resistant prostate cancer subtype-specific transcription factors that modulate oncogenic programs.
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Affiliation(s)
- Raunak Shrestha
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California
| | - Lisa N Chesner
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California
| | - Meng Zhang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California
| | - Stanley Zhou
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Arian Lundberg
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California
- The Institute of Cancer Research and The Royal Marsden Hospital, London, United Kingdom
| | - Alana S Weinstein
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California
| | - Martin Sjöström
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California
| | - Xiaolin Zhu
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Thaidy Moreno-Rodriguez
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Urology, University of California, San Francisco, San Francisco, California
| | - Haolong Li
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California
| | - Joshi J Alumkal
- Division of Hematology and Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, Michigan
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California
- Department of Urology, University of California, San Francisco, San Francisco, California
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Ontario Institute for Cancer Research, Toronto, Canada
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Urology, University of California, San Francisco, San Francisco, California
- Department of Epidemiology & Biostatistics, University of California, San Francisco, San Francisco, California
| | - Felix Y Feng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California
- Department of Urology, University of California, San Francisco, San Francisco, California
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3
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Zhang M, Sjöström M, Cui X, Foye A, Farh K, Shrestha R, Lundberg A, Dang HX, Li H, Febbo PG, Aggarwal R, Alumkal JJ, Small EJ, Maher CA, Feng FY, Quigley DA. Integrative analysis of ultra-deep RNA-seq reveals alternative promoter usage as a mechanism of activating oncogenic programmes during prostate cancer progression. Nat Cell Biol 2024; 26:1176-1186. [PMID: 38871824 PMCID: PMC11844022 DOI: 10.1038/s41556-024-01438-3] [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: 02/13/2023] [Accepted: 05/11/2024] [Indexed: 06/15/2024]
Abstract
Transcription factor (TF) proteins regulate gene activity by binding to regulatory regions, most importantly at gene promoters. Many genes have alternative promoters (APs) bound by distinct TFs. The role of differential TF activity at APs during tumour development is poorly understood. Here we show, using deep RNA sequencing in 274 biopsies of benign prostate tissue, localized prostate tumours and metastatic castration-resistant prostate cancer, that AP usage increases as tumours progress and APs are responsible for a disproportionate amount of tumour transcriptional activity. Expression of the androgen receptor (AR), the key driver of prostate tumour activity, is correlated with elevated AP usage. We identified AR, FOXA1 and MYC as potential drivers of AP activation. DNA methylation is a likely mechanism for AP activation during tumour progression and lineage plasticity. Our data suggest that prostate tumours activate APs to magnify the transcriptional impact of tumour drivers, including AR and MYC.
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Affiliation(s)
- Meng Zhang
- Department of Radiation Oncology, University of California at San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA
| | - Martin Sjöström
- Department of Radiation Oncology, University of California at San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA
| | - Xiekui Cui
- Department of Radiation Oncology, University of California at San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California at San Francisco, San Francisco, CA, USA
| | - Adam Foye
- Department of Radiation Oncology, University of California at San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA
| | | | - Raunak Shrestha
- Department of Radiation Oncology, University of California at San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA
| | - Arian Lundberg
- Department of Radiation Oncology, University of California at San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA
| | - Ha X Dang
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
- Department of Internal Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Bristol Myers Squibb, San Diego, CA, USA
| | - Haolong Li
- Department of Radiation Oncology, University of California at San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA
| | | | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA
- Division of Hematology and Oncology, Department of Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Joshi J Alumkal
- Division of Hematology and Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA
- Division of Hematology and Oncology, Department of Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Christopher A Maher
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA
- Department of Internal Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Felix Y Feng
- Department of Radiation Oncology, University of California at San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA
- Division of Hematology and Oncology, Department of Medicine, University of California at San Francisco, San Francisco, CA, USA
- Department of Urology, University of California at San Francisco, San Francisco, CA, USA
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA.
- Department of Urology, University of California at San Francisco, San Francisco, CA, USA.
- Department of Epidemiology & Biostatistics, University of California at San Francisco, San Francisco, CA, USA.
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4
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Naseer QA, Malik A, Zhang F, Chen S. Exploring the enigma: history, present, and future of long non-coding RNAs in cancer. Discov Oncol 2024; 15:214. [PMID: 38847897 PMCID: PMC11161455 DOI: 10.1007/s12672-024-01077-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024] Open
Abstract
Long noncoding RNAs (lncRNAs), which are more than 200 nucleotides in length and do not encode proteins, play crucial roles in governing gene expression at both the transcriptional and posttranscriptional levels. These molecules demonstrate specific expression patterns in various tissues and developmental stages, suggesting their involvement in numerous developmental processes and diseases, notably cancer. Despite their widespread acknowledgment and the growing enthusiasm surrounding their potential as diagnostic and prognostic biomarkers, the precise mechanisms through which lncRNAs function remain inadequately understood. A few lncRNAs have been studied in depth, providing valuable insights into their biological activities and suggesting emerging functional themes and mechanistic models. However, the extent to which the mammalian genome is transcribed into functional noncoding transcripts is still a matter of debate. This review synthesizes our current understanding of lncRNA biogenesis, their genomic contexts, and their multifaceted roles in tumorigenesis, highlighting their potential in cancer-targeted therapy. By exploring historical perspectives alongside recent breakthroughs, we aim to illuminate the diverse roles of lncRNA and reflect on the broader implications of their study for understanding genome evolution and function, as well as for advancing clinical applications.
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Affiliation(s)
- Qais Ahmad Naseer
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China
| | - Abdul Malik
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China
| | - Fengyuan Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China
| | - Shengxia Chen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China.
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5
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Lundberg A, Zhang M, Aggarwal R, Li H, Zhang L, Foye A, Sjöström M, Chou J, Chang K, Moreno-Rodriguez T, Shrestha R, Baskin A, Zhu X, Weinstein AS, Younger N, Alumkal JJ, Beer TM, Chi KN, Evans CP, Gleave M, Lara PN, Reiter RE, Rettig MB, Witte ON, Wyatt AW, Feng FY, Small EJ, Quigley DA. The Genomic and Epigenomic Landscape of Double-Negative Metastatic Prostate Cancer. Cancer Res 2023; 83:2763-2774. [PMID: 37289025 PMCID: PMC10425725 DOI: 10.1158/0008-5472.can-23-0593] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/20/2023] [Accepted: 06/02/2023] [Indexed: 06/09/2023]
Abstract
Systemic targeted therapy in prostate cancer is primarily focused on ablating androgen signaling. Androgen deprivation therapy and second-generation androgen receptor (AR)-targeted therapy selectively favor the development of treatment-resistant subtypes of metastatic castration-resistant prostate cancer (mCRPC), defined by AR and neuroendocrine (NE) markers. Molecular drivers of double-negative (AR-/NE-) mCRPC are poorly defined. In this study, we comprehensively characterized treatment-emergent mCRPC by integrating matched RNA sequencing, whole-genome sequencing, and whole-genome bisulfite sequencing from 210 tumors. AR-/NE- tumors were clinically and molecularly distinct from other mCRPC subtypes, with the shortest survival, amplification of the chromatin remodeler CHD7, and PTEN loss. Methylation changes in CHD7 candidate enhancers were linked to elevated CHD7 expression in AR-/NE+ tumors. Genome-wide methylation analysis nominated Krüppel-like factor 5 (KLF5) as a driver of the AR-/NE- phenotype, and KLF5 activity was linked to RB1 loss. These observations reveal the aggressiveness of AR-/NE- mCRPC and could facilitate the identification of therapeutic targets in this highly aggressive disease. SIGNIFICANCE Comprehensive characterization of the five subtypes of metastatic castration-resistant prostate cancer identified transcription factors that drive each subtype and showed that the double-negative subtype has the worst prognosis.
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Affiliation(s)
- Arian Lundberg
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Meng Zhang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Haolong Li
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Li Zhang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Martin Sjöström
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Jonathan Chou
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Kevin Chang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Thaidy Moreno-Rodriguez
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Urology, University of California San Francisco, San Francisco, California
| | - Raunak Shrestha
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Avi Baskin
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Xiaolin Zhu
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Alana S. Weinstein
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Noah Younger
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Joshi J. Alumkal
- Division of Hematology and Oncology, University of Michigan Rogel Cancer Center, Ann Arbor, Michigan
| | - Tomasz M. Beer
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Kim N. Chi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Christopher P. Evans
- Comprehensive Cancer Center, University of California Davis, Sacramento, California
- Department of Urologic Surgery, University of California Davis, Sacramento, California
| | - Martin Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Primo N. Lara
- Comprehensive Cancer Center, University of California Davis, Sacramento, California
- Division of Hematology Oncology, Department of Internal Medicine, University of California Davis, Sacramento, California
| | - Rob E. Reiter
- Departments of Medicine, Hematology/Oncology and Urology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, California
| | - Matthew B. Rettig
- Departments of Medicine, Hematology/Oncology and Urology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, California
- VA Greater Los Angeles Healthcare System, Los Angeles, California
| | - Owen N. Witte
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Alexander W. Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Felix Y. Feng
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, California
- Department of Urology, University of California San Francisco, San Francisco, California
| | - Eric J. Small
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - David A. Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Urology, University of California San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
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6
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Le Hars M, Castro-Vega LJ, Rajabi F, Tabatadze D, Romero M, Pinskaya M, Groisman I. Pro-tumorigenic role of lnc-ZNF30-3 as a sponge counteracting miR-145-5p in prostate cancer. Biol Direct 2023; 18:38. [PMID: 37434219 PMCID: PMC10334624 DOI: 10.1186/s13062-023-00393-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 06/23/2023] [Indexed: 07/13/2023] Open
Abstract
BACKGROUND Prostate cancer remains one of the deadliest neoplasms in developed countries. Identification of new molecular markers that predict the onset and progression of the disease could improve its clinical management. Low miR-145-5p expression is consistently found in primary tumors and metastases, but the regulatory mechanisms governing its functions remain largely unknown. METHODS Bioinformatics analysis was conducted to identify [1] a set of novel potential competing endogenous lncRNAs for sponging of miRNA-145-5p in prostate cancer and [2] miR-145-5p and other EMT-related miRNAs response elements in lnc-ZNF30-3. Quantification of miR-145-5p, lnc-ZNF30-3, and TWIST1 expression levels in tumor tissues in RNA sequencing datasets of our and TCGA PRAD cohorts revealed a correlation with clinical outcome of prostate cancer patients. Biochemical and cell biology approaches, such as RNA pull-down, western blot, immunostaining, and wound healing assays were used for evaluation of the impact of TWIST1/miR-145/ lnc-ZNF30-3 interactions in prostate cancer cells altered in miRNA and lncRNA expression. RESULTS We identified a few potential lncRNA sponges of miR-145-5p, including lnc-ZNF30-3. It contains five response elements for miR-145-5p, but also other miRNAs targeting EMT transcription factors. Lnc-ZNF30-3 is significantly upregulated in prostate cancer cell lines and tumor tissues, and its high expression is correlated with poor patient prognosis. We demonstrated that lnc-ZNF30-3 is associated with AGO2 and specifically interacts with the miR-145-5p seed region. Knockdown of lnc-ZNF30-3 results in decreased migration of prostate cancer cells and downregulation of EMT drivers such as TWIST1 and ZEB1 at both the RNA and protein levels. These phenotypic and molecular features of lnc-ZNF30-3-depleted cells are partially rescued by miR-145-5p inhibition. CONCLUSIONS Collectively, our results point to lnc-ZNF30-3 as a novel competing endogenous lncRNA for miR-145-5p and other miRNAs that target TWIST1 as well as other EMT transcription factors. Prostate cancer patients with high lncRNA expression in primary tumors show lower survival rate suggesting that lnc-ZNF30-3 may contribute to prostate cancer progression and metastasis.
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Affiliation(s)
- Matthieu Le Hars
- Institut Curie, Sorbonne Universités, Paris Sciences et Lettres Research University, CNRS UMR3244, Paris, France
| | - Luis Jaime Castro-Vega
- Paris Brain Institute (ICM), Hôpital Pitié-Salpêtrière, Inserm U1127, CNRS UMR7225, Sorbonne Universités, Paris, France
| | - Fatemeh Rajabi
- Institut Curie, Sorbonne Universités, Paris Sciences et Lettres Research University, CNRS UMR3244, Paris, France
- Cancer Genomics lab, Inserm U981, Gustave Roussy Cancer Center Grand Paris, Villejuif, France
| | | | - Martha Romero
- Department of Pathology, Hospital Universitario-Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - Marina Pinskaya
- Institut Curie, Sorbonne Universités, Paris Sciences et Lettres Research University, CNRS UMR3244, Paris, France.
| | - Irina Groisman
- Institut Curie, Sorbonne Universités, Paris Sciences et Lettres Research University, CNRS UMR3244, Paris, France.
- Cancer Genomics lab, Inserm U981, Gustave Roussy Cancer Center Grand Paris, Villejuif, France.
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7
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de la Rubia I, Srivastava A, Xue W, Indi JA, Carbonell-Sala S, Lagarde J, Albà MM, Eyras E. RATTLE: reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing. Genome Biol 2022; 23:153. [PMID: 35804393 PMCID: PMC9264490 DOI: 10.1186/s13059-022-02715-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 06/20/2022] [Indexed: 11/04/2022] Open
Abstract
Nanopore sequencing enables the efficient and unbiased measurement of transcriptomes. Current methods for transcript identification and quantification rely on mapping reads to a reference genome, which precludes the study of species with a partial or missing reference or the identification of disease-specific transcripts not readily identifiable from a reference. We present RATTLE, a tool to perform reference-free reconstruction and quantification of transcripts using only Nanopore reads. Using simulated data and experimental data from isoform spike-ins, human tissues, and cell lines, we show that RATTLE accurately determines transcript sequences and their abundances, and shows good scalability with the number of transcripts.
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Affiliation(s)
- Ivan de la Rubia
- EMBL Australia Partner Laboratory Network at the Australian National University, Acton, Canberra, ACT, 2601, Australia.,Pompeu Fabra University (UPF), E08003, Barcelona, Spain
| | - Akanksha Srivastava
- EMBL Australia Partner Laboratory Network at the Australian National University, Acton, Canberra, ACT, 2601, Australia.,Australian National University, Acton, Canberra, ACT, 2601, Australia
| | - Wenjing Xue
- EMBL Australia Partner Laboratory Network at the Australian National University, Acton, Canberra, ACT, 2601, Australia.,Australian National University, Acton, Canberra, ACT, 2601, Australia
| | - Joel A Indi
- EMBL Australia Partner Laboratory Network at the Australian National University, Acton, Canberra, ACT, 2601, Australia.,Universidade de Lisboa, Lisboa, Portugal
| | - Silvia Carbonell-Sala
- Pompeu Fabra University (UPF), E08003, Barcelona, Spain.,Centre for Regulatory Genomics (CRG), E08001, Barcelona, Spain
| | - Julien Lagarde
- Pompeu Fabra University (UPF), E08003, Barcelona, Spain.,Centre for Regulatory Genomics (CRG), E08001, Barcelona, Spain
| | - M Mar Albà
- Pompeu Fabra University (UPF), E08003, Barcelona, Spain. .,Catalan Institution for Research and Advanced Studies (ICREA), E08010, Barcelona, Spain. .,Hospital del Mar Medical Research Institute (IMIM), E08001, Barcelona, Spain.
| | - Eduardo Eyras
- EMBL Australia Partner Laboratory Network at the Australian National University, Acton, Canberra, ACT, 2601, Australia. .,Australian National University, Acton, Canberra, ACT, 2601, Australia. .,Catalan Institution for Research and Advanced Studies (ICREA), E08010, Barcelona, Spain. .,Hospital del Mar Medical Research Institute (IMIM), E08001, Barcelona, Spain.
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8
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Almeida A, Gabriel M, Firlej V, Martin‐Jaular L, Lejars M, Cipolla R, Petit F, Vogt N, San‐Roman M, Dingli F, Loew D, Destouches D, Vacherot F, de la Taille A, Théry C, Morillon A. Urinary extracellular vesicles contain mature transcriptome enriched in circular and long noncoding RNAs with functional significance in prostate cancer. J Extracell Vesicles 2022; 11:e12210. [PMID: 35527349 PMCID: PMC9081490 DOI: 10.1002/jev2.12210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/22/2022] [Accepted: 03/15/2022] [Indexed: 12/14/2022] Open
Abstract
Long noncoding (lnc)RNAs modulate gene expression alongside presenting unexpected source of neoantigens. Despite their immense interest, their ability to be transferred and control adjacent cells is unknown. Extracellular Vesicles (EVs) offer a protective environment for nucleic acids, with pro and antitumourigenic functions by controlling the immune response. In contrast to extracellular nonvesicular RNA, few studies have addressed the full RNA content within human fluids' EVs and have compared them with their tissue of origin. Here, we performed Total RNA-Sequencing on six Formalin-Fixed-Paraffin-Embedded (FFPE) prostate cancer (PCa) tumour tissues and their paired urinary (u)EVs to provide the first whole transcriptome comparison from the same patients. UEVs contain simplified transcriptome with intron-free cytoplasmic transcripts and enriched lnc/circular (circ)RNAs, strikingly common to an independent 20 patients' urinary cohort. Our full cellular and EVs transcriptome comparison within three PCa cell lines identified a set of overlapping 14 uEV-circRNAs characterized as essential for prostate cell proliferation in vitro and 28 uEV-lncRNAs belonging to the cancer-related lncRNA census (CLC2). In addition, we found 15 uEV-lncRNAs, predicted to encode 768 high-affinity neoantigens, and for which three of the encoded-ORF produced detectable unmodified peptides by mass spectrometry. Our dual analysis of EVs-lnc/circRNAs both in urines' and in vitro's EVs provides a fundamental resource for future uEV-lnc/circRNAs phenotypic characterization involved in PCa.
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Affiliation(s)
- Anna Almeida
- CNRS UMR3244Sorbonne UniversityPSL UniversityInstitut Curie, Centre de RechercheParisFrance
- Departement de Recherche TranslationnellePSL UniversityInstitut Curie, Centre de RechercheParisFrance
| | - Marc Gabriel
- CNRS UMR3244Sorbonne UniversityPSL UniversityInstitut Curie, Centre de RechercheParisFrance
| | - Virginie Firlej
- AP‐HPHôpital H. MondorPlateforme de Ressources BiologiquesCréteilFrance
- Univ Paris Est CreteilUR TRePCaCréteilFrance
| | - Lorena Martin‐Jaular
- INSERM U932PSL UniversityInstitut Curie, Centre de RechercheParisFrance
- Curie Core Tech Extracellular VesiclesInstitut Curie, Centre de RechercheParisFrance
| | - Matthieu Lejars
- CNRS UMR3244Sorbonne UniversityPSL UniversityInstitut Curie, Centre de RechercheParisFrance
| | - Rocco Cipolla
- CNRS UMR3244Sorbonne UniversityPSL UniversityInstitut Curie, Centre de RechercheParisFrance
| | - Floriane Petit
- Tumour BiologyINSERM U820, Sorbonne Université, PSL University, Institut CurieCentre de RechercheParisFrance
| | - Nicolas Vogt
- CNRS UMR3244Sorbonne UniversityPSL UniversityInstitut Curie, Centre de RechercheParisFrance
| | - Mabel San‐Roman
- CNRS UMR3215, Sorbonne Université, PSL University, Institut CurieCentre de RechercheParisFrance
| | - Florent Dingli
- Laboratoire de Spectrométrie de Masse ProtéomiquePSL Research University, Institut Curie Centre de RechercheParisFrance
| | - Damarys Loew
- Laboratoire de Spectrométrie de Masse ProtéomiquePSL Research University, Institut Curie Centre de RechercheParisFrance
| | | | | | | | - Clotilde Théry
- INSERM U932PSL UniversityInstitut Curie, Centre de RechercheParisFrance
- Curie Core Tech Extracellular VesiclesInstitut Curie, Centre de RechercheParisFrance
| | - Antonin Morillon
- CNRS UMR3244Sorbonne UniversityPSL UniversityInstitut Curie, Centre de RechercheParisFrance
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9
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Firlej V, Soyeux P, Nourieh M, Huet E, Semprez F, Allory Y, Londono-Vallejo A, de la Taille A, Vacherot F, Destouches D. Overexpression of Nucleolin and Associated Genes in Prostate Cancer. Int J Mol Sci 2022; 23:4491. [PMID: 35562881 PMCID: PMC9101690 DOI: 10.3390/ijms23094491] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/04/2022] [Accepted: 04/07/2022] [Indexed: 12/09/2022] Open
Abstract
Prostate cancer (PCa) is the second most frequent cancer and the fifth leading cause of cancer death in men worldwide. If local PCa presents a favorable prognosis, available treatments for advanced PCa display limiting benefits due to therapeutic resistances. Nucleolin (NCL) is a ubiquitous protein involved in numerous cell processes, such as ribosome biogenesis, cell cycles, or angiogenesis. NCL is overexpressed in several tumor types in which it has been proposed as a diagnostic and prognostic biomarker. In PCa, NCL has mainly been studied as a target for new therapeutic agents. Nevertheless, little data are available concerning its expression in patient tissues. Here, we investigated the expression of NCL using a new cohort from Mondor Hospital and data from published cohorts. Results were then compared with NCL expression using in vitro models. NCL was overexpressed in PCa tissues compared to the normal tissues, but no prognostic values were demonstrated. Nine genes were highly co-expressed with NCL in patient tissues and tumor prostate cell lines. Our data demonstrate that NCL is an interesting diagnostic biomarker and propose a signature of genes co-expressed with NCL.
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Affiliation(s)
- Virginie Firlej
- Univ Paris Est Creteil, TRePCa, F-94010 Creteil, France; (V.F.); (P.S.); (E.H.); (A.d.l.T.); (F.V.)
| | - Pascale Soyeux
- Univ Paris Est Creteil, TRePCa, F-94010 Creteil, France; (V.F.); (P.S.); (E.H.); (A.d.l.T.); (F.V.)
| | - Maya Nourieh
- Department of Pathology, Institut Curie, F-92210 Saint-Cloud, France; (M.N.); (Y.A.)
| | - Eric Huet
- Univ Paris Est Creteil, TRePCa, F-94010 Creteil, France; (V.F.); (P.S.); (E.H.); (A.d.l.T.); (F.V.)
| | - Fannie Semprez
- SPPIN—Saints-Pères Paris Institute for the Neurosciences, Université de Paris, CNRS, F-75006 Paris, France;
| | - Yves Allory
- Department of Pathology, Institut Curie, F-92210 Saint-Cloud, France; (M.N.); (Y.A.)
- Institut Curie, PSL Research University, CNRS UMR 144, F-75005 Paris, France
| | - Arturo Londono-Vallejo
- Institut Curie, PSL Research University, CNRS UMR 3244 « Telomeres and Cancer », F-75005 Paris, France;
| | - Alexandre de la Taille
- Univ Paris Est Creteil, TRePCa, F-94010 Creteil, France; (V.F.); (P.S.); (E.H.); (A.d.l.T.); (F.V.)
- AP-HP, Hôpital Henri-Mondor, Service Urologie, F-94010 Creteil, France
| | - Francis Vacherot
- Univ Paris Est Creteil, TRePCa, F-94010 Creteil, France; (V.F.); (P.S.); (E.H.); (A.d.l.T.); (F.V.)
| | - Damien Destouches
- Univ Paris Est Creteil, TRePCa, F-94010 Creteil, France; (V.F.); (P.S.); (E.H.); (A.d.l.T.); (F.V.)
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10
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Salachan PV, Rasmussen M, Fredsøe J, Ulhøi B, Borre M, Sørensen KD. Microbiota of the prostate tumor environment investigated by whole-transcriptome profiling. Genome Med 2022; 14:9. [PMID: 35078527 PMCID: PMC8787950 DOI: 10.1186/s13073-022-01011-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 01/05/2022] [Indexed: 02/08/2023] Open
Abstract
Background With over 350,000 estimated deaths worldwide in 2018, prostate cancer (PCa) continues to be a major health concern and a significant cause of cancer-associated mortality among men. While cancer in general is considered a disease of the human genome, there is a growing body of evidence suggesting that changes to the healthy microbiota could play a vital role in cancer development, progression, and/or treatment outcome. Methods Using a metatranscriptomic approach, we annotated the microbial reads obtained from total RNA sequencing of 106 prostate tissue samples from 94 PCa patients (discovery cohort). We investigated microbial dysbiosis associated with PCa by systematically comparing the microbiomes between benign and malignant tissue samples, between less vs. more-aggressive PCa, and between patients who had biochemical recurrence as opposed to those who did not. We further performed differential gene expression and cell type enrichment analysis to explore the host transcriptomic and cellular responses to selected microbial genera. A public dataset (GSE115414) of total RNA sequencing reads from 24 prostate tissue samples (8 benign and 16 malignant) served as the validation cohort. Results We observed decreased species diversity and significant under-representation of Staphylococcus saprophyticus and Vibrio parahaemolyticus, as well as significant over-abundance of Shewanella in malignant as compared to benign prostate tissue samples in both the discovery (p < 0.01) and validation (p < 0.05) cohorts. In addition, we identified Microbacterium species (p < 0.01) to be significantly over-abundant in pathologically advanced T3 tumors compared to T2 in the discovery cohort. Malignant samples having high vs. low Shewanella counts were associated with downregulated Toll-like receptor signaling pathways and decreased enrichment of dendritic cells. Malignant samples having low vs. high V. parahaemolyticus counts were enriched for olfactory transduction and drug metabolism pathways. Finally, malignant samples were enriched for M1 and M2 macrophages as compared to benign tissue samples. Conclusions The results from this exploratory study support the existence of an important biological link between the prostate microbiota and PCa development/progression. Our results highlight Shewanella, V. parahaemolyticus, and Microbacterium sp. as interesting candidates for further investigation of their association with PCa. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01011-3.
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11
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Nguyen HTN, Xue H, Firlej V, Ponty Y, Gallopin M, Gautheret D. Reference-free transcriptome signatures for prostate cancer prognosis. BMC Cancer 2021; 21:394. [PMID: 33845808 PMCID: PMC8040209 DOI: 10.1186/s12885-021-08021-1] [Citation(s) in RCA: 5] [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: 12/18/2020] [Accepted: 03/09/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND RNA-seq data are increasingly used to derive prognostic signatures for cancer outcome prediction. A limitation of current predictors is their reliance on reference gene annotations, which amounts to ignoring large numbers of non-canonical RNAs produced in disease tissues. A recently introduced kind of transcriptome classifier operates entirely in a reference-free manner, relying on k-mers extracted from patient RNA-seq data. METHODS In this paper, we set out to compare conventional and reference-free signatures in risk and relapse prediction of prostate cancer. To compare the two approaches as fairly as possible, we set up a common procedure that takes as input either a k-mer count matrix or a gene expression matrix, extracts a signature and evaluates this signature in an independent dataset. RESULTS We find that both gene-based and k-mer based classifiers had similarly high performances for risk prediction and a markedly lower performance for relapse prediction. Interestingly, the reference-free signatures included a set of sequences mapping to novel lncRNAs or variable regions of cancer driver genes that were not part of gene-based signatures. CONCLUSIONS Reference-free classifiers are thus a promising strategy for the identification of novel prognostic RNA biomarkers.
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Affiliation(s)
- Ha T N Nguyen
- Institute for Integrative Biology of the Cell, UMR 9198, CEA, CNRS, Université Paris-Saclay, Gif-Sur-Yvette, France
| | - Haoliang Xue
- Institute for Integrative Biology of the Cell, UMR 9198, CEA, CNRS, Université Paris-Saclay, Gif-Sur-Yvette, France
| | - Virginie Firlej
- Institute of Biology, Université Paris Est Creteil, Creteil, Creteil, France
| | - Yann Ponty
- LIX CNRS UMR 7161, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France
| | - Melina Gallopin
- Institute for Integrative Biology of the Cell, UMR 9198, CEA, CNRS, Université Paris-Saclay, Gif-Sur-Yvette, France
| | - Daniel Gautheret
- Institute for Integrative Biology of the Cell, UMR 9198, CEA, CNRS, Université Paris-Saclay, Gif-Sur-Yvette, France.
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12
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Kleshnin A, Monet L, Plays M, Vaysset H, Rougeulle C, Vagner S. Amid darkness, light will prevail – a report on the 2020 annual SFC meeting on “Dark genome and Cancer”. Bull Cancer 2021; 108:129-132. [PMID: 33422339 DOI: 10.1016/j.bulcan.2020.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Andrey Kleshnin
- École polytechnique, route de Saclay, 91128 Palaiseau cedex, France
| | - Léa Monet
- École polytechnique, route de Saclay, 91128 Palaiseau cedex, France
| | - Marina Plays
- École polytechnique, route de Saclay, 91128 Palaiseau cedex, France
| | - Hugo Vaysset
- École polytechnique, route de Saclay, 91128 Palaiseau cedex, France
| | - Claire Rougeulle
- Université de Paris, epigenetics and cell fate, CNRS, 75013 Paris, France.
| | - Stéphan Vagner
- Institut Curie, PSL research university, Paris-Saclay university, CNRS UMR3348, Inserm U1278, 91405 Orsay cedex, France.
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13
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Wang Y, Yang Z. A Gleason score-related outcome model for human prostate cancer: a comprehensive study based on weighted gene co-expression network analysis. Cancer Cell Int 2020; 20:159. [PMID: 32425694 PMCID: PMC7216484 DOI: 10.1186/s12935-020-01230-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/23/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Prostate cancer (PCa) is the second leading cause of cancer death in men in 2018. Thus, the evaluation of prognosis is crucial for clinical treatment decision of human PCa patients. We aim to establishing an effective and reliable model to predict the outcome of PCa patients. METHODS We first identified differentially expressed genes between prostate cancer and normal prostate in TCGA-PRAD and then performed WGCNA to initially identify the candidate Gleason score related genes. Then, the candidate genes were applied to construct a LASSO Cox regression analysis model. Numerous independent validation cohorts, time-dependent receiver operating characteristic (ROC), univariate cox regression analysis, nomogram were used to test the effectiveness, accuracy and clinical utility of the prognostic model. Furthermore, functional analysis and immune cells infiltration were performed. RESULTS Gleason score-related differentially expressed candidates were identified and used to build up the outcome model in TCGA-PRAD cohort and was validated in MSKCC cohort. We found the 3-gene outcome model (CDC45, ESPL1 and RAD54L) had good performance in predicting recurrence free survival, metastasis free survival and overall survival of PCa patients. Time-dependent ROC and nomogram indicated an ideal predictive accuracy and clinical utility of the outcome model. Moreover, outcome model was enriched in 28 pathways by GSVA and GSEA. In addition, the risk score was positively correlated with memory B cells, native CD4 T cells, activated CD4 memory T cells and eosinophil, and negatively correlated with plasma cells, resting CD4 memory T cells, resting mast cells and neutrophil. CONCLUSIONS In summary, our outcome model proves to be an effective prognostic model for predicting the risk of prognosis in PCa.
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Affiliation(s)
- Yongzhi Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, 430071 China
| | - Zhonghua Yang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, 430071 China
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14
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Huo W, Qi F, Wang K. Long non-coding RNA FER1L4 inhibits prostate cancer progression via sponging miR-92a-3p and upregulation of FBXW7. Cancer Cell Int 2020; 20:64. [PMID: 32140077 PMCID: PMC7049228 DOI: 10.1186/s12935-020-1143-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 02/19/2020] [Indexed: 02/07/2023] Open
Abstract
Background Dysregulation of long non-coding RNAs (lncRNAs) is involved in development of prostate cancer. However, the molecular mechanisms of many lncRNAs in prostate cancer have not been studied yet. Methods The lncRNA Fer-1-like protein 4 (FER1L4) expression was explored in prostate tumors and normal prostate tissues by RT-qPCR and bioinformatic analysis. Overexpression of FER1L4 was performed to evaluate its role in prostate cancer cell proliferation and survival. The molecular mechanism of FER1L4 was investigated by dual luciferase reporter assay, RNA pull down assay, western blotting and RT-qPCR. Results It was found that FER1L4 was lower in prostate cancer tissues than normal tissues. Higher expression of FER1L4 was associated with prostate cancer tissues of early stage (AJCC stage I/II). Overexpression of FER1L4 inhibited cell proliferation and promoted cell apoptosis in prostate cancer cells. Bioinformatic analysis, RT-qPCR, RNA pull down assay and dual luciferase assay showed that FER1L4 upregulated F-box/WD repeat-containing protein 7 (FBXW7) tumor suppressor via sponging miR-92a-3p. Silencing of FBXW7 reversed the cell phenotypes caused by FER1L4 overexpression in prostate cancer cells. Conclusion The data demonstrated that FER1L4, a downregulated lncRNA in prostate cancer, was pivotal for cell proliferation and survival of prostate cancer. The study provided new sights into understanding of the signaling network in prostate cancer and implied that FER1L4 might be a biomarker for patients with prostate cancer.
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Affiliation(s)
- Wei Huo
- 1Department of Urology, China-Japan Union Hospital, Jilin University, 126 Xiantai Street, Changchun, 130001 People's Republic of China
| | - Fei Qi
- 2Department of Operating Room, China-Japan Union Hospital, Jilin University, Changchun, 130001 People's Republic of China
| | - Kaichen Wang
- 1Department of Urology, China-Japan Union Hospital, Jilin University, 126 Xiantai Street, Changchun, 130001 People's Republic of China
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