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Archer M, Begemann D, Gonzalez-Kozlova E, Nepali PR, Labanca E, Shepherd P, Dogra N, Navone N, Kyprianou N. Kinesin Facilitates Phenotypic Targeting of Therapeutic Resistance in Advanced Prostate Cancer. Mol Cancer Res 2024; 22:730-745. [PMID: 38648082 PMCID: PMC11296928 DOI: 10.1158/1541-7786.mcr-23-1047] [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: 12/15/2023] [Revised: 02/16/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Abstract
Understanding the mechanisms underlying resistance is critical to improving therapeutic outcomes in patients with metastatic castration-resistant prostate cancer. Previous work showed that dynamic interconversions between epithelial-mesenchymal transition to mesenchymal-epithelial transition defines the phenotypic landscape of prostate tumors, as a potential driver of the emergence of therapeutic resistance. In this study, we use in vitro and in vivo preclinical MDA PCa patient-derived xenograft models of resistant human prostate cancer to determine molecular mechanisms of cross-resistance between antiandrogen therapy and taxane chemotherapy, underlying the therapeutically resistant phenotype. Transcriptomic profiling revealed that resistant and sensitive prostate cancer C4-2B cells have a unique differential gene signature response to cabazitaxel. Gene pathway analysis showed that sensitive cells exhibit an increase in DNA damage, while resistant cells express genes associated with protein regulation in response to cabazitaxel. The patient-derived xenograft model specimens are from patients who have metastatic lethal castration-resistant prostate cancer, treated with androgen deprivation therapy, antiandrogens, and chemotherapy including second-line taxane chemotherapy, cabazitaxel. Immunohistochemistry revealed high expression of E-cadherin and low expression of vimentin resulting in redifferentiation toward an epithelial phenotype. Furthermore, the mitotic kinesin-related protein involved in microtubule binding and the SLCO1B3 transporter (implicated in cabazitaxel intracellular transport) are associated with resistance in these prostate tumors. Combinational targeting of kinesins (ispinesib) with cabazitaxel was more effective than single monotherapies in inducing cell death in resistant prostate tumors. Implications: Our findings are of translational significance in identifying kinesin as a novel target of cross-resistance toward enhancing therapeutic vulnerability and improved clinical outcomes in patients with advanced prostate cancer.
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Affiliation(s)
- Maddison Archer
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Diane Begemann
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Toxicology and Cancer Biology, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Edgar Gonzalez-Kozlova
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Prerna R. Nepali
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Estefania Labanca
- Department of GU Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Peter Shepherd
- Department of GU Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Navneet Dogra
- Department of Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology and Molecular & Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nora Navone
- Department of GU Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Natasha Kyprianou
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology and Molecular & Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Jia T, Liu C, Guo P, Xu Y, Wang W, Liu X, Wang S, Zhang X, Guo H. FOXA1 regulates ribosomal RNA transcription in prostate cancer. Prostate 2024; 84:967-976. [PMID: 38632701 DOI: 10.1002/pros.24714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/20/2024] [Accepted: 04/08/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Ribosome biogenesis is excessively activated in tumor cells, yet it is little known whether oncogenic transcription factors (TFs) are involved in the ribosomal RNA (rRNA) transactivation. METHODS Nucleolar proteomics data and large-scale immunofluorescence were re-analyzed to jointly identify the proteins localized at nucleolus. RNA-Seq data of five prostate cancer (PCa) cohorts were combined and integrated with multi-dimensional data to define the upregulated nucleolar TFs in PCa tissues. Then, ChIP-Seq data of PCa cell lines and two PCa clinical cohorts were re-analyzed to reveal the TF binding patterns at ribosomal DNA (rDNA) repeats. The TF binding at rDNA was validated by ChIP-qPCR. The effect of the TF on rRNA transcription was determined by rDNA luciferase reporter, nascent RNA synthesis, and global protein translation assays. RESULTS In this study, we reveal the role of oncogenic TF FOXA1 in regulating rRNA transcription within nucleolar organization regions. By analyzing human TFs in prostate cancer clinical datasets and nucleolar proteomics data, we identified that FOXA1 is partially localized in the nucleolus and correlated with global protein translation. Our extensive FOXA1 ChIP-Seq analysis provides robust evidence of FOXA1 binding across rDNA repeats in prostate cancer cell lines, primary tumors, and castration-resistant variants. Notably, FOXA1 occupancy at rDNA repeats correlates with histone modifications associated with active transcription, namely H3K27ac and H3K4me3. Reducing FOXA1 expression results in decreased transactivation at rDNA, subsequently diminishing global protein synthesis. CONCLUSIONS Our results suggest FOXA1 regulates aberrant ribosome biogenesis downstream of oncogenic signaling in prostate cancer.
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Affiliation(s)
- Tianwei Jia
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Chenxu Liu
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Ping Guo
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Yaning Xu
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Wenzheng Wang
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Xiaoyu Liu
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Song Wang
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Xianglin Zhang
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Haiyang Guo
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
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3
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Karthikeyan SK, Nuo X, Ferguson JE, Rais-Bahrami S, Qin ZS, Manne U, Netto GJ, Chandrashekar DS, Varambally S. Identification of androgen response-related lncRNAs in prostate cancer. Prostate 2023; 83:590-601. [PMID: 36760203 PMCID: PMC10038919 DOI: 10.1002/pros.24494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 11/11/2022] [Accepted: 01/16/2023] [Indexed: 02/11/2023]
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) are RNA molecules with over 200 nucleotides that do not code for proteins, but are known to be widely expressed and have key roles in gene regulation and cellular functions. They are also found to be involved in the onset and development of various cancers, including prostate cancer (PCa). Since PCa are commonly driven by androgen regulated signaling, mainly stimulated pathways, identification and determining the influence of lncRNAs in androgen response is useful and necessary. LncRNAs regulated by the androgen receptor (AR) can serve as potential biomarkers for PCa. In the present study, gene expression data analysis were performed to distinguish lncRNAs related to the androgen response pathway. METHODS AND RESULTS We used publicly available RNA-sequencing and ChIP-seq data to identify lncRNAs that are associated with the androgen response pathway. Using Universal Correlation Coefficient (UCC) and Pearson Correlation Coefficient (PCC) analyses, we found 15 lncRNAs that have (a) highly correlated expression with androgen response genes in PCa and are (b) differentially expressed in the setting of treatment with an androgen agonist as well as antagonist compared to controls. Using publicly available ChIP-seq data, we investigated the role of androgen/AR axis in regulating expression of these lncRNAs. We observed AR binding in the promoter regions of 5 lncRNAs (MIR99AHG, DUBR, DRAIC, PVT1, and COLCA1), showing the direct influence of AR on their expression and highlighting their association with the androgen response pathway. CONCLUSION By utilizing publicly available multiomics data and by employing in silico methods, we identified five candidate lncRNAs that are involved in the androgen response pathway. These lncRNAs should be investigated as potential biomarkers for PCa.
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Affiliation(s)
| | - Xu Nuo
- Collat School of Business, University of Alabama at Birmingham, Birmingham, AL, USA
| | - James E. Ferguson
- Department of Urology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Soroush Rais-Bahrami
- Department of Urology, University of Alabama at Birmingham, Birmingham, AL, USA
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Zhaohui S. Qin
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA
| | - Upender Manne
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - George J. Netto
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Sooryanarayana Varambally
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
- Informatics Institute, University of Alabama at Birmingham, Birmingham, AL, USA
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4
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Kakkat S, Pramanik P, Singh S, Singh AP, Sarkar C, Chakroborty D. Cardiovascular Complications in Patients with Prostate Cancer: Potential Molecular Connections. Int J Mol Sci 2023; 24:ijms24086984. [PMID: 37108147 PMCID: PMC10138415 DOI: 10.3390/ijms24086984] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/21/2023] [Accepted: 03/30/2023] [Indexed: 04/29/2023] Open
Abstract
Cardiovascular diseases (CVDs) and complications are often seen in patients with prostate cancer (PCa) and affect their clinical management. Despite acceptable safety profiles and patient compliance, androgen deprivation therapy (ADT), the mainstay of PCa treatment and chemotherapy, has increased cardiovascular risks and metabolic syndromes in patients. A growing body of evidence also suggests that patients with pre-existing cardiovascular conditions show an increased incidence of PCa and present with fatal forms of the disease. Therefore, it is possible that a molecular link exists between the two diseases, which has not yet been unraveled. This article provides insight into the connection between PCa and CVDs. In this context, we present our findings linking PCa progression with patients' cardiovascular health by performing a comprehensive gene expression study, gene set enrichment (GSEA) and biological pathway analysis using publicly available data extracted from patients with advanced metastatic PCa. We also discuss the common androgen deprivation strategies and CVDs most frequently reported in PCa patients and present evidence from various clinical trials that suggest that therapy induces CVD in PCa patients.
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Affiliation(s)
- Sooraj Kakkat
- Department of Pathology, University of South Alabama, Mobile, AL 36617, USA
- Cancer Biology Program, Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
| | - Paramahansa Pramanik
- Department of Mathematics and Statistics, University of South Alabama, Mobile, AL 36688, USA
| | - Seema Singh
- Department of Pathology, University of South Alabama, Mobile, AL 36617, USA
- Cancer Biology Program, Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Ajay Pratap Singh
- Department of Pathology, University of South Alabama, Mobile, AL 36617, USA
- Cancer Biology Program, Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Chandrani Sarkar
- Department of Pathology, University of South Alabama, Mobile, AL 36617, USA
- Cancer Biology Program, Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Debanjan Chakroborty
- Department of Pathology, University of South Alabama, Mobile, AL 36617, USA
- Cancer Biology Program, Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
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Zheng Y, Wang Y, He H, Zou Z, Lu H, Li J, Cai J, Wang K. Transcriptome Data Reveal Geographic Heterogeneity in Gene Expression in Patients with Prostate Cancer. Rep Biochem Mol Biol 2023; 12:92-101. [PMID: 37724140 PMCID: PMC10505463 DOI: 10.52547/rbmb.12.1.92] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/07/2023] [Indexed: 09/20/2023]
Abstract
Background The incidence of prostate cancer (PC) exhibits geographical heterogeneity. However, the metabolic mechanisms underlying this geographic heterogeneity remain unclear. This study aimed to reveal the metabolic mechanism of the geographic heterogeneity in the incidence of PC.This study aimed to investigate the anti-cancer effects of different gum extracts on metabolic changes and their impact on gene expression in HT-29 cell. Methods Transcriptomic data from public databases were obtained and analyzed to screen geographic-differentially expressed genes and metabolic pathways. Associations between these differentially expressed genes and the incidence of PC were determined to identify genes that were highly associated with PC incidence. A co-expression network analysis was performed to identify geographic-specific regulatory pathways. Results A total of 175 differentially expressed genes were identified in four countries and were associated with the regulation of DNA replication and the metabolism of pyrimidine, nucleotides, purines, and galactose.Additionally, the expression of the genes CLVS2, SCGB1A1, KCNK3, HHIPL2, MMP26, KCNJ15, and PNMT was highly correlated with the incidence of PC. Geographic-specific differentially expressed genes in low-incidence areas were highly correlated with KCNJ15, MMP26, KCNK3, and SCCB1A1, which play a major role in ion channel-related functions. Conclusions This study suggests that geographic heterogeneity in PC incidence is associated with the expression levels of genes associated with amino acid metabolism, lipid metabolism, and ion channels.
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Affiliation(s)
- Yi Zheng
- Center for Medical Experiments (CME), University of Chinese Academy Sciences-Shenzhen Hospital, Shenzhen, China.
| | - Yang Wang
- The Department of Urology of Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, China.
| | - Haitian He
- The Department of Urology of Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, China.
| | - Zhuping Zou
- The Operating Room of Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, China.
| | - Huiling Lu
- The Operating Room of Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, China.
| | | | - Jun Cai
- TB Healthcare Co., Ltd., Foshan, China.
| | - Kebing Wang
- The Department of Urology of Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, China.
- The Department of Urology of Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China.
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Li Y, Shi H, Zhao Z, Xu M. Identification of castration-dependent and -independent driver genes and pathways in castration-resistant prostate cancer (CRPC). BMC Urol 2022; 22:162. [PMID: 36258196 PMCID: PMC9580185 DOI: 10.1186/s12894-022-01113-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
Abstract
Background Prostate cancer (PCa) is one of the most diagnosed cancers in the world. PCa inevitably progresses to castration-resistant prostate cancer (CRPC) after androgen deprivation therapy treatment, and castration-resistant state means a shorter survival time than other causes. Here we aimed to define castration-dependent and -independent diver genes and molecular pathways in CRPC which are responsible for such lethal metastatic events. Methods By employing digital gene expression (DGE) profiling, the alterations of the epididymal gene expression profile in the mature and bilateral castrated rat were explored. Then we detect and characterize the castration-dependent and -independent genes and pathways with two data set of CPRC-associated gene expression profiles publicly available on the NCBI. Results We identified 1,632 up-regulated and 816 down-regulated genes in rat’s epididymis after bilateral castration. Differential expression analysis of CRPC samples compared with the primary PCa samples was also done. In contrast to castration, we identified 97 up-regulated genes and 128 down-regulated genes that changed in both GEO dataset and DGE profile, and 120 up-regulated genes and 136 down-regulated genes changed only in CRPC, considered as CRPC-specific genes independent of castration. CRPC-specific DEGs were mainly enriched in cell proliferation, while CRPC-castration genes were associated with prostate gland development. NUSAP1 and NCAPG were identified as key genes, which might be promising biomarkers of the diagnosis and prognosis of CRPC. Conclusion Our study will provide insights into gene regulation of CRPC dependent or independent of castration and will improve understandings of CRPC development and progression. Supplementary Information The online version contains supplementary material available at 10.1186/s12894-022-01113-5.
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Affiliation(s)
- Yan Li
- College of Life Sciences, Yantai University, 30th Qingquan Road, 264005, Yantai, Shandong Province, China.
| | - Hui Shi
- College of Life Sciences, Yantai University, 30th Qingquan Road, 264005, Yantai, Shandong Province, China
| | - Zhenjun Zhao
- College of Life Sciences, Yantai University, 30th Qingquan Road, 264005, Yantai, Shandong Province, China
| | - Minghui Xu
- School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, Guangdong Province, China
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Histone lysine demethylase inhibition reprograms prostate cancer metabolism and mechanics. Mol Metab 2022; 64:101561. [PMID: 35944897 PMCID: PMC9403566 DOI: 10.1016/j.molmet.2022.101561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 11/20/2022] Open
Abstract
Objective Methods Results Conclusions KDMs inhibition promotes increases H3K4me2 and H3K27me3 in PCa and CRPC, which causes cancer selective pro-apoptotic pathways. KDMs regulate AR expression in PCa and CRPC, reducing ATP production, mitochondrial respiration and intermediate metabolites availability. Epigenetic controls metabolic pathways and redirects lipid metabolic cascade. KDMs inhibition alters lipid distribution and composition, impacting on physical and mechanical properties of PCa and CRPC.
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8
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Jha A, Quesnel-Vallières M, Wang D, Thomas-Tikhonenko A, Lynch KW, Barash Y. Identifying common transcriptome signatures of cancer by interpreting deep learning models. Genome Biol 2022; 23:117. [PMID: 35581644 PMCID: PMC9112525 DOI: 10.1186/s13059-022-02681-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/27/2022] [Indexed: 01/01/2023] Open
Abstract
Background Cancer is a set of diseases characterized by unchecked cell proliferation and invasion of surrounding tissues. The many genes that have been genetically associated with cancer or shown to directly contribute to oncogenesis vary widely between tumor types, but common gene signatures that relate to core cancer pathways have also been identified. It is not clear, however, whether there exist additional sets of genes or transcriptomic features that are less well known in cancer biology but that are also commonly deregulated across several cancer types. Results Here, we agnostically identify transcriptomic features that are commonly shared between cancer types using 13,461 RNA-seq samples from 19 normal tissue types and 18 solid tumor types to train three feed-forward neural networks, based either on protein-coding gene expression, lncRNA expression, or splice junction use, to distinguish between normal and tumor samples. All three models recognize transcriptome signatures that are consistent across tumors. Analysis of attribution values extracted from our models reveals that genes that are commonly altered in cancer by expression or splicing variations are under strong evolutionary and selective constraints. Importantly, we find that genes composing our cancer transcriptome signatures are not frequently affected by mutations or genomic alterations and that their functions differ widely from the genes genetically associated with cancer. Conclusions Our results highlighted that deregulation of RNA-processing genes and aberrant splicing are pervasive features on which core cancer pathways might converge across a large array of solid tumor types. Supplementary Information The online version contains supplementary material available at (10.1186/s13059-022-02681-3).
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Affiliation(s)
- Anupama Jha
- Department of Computer and Information Science, School of Engineering and Applied Science, Philadelphia, USA.
| | - Mathieu Quesnel-Vallières
- Department of Genetics, Philadelphia, USA. .,Department of Biochemistry and Biophysics, Philadelphia, USA.
| | - David Wang
- Department of Genetics, Philadelphia, USA
| | - Andrei Thomas-Tikhonenko
- Department of Pathology and Laboratory Medicine, Philadelphia, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.,Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, Philadelphia, USA
| | - Yoseph Barash
- Department of Computer and Information Science, School of Engineering and Applied Science, Philadelphia, USA. .,Department of Genetics, Philadelphia, USA.
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Hawthorne B, Lund K, Freggiaro S, Kaga R, Meng J. The mechanism of the cytotoxic effect of Panax notoginseng extracts on prostate cancer cells. Biomed Pharmacother 2022; 149:112887. [PMID: 35367754 DOI: 10.1016/j.biopha.2022.112887] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 11/02/2022] Open
Abstract
INTRODUCTION Panax notoginseng (Burkill) F.H. commonly referred to as Sanqi, is a Chinese herb that has long been used to treat various conditions including blood disorders and cardiovascular diseases. While Panax notoginseng has been used as an anti-cancer medicinal herb in recent years, how it achieves this therapeutic effect has not been thoroughly elucidated. The purpose of this study was to reveal more about the mechanism of the cytotoxic effect of Panax notoginseng on prostate cancer (PCa) cells. METHODS Ethanol extract of Panax notoginseng root was authenticated using high-performance liquid chromatography (HPLC). The cytotoxic activity of this herb against PCa cells was determined using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) method, flow cytometry, and enzyme-linked immunosorbent assay (ELISA). RESULTS The assessment of cellular metabolic activity demonstrated that Panax notoginseng reduces the viability of LNCaP and 22Rv1 cells in a dose-dependent manner. Annexin-V binding flow cytometry assay showed that Panax notoginseng induces apoptosis in PCa cells. Cell cycle analysis by quantification of DNA content using flow cytometry showed that Panax notoginseng arrests the cell cycle at the G2/M phase in both LNCaP and 22Rv1 cells. Moreover, ELISA demonstrated that Panax notoginseng-treated PCa cells secrete significantly less tumor-promoting cytokine interleukin-4 (IL-4) to the supernatant compared with controls. CONCLUSIONS These results provide evidence for the cytotoxic effects of Panax notoginseng on PCa cell lines. This botanical is a promising candidate for the complementary and integrative medicine treatment of PCa and further studies are indicated to determine the anti-cancer mechanism of Panax notoginseng.
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Affiliation(s)
- Benjamin Hawthorne
- School of Naturopathic Medicine, Bastyr University, 14500 Juanita Drive NE, Kenmore, WA 98028, USA
| | - Kaleb Lund
- School of Naturopathic Medicine, Bastyr University, 14500 Juanita Drive NE, Kenmore, WA 98028, USA
| | - Sydney Freggiaro
- School of Naturopathic Medicine, Bastyr University, 14500 Juanita Drive NE, Kenmore, WA 98028, USA
| | - Risa Kaga
- School of Natural Health Arts & Sciences, Bastyr University, 14500 Juanita Drive NE, Kenmore, WA 98028, USA
| | - Jing Meng
- School of Natural Health Arts & Sciences, Bastyr University, 14500 Juanita Drive NE, Kenmore, WA 98028, USA.
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10
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Goel S, Bhatia V, Kundu S, Biswas T, Carskadon S, Gupta N, Asim M, Morrissey C, Palanisamy N, Ateeq B. Transcriptional network involving ERG and AR orchestrates Distal-less homeobox-1 mediated prostate cancer progression. Nat Commun 2021; 12:5325. [PMID: 34493733 PMCID: PMC8423767 DOI: 10.1038/s41467-021-25623-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 08/20/2021] [Indexed: 02/07/2023] Open
Abstract
Distal-less homeobox-1 (DLX1) is a well-established non-invasive biomarker for prostate cancer (PCa) diagnosis, however, its mechanistic underpinnings in disease pathobiology are not known. Here, we reveal the oncogenic role of DLX1 and show that abrogating its function leads to reduced tumorigenesis and metastases. We observed that ~60% of advanced-stage and metastatic patients display higher DLX1 levels. Moreover, ~96% of TMPRSS2-ERG fusion-positive and ~70% of androgen receptor (AR)-positive patients show elevated DLX1, associated with aggressive disease and poor survival. Mechanistically, ERG coordinates with enhancer-bound AR and FOXA1 to drive transcriptional upregulation of DLX1 in ERG-positive background. However, in ERG-negative context, AR/AR-V7 and FOXA1 suffice to upregulate DLX1. Notably, inhibiting ERG/AR-mediated DLX1 transcription using BET inhibitor (BETi) or/and anti-androgen drugs reduce its expression and downstream oncogenic effects. Conclusively, this study establishes DLX1 as a direct-target of ERG/AR with an oncogenic role and demonstrates the clinical significance of BETi and anti-androgens for DLX1-positive patients.
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Affiliation(s)
- Sakshi Goel
- grid.417965.80000 0000 8702 0100Molecular Oncology Laboratory, Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, U.P. India
| | - Vipul Bhatia
- grid.417965.80000 0000 8702 0100Molecular Oncology Laboratory, Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, U.P. India
| | - Sushmita Kundu
- grid.417965.80000 0000 8702 0100Molecular Oncology Laboratory, Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, U.P. India
| | - Tanay Biswas
- grid.417965.80000 0000 8702 0100Molecular Oncology Laboratory, Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, U.P. India
| | - Shannon Carskadon
- grid.239864.20000 0000 8523 7701Vattikuti Urology Institute, Department of Urology, Henry Ford Health System, Detroit, MI USA
| | - Nilesh Gupta
- grid.239864.20000 0000 8523 7701Department of Pathology, Henry Ford Health System, Detroit, MI USA
| | - Mohammad Asim
- grid.5475.30000 0004 0407 4824Department of Clinical and Experimental Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Colm Morrissey
- grid.34477.330000000122986657Department of Urology, University of Washington, Seattle, WA USA
| | - Nallasivam Palanisamy
- grid.239864.20000 0000 8523 7701Vattikuti Urology Institute, Department of Urology, Henry Ford Health System, Detroit, MI USA
| | - Bushra Ateeq
- grid.417965.80000 0000 8702 0100Molecular Oncology Laboratory, Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, U.P. India ,grid.417965.80000 0000 8702 0100The Mehta Family Center for Engineering in Medicine, Indian Institute of Technology Kanpur, Kanpur, U.P. India
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11
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Segura-Moreno YY, Sanabria-Salas MC, Varela R, Mesa JA, Serrano ML. Decoding the heterogeneous landscape in the development prostate cancer. Oncol Lett 2021; 21:376. [PMID: 33777200 PMCID: PMC7988715 DOI: 10.3892/ol.2021.12637] [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: 01/07/2020] [Accepted: 06/02/2020] [Indexed: 01/02/2023] Open
Abstract
Prostate cancer (PCa) is characterized as being histologically and molecularly heterogeneous; however, this is not only incorrect among individuals, but also at the multiple foci level, which originates in the prostate gland itself. The reasons for such heterogeneity have not been fully elucidated; however, understanding these may be crucial in determining the course of the disease. PCa is characterized by a complex network of chromosomal rearrangements, which simultaneously deregulate multiple genes; this could explain the appearance of exclusive events associated with molecular subtypes, which have been extensively investigated to establish clinical management and the development of therapies targeted to this type of cancer. From a clinical aspect, the prognosis of the patient has focused on the characteristics of the index lesion (the largest focus in PCa); however, a significant percentage of patients (11%) also exhibit an aggressive secondary foci, which may determine the prognosis of the disease, and could be the determining factor of why, in different studies, the classification of the subtypes does not have an association with prognosis. Due to the aforementioned reasons, the analysis of molecular subtypes in several foci, from the same individual could assist in determining the association between clinical evolution and management of patients with PCa. Castration-resistant PCa (CRPC) has the worst prognosis and develops following androgen ablation therapy. Currently, there are two models to explain the development of CRPC: i) The selection model and ii) the adaptation model; both of which, have been found to include alterations described in the molecular subtypes, such as Enhancer of zeste 2 polycomb repressive complex 2 subunit overexpression, isocitrate dehydrogenase (NAPD+)1 and forkhead box A1 mutations, suggesting that the presence of specific molecular alterations could predict the development of CRPC. This type of analysis could lead to a biological understanding of PCa, to develop personalized medicine strategies, which could improve the response to treatment thus, avoiding the development of resistance. Therefore, the present review discusses the primary molecular factors, to which variable heterogeneity in PCa progress has been attributed.
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Affiliation(s)
- Yenifer Yamile Segura-Moreno
- Cancer Biology Research Group, National Institute of Cancerology, Bogota 110411, Colombia.,Department of Chemistry, Faculty of Sciences, National University of Colombia, University City, Bogota 111321, Colombia
| | | | - Rodolfo Varela
- Department of Urology, National Institute of Cancerology, Bogota 110411, Colombia.,Department of Urology, National University of Colombia, University City, Bogota 111321, Colombia
| | - Jorge Andrés Mesa
- Department of Pathology, National Institute of Cancerology, Bogota 110411, Colombia
| | - Martha Lucia Serrano
- Cancer Biology Research Group, National Institute of Cancerology, Bogota 110411, Colombia.,Department of Chemistry, Faculty of Sciences, National University of Colombia, University City, Bogota 111321, Colombia
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12
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Epigenetic reprogramming during prostate cancer progression: A perspective from development. Semin Cancer Biol 2021; 83:136-151. [PMID: 33545340 DOI: 10.1016/j.semcancer.2021.01.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/27/2021] [Accepted: 01/27/2021] [Indexed: 12/15/2022]
Abstract
Conrad Waddington's theory of epigenetic landscape epitomize the process of cell fate and cellular decision-making during development. Wherein the epigenetic code maintains patterns of gene expression in pluripotent and differentiated cellular states during embryonic development and differentiation. Over the years disruption or reprogramming of the epigenetic landscape has been extensively studied in the course of cancer progression. Cellular dedifferentiation being a key hallmark of cancer allow us to take cues from the biological processes involved during development. Here, we discuss the role of epigenetic landscape and its modifiers in cell-fate determination, differentiation and prostate cancer progression. Lately, the emergence of RNA-modifications has also furthered our understanding of epigenetics in cancer. The overview of the epigenetic code regulating androgen signalling, and progression to aggressive neuroendocrine stage of PCa reinforces its gene regulatory functions during the development of prostate gland as well as cancer progression. Additionally, we also highlight the clinical implications of cancer cell epigenome, and discuss the recent advancements in the therapeutic strategies targeting the advanced stage disease.
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13
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Identification of key genes and pathways in castrate-resistant prostate cancer by integrated bioinformatics analysis. Pathol Res Pract 2020; 216:153109. [DOI: 10.1016/j.prp.2020.153109] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 07/03/2020] [Accepted: 07/08/2020] [Indexed: 12/24/2022]
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14
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Immune signature driven by ADT-induced immune microenvironment remodeling in prostate cancer is correlated with recurrence-free survival and immune infiltration. Cell Death Dis 2020; 11:779. [PMID: 32951005 PMCID: PMC7502080 DOI: 10.1038/s41419-020-02973-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 08/12/2020] [Accepted: 08/27/2020] [Indexed: 12/09/2022]
Abstract
Androgen deprivation therapy (ADT) is a cornerstone treatment for locally advanced or metastatic prostate cancer (PCa). However, its potential effects on the tumor immune microenvironment (TIM) of PCa patients and the underlying mechanism remain largely unclear. To explore the effects of ADT on PCa TIM, RNA sequencing was performed on six paired pre-ADT biopsy and post-ADT PCa lesions, and five paired paracancerous benign tissues from patients receiving neoadjuvant ADT with locally advanced PCa. Bioinformatics methods including ESTIMATE and ssGSEA were used to evaluate the stromal immune score and immune cell infiltration in PCa and paracancerous tissues. Weighted correlation network analysis was used to screen hub genes in the ADT-induced immune remodeling process. The results showed differences exist between PCa and paracancerous tissues in response to ADT. Compared with paracancerous tissues, the immune remodeling effect of ADT in PCa was more intense. ZFP36, JUNB, and SOCS3 served as hub genes in the ADT-induced immune remodeling process and were associated with PSA recurrent-free survival in the TCGA and our neoadjuvant ADT cohort. To investigate the joint action of the above three hub genes, an immune signature score was constructed. The results showed that immune signature score-based immune subtypes reveal the heterogeneity of the immune microenvironment of PCa and showed significant differences in patient prognosis, tumor immune infiltration, mutation burden, and landscape.
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15
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Androgen receptor signaling regulates the transcriptome of prostate cancer cells by modulating global alternative splicing. Oncogene 2020; 39:6172-6189. [PMID: 32820253 PMCID: PMC7515832 DOI: 10.1038/s41388-020-01429-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 07/28/2020] [Accepted: 08/10/2020] [Indexed: 12/13/2022]
Abstract
Androgen receptor (AR), is a transcription factor and a member of a hormone receptor superfamily. AR plays a vital role in the progression of prostate cancer and is a crucial target for therapeutic interventions. While the majority of advanced-stage prostate cancer patients will initially respond to the androgen deprivation, the disease often progresses to castrate-resistant prostate cancer (CRPC). Interestingly, CRPC tumors continue to depend on hyperactive AR signaling and will respond to potent second-line antiandrogen therapies, including bicalutamide (CASODEX®) and enzalutamide (XTANDI®). However, the progression-free survival rate for the CRPC patients on antiandrogen therapies is only 8–19 months. Hence, there is a need to understand the mechanisms underlying CRPC progression and eventual treatment resistance. Here, we have leveraged next-generation sequencing and newly developed analytical methodologies to evaluate the role of AR signaling in regulating the transcriptome of prostate cancer cells. The genomic and pharmacologic stimulation and inhibition of AR activity demonstrates that AR regulates alternative splicing within cancer-relevant genes. Furthermore, by integrating transcriptomic data from in vitro experiments and in prostate cancer patients, we found that a significant number of AR-regulated splicing events are associated with tumor progression. For example, we found evidence for an inadvertent AR-antagonist-mediated switch in IDH1 and PL2G2A isoform expression, which is associated with a decrease in overall survival of patients. Mechanistically, we discovered that the epithelial-specific splicing regulators (ESRP1 and ESRP2), flank many AR-regulated alternatively spliced exons. And, using 2D invasion assays, we show that the inhibition of ESRPs can suppress AR-antagonist-driven tumor invasion. Our work provides evidence for a new mechanism by which AR alters the transcriptome of prostate cancer cells by modulating alternative splicing. As such, our work has important implications for CRPC progression and development of resistance to treatment with bicalutamide and enzalutamide.
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16
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Traka MH, Melchini A, Coode-Bate J, Al Kadhi O, Saha S, Defernez M, Troncoso-Rey P, Kibblewhite H, O'Neill CM, Bernuzzi F, Mythen L, Hughes J, Needs PW, Dainty JR, Savva GM, Mills RD, Ball RY, Cooper CS, Mithen RF. Transcriptional changes in prostate of men on active surveillance after a 12-mo glucoraphanin-rich broccoli intervention-results from the Effect of Sulforaphane on prostate CAncer PrEvention (ESCAPE) randomized controlled trial. Am J Clin Nutr 2019; 109:1133-1144. [PMID: 30982861 PMCID: PMC6462431 DOI: 10.1093/ajcn/nqz012] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 01/18/2019] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Epidemiological evidence suggests that consumption of cruciferous vegetables is associated with reduced risk of prostate cancer progression, largely attributed to the biological activity of glucosinolate degradation products, such as sulforaphane derived from glucoraphanin. Because there are few therapeutic interventions for men on active surveillance for prostate cancer to reduce the risk of cancer progression, dietary approaches are an appealing option for patients. OBJECTIVE We evaluated whether consumption of a glucoraphanin-rich broccoli soup for 1 y leads to changes in gene expression in prostate tissue of men with localized prostate cancer. METHODS Forty-nine men on active surveillance completed a 3-arm parallel randomized double-blinded intervention study for 12 mo and underwent transperineal template biopsy procedures and dietary assessment at the start and end of the study. Patients received a weekly 300 mL portion of soup made from a standard broccoli (control) or from 1 of 2 experimental broccoli genotypes with enhanced concentrations of glucoraphanin, delivering 3 and 7 times that of the control, respectively. Gene expression in tissues from each patient obtained before and after the dietary intervention was quantified by RNA sequencing followed by gene set enrichment analyses. RESULTS In the control arm, there were several hundred changes in gene expression in nonneoplastic tissue during the 12 mo. These were associated with an increase in expression of potentially oncogenic pathways including inflammation processes and epithelial-mesenchymal transition. Changes in gene expression and associated oncogenic pathways were attenuated in men on the glucoraphanin-rich broccoli soup in a dose-dependent manner. Although the study was not powered to assess clinical progression, an inverse association between consumption of cruciferous vegetables and cancer progression was observed. CONCLUSION Consuming glucoraphanin-rich broccoli soup affected gene expression in the prostate of men on active surveillance, consistent with a reduction in the risk of cancer progression. This trial was registered at clinicaltrials.gov as NCT01950143.
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Affiliation(s)
- Maria H Traka
- Quadram Institute Bioscience, Norwich, United Kingdom
| | | | - Jack Coode-Bate
- Quadram Institute Bioscience, Norwich, United Kingdom,Department of Urology, Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, United Kingdom
| | - Omar Al Kadhi
- Quadram Institute Bioscience, Norwich, United Kingdom,Department of Urology, Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, United Kingdom
| | - Shikha Saha
- Quadram Institute Bioscience, Norwich, United Kingdom
| | | | | | | | | | | | - Laura Mythen
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Jackie Hughes
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Paul W Needs
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Jack R Dainty
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | | | - Robert D Mills
- Department of Urology, Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, United Kingdom
| | - Richard Y Ball
- Norfolk and Waveney Cellular Pathology Service, Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, United Kingdom
| | - Colin S Cooper
- Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Richard F Mithen
- Quadram Institute Bioscience, Norwich, United Kingdom,Liggins Institute, University of Auckland, New Zealand,Address correspondence to RFM (e-mail: )
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