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Nurminen A, Jaatinen S, Taavitsainen S, Högnäs G, Lesluyes T, Ansari-Pour N, Tolonen T, Haase K, Koskenalho A, Kankainen M, Jasu J, Rauhala H, Kesäniemi J, Nikupaavola T, Kujala P, Rinta-Kiikka I, Riikonen J, Kaipia A, Murtola T, Tammela TL, Visakorpi T, Nykter M, Wedge DC, Van Loo P, Bova GS. Cancer origin tracing and timing in two high-risk prostate cancers using multisample whole genome analysis: prospects for personalized medicine. Genome Med 2023; 15:82. [PMID: 37828555 PMCID: PMC10571458 DOI: 10.1186/s13073-023-01242-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 10/02/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND Prostate cancer (PrCa) genomic heterogeneity causes resistance to therapies such as androgen deprivation. Such heterogeneity can be deciphered in the context of evolutionary principles, but current clinical trials do not include evolution as an essential feature. Whether or not analysis of genomic data in an evolutionary context in primary prostate cancer can provide unique added value in the research and clinical domains remains an open question. METHODS We used novel processing techniques to obtain whole genome data together with 3D anatomic and histomorphologic analysis in two men (GP5 and GP12) with high-risk PrCa undergoing radical prostatectomy. A total of 22 whole genome-sequenced sites (16 primary cancer foci and 6 lymph node metastatic) were analyzed using evolutionary reconstruction tools and spatio-evolutionary models. Probability models were used to trace spatial and chronological origins of the primary tumor and metastases, chart their genetic drivers, and distinguish metastatic and non-metastatic subclones. RESULTS In patient GP5, CDK12 inactivation was among the first mutations, leading to a PrCa tandem duplicator phenotype and initiating the cancer around age 50, followed by rapid cancer evolution after age 57, and metastasis around age 59, 5 years prior to prostatectomy. In patient GP12, accelerated cancer progression was detected after age 54, and metastasis occurred around age 56, 3 years prior to prostatectomy. Multiple metastasis-originating events were identified in each patient and tracked anatomically. Metastasis from prostate to lymph nodes occurred strictly ipsilaterally in all 12 detected events. In this pilot, metastatic subclone content analysis appears to substantially enhance the identification of key drivers. Evolutionary analysis' potential impact on therapy selection appears positive in these pilot cases. CONCLUSIONS PrCa evolutionary analysis allows tracking of anatomic site of origin, timing of cancer origin and spread, and distinction of metastatic-capable from non-metastatic subclones. This enables better identification of actionable targets for therapy. If extended to larger cohorts, it appears likely that similar analyses could add substantial biological insight and clinically relevant value.
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Affiliation(s)
- Anssi Nurminen
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Serafiina Jaatinen
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Sinja Taavitsainen
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Gunilla Högnäs
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Tom Lesluyes
- The Francis Crick Institute, London, NW1 1AT, UK
| | - Naser Ansari-Pour
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Teemu Tolonen
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere, Finland
| | - Kerstin Haase
- The Francis Crick Institute, London, NW1 1AT, UK
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität Zu Berlin, ECRC Experimental and Clinical Research Center, Berlin, Germany
| | - Antti Koskenalho
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Matti Kankainen
- Institute for Molecular Medicine Finland, University of Helsinki, Tukholmankatu 8, Helsinki, 00290, Finland
| | - Juho Jasu
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Hanna Rauhala
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Jenni Kesäniemi
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Tiia Nikupaavola
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Paula Kujala
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere, Finland
| | - Irina Rinta-Kiikka
- Imaging Centre, Department of Radiology, Tampere University Hospital, Tampere, Finland
| | - Jarno Riikonen
- Department of Urology, TAYS Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Antti Kaipia
- Department of Urology, TAYS Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Teemu Murtola
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
- Department of Urology, TAYS Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Teuvo L Tammela
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
- Department of Urology, TAYS Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Tapio Visakorpi
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere, Finland
| | - Matti Nykter
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - David C Wedge
- Manchester Cancer Research Centre, Division of Cancer Sciences, University of Manchester, Manchester, M20 4GJ, UK
| | - Peter Van Loo
- The Francis Crick Institute, London, NW1 1AT, UK
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - G Steven Bova
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland.
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2
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Sattari M, Kohvakka A, Moradi E, Rauhala H, Urhonen H, Isaacs WB, Nykter M, Murtola TJ, Tammela TLJ, Latonen L, Bova GS, Kesseli J, Visakorpi T. Identification of long noncoding RNAs with aberrant expression in prostate cancer metastases. Endocr Relat Cancer 2023:ERC-22-0247. [PMID: 37140987 DOI: 10.1530/erc-22-0247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 05/03/2023] [Indexed: 05/05/2023]
Abstract
Prostate cancer (PCa) is the second-most common cause of male cancer-related death in western industrialized countries, and the emergence of metastases is a key challenge in the treatment of PCa. Accumulating studies have shown that long noncoding RNAs (lncRNAs) play an important role in the regulation of diverse cellular and molecular processes during the development and progression of cancer. Here, we utilized a unique cohort of castration-resistant prostate cancer metastases (mCRPC) and corresponding localized tumors and RNA sequencing (RNA-seq). First, we showed that patient-to-patient variability accounted for most of the variance in lncRNA expression between the samples, suggesting that genomic alterations in the samples are the main drivers of lncRNA expression in PCa metastasis. Subsequently, we identified 27 lncRNAs with differential expression (DE-lncRNAs) between metastases and corresponding primary tumors, suggesting that they are mCRPC-specific lncRNAs. Analyses of potential regulation by transcription factors (TFs) revealed that approximately half of the DE-lncRNAs have at least one binding site for the androgen receptor (AR) in their regulatory regions. In addition, transcription factor enrichment analysis revealed the enrichment of binding sites for PCa-associated TFs, such as FOXA1 and HOXB13, in the regulatory regions of the DE-lncRNAs. In a cohort of prostatectomy-treated prostate tumors, four of the DE-lncRNAs showed association with progression-free time, and two of them (lnc-SCFD2-2, and lnc-R3HCC1L-8) were independent prognostic markers. Our study highlights several mCRPC-specific lncRNAs that might be important in the progression of the disease to the metastatic stage and may also serve as potential biomarkers for aggressive PCa.
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Affiliation(s)
- Mina Sattari
- M Sattari, faculty of medicine and health technology, Tampere University, Tampere, 33014, Finland
| | - Annika Kohvakka
- A Kohvakka, Faculty of medicine and health technology, Tampere University, Tampere, Finland
| | - Elaheh Moradi
- E Moradi, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland - Kuopio Campus, Kuopio, Finland
| | - Hanna Rauhala
- H Rauhala, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Henna Urhonen
- H Urhonen, Faculty of medicine and health technology, Tampere University, Tampere, Finland
| | - William B Isaacs
- W Isaacs, The James Buchanan Brady Urological Institute, Johns Hopkins, Baltimore, United States
| | - Matti Nykter
- M Nykter, Faculty of medicine and health technology, Tays Cancer Center, Tampere, Finland
| | - Teemu J Murtola
- T Murtola, Faculty of Medicine and Health Technology, Tampere Universities, Tampere, Finland
| | - Teuvo L J Tammela
- T Tammela, Faculty of medicine and health technology, Tampere University, Tampere, Finland
| | - Leena Latonen
- L Latonen, Institute of Biomedicine, University of Eastern Finland School of Medicine, Kuopio, Finland
| | - G Steven Bova
- G Bova, Faculty of medicine and health technology, Tampere University, Tampere, Finland
| | - Juha Kesseli
- J Kesseli, Faculty of medicine and health technology, Tampere University, Tampere, Finland
| | - Tapio Visakorpi
- T Visakorpi, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
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3
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Kiviaho A, Kallio HM, Eerola SK, Vuorinen EM, Häkkinen T, Taavitsainen S, Afyounian E, Tolonen T, Kesseli J, Urbanucci A, Rautajoki KJ, Tammela TL, Visakorpi T, Nykter M. Abstract 5644: Spatially resolved transcriptomics points to distinct malignant cell populations within primary and castration resistant prostate cancer. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-5644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Background: Prostate cancer (PCa) is the second most common cancer in men. Despite its high prevalence, many patients carry an indolent form of the disease and are thus suspect to overtreatment. Conversely, some cases treated with androgen deprivation therapy can develop into castration resistant prostate cancer (CRPC), for which there is no curative treatment. Understanding why some tumors are more aggressive than others could lead to more accurate patient risk stratification. Here we characterize cancer and normal cell subpopulations within prostate tissue in their spatial context using a multimodal integrative approach.
Methods: We performed spatially resolved transcriptomics (ST) on a set of primary tumor PCa, CRPC and benign prostatic hyperplasia (BPH) patient samples. In addition to ST, we produced RNA-seq, DNA-seq and assay for transposase accessible chromatin using sequencing (ATAC-seq) data, allowing for multiomic integration within and across sample categories. We performed extensive analysis of ST data, employing unsupervised clustering, spot expression signal deconvolution, differential gene expression analysis and copy number variation (CNV) inference.
Main Results: The systematic analysis of spot expression profiles revealed a high degree of variation in nearby tissue regions, as we found up to three unique luminal cell populations inside a one millimeter radius in PCa. Similarly in locally recurrent CRPC, we identified cumulative CNVs in proximal luminal cell populations, with the inferred CNV profiles validated through DNA-seq. A set of marker genes was calculated for each unique cell population, with multiple PCa associated genes found to be differentially expressed. Although we observed significant variation in the luminal cell populations, the stromal gene expression was markedly similar across all samples.
Conclusions: We discovered shared, similar and unique cell populations both within and across different PCa and CRPC sections. We observed various luminal cell populations with distinct gene expression profiles in samples from both progression stages. The close spatial proximity of these cell clusters suggests that ST can be used to discover and examine finely detailed populations in their original spatial environment.
Citation Format: Antti Kiviaho, Heini M. Kallio, Sini K. Eerola, Elisa M. Vuorinen, Tomi Häkkinen, Sinja Taavitsainen, Ebrahim Afyounian, Teemu Tolonen, Juha Kesseli, Alfonso Urbanucci, Kirsi J. Rautajoki, Teuvo L. Tammela, Tapio Visakorpi, Matti Nykter. Spatially resolved transcriptomics points to distinct malignant cell populations within primary and castration resistant prostate cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5644.
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Affiliation(s)
- Antti Kiviaho
- 1Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Heini M. Kallio
- 1Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Sini K. Eerola
- 1Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Elisa M. Vuorinen
- 1Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Tomi Häkkinen
- 1Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Sinja Taavitsainen
- 1Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Ebrahim Afyounian
- 1Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Teemu Tolonen
- 1Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Juha Kesseli
- 1Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Alfonso Urbanucci
- 1Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Kirsi J. Rautajoki
- 1Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Teuvo L. Tammela
- 1Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Tapio Visakorpi
- 1Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Matti Nykter
- 1Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
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4
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Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD, Spellman PT, Wedge DC, Van Loo P, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Gonzalez S, Rubanova Y, Macintyre G, Adams DJ, Anur P, Beroukhim R, Boutros PC, Bowtell DD, Campbell PJ, Cao S, Christie EL, Cmero M, Cun Y, Dawson KJ, Demeulemeester J, Donmez N, Drews RM, Eils R, Fan Y, Fittall M, Garsed DW, Getz G, Ha G, Imielinski M, Jerman L, Ji Y, Kleinheinz K, Lee J, Lee-Six H, Livitz DG, Malikic S, Markowetz F, Martincorena I, Mitchell TJ, Mustonen V, Oesper L, Peifer M, Peto M, Raphael BJ, Rosebrock D, Sahinalp SC, Salcedo A, Schlesner M, Schumacher S, Sengupta S, Shi R, Shin SJ, Spiro O, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Stein LD, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Vázquez-García I, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Vembu S, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Wheeler DA, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Yang TP, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Yao X, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Yuan K, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Zhu H, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Wang W, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Morris QD, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Spellman PT, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Wedge DC, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Van Loo P, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Spellman PT, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Wedge DC, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Van Loo P, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Aaltonen LA, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Abascal F, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Abeshouse A, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Aburatani H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Adams DJ, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Agrawal N, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Ahn KS, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Ahn SM, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Aikata H, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Akbani R, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Akdemir KC, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Al-Ahmadie H, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Al-Sedairy ST, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Al-Shahrour F, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Alawi M, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Albert M, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Aldape K, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Alexandrov LB, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Ally A, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Alsop K, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Alvarez EG, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Amary F, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Amin SB, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Aminou B, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Ammerpohl O, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Anderson MJ, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Ang Y, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, Antonello D, von Mering C, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, 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D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen 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Author Correction: The evolutionary history of 2,658 cancers. Nature 2023; 614:E42. [PMID: 36697833 PMCID: PMC9931577 DOI: 10.1038/s41586-022-05601-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK. .,European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany. .,Wellcome Sanger Institute, Cambridge, UK.
| | - Clemency Jolly
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Ignaty Leshchiner
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Stefan C. Dentro
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK
| | - Santiago Gonzalez
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Daniel Rosebrock
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Thomas J. Mitchell
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Yulia Rubanova
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Pavana Anur
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - Kaixian Yu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Maxime Tarabichi
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Amit Deshwar
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Jeff Wintersinger
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Kortine Kleinheinz
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Heidelberg University, Heidelberg, Germany
| | - Ignacio Vázquez-García
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Kerstin Haase
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Lara Jerman
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK ,grid.8954.00000 0001 0721 6013University of Ljubljana, Ljubljana, Slovenia
| | - Subhajit Sengupta
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA
| | - Geoff Macintyre
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Salem Malikic
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Nilgun Donmez
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Dimitri G. Livitz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Marek Cmero
- grid.1008.90000 0001 2179 088XUniversity of Melbourne, Melbourne, Victoria Australia ,grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute, Melbourne, Victoria Australia
| | - Jonas Demeulemeester
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.5596.f0000 0001 0668 7884University of Leuven, Leuven, Belgium
| | - Steven Schumacher
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Yu Fan
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Xiaotong Yao
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Juhee Lee
- grid.205975.c0000 0001 0740 6917University of California Santa Cruz, Santa Cruz, CA USA
| | - Matthias Schlesner
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul C. Boutros
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.419890.d0000 0004 0626 690XOntario Institute for Cancer Research, Toronto, Ontario Canada ,grid.19006.3e0000 0000 9632 6718University of California, Los Angeles, CA USA
| | - David D. Bowtell
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, Victoria Australia
| | - Hongtu Zhu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Gad Getz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA USA ,grid.32224.350000 0004 0386 9924Department of Pathology, Massachusetts General Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Marcin Imielinski
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Rameen Beroukhim
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - S. Cenk Sahinalp
- grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada ,grid.411377.70000 0001 0790 959XIndiana University, Bloomington, IN USA
| | - Yuan Ji
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA ,grid.170205.10000 0004 1936 7822The University of Chicago, Chicago, IL USA
| | - Martin Peifer
- grid.6190.e0000 0000 8580 3777University of Cologne, Cologne, Germany
| | - Florian Markowetz
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ville Mustonen
- grid.7737.40000 0004 0410 2071University of Helsinki, Helsinki, Finland
| | - Ke Yuan
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK ,grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Wenyi Wang
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Quaid D. Morris
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | | | - Paul T. Spellman
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - David C. Wedge
- grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK ,grid.454382.c0000 0004 7871 7212Oxford NIHR Biomedical Research Centre, Oxford, UK
| | - Peter Van Loo
- The Francis Crick Institute, London, UK. .,University of Leuven, Leuven, Belgium.
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Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z, Wu K, Yang H, Fonseca NA, Kahles A, Lehmann KV, Urban L, Soulette CM, Shiraishi Y, Liu F, He Y, Demircioğlu D, Davidson NR, Calabrese C, Zhang J, Perry MD, Xiang Q, Greger L, Li S, Liu D, Stark SG, Zhang F, Amin SB, Bailey P, Chateigner A, Cortés-Ciriano I, Craft B, Erkek S, Frenkel-Morgenstern M, Goldman M, Hoadley KA, Hou Y, Huska MR, Khurana E, Kilpinen H, Korbel JO, Lamaze FC, Li C, Li X, Li X, Liu X, Marin MG, Markowski J, Nandi T, Nielsen MM, Ojesina AI, Pan-Hammarström Q, Park PJ, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Pedamallu CS, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pedersen JS, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Siebert R, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Su H, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Tan P, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Teh BT, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Wang J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Waszak SM, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Xiong H, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Yakneen S, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Ye C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Yung C, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Zhang X, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Zheng L, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Zhu J, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Zhu S, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Awadalla P, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Creighton CJ, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Meyerson M, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Ouellette BFF, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Wu K, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Yang H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Göke J, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Schwarz RF, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Stegle O, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Zhang Z, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Brazma A, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Rätsch G, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Brooks AN, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Brazma A, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Brooks AN, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Göke J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Rätsch G, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Schwarz RF, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Stegle O, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Zhang Z, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Aaltonen LA, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Abascal F, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Abeshouse A, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Aburatani H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Adams DJ, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Agrawal N, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Ahn KS, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Ahn SM, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Aikata H, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, Akbani R, von Mering C, Akdemir KC, Al-Ahmadie H, Al-Sedairy ST, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov LB, Ally A, Alsop K, Alvarez EG, Amary F, Amin SB, Aminou B, Ammerpohl O, Anderson MJ, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV. Author Correction: Genomic basis for RNA alterations in cancer. Nature 2023; 614:E37. [PMID: 36697831 PMCID: PMC9931574 DOI: 10.1038/s41586-022-05596-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
| | - Claudia Calabrese
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Natalie R. Davidson
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medical College, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Deniz Demircioğlu
- grid.4280.e0000 0001 2180 6431National University of Singapore, Singapore, Singapore ,grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Nuno A. Fonseca
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Yao He
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - André Kahles
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Kjong-Van Lehmann
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Fenglin Liu
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Yuichi Shiraishi
- grid.26999.3d0000 0001 2151 536XThe University of Tokyo, Minato-ku, Japan
| | - Cameron M. Soulette
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Lara Urban
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Liliana Greger
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Siliang Li
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Dongbing Liu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Marc D. Perry
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.266102.10000 0001 2297 6811University of California, San Francisco, San Francisco, CA USA
| | - Qian Xiang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Fan Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Junjun Zhang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Peter Bailey
- grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Serap Erkek
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Katherine A. Hoadley
- grid.10698.360000000122483208The University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Yong Hou
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Matthew R. Huska
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Helena Kilpinen
- grid.83440.3b0000000121901201University College London, London, UK
| | - Jan O. Korbel
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Maximillian G. Marin
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Julia Markowski
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Tannistha Nandi
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Qiang Pan-Hammarström
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.4714.60000 0004 1937 0626Karolinska Institutet, Stockholm, Sweden
| | - Chandra Sekhar Pedamallu
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Reiner Siebert
- grid.410712.10000 0004 0473 882XUlm University and Ulm University Medical Center, Ulm, Germany
| | - Stefan G. Stark
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Hong Su
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Patrick Tan
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Singapore, Singapore
| | - Sebastian M. Waszak
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Christina Yung
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Shida Zhu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Philip Awadalla
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada
| | - Chad J. Creighton
- grid.39382.330000 0001 2160 926XBaylor College of Medicine, Houston, TX USA
| | - Matthew Meyerson
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | | | - Kui Wu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Huanming Yang
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China
| | | | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
| | - Angela N. Brooks
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA ,grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - Jonathan Göke
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745National Cancer Centre Singapore, Singapore, Singapore
| | - Gunnar Rätsch
- ETH Zurich, Zurich, Switzerland. .,Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Weill Cornell Medical College, New York, NY, USA. .,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,University Hospital Zurich, Zurich, Switzerland.
| | - Roland F. Schwarz
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), partner site Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Stegle
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zemin Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
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6
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Kukkonen K, Autio-Kimura B, Rauhala H, Kesseli J, Nykter M, Latonen L, Visakorpi T. Nonmalignant AR-positive prostate epithelial cells and cancer cells respond differently to androgen. Endocr Relat Cancer 2022; 29:717-733. [PMID: 36219867 PMCID: PMC9644224 DOI: 10.1530/erc-22-0108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 10/10/2022] [Indexed: 11/07/2022]
Abstract
Prostate cancer research suffers from the lack of suitable models to study the role of normal cells in prostate carcinogenesis. To address this challenge, we developed a cell line model mimicking luminal prostate epithelial cells by modifying the immortalized prostate epithelial cell line RWPE-1 to constitutively express the androgen receptor (AR). RWPE-1-AR cells express known AR target genes, and exhibit coexpression of luminal and basal markers characteristic of transient amplifying cells, and an RNA signature resembling prostate luminal progenitor cells. Under unstimulated conditions, constitutive AR expression does not have a biologically significant effect on the proliferation of RWPE-1 cells, but when stimulated by androgens, growth is retarded. The transcriptional response of RWPE-1-AR cells to androgen stimulation involves suppression of the growth-related KRAS pathway and is thus markedly different from that of the prostate cancer cell line LNCaP and its derivative AR-overexpressing LNCaP-ARhi cells, in which growth- and cancer-related pathways are upregulated. Hence, the nonmalignant AR-positive RWPE-1-AR cell line model could be used to study the transformation of the prostate epithelium.
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Affiliation(s)
- Konsta Kukkonen
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Bryn Autio-Kimura
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Hanna Rauhala
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Juha Kesseli
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Matti Nykter
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
- Foundation for the Finnish Cancer Institute, Helsinki, Finland
| | - Leena Latonen
- Foundation for the Finnish Cancer Institute, Helsinki, Finland
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Tapio Visakorpi
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
- Fimlab Laboratories Ltd, Tampere, Finland
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Siltari A, Lönnerbro R, Pang K, Shiranov K, Asiimwe A, Evans-Axelsson S, Franks B, Kiran A, Murtola TJ, Schalken J, Steinbeisser C, Bjartell A, Auvinen A, Smith E, N'Dow J, Plass K, Ribal M, Mottet N, Moris L, Lardas M, Van den Broeck T, Willemse PP, Gandaglia G, Campi R, Greco I, Gacci M, Serni S, Briganti A, Crosti D, Meoni M, Garzonio R, Bangma R, Roobol M, Remmers S, Tilki D, Visakorpi T, Talala K, Tammela T, van Hemelrijck M, Bayer K, Lejeune S, Taxiarchopoulou G, van Diggelen F, Senthilkumar K, Schutte S, Byrne S, Fialho L, Cardone A, Gono P, De Vetter M, Ceke K, De Meulder B, Auffray C, Balaur IA, Taibi N, Power S, Kermani NZ, van Bochove K, Cavelaars M, Moinat M, Voss E, Bernini C, Horgan D, Fullwood L, Holtorf M, Lancet D, Bernstein G, Omar I, MacLennan S, Maclennan S, Healey J, Huber J, Wirth M, Froehner M, Brenner B, Borkowetz A, Thomas C, Horn F, Reiche K, Kreux M, Josefsson A, Tandefekt DG, Hugosson J, Huisman H, Hofmacher T, Lindgren P, Andersson E, Fridhammar A, Vizcaya D, Verholen F, Zong J, Butler-Ransohoff JE, Williamson T, Chandrawansa K, Dlamini D, waldeck R, Molnar M, Bruno A, Herrera R, Jiang S, Nevedomskaya E, Fatoba S, Constantinovici N, Maass M, Torremante P, Voss M, Devecseri Z, Cuperus G, Abott T, Dau C, Papineni K, Wang-Silvanto J, Hass S, Snijder R, Doye V, Wang X, Garnham A, Lambrecht M, Wolfinger R, Rogiers S, Servan A, Lefresne F, Caseriego J, Samir M, Lawson J, Pacoe K, Robinson P, Jaton B, Bakkard D, Turunen H, Kilkku O, Pohjanjousi P, Voima O, Nevalaita L, Reich C, Araujo S, Longden-Chapman E, Burke D, Agapow P, Derkits S, Licour M, McCrea C, Payne S, Yong A, Thompson L, Lujan F, Bussmann M, Köhler I. How well do polygenic risk scores identify men at high risk for prostate cancer? Systematic review and meta-analysis. Clin Genitourin Cancer 2022; 21:316.e1-316.e11. [PMID: 36243664 DOI: 10.1016/j.clgc.2022.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 11/27/2022]
Abstract
OBJECTIVES Genome-wide association studies have revealed over 200 genetic susceptibility loci for prostate cancer (PCa). By combining them, polygenic risk scores (PRS) can be generated to predict risk of PCa. We summarize the published evidence and conduct meta-analyses of PRS as a predictor of PCa risk in Caucasian men. PATIENTS AND METHODS Data were extracted from 59 studies, with 16 studies including 17 separate analyses used in the main meta-analysis with a total of 20,786 cases and 69,106 controls identified through a systematic search of ten databases. Random effects meta-analysis was used to obtain pooled estimates of area under the receiver-operating characteristic curve (AUC). Meta-regression was used to assess the impact of number of single-nucleotide polymorphisms (SNPs) incorporated in PRS on AUC. Heterogeneity is expressed as I2 scores. Publication bias was evaluated using funnel plots and Egger tests. RESULTS The ability of PRS to identify men with PCa was modest (pooled AUC 0.63, 95% CI 0.62-0.64) with moderate consistency (I2 64%). Combining PRS with clinical variables increased the pooled AUC to 0.74 (0.68-0.81). Meta-regression showed only negligible increase in AUC for adding incremental SNPs. Despite moderate heterogeneity, publication bias was not evident. CONCLUSION Typically, PRS accuracy is comparable to PSA or family history with a pooled AUC value 0.63 indicating mediocre performance for PRS alone.
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8
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Taavitsainen S, Engedal N, Cao S, Handle F, Erickson A, Prekovic S, Wetterskog D, Tolonen T, Vuorinen EM, Kiviaho A, Nätkin R, Häkkinen T, Devlies W, Henttinen S, Kaarijärvi R, Lahnalampi M, Kaljunen H, Nowakowska K, Syvälä H, Bläuer M, Cremaschi P, Claessens F, Visakorpi T, Tammela TL, Murtola T, Granberg KJ, Lamb AD, Ketola K, Mills IG, Attard G, Wang W, Nykter M, Urbanucci A. Abstract 401: Single-cell transcriptome and chromatin sequencing uncover gene expression and gene regulatory patterns associated with enzalutamide resistance. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Resistance to androgen receptor-targeted therapy due to tumor heterogeneity and clonal evolution is a key challenge for improving prostate cancer outcomes. Despite this, the transcriptomic and chromatin accessibility changes contributing to the emergence of resistance remain incompletely understood at the level of individual cells. Using single-cell assays for transposase-accessible chromatin (ATAC) and RNA sequencing in models of early treatment response and resistance to enzalutamide, we previously identified pre-existing and persistent cell subpopulations that possess regenerative potential when subjected to treatment. Here we analyze the chromatin and transcriptomes of these single cells to characterize their gene regulation and gene expression trajectories. We present evidence of a model of enzalutamide resistance emergence in which the pre-existing and treatment-persistent cells regenerate the bulk of resistant cells. This process is underpinned by chromatin reprogramming that increases the overall relaxation of chromatin upon resistance. We show that the reprogramming of the chromatin further differentially contributes to transcription factor-mediated transcriptional reprogramming via DNA motif exposure in different cell subpopulations. For example, in the treatment-persistent cells, we identify chromatin configurations characterized by the exposure of DNA motifs for GATA2, RELA (a NFkB subunit), CREB1, and E2F1. Pre-existing and treatment-persistent cells consistently display transcriptional features of high developmental potential and RNA velocity analysis identifies them as precursors of cell populations that arise from enzalutamide treatment. We also analyze the pre-existing and treatment-persistent cells in spatial transcriptomics of prostate cancer patient specimens based on their characteristic gene expression profiles. We find these cells to be enriched in cancerous regions of the tissue but also detect them within apparent benign regions, which has potential implications for treatment choice. In summary, we show patterns of gene expression regulation in preclinical models and patient samples that uncover mechanisms of resistance to androgen receptor-targeted therapy in prostate cancer.
Citation Format: Sinja Taavitsainen, Nikolai Engedal, Shaolong Cao, Florian Handle, Andrew Erickson, Stefan Prekovic, Daniel Wetterskog, Teemu Tolonen, Elisa M. Vuorinen, Antti Kiviaho, Reetta Nätkin, Tomi Häkkinen, Wout Devlies, Sallamari Henttinen, Roosa Kaarijärvi, Mari Lahnalampi, Heidi Kaljunen, Karolina Nowakowska, Heimo Syvälä, Merja Bläuer, Paolo Cremaschi, Frank Claessens, Tapio Visakorpi, Teuvo L. Tammela, Teemu Murtola, Kirsi J. Granberg, Alastair D. Lamb, Kirsi Ketola, Ian G. Mills, Gerhardt Attard, Wenyi Wang, Matti Nykter, Alfonso Urbanucci. Single-cell transcriptome and chromatin sequencing uncover gene expression and gene regulatory patterns associated with enzalutamide resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 401.
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Affiliation(s)
| | - Nikolai Engedal
- 2Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Shaolong Cao
- 3The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Stefan Prekovic
- 6Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Teemu Tolonen
- 8Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | | | - Antti Kiviaho
- 1Tampere University and Tays Cancer Center, Tampere, Finland
| | - Reetta Nätkin
- 1Tampere University and Tays Cancer Center, Tampere, Finland
| | - Tomi Häkkinen
- 1Tampere University and Tays Cancer Center, Tampere, Finland
| | | | | | | | | | | | | | - Heimo Syvälä
- 1Tampere University and Tays Cancer Center, Tampere, Finland
| | - Merja Bläuer
- 1Tampere University and Tays Cancer Center, Tampere, Finland
| | - Paolo Cremaschi
- 7University College London Cancer Institute, London, United Kingdom
| | | | - Tapio Visakorpi
- 1Tampere University and Tays Cancer Center, Tampere, Finland
| | | | - Teemu Murtola
- 1Tampere University and Tays Cancer Center, Tampere, Finland
| | | | | | - Kirsi Ketola
- 10University of Eastern Finland, Kuopio, Finland
| | | | - Gerhardt Attard
- 7University College London Cancer Institute, London, United Kingdom
| | - Wenyi Wang
- 3The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Matti Nykter
- 1Tampere University and Tays Cancer Center, Tampere, Finland
| | - Alfonso Urbanucci
- 2Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
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9
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Ruusuvuori P, Valkonen M, Kartasalo K, Valkonen M, Visakorpi T, Nykter M, Latonen L. Spatial analysis of histology in 3D: quantification and visualization of organ and tumor level tissue environment. Heliyon 2022; 8:e08762. [PMID: 35128089 PMCID: PMC8800033 DOI: 10.1016/j.heliyon.2022.e08762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/24/2021] [Accepted: 01/11/2022] [Indexed: 10/25/2022] Open
Abstract
Histological changes in tissue are of primary importance in pathological research and diagnosis. Automated histological analysis requires ability to computationally separate pathological alterations from normal tissue. Conventional histopathological assessments are performed from individual tissue sections, leading to the loss of three-dimensional context of the tissue. Yet, the tissue context and spatial determinants are critical in several pathologies, such as in understanding growth patterns of cancer in its local environment. Here, we develop computational methods for visualization and quantitative assessment of histopathological alterations in three dimensions. First, we reconstruct the 3D representation of the whole organ from serial sectioned tissue. Then, we proceed to analyze the histological characteristics and regions of interest in 3D. As our example cases, we use whole slide images representing hematoxylin-eosin stained whole mouse prostates in a Pten+/- mouse prostate tumor model. We show that quantitative assessment of tumor sizes, shapes, and separation between spatial locations within the organ enable characterizing and grouping tumors. Further, we show that 3D visualization of tissue with computationally quantified features provides an intuitive way to observe tissue pathology. Our results underline the heterogeneity in composition and cellular organization within individual tumors. As an example, we show how prostate tumors have nuclear density gradients indicating areas of tumor growth directions and reflecting varying pressure from the surrounding tissue. The methods presented here are applicable to any tissue and different types of pathologies. This work provides a proof-of-principle for gaining a comprehensive view from histology by studying it quantitatively in 3D.
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Affiliation(s)
- Pekka Ruusuvuori
- Institute of Biomedicine, University of Turku, Turku, Finland
- Faculty of Medicine and Health Technology, Tampere University, Finland
| | - Masi Valkonen
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Kimmo Kartasalo
- Faculty of Medicine and Health Technology, Tampere University, Finland
| | - Mira Valkonen
- Faculty of Medicine and Health Technology, Tampere University, Finland
| | - Tapio Visakorpi
- Faculty of Medicine and Health Technology, Tampere University, Finland
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- Fimlab Laboratories Ltd, Tampere University Hospital, Tampere, Finland
| | - Matti Nykter
- Faculty of Medicine and Health Technology, Tampere University, Finland
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Leena Latonen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
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10
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Jeyapala R, Kamdar S, Olkhov-Mitsel E, Zlotta A, Fleshner N, Visakorpi T, van der Kwast T, Bapat B. Combining CAPRA-S with tumor IDC/C features improves the prognostication of biochemical recurrence in prostate cancer patients. Clin Genitourin Cancer 2022; 20:e217-e226. [DOI: 10.1016/j.clgc.2022.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 12/18/2022]
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11
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Taavitsainen S, Engedal N, Cao S, Handle F, Erickson A, Prekovic S, Wetterskog D, Tolonen T, Vuorinen EM, Kiviaho A, Nätkin R, Häkkinen T, Devlies W, Henttinen S, Kaarijärvi R, Lahnalampi M, Kaljunen H, Nowakowska K, Syvälä H, Bläuer M, Cremaschi P, Claessens F, Visakorpi T, Tammela TLJ, Murtola T, Granberg KJ, Lamb AD, Ketola K, Mills IG, Attard G, Wang W, Nykter M, Urbanucci A. Single-cell ATAC and RNA sequencing reveal pre-existing and persistent cells associated with prostate cancer relapse. Nat Commun 2021; 12:5307. [PMID: 34489465 PMCID: PMC8421417 DOI: 10.1038/s41467-021-25624-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/23/2021] [Indexed: 02/08/2023] Open
Abstract
Prostate cancer is heterogeneous and patients would benefit from methods that stratify those who are likely to respond to systemic therapy. Here, we employ single-cell assays for transposase-accessible chromatin (ATAC) and RNA sequencing in models of early treatment response and resistance to enzalutamide. In doing so, we identify pre-existing and treatment-persistent cell subpopulations that possess regenerative potential when subjected to treatment. We find distinct chromatin landscapes associated with enzalutamide treatment and resistance that are linked to alternative transcriptional programs. Transcriptional profiles characteristic of persistent cells are able to stratify the treatment response of patients. Ultimately, we show that defining changes in chromatin and gene expression in single-cell populations from pre-clinical models can reveal as yet unrecognized molecular predictors of treatment response. This suggests that the application of single-cell methods with high analytical resolution in pre-clinical models may powerfully inform clinical decision-making.
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Affiliation(s)
- S Taavitsainen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - N Engedal
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - S Cao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - F Handle
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
- Department of Urology, Division of Experimental Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - A Erickson
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - S Prekovic
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - D Wetterskog
- University College London Cancer Institute, London, UK
| | - T Tolonen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
- Department of Pathology, Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - E M Vuorinen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - A Kiviaho
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - R Nätkin
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - T Häkkinen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - W Devlies
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
- Department of Urology, UZ Leuven, Leuven, Belgium
| | - S Henttinen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - R Kaarijärvi
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - M Lahnalampi
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - H Kaljunen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - K Nowakowska
- University College London Cancer Institute, London, UK
| | - H Syvälä
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - M Bläuer
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - P Cremaschi
- University College London Cancer Institute, London, UK
| | - F Claessens
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - T Visakorpi
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
- Fimlab Laboratories, Ltd, Tampere University Hospital, Tampere, Finland
| | - T L J Tammela
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - T Murtola
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - K J Granberg
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - A D Lamb
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- Department of Urology, Churchill Hospital Cancer Centre, Oxford, UK
| | - K Ketola
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - I G Mills
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- Patrick G Johnston Centre for Cancer Research, Queen's University of Belfast, Belfast, UK
- Centre for Cancer Biomarkers (CCBIO), University of Bergen, Bergen, Norway
| | - G Attard
- University College London Cancer Institute, London, UK
| | - W Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - M Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland.
| | - A Urbanucci
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.
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12
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Eerola SK, Kohvakka A, Tammela TLJ, Koskinen PJ, Latonen L, Visakorpi T. Expression and ERG regulation of PIM kinases in prostate cancer. Cancer Med 2021; 10:3427-3436. [PMID: 33932111 PMCID: PMC8124112 DOI: 10.1002/cam4.3893] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/04/2021] [Accepted: 03/23/2021] [Indexed: 11/26/2022] Open
Abstract
The three oncogenic PIM family kinases have been implicated in the development of prostate cancer (PCa). The aim of this study was to examine the mRNA and protein expression levels of PIM1, PIM2, and PIM3 in PCa and their associations with the MYC and ERG oncogenes. We utilized prostate tissue specimens of normal, benign prostatic hyperplasia (BPH), prostatic intraepithelial neoplasia (PIN), untreated PCa, and castration‐resistant prostate cancer (CRPC) for immunohistochemical (IHC) analysis. In addition, we analyzed data from publicly available mRNA expression and chromatin immunoprecipitation sequencing (ChIP‐Seq) datasets. Our data demonstrated that PIM expression levels are significantly elevated in PCa compared to benign samples. Strikingly, the expression of both PIM1 and PIM2 was further increased in CRPC compared to PCa. We also demonstrated a significant association between upregulated PIM family members and both the ERG and MYC oncoproteins. Interestingly, ERG directly binds to the regulatory regions of all PIM genes and upregulates their expression. Furthermore, ERG suppression with siRNA reduced the expression of PIM in PCa cells. These results provide evidence for cooperation of PIM and the MYC and ERG oncoproteins in PCa development and progression and may help to stratify suitable patients for PIM‐targeted therapies.
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Affiliation(s)
- Sini K Eerola
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Annika Kohvakka
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Teuvo L J Tammela
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland.,Department of Urology, Tampere University Hospital, Tampere, Finland
| | | | - Leena Latonen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Tapio Visakorpi
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland.,Fimlab Laboratories Ltd, Tampere University Hospital, Tampere, Finland
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13
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Launonen KM, Paakinaho V, Sigismondo G, Malinen M, Sironen R, Hartikainen JM, Laakso H, Visakorpi T, Krijgsveld J, Niskanen EA, Palvimo JJ. Chromatin-directed proteomics-identified network of endogenous androgen receptor in prostate cancer cells. Oncogene 2021; 40:4567-4579. [PMID: 34127815 PMCID: PMC8266679 DOI: 10.1038/s41388-021-01887-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/18/2021] [Accepted: 06/01/2021] [Indexed: 02/05/2023]
Abstract
Treatment of prostate cancer confronts resistance to androgen receptor (AR)-targeted therapies. AR-associated coregulators and chromatin proteins hold a great potential for novel therapy targets. Here, we employed a powerful chromatin-directed proteomics approach termed ChIP-SICAP to uncover the composition of chromatin protein network, the chromatome, around endogenous AR in castration resistant prostate cancer (CRPC) cells. In addition to several expected AR coregulators, the chromatome contained many nuclear proteins not previously associated with the AR. In the context of androgen signaling in CRPC cells, we further investigated the role of a known AR-associated protein, a chromatin remodeler SMARCA4 and that of SIM2, a transcription factor without a previous association with AR. To understand their role in chromatin accessibility and AR target gene expression, we integrated data from ChIP-seq, RNA-seq, ATAC-seq and functional experiments. Despite the wide co-occurrence of SMARCA4 and AR on chromatin, depletion of SMARCA4 influenced chromatin accessibility and expression of a restricted set of AR target genes, especially those involved in cell morphogenetic changes in epithelial-mesenchymal transition. The depletion also inhibited the CRPC cell growth, validating SMARCA4's functional role in CRPC cells. Although silencing of SIM2 reduced chromatin accessibility similarly, it affected the expression of a much larger group of androgen-regulated genes, including those involved in cellular responses to external stimuli and steroid hormone stimulus. The silencing also reduced proliferation of CRPC cells and tumor size in chick embryo chorioallantoic membrane assay, further emphasizing the importance of SIM2 in CRPC cells and pointing to the functional relevance of this potential prostate cancer biomarker in CRPC cells. Overall, the chromatome of AR identified in this work is an important resource for the field focusing on this important drug target.
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Affiliation(s)
- Kaisa-Mari Launonen
- grid.9668.10000 0001 0726 2490Institute of Biomedicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ville Paakinaho
- grid.9668.10000 0001 0726 2490Institute of Biomedicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Gianluca Sigismondo
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marjo Malinen
- grid.9668.10000 0001 0726 2490Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Reijo Sironen
- grid.9668.10000 0001 0726 2490Institute of Clinical Medicine, Clinical Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland ,grid.410705.70000 0004 0628 207XDepartment of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Jaana M. Hartikainen
- grid.9668.10000 0001 0726 2490Institute of Clinical Medicine, Clinical Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
| | - Hanna Laakso
- grid.9668.10000 0001 0726 2490Institute of Biomedicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Tapio Visakorpi
- grid.412330.70000 0004 0628 2985Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland ,grid.511163.10000 0004 0518 4910Fimlab Laboratories, Tampere, Finland
| | - Jeroen Krijgsveld
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Einari A. Niskanen
- grid.9668.10000 0001 0726 2490Institute of Biomedicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Jorma J. Palvimo
- grid.9668.10000 0001 0726 2490Institute of Biomedicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
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14
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Gundem G, Van Loo P, Kremeyer B, Alexandrov LB, Tubio JMC, Papaemmanuil E, Brewer DS, Kallio HML, Hägnäs G, Annala M, Kivinummi K, Goody V, Latimer C, O'Meara S, Dawson KJ, Isaacs W, Emmert-Buck MR, Nykter M, Foster C, Kote-Jarai Z, Easton D, Whitaker HC, Neal DE, Cooper CS, Eeles RA, Visakorpi T, Campbell PJ, McDermott U, Wedge DC, Bova GS. Author Correction: The evolutionary history of lethal metastatic prostate cancer. Nature 2020; 584:E18. [PMID: 32728210 DOI: 10.1038/s41586-020-2581-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Gunes Gundem
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Peter Van Loo
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.,Department of Human Genetics, KU Leuven, Herestraat 49 Box 602, B-3000, Leuven, Belgium.,Cancer Research UK London Research Institute, London, WC2A3LY, UK
| | - Barbara Kremeyer
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Ludmil B Alexandrov
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Jose M C Tubio
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Elli Papaemmanuil
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Daniel S Brewer
- Norwich Medical School and Department of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.,The Genome Analysis Centre, Norwich, NR4 7UH, UK
| | - Heini M L Kallio
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, FI-33520, Finland
| | - Gunilla Hägnäs
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, FI-33520, Finland
| | - Matti Annala
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, FI-33520, Finland
| | - Kati Kivinummi
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, FI-33520, Finland
| | - Victoria Goody
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Calli Latimer
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Sarah O'Meara
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Kevin J Dawson
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - William Isaacs
- The James Buchanan Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, Maryland, 21287, USA
| | - Michael R Emmert-Buck
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Maryland, 20892, USA.,Avoneaux Medical Institute, Oxford, Maryland, 21654, USA
| | - Matti Nykter
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, FI-33520, Finland
| | - Christopher Foster
- University of Liverpool andHCA Pathology Laboratories, London, WC1E6JA, UK
| | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, SW73RP, UK
| | - Douglas Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB18RN, UK
| | - Hayley C Whitaker
- Uro-oncology Research Group, Cancer ResearchUKCambridge Institute, Cambridge, CB20RE, UK
| | | | - David E Neal
- Uro-oncology Research Group, Cancer ResearchUKCambridge Institute, Cambridge, CB20RE, UK.,Department of Surgical Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - Colin S Cooper
- Norwich Medical School and Department of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.,Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, SW73RP, UK
| | - Rosalind A Eeles
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, SW73RP, UK.,Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; and, Sutton, SM2 5PT, UK
| | - Tapio Visakorpi
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, FI-33520, Finland
| | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Ultan McDermott
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - David C Wedge
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.
| | - G Steven Bova
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, FI-33520, Finland
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15
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Savolainen K, Scaravilli M, Ilvesmäki A, Staff S, Tolonen T, Mäenpää JU, Visakorpi T, Auranen A. Expression of the miR-200 family in tumor tissue, plasma and urine of epithelial ovarian cancer patients in comparison to benign counterparts. BMC Res Notes 2020; 13:311. [PMID: 32611374 PMCID: PMC7329467 DOI: 10.1186/s13104-020-05155-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 06/25/2020] [Indexed: 02/07/2023] Open
Abstract
Objective Plasma, but also urine sample could represent a simple liquid biopsy for ovarian cancer biomarker detection. The miRNA-200 family has been shown to be dysregulated in ovarian cancer. The aim of this study was to isolate three members of miR-200 family from tumor tissue, plasma and urine of high-grade serous ovarian cancer patients in comparison with samples from patients with benign ovarian tumors. This is a methodological pilot study of a prospective ovarian cancer patient cohort investigating the potential of liquid biopsies and the role of miRNAs in ovarian cancer treatment. Results MiR-200a, miR-200b and miR-200c were isolated from samples of nine ovarian cancer patients and seven patients with benign ovarian tumor. The most significant finding is that all three miRNAs were detectable in all sample types. Tumor tissue and plasma, but not urine analysis was able to discriminate malignant and benign samples. A correlation between the miRNA-200 expression in urine and plasma was observed in malignant samples only. Plasma and urine with respect to miRNA detection show potential according to this study, but larger studies are needed to clarify the usefulness of these liquid biopsies in ovarian cancer. Trial registration: ClinicalTrials.gov NCT02758652, May 2, 2016.
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Affiliation(s)
- Kalle Savolainen
- Department of Obstetrics and Gynecology, Tampere University Hospital, P.O.box 2000, 33521, Tampere, Finland. .,Tays Cancer Centre, Tampere University Hospital and Tampere University, Tampere, Finland.
| | - Mauro Scaravilli
- Tays Cancer Centre, Tampere University Hospital and Tampere University, Tampere, Finland.,Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland.,Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Antti Ilvesmäki
- Department of Obstetrics and Gynecology, Tampere University Hospital, P.O.box 2000, 33521, Tampere, Finland
| | - Synnöve Staff
- Department of Obstetrics and Gynecology, Tampere University Hospital, P.O.box 2000, 33521, Tampere, Finland.,Tays Cancer Centre, Tampere University Hospital and Tampere University, Tampere, Finland.,Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Teemu Tolonen
- Tays Cancer Centre, Tampere University Hospital and Tampere University, Tampere, Finland.,Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Johanna U Mäenpää
- Department of Obstetrics and Gynecology, Tampere University Hospital, P.O.box 2000, 33521, Tampere, Finland.,Tays Cancer Centre, Tampere University Hospital and Tampere University, Tampere, Finland.,Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Tapio Visakorpi
- Tays Cancer Centre, Tampere University Hospital and Tampere University, Tampere, Finland.,Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Annika Auranen
- Department of Obstetrics and Gynecology, Tampere University Hospital, P.O.box 2000, 33521, Tampere, Finland.,Tays Cancer Centre, Tampere University Hospital and Tampere University, Tampere, Finland
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16
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Kohvakka A, Sattari M, Shcherban A, Annala M, Urbanucci A, Kesseli J, Tammela TLJ, Kivinummi K, Latonen L, Nykter M, Visakorpi T. AR and ERG drive the expression of prostate cancer specific long noncoding RNAs. Oncogene 2020; 39:5241-5251. [PMID: 32555329 DOI: 10.1038/s41388-020-1365-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/25/2020] [Accepted: 06/08/2020] [Indexed: 01/04/2023]
Abstract
Long noncoding RNAs (lncRNAs) play pivotal roles in cancer development and progression, and some function in a highly cancer-specific manner. However, whether the cause of their expression is an outcome of a specific regulatory mechanism or nonspecific transcription induced by genome reorganization in cancer remains largely unknown. Here, we investigated a group of lncRNAs that we previously identified to be aberrantly expressed in prostate cancer (PC), called TPCATs. Our high-throughput real-time PCR experiments were integrated with publicly available RNA-seq and ChIP-seq data and revealed that the expression of a subset of TPCATs is driven by PC-specific transcription factors (TFs), especially androgen receptor (AR) and ETS-related gene (ERG). Our in vitro validations confirmed that AR and ERG regulated a subset of TPCATs, most notably for EPCART. Knockout of EPCART was found to reduce migration and proliferation of the PC cells in vitro. The high expression of EPCART and two other TPCATs (TPCAT-3-174133 and TPCAT-18-31849) were also associated with the biochemical recurrence of PC in prostatectomy patients and were independent prognostic markers. Our findings suggest that the expression of numerous PC-associated lncRNAs is driven by PC-specific mechanisms and not by random cellular events that occur during cancer development. Furthermore, we report three prospective prognostic markers for the early detection of advanced PC and show EPCART to be a functionally relevant lncRNA in PC.
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Affiliation(s)
- Annika Kohvakka
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Mina Sattari
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Anastasia Shcherban
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Matti Annala
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Alfonso Urbanucci
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Juha Kesseli
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Teuvo L J Tammela
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland.,Department of Urology, Tampere University Hospital, Tampere, Finland
| | - Kati Kivinummi
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Leena Latonen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Matti Nykter
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Tapio Visakorpi
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland. .,Fimlab Laboratories Ltd, Tampere University Hospital, Tampere, Finland.
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17
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Aaltonen LA, Abascal F, Abeshouse A, Aburatani H, Adams DJ, Agrawal N, Ahn KS, Ahn SM, Aikata H, Akbani R, Akdemir KC, Al-Ahmadie H, Al-Sedairy ST, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov LB, Ally A, Alsop K, Alvarez EG, Amary F, Amin SB, Aminou B, Ammerpohl O, Anderson MJ, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, von Mering C. Pan-cancer analysis of whole genomes. Nature 2020; 578:82-93. [PMID: 32025007 PMCID: PMC7025898 DOI: 10.1038/s41586-020-1969-6] [Citation(s) in RCA: 1435] [Impact Index Per Article: 358.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 12/11/2019] [Indexed: 02/07/2023]
Abstract
Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.
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18
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Eerola SK, Santio NM, Rinne S, Kouvonen P, Corthals GL, Scaravilli M, Scala G, Serra A, Greco D, Ruusuvuori P, Latonen L, Rainio EM, Visakorpi T, Koskinen PJ. Phosphorylation of NFATC1 at PIM1 target sites is essential for its ability to promote prostate cancer cell migration and invasion. Cell Commun Signal 2019; 17:148. [PMID: 31730483 PMCID: PMC6858710 DOI: 10.1186/s12964-019-0463-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 10/22/2019] [Indexed: 12/11/2022] Open
Abstract
Background Progression of prostate cancer from benign local tumors to metastatic carcinomas is a multistep process. Here we have investigated the signaling pathways that support migration and invasion of prostate cancer cells, focusing on the role of the NFATC1 transcription factor and its post-translational modifications. We have previously identified NFATC1 as a substrate for the PIM1 kinase and shown that PIM1-dependent phosphorylation increases NFATC1 activity without affecting its subcellular localization. Both PIM kinases and NFATC1 have been reported to promote cancer cell migration, invasion and angiogenesis, but it has remained unclear whether the effects of NFATC1 are phosphorylation-dependent and which downstream targets are involved. Methods We used mass spectrometry to identify PIM1 phosphorylation target sites in NFATC1, and analysed their functional roles in three prostate cancer cell lines by comparing phosphodeficient mutants to wild-type NFATC1. We used luciferase assays to determine effects of phosphorylation on NFAT-dependent transcriptional activity, and migration and invasion assays to evaluate effects on cell motility. We also performed a microarray analysis to identify novel PIM1/NFATC1 targets, and validated one of them with both cellular expression analyses and in silico in clinical prostate cancer data sets. Results Here we have identified ten PIM1 target sites in NFATC1 and found that prevention of their phosphorylation significantly decreases the transcriptional activity as well as the pro-migratory and pro-invasive effects of NFATC1 in prostate cancer cells. We observed that also PIM2 and PIM3 can phosphorylate NFATC1, and identified several novel putative PIM1/NFATC1 target genes. These include the ITGA5 integrin, which is differentially expressed in the presence of wild-type versus phosphorylation-deficient NFATC1, and which is coexpressed with PIM1 and NFATC1 in clinical prostate cancer specimens. Conclusions Based on our data, phosphorylation of PIM1 target sites stimulates NFATC1 activity and enhances its ability to promote prostate cancer cell migration and invasion. Therefore, inhibition of the interplay between PIM kinases and NFATC1 may have therapeutic implications for patients with metastatic forms of cancer. Graphical abstract ![]()
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Affiliation(s)
- Sini K Eerola
- Department of Biology, University of Turku, Vesilinnantie 5, FI-20500, Turku, Finland.,Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Niina M Santio
- Department of Biology, University of Turku, Vesilinnantie 5, FI-20500, Turku, Finland
| | - Sanni Rinne
- Department of Biology, University of Turku, Vesilinnantie 5, FI-20500, Turku, Finland
| | - Petri Kouvonen
- Turku Centre for Biotechnology, University of Turku, Turku, Finland
| | - Garry L Corthals
- Turku Centre for Biotechnology, University of Turku, Turku, Finland
| | - Mauro Scaravilli
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland.,Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Giovanni Scala
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland.,University of Helsinki, Helsinki, Finland
| | - Angela Serra
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Dario Greco
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland.,University of Helsinki, Helsinki, Finland
| | - Pekka Ruusuvuori
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland.,Signal processing laboratory, Tampere University of Technology, Pori, Finland
| | - Leena Latonen
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland.,Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Eeva-Marja Rainio
- Department of Biology, University of Turku, Vesilinnantie 5, FI-20500, Turku, Finland
| | - Tapio Visakorpi
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland.,Fimlab Laboratories, Tampere, Finland
| | - Päivi J Koskinen
- Department of Biology, University of Turku, Vesilinnantie 5, FI-20500, Turku, Finland.
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19
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Granberg KJ, Raita A, Lehtinen B, Tiihonen AM, Kesseli J, Annala M, Rodriguez-Martinez A, Nordfors K, Zhang W, Visakorpi T, Nykter M, Haapasalo H. Moderate-to-strong expression of FGFR3 and TP53 alterations in a subpopulation of choroid plexus tumors. Histol Histopathol 2019; 35:673-680. [PMID: 31660579 DOI: 10.14670/hh-18-180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Deregulation of fibroblast growth factor receptor (FGFR) signaling is tightly associated with numerous human malignancies, including cancer. Indeed, FGFR inhibitors are being tested as anti-tumor drugs in clinical trials. Among gliomas, FGFR3 fusions occur in IDH wild-type diffuse gliomas leading to high FGFR3 protein expression and both, FGFR3 and FGFR1, show elevated expression in aggressive ependymomas. The aim of this study was to uncover the expression of FGFR1 and FGFR3 proteins in choroid plexus tumors and to further characterize FGFR-related as well as other genetic alterations in FGFR3 expressing tumors. Expression levels of FGFR1 and FGFR3 were detected in 15 choroid plexus tumor tissues using immunohistochemistry of tissue microarrays and 6 samples were subjected to whole mount FGFR3 staining. Targeted sequencing was used for deeper molecular analysis of two FGFR3 positive cases. Moderate expression of FGFR1 or FGFR3 was evidenced in one third of the studied choroid plexus tumors. Targeted sequencing of a choroid plexus carcinoma and an atypical choroid plexus papilloma, both with moderate-to-strong FGFR3 expression, revealed lack of protein-altering mutations or fusions in FGFR1 or FGFR3, but TP53 was altered in both tumors. FGFR3 and FGFR1 proteins are expressed in a subpopulation of choroid plexus tumors. Further studies using larger cohorts of patients will allow identification of the clinicopathological implications of FGFR1 and FGFR3 expression in choroid plexus tumors.
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Affiliation(s)
- Kirsi J Granberg
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland. .,Tays Cancer Center, Tampere University Hospital, Tampere, Finland.,Science Center, Tampere University Hospital, Tampere, Finland
| | - Annina Raita
- Fimlab Laboratories Ltd., Tampere University Hospital, Tampere, Finland.,Department of Pathology, Tampere University, Tampere, Finland
| | - Birgitta Lehtinen
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland.,BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Aliisa M Tiihonen
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland.,BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Juha Kesseli
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland.,BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Matti Annala
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland.,BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Alejandra Rodriguez-Martinez
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland.,BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Kristiina Nordfors
- Department of Pediatrics, Tampere University Hospital, Tampere, Finland.,Tampere Center for Child Health Research, Tampere University, Tampere, Finland
| | - Wei Zhang
- Department of Cancer Biology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, NC USA
| | - Tapio Visakorpi
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland.,Fimlab Laboratories Ltd., Tampere University Hospital, Tampere, Finland.,BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Matti Nykter
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland.,Science Center, Tampere University Hospital, Tampere, Finland.,BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Hannu Haapasalo
- Fimlab Laboratories Ltd., Tampere University Hospital, Tampere, Finland.,Department of Pathology, Tampere University, Tampere, Finland
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Kartasalo K, Latonen L, Vihinen J, Visakorpi T, Nykter M, Ruusuvuori P. Comparative analysis of tissue reconstruction algorithms for 3D histology. Bioinformatics 2019; 34:3013-3021. [PMID: 29684099 PMCID: PMC6129300 DOI: 10.1093/bioinformatics/bty210] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 04/18/2018] [Indexed: 12/05/2022] Open
Abstract
Motivation Digital pathology enables new approaches that expand beyond storage, visualization or analysis of histological samples in digital format. One novel opportunity is 3D histology, where a three-dimensional reconstruction of the sample is formed computationally based on serial tissue sections. This allows examining tissue architecture in 3D, for example, for diagnostic purposes. Importantly, 3D histology enables joint mapping of cellular morphology with spatially resolved omics data in the true 3D context of the tissue at microscopic resolution. Several algorithms have been proposed for the reconstruction task, but a quantitative comparison of their accuracy is lacking. Results We developed a benchmarking framework to evaluate the accuracy of several free and commercial 3D reconstruction methods using two whole slide image datasets. The results provide a solid basis for further development and application of 3D histology algorithms and indicate that methods capable of compensating for local tissue deformation are superior to simpler approaches. Availability and implementation Code: https://github.com/BioimageInformaticsTampere/RegBenchmark. Whole slide image datasets: http://urn.fi/urn: nbn: fi: csc-kata20170705131652639702. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Kimmo Kartasalo
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland.,Faculty of Biomedical Sciences and Engineering, Tampere University of Technology, Tampere, Finland.,BioMediTech Institute, Tampere, Finland
| | - Leena Latonen
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland.,BioMediTech Institute, Tampere, Finland.,Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Jorma Vihinen
- Faculty of Engineering Sciences, Tampere University of Technology, Tampere, Finland
| | - Tapio Visakorpi
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland.,BioMediTech Institute, Tampere, Finland.,Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Matti Nykter
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland.,Faculty of Biomedical Sciences and Engineering, Tampere University of Technology, Tampere, Finland.,BioMediTech Institute, Tampere, Finland
| | - Pekka Ruusuvuori
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland.,BioMediTech Institute, Tampere, Finland.,Faculty of Computing and Electrical Engineering, Tampere University of Technology, Tampere 33101, Finland
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Tuominen JI, Afyounian E, Tabaro F, Häkkinen T, Shcherban A, Annala M, Kivinummi K, Tammela T, Kesseli J, Latonen L, Granberg K, Visakorpi T, Nykter M. Abstract LB-096: Chromatin alterations in human prostate cancer. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-lb-096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Whole human genome is packed into chromatin, which is dynamically remodeled. Chromatin structure has been extensively studied with cell lines, but information about chromatin structure in tissue context is lacking. We present genome-wide chromatin accessibility analysis of clinical tissue samples using transposase-accessible chromatin sequencing (ATAC-seq). Our sample cohort consist 11 benign prostatic hyperplasia (BPH), 16 primary prostate cancer (PC), and 11 castration resistant prostate cancer (CRPC) samples. We identified 23,307 to 136,104 regions of accessible chromatin per sample using MACS2 peak calling. Utilizing a peak unification method resulted in a unified set of 178,333 high confidence peaks across sample set. To find out which loci are differentially accessible during disease progression, we further compared normalized ATAC-seq signal between sample groups across the genome. We identified 4747 and 9445 differentially accessible regions (DARs) for BPH to PC and PC to CRPC comparison, respectively. Out of these, in 2961 and 6652 chromatin was opening and in 1786 and 2793 chromatin was closing in respective comparison. Using DARs, we observe clear separation of the sample groups. Earlier, we have characterized this cohort using DNA, RNA and DNA methylation sequencing as well as SWATH proteomics. Using these data and the same analysis approach as with DARs, we identified 2061 and 2723 differentially methylated regions (DMRs) in BPH to PC and PC to CRPC comparisons, respectively. We compared locations of DARs and DMRs and found out that these occur in different loci overlapping only in 27 and 35 loci in respective comparisons. When integrated with gene expression data, the chromatin accessibility correlated (|coefficient| >0.5) with the expression of at least one gene located in the same topologically associating domain (TAD) in altogether 2713 DARs. Next, we examined which transcription factors (TFs) are binding to DARs and thus putatively regulating gene-expression. Using HOMER database, we found several TFs with binding motif enrichment in our DARs. In BPH to PC comparison, opening DARs contain binding sites e.g. for AR and FOXA1 and, in PC to CRPC comparison, opening DARs contain binding sites e.g. for HOXB13, as expected. Interestingly, in PC to CRPC comparison closing DARs contain binding sites for AR and FOXA1 indicating that these TFs have smaller role or alternative regulatory programs when disease progresses. We utilized publicly available CHIP-seq datasets to study this more closely in DARs where ATAC-seq signal correlates with gene-expression within a TAD. Here, while the total number of AR binding sites doubles, the number of AR binding sites in closing DARs is ten times higher in CRPC to PC comparison than in PC to BPH comparison. These results suggest that chromatin accessibility is an important regulator of prostate cancer progression and changes occur in specific loci to where several relevant prostate cancer TFs can bind.
Citation Format: Joonas I. Tuominen, Ebrahim Afyounian, Francesco Tabaro, Tomi Häkkinen, Anastasia Shcherban, Matti Annala, Kati Kivinummi, Teuvo Tammela, Juha Kesseli, Leena Latonen, Kirsi Granberg, Tapio Visakorpi, Matti Nykter. Chromatin alterations in human prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-096.
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Scaravilli M, Kohvakka A, Ruusuvuori P, Afyounian E, Nykter M, Visakorpi T, Latonen L. Abstract 4393: Integrative proteomic analysis of prostate cancer reveals distinct regulation of RNA binding proteins during disease progression. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-4393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
To understand the etiology of the disease, and to find novel and more specific drug targets, the driver mutations and expressional changes in prostate cancer have been examined through extensive genomic and transcriptomic characterization. Although significant insight has been gained through these efforts, it is clear that not all molecular alterations influencing the tumor outcome can be captured through these approaches, and that a comprehensive understanding of the molecular events in cancer require thorough investigation of the proteome.
To understand the functional consequences of genetic and transcriptional aberrations in prostate cancer, we aimed to reveal the proteomic changes during disease formation and progression. We performed high throughput mass spectrometry on clinical tissue samples of benign prostatic hyperplasia (BPH), untreated primary prostate cancer (PC) and castration resistant prostate cancer (CRPC). We performed an integrative analysis of the proteomic data with gene copy number, DNA methylation, and RNA expression data from the same samples. Furthermore, proteomic events correlating with the androgen receptor (AR) status of the tumors were analysed.
We uncovered previously unrecognized molecular and pathway events and several novel AR-associated events in the prostate cancer proteomes to study further. We found significant changes in expression of RNA-binding proteins during disease formation and progression. Examining the relationship of RNA binding proteins at the RNA and protein expression level reveal that while many RNA binding proteins exhibit correlation between the expression levels, some seem regulated at the posttranslational level. Two RNA binding proteins, TDP-43 and FUS, which regulated at the protein, but not at RNA level during prostate cancer progression, show opposite behavior during disease progression and correlation with AR status of the tumors. In cultured prostate cancer cell models, we show that these proteins have specific, but divergent interactions with AR at the RNA and protein levels, and that they contribute differentially to AR activity-mediated responses. Thus, these proteins may significantly contribute to prostate cancer molecular evolution and may pinpoint possible targetable pathways in future prostate cancer therapy.
Citation Format: Mauro Scaravilli, Annika Kohvakka, Pekka Ruusuvuori, Ebrahim Afyounian, Matti Nykter, Tapio Visakorpi, Leena Latonen. Integrative proteomic analysis of prostate cancer reveals distinct regulation of RNA binding proteins during disease progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4393.
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Schiewer MJ, Mandigo AC, Gordon N, Huang F, Gaur S, de Leeuw R, Zhao SG, Evans J, Han S, Parsons T, Birbe R, McCue P, McNair C, Chand SN, Cendon-Florez Y, Gallagher P, McCann JJ, Poudel Neupane N, Shafi AA, Dylgjeri E, Brand LJ, Visakorpi T, Raj GV, Lallas CD, Trabulsi EJ, Gomella LG, Dicker AP, Kelly WK, Leiby BE, Knudsen B, Feng FY, Knudsen KE. PARP-1 regulates DNA repair factor availability. EMBO Mol Med 2018; 10:e8816. [PMID: 30467127 PMCID: PMC6284389 DOI: 10.15252/emmm.201708816] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 10/10/2018] [Accepted: 10/25/2018] [Indexed: 12/22/2022] Open
Abstract
PARP-1 holds major functions on chromatin, DNA damage repair and transcriptional regulation, both of which are relevant in the context of cancer. Here, unbiased transcriptional profiling revealed the downstream transcriptional profile of PARP-1 enzymatic activity. Further investigation of the PARP-1-regulated transcriptome and secondary strategies for assessing PARP-1 activity in patient tissues revealed that PARP-1 activity was unexpectedly enriched as a function of disease progression and was associated with poor outcome independent of DNA double-strand breaks, suggesting that enhanced PARP-1 activity may promote aggressive phenotypes. Mechanistic investigation revealed that active PARP-1 served to enhance E2F1 transcription factor activity, and specifically promoted E2F1-mediated induction of DNA repair factors involved in homologous recombination (HR). Conversely, PARP-1 inhibition reduced HR factor availability and thus acted to induce or enhance "BRCA-ness". These observations bring new understanding of PARP-1 function in cancer and have significant ramifications on predicting PARP-1 inhibitor function in the clinical setting.
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Affiliation(s)
- Matthew J Schiewer
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
- Sidney Kimmel Cancer Center Thomas Jefferson University, Philadelphia, PA, USA
| | - Amy C Mandigo
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
- Sidney Kimmel Cancer Center Thomas Jefferson University, Philadelphia, PA, USA
| | - Nicolas Gordon
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
- Sidney Kimmel Cancer Center Thomas Jefferson University, Philadelphia, PA, USA
| | | | | | - Renée de Leeuw
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
- Sidney Kimmel Cancer Center Thomas Jefferson University, Philadelphia, PA, USA
| | - Shuang G Zhao
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Joseph Evans
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Sumin Han
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Theodore Parsons
- Sidney Kimmel Cancer Center Thomas Jefferson University, Philadelphia, PA, USA
- Department of Pathology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Ruth Birbe
- Cooper University Health, Camden, NJ, USA
| | - Peter McCue
- Sidney Kimmel Cancer Center Thomas Jefferson University, Philadelphia, PA, USA
- Department of Pathology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Christopher McNair
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
- Sidney Kimmel Cancer Center Thomas Jefferson University, Philadelphia, PA, USA
| | - Saswati N Chand
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
- Sidney Kimmel Cancer Center Thomas Jefferson University, Philadelphia, PA, USA
| | - Ylenia Cendon-Florez
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
- Sidney Kimmel Cancer Center Thomas Jefferson University, Philadelphia, PA, USA
| | - Peter Gallagher
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
- Sidney Kimmel Cancer Center Thomas Jefferson University, Philadelphia, PA, USA
| | - Jennifer J McCann
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
- Sidney Kimmel Cancer Center Thomas Jefferson University, Philadelphia, PA, USA
| | - Neermala Poudel Neupane
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
- Sidney Kimmel Cancer Center Thomas Jefferson University, Philadelphia, PA, USA
| | - Ayesha A Shafi
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
- Sidney Kimmel Cancer Center Thomas Jefferson University, Philadelphia, PA, USA
| | - Emanuela Dylgjeri
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
- Sidney Kimmel Cancer Center Thomas Jefferson University, Philadelphia, PA, USA
| | - Lucas J Brand
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
- Sidney Kimmel Cancer Center Thomas Jefferson University, Philadelphia, PA, USA
| | | | | | - Costas D Lallas
- Sidney Kimmel Cancer Center Thomas Jefferson University, Philadelphia, PA, USA
- Department of Urology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Edouard J Trabulsi
- Sidney Kimmel Cancer Center Thomas Jefferson University, Philadelphia, PA, USA
- Department of Urology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Leonard G Gomella
- Sidney Kimmel Cancer Center Thomas Jefferson University, Philadelphia, PA, USA
- Department of Urology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Adam P Dicker
- Sidney Kimmel Cancer Center Thomas Jefferson University, Philadelphia, PA, USA
- Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Wm Kevin Kelly
- Sidney Kimmel Cancer Center Thomas Jefferson University, Philadelphia, PA, USA
- Department of Medical Oncology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Benjamin E Leiby
- Sidney Kimmel Cancer Center Thomas Jefferson University, Philadelphia, PA, USA
- Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA, USA
| | | | - Felix Y Feng
- Departments of Radiation Oncology, Urology, and Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Karen E Knudsen
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
- Sidney Kimmel Cancer Center Thomas Jefferson University, Philadelphia, PA, USA
- Department of Urology, Thomas Jefferson University, Philadelphia, PA, USA
- Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, PA, USA
- Department of Medical Oncology, Thomas Jefferson University, Philadelphia, PA, USA
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Veskimäe K, Scaravilli M, Niininen W, Karvonen H, Jaatinen S, Nykter M, Visakorpi T, Mäenpää J, Ungureanu D, Staff S. Expression Analysis of Platinum Sensitive and Resistant Epithelial Ovarian Cancer Patient Samples Reveals New Candidates for Targeted Therapies. Transl Oncol 2018; 11:1160-1170. [PMID: 30056367 PMCID: PMC6079561 DOI: 10.1016/j.tranon.2018.07.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/09/2018] [Accepted: 07/10/2018] [Indexed: 12/21/2022] Open
Abstract
Ovarian cancer has the highest mortality rate of all gynecologic malignancies. Identification of new biomarkers is highly needed due to its late diagnosis and high recurrence rate. The objective of this study was to identify mechanisms of therapy resistance and potential biomarkers by analyzing mRNA and protein expression from samples derived from patients with platinum-sensitive and -resistant ovarian cancer (total cohort n = 53). The data revealed new candidates for targeted therapies, such as GREB1 and ROR2. We showed that the development of platinum resistance correlated with upregulation of ROR2, whereas GREB1 was downregulated. Moreover, we demonstrated that high levels of ROR2 in platinum-resistant samples were associated with upregulation of Wnt5a, STAT3 and NF-kB levels, suggesting that a crosstalk between the non-canonical Wnt5a-ROR2 and STAT3/NF-kB signaling pathways. Upregulation of ROR2, Wnt5a, STAT3 and NF-kB was further detected in a platinum-resistant cell-line model. The results of the present study provided insight into molecular mechanisms associated with platinum resistance that could be further investigated to improve treatment strategies in this clinically challenging gynecological cancer.
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Affiliation(s)
- K Veskimäe
- Department of Obstetrics and Gynecology, Tampere University Hospital, Tampere, Finland.
| | - M Scaravilli
- BioMediTech Institute, University of Tampere, Tampere, Finland.; Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - W Niininen
- BioMediTech Institute, University of Tampere, Tampere, Finland.; Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - H Karvonen
- BioMediTech Institute, University of Tampere, Tampere, Finland.; Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - S Jaatinen
- BioMediTech Institute, University of Tampere, Tampere, Finland.; Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - M Nykter
- BioMediTech Institute, University of Tampere, Tampere, Finland.; Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - T Visakorpi
- BioMediTech Institute, University of Tampere, Tampere, Finland.; Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland; Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - J Mäenpää
- Department of Obstetrics and Gynecology, Tampere University Hospital, Tampere, Finland; Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - D Ungureanu
- BioMediTech Institute, University of Tampere, Tampere, Finland.; Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - S Staff
- Department of Obstetrics and Gynecology, Tampere University Hospital, Tampere, Finland; BioMediTech Institute, University of Tampere, Tampere, Finland
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Tuominen J, Häkkinen T, Annala M, Kivinummi K, Tammela T, Latonen L, Granberg K, Visakorpi T, Nykter M. Abstract A077: Chromatin state alterations in human prostate cancer progression. Cancer Res 2018. [DOI: 10.1158/1538-7445.prca2017-a077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Understanding the mechanisms of prostate cancer (PC) development into castration-resistant prostate cancer (CRPC) is a key factor in finding better diagnostic and treatment tools. Although a number of studies have tried to explain the molecular evolution of CRPC, more refined understanding on molecular mechanisms is still needed for improved patient care. While increasing amounts of genomic aberrations are accumulating in prostate cancer genome during the disease progression, we still lack understanding on the functional impact of the majority of these aberrations or their combinations. Identification of the regulatory regions from tissue samples enables in-depth analysis of regulatory elements and upstream regulators that are driving tumor development. Thus, we can gain detailed understanding of how the genomic alterations reorganize the chromatin and enable the emergence of cancer phenotype.
We have previously characterized a cohort of 60 clinical prostate tissue samples including benign prostatic hyperplasia (BPH), PC, and CRPC with RNA-seq, MeDIP-seq, DNA-seq, small-RNA-seq, and mass spectrometry. To gain insight into the epigenetic regulation during the disease progression, we decided to use assay for transposase-accessible chromatin using sequencing (ATAC-seq). We first developed a method that allows us to use freshly frozen prostate samples as starting material, and performed ATAC-seq for BPH, PC, and CRPC samples from the above-mentioned cohort.
High quality peaks were identified from all the samples, ranging from tens of thousands to over one hundred thousand peaks per sample. Large variation in the chromatin structure was observed across the cohort. Unsupervised clustering based on peak intensities was able to separate the three different sample types into separate clusters with distinct chromatin state profile for each sample cluster. Next we extracted nucleosome signals from the data. This signal is able to illustrate nucleosome occupancy and positioning with high resolution in the areas of open chromatin. We observed organized nucleosome patterns in our BPH samples, but this organization start to fall apart in PC and especially in CRPC samples where nucleosome localization is no longer uniform inside the group. The results imply increased heterogeneity in chromatin structure as a result of disease progression.
Our data show that ATAC-seq data from clinical prostate material are sufficient to separate different sample groups to their own clusters, and it is possible to have detailed information about nucleosome binding in tumor tissues. These data allow us to reveal novel changes in chromatin state and integrate those changes to other features such as gene expression. With these data we aim to connect specific regulatory elements and upstream regulators to cancer phenotypes and genomic alterations. This new layer of information will bring us closer to understanding the mechanisms that drive molecular evolution of CRPC with potential implications in clinical practice for patients suffering from this devastating disease.
Citation Format: Joonas Tuominen, Tomi Häkkinen, Matti Annala, Kati Kivinummi, Teuvo Tammela, Leena Latonen, Kirsi Granberg, Tapio Visakorpi, Matti Nykter. Chromatin state alterations in human prostate cancer progression [abstract]. In: Proceedings of the AACR Special Conference: Prostate Cancer: Advances in Basic, Translational, and Clinical Research; 2017 Dec 2-5; Orlando, Florida. Philadelphia (PA): AACR; Cancer Res 2018;78(16 Suppl):Abstract nr A077.
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McNair C, Xu K, Mandigo AC, Benelli M, Leiby B, Rodrigues D, Lindberg J, Gronberg H, Crespo M, Laere BD, Dirix L, Visakorpi T, Li F, Feng FY, Bono JD, Demichelis F, Rubin MA, Brown M, Knudsen KE. Abstract B040: Differential impact of RB status on E2F1 reprogramming in human cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.prca2017-b040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Recent examination of advanced prostate cancer (PCa) has suggested a major mechanism of progression to castration-resistant disease (CRPC) to be loss of the retinoblastoma (RB) protein. Along with its critical role in controlling cell cycle progression, RB is known to have important tumor-suppressor functions, and has been shown in PCa to be lost exclusively in late-stage disease. Additionally, loss of RB has been shown to correlate with increased E2F1 transcript and protein expression, via E2F-dependent mechanisms. Despite the vital role RB loss has been shown to play in this fatal stage of disease, the molecular underpinnings remain undefined. Thus, in order to elucidate these CRPC specific alterations, the current study utilizes isogenic models of RB loss in combination with genome-wide binding and transcriptional studies. Data presented herein demonstrate that loss of RB is frequent in CRPC, and represents the main mechanism of RB pathways disruption in PCa as detected through analyses of tumor samples and cell-free DNA. However, this phenomenon is not correlated with changes in proliferative indices, suggesting a role for RB loss outside of canonical cell cycle control. Further, RB loss induces significant genome-wide transcriptional alterations, including upregulation in Myc, E2F, and DNA-repair related pathways. Additionally, loss of RB significantly expands E2F1 binding capacity in castrate conditions, while largely maintaining the RB-intact E2F1 cistrome. Strikingly, while the current RB/E2F1 paradigm suggests that E2F1 exclusively occupies promoter regions of DNA in order to regulate transcriptional changes, RB loss induces marked reprogramming of E2F1 occupied regions, with a distinct increase in enhancer-bound E2F1. Further, motif analyses suggest divergence away from canonical E2F1 binding motifs after RB loss, specifically in regions of expanded E2F1 binding, and additionally suggest likely interaction of novel E2F1 cofactors under RB loss conditions. Interestingly, changes in E2F1 binding capacity after RB loss were seen to be distinct from those detected after androgen-induced RB inactivation, suggesting that the molecular alterations underlying RB loss are discrete from those resulting from functional inactivation. With respect to putative mechanism, it is of note that chromatin accessibility was not significantly altered to sufficiently explain the widespread changes in E2F1 cistrome, regardless of RB status, suggesting a mechanism outside simple opportunistic E2F1 binding after RB loss. Finally, interrogation of a CRPC patient tumor cohort showed predictive capacity for an “Expanded E2F1 Signature,” resulting from genes exhibiting gained E2F1 binding and differential expression after RB loss, in predicting loss of RB in patient samples, and indicating a novel E2F1-driven set of targets vital for CRPC transition in human disease. Together, these data present the first insight into E2F1 activity resulting from RB loss, and the role these changes play in progression to CRPC.
Citation Format: Christopher McNair, Kexin Xu, Amy C. Mandigo, Matteo Benelli, Benjamin Leiby, Daniel Rodrigues, Johan Lindberg, Henrik Gronberg, Mateus Crespo, Bram De Laere, Luc Dirix, Tapio Visakorpi, Fugen Li, Felix Y. Feng, Johann de Bono, Francesca Demichelis, Mark A. Rubin, Myles Brown, Karen E. Knudsen. Differential impact of RB status on E2F1 reprogramming in human cancer [abstract]. In: Proceedings of the AACR Special Conference: Prostate Cancer: Advances in Basic, Translational, and Clinical Research; 2017 Dec 2-5; Orlando, Florida. Philadelphia (PA): AACR; Cancer Res 2018;78(16 Suppl):Abstract nr B040.
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Affiliation(s)
| | - Kexin Xu
- 2University of Health Science Center at San Antonio, San Antonio, TX,
| | | | | | | | | | | | | | - Mateus Crespo
- 4Institute of Cancer Research UK, London, United Kingdom,
| | | | - Luc Dirix
- 6University of Antwerp, Antwerp, Belgium,
| | | | - Fugen Li
- 8Dana Farber Cancer Institute, Boston, MA,
| | - Felix Y. Feng
- 9University of California at San Francisco, San Francisco, CA,
| | - Johann de Bono
- 4Institute of Cancer Research UK, London, United Kingdom,
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Ruusuvuori P, Valkonen M, Kartasalo K, Visakorpi T, Nykter M, Latonen L. Abstract B077: 3D reconstruction and machine learning-based analysis of prostate cancer from histologic images. Cancer Res 2018. [DOI: 10.1158/1538-7445.prca2017-b077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Prostate cancer is multifocal in nature, and histologic grading is the key clinical prognostic factor. Imaging-based tools are required for decreasing the subjectivity of histologic grading, providing quantitative information of the tissue and the pathologic changes in it, and to allow quantitative associations of histologic alterations with other types of information collected from the tissues, such as genomic data.
To enable imaging-based diagnosis, methods for quantifying both the naturally occurring heterogeneity of normal tissue and morphologic changes due to pathology need to be developed. On the other hand, accurate distinction of early pathologic changes from natural variation could provide novel information about development of tumors. Furthermore, the 3-dimensional evolution and growth patterns of tumors should be considered as, traditionally, histologic scoring mostly relies on individual tissue sections extracted from their spatial context.
To build nonsubjective histologic analysis tools, and to model the multifocality of prostate cancer within the organ, we use analysis of histologic images to quantitatively describe prostate cancer. We present an approach for 1) imaging the whole organ into digital pathology slides, 2) reconstruction of the 3D structure of the organ based on the histologic images, and 3) both feature-based and deep learning-based quantitative analysis of the digital images. Our approach enables characterization of tissue morphology with numerical descriptors, enabling subsequent analysis, such as determining the likelihood of pathologic changes. Our current efforts show how heterogeneity in prostate tissue due to spatial location or cancer can be quantified with image-derived features. In addition, we use mouse prostate as a model to visualize and reconstruct a whole organ from high-resolution whole-slide images, and combine tissue type classification in the 3D reconstruction. Further development of these methods and their application for human samples will improve our understanding of human prostate pathologies and cancer evolution within the 3D environment of the organ.
Citation Format: Pekka Ruusuvuori, Mira Valkonen, Kimmo Kartasalo, Tapio Visakorpi, Matti Nykter, Leena Latonen. 3D reconstruction and machine learning-based analysis of prostate cancer from histologic images [abstract]. In: Proceedings of the AACR Special Conference: Prostate Cancer: Advances in Basic, Translational, and Clinical Research; 2017 Dec 2-5; Orlando, Florida. Philadelphia (PA): AACR; Cancer Res 2018;78(16 Suppl):Abstract nr B077.
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Schiewer MJ, Mandigo A, Gordon N, Huang F, Gaur S, Zhao G, Evans J, Han S, Parsons T, Birbe R, McCue P, Visakorpi T, Raj G, Rubin M, Bono JD, Lallas C, Trabulsi E, Gomella L, Dicker A, Kelly WK, Knudsen B, Feng F, Knudsen KE. Abstract B017: PARP-1 and E2F1 collaborate to transcriptionally regulate DNA repair factor availability. Cancer Res 2018. [DOI: 10.1158/1538-7445.prca2017-b017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
PARP-1 holds at least four major functions on chromatin: DNA damage repair, telomeric maintenance, chromatin dynamics, and transcriptional regulation—all of which are relevant in the context of cancer. Notably, PARP-1 has been found to be a key modulator of androgen receptor (AR) function and AR-dependent phenotypes, which is a driving factor in prostate cancer (PCa) biology and therapeutic management. Recent studies indicate an unanticipated prevalence of DNA repair alterations in advanced PCa and showed that PARP-1 inhibitors (PARPi) can effectively manage a subset of these tumors. Despite the functions of PARP-1 in DNA repair having been exploited as a therapeutic target for tumors with BRCA1/2 aberrations, factors beyond DNA repair alterations clearly play a role in the response to PARPi. Notably, while DNA repair defects enrich for PARPi responders, BRCA1/2 alterations do not appear to be necessary or sufficient to induce PARPi clinical response. Given the preclinical and clinical data, pursuing a deeper understanding of the molecular underpinnings of PARPi action in PCa may yield significant benefit. Human tissue microarrays were utilized to quantify PARP-1 levels and activity as a function of PCa progression. Genome-wide transcriptional profiling in response to PARPi was performed and the PARP-1-regulated transcriptome was identified. Both the PARP-1-regulated transcriptome and PARP-1 enzymatic activity were found to be elevated as a function of PCa progression. Further interrogation of the PARP-1-regulated transcriptome revealed a major impact on E2F1-regulated genes, and chromatin immunoprecipitation analyses indicated that PARP-1 functions to regulate the chromatin architecture and E2F1 occupancy at E2F1 target gene loci. Most prominent among the E2F1-regulated genes responsive to PARPi were genes associated with DNA damage repair, with a particular enrichment for genes involved in homologous recombination (HR). In sum, these data indicate that PARP-1 regulates the function of key oncogenic transcription factors (AR and E2F1) in PCa, and part of the effect of PARPi may be through downregulation of DNA repair factors.
Citation Format: Matthew J. Schiewer, Amy Mandigo, Nicolas Gordon, Fangjin Huang, Sanchaika Gaur, George Zhao, Joseph Evans, Sumin Han, Theodore Parsons, Ruth Birbe, Peter McCue, Tapio Visakorpi, Ganesh Raj, Mark Rubin, Johann de Bono, Costas Lallas, Edouard Trabulsi, Leonard Gomella, Adam Dicker, Wm. Kevin Kelly, Beatrice Knudsen, Felix Feng, Karen E. Knudsen. PARP-1 and E2F1 collaborate to transcriptionally regulate DNA repair factor availability [abstract]. In: Proceedings of the AACR Special Conference: Prostate Cancer: Advances in Basic, Translational, and Clinical Research; 2017 Dec 2-5; Orlando, Florida. Philadelphia (PA): AACR; Cancer Res 2018;78(16 Suppl):Abstract nr B017.
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Affiliation(s)
| | - Amy Mandigo
- 1Thomas Jefferson University, Philadelphia, PA,
| | | | | | | | | | | | - Sumin Han
- 3University of Michigan, Ann Arbor, MI,
| | | | - Ruth Birbe
- 1Thomas Jefferson University, Philadelphia, PA,
| | - Peter McCue
- 1Thomas Jefferson University, Philadelphia, PA,
| | | | | | | | - Johann de Bono
- 7Institute for Cancer Research, Royal Marsden, London, United Kingdom,
| | | | | | | | - Adam Dicker
- 1Thomas Jefferson University, Philadelphia, PA,
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Latonen L, Afyounian E, Jylhä A, Nättinen J, Aapola U, Annala M, Kivinummi K, Tammela T, Beuerman RW, Uusitalo H, Nykter M, Visakorpi T. Abstract A020: Integrative analysis of the proteome in primary and advanced prostate cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.prca2017-a020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
To fully understand the output of alterations in cancer genomes and transcriptomes, we need to know how these aberrations are translated into the functional protein units in cells. We assessed proteomic changes during disease formation and progression in prostate cancer by performing high-throughput mass spectrometry on clinical tissue samples of benign prostatic hyperplasia (BPH), untreated primary prostate cancer (PC), and castration-resistant prostate cancer (CRPC). With SWATH-MS quantitation-based proteomics we found that each of these sample groups show a distinct protein profile. By integrative analysis of this mass spectrometry dataset with genetic, epigenetic, and transcriptional data from the same samples, we show that, especially in CRPC, gene copy number, DNA methylation, and RNA expression levels do not reliably predict proteomic changes. From our analysis, we have identified sets of novel expression changes occurring primarily at the protein level, in addition to identification of several miRNA-target correlations present at protein but not at mRNA level. We find novel expression changes in previously unrecognized pathways in prostate cancer that are likely to affect disease development and progression. For example, we identify two metabolic shifts in the citric acid cycle (TCA cycle), one occurring during primary cancer development and the second during castration resistance, having implications on drug targeting against cancer metabolism. Our proteogenomic analysis of prostate cancer uncovers robustness against genomic and transcriptomic aberrations during disease progression, reveals new disease mechanisms, and significantly extends understanding of prostate cancer biology.
Citation Format: Leena Latonen, Ebrahim Afyounian, Antti Jylhä, Janika Nättinen, Ulla Aapola, Matti Annala, Kati Kivinummi, Teuvo Tammela, Roger W. Beuerman, Hannu Uusitalo, Matti Nykter, Tapio Visakorpi. Integrative analysis of the proteome in primary and advanced prostate cancer [abstract]. In: Proceedings of the AACR Special Conference: Prostate Cancer: Advances in Basic, Translational, and Clinical Research; 2017 Dec 2-5; Orlando, Florida. Philadelphia (PA): AACR; Cancer Res 2018;78(16 Suppl):Abstract nr A020.
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30
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McNair C, Xu K, Mandigo AC, Benelli M, Leiby B, Rodrigues D, Lindberg J, Gronberg H, Laere BD, Dirix L, Visakorpi T, Li F, Feng FY, Bono JD, Demichelis F, Rubin MA, Brown M, Knudsen KE. Abstract IA03: Differential impact of RB pathway status on E2F1 reprogramming and disease progression in human prostate cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.prca2017-ia03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The retinoblastoma tumor suppressor (RB) is mechanistically linked to suppression of E2F1-mediated cell cycle regulation. Abrogation of RB function is associated with poor clinical outcome across various tumor types, which frequently elicit a preference for either RB depletion or functional inactivation, yet the basis for selectivity is unknown. Here, examination of RB pathway alterations in advanced prostate cancer revealed that cyclin dependent kinase (CDK)/cyclin/CDKi alterations are infrequent, and identify RB loss as the major mechanism of pathway disruption in human disease. Furthermore, RB status was readily traced through cell-free DNA analyses in human specimens, thus identifying new ways to assign RB status in the clinical setting. Strikingly, RB depletion in human disease was not associated with a higher Ki67 index, indicating a role for the RB/E2F1 pathway in regulating processes distinct from cell cycle control and associated with lethal-stage disease. Subsequent mechanistic investigation utilized isogenic prostate cancer models, wherein RB could be differentially inactivated through depletion or through hormone-induced, CDK-mediated phosphorylation. Unbiased molecular interrogation uncovered a novel E2F1 cistrome and downstream engagement of transcriptional networks exclusively observed after RB loss, with binding specificity divergent from canonically described E2F1 binding patterns. Additionally, E2F1 cistrome alterations elicited by RB depletion were seen to be distinct from those after phosphorylation-induced RB functional inactivation, providing needed insight into the basis of selectivity for RB loss versus CDK-mediated inactivation observed in human disease. Analyses of human CRPC tumor samples further underscored the clinical relevance of RB loss-induced gene expression programs, which were significantly correlated with reprogrammed E2F1 binding identified herein. Taken together, the studies presented are the first to identify the consequences of RB loss, demonstrating molecular distinction from RB inactivation and illustrating the clinical relevance of RB loss-induced E2F rewiring.
Citation Format: Christopher McNair, Kexin Xu, Amy C. Mandigo, Matteo Benelli, Benjamin Leiby, Daniel Rodrigues, Johan Lindberg, Henrik Gronberg, Bram De Laere, Luc Dirix, Tapio Visakorpi, Fugen Li, Felix Y. Feng, Johann de Bono, Francesca Demichelis, Mark A Rubin, Myles Brown, Karen E. Knudsen. Differential impact of RB pathway status on E2F1 reprogramming and disease progression in human prostate cancer [abstract]. In: Proceedings of the AACR Special Conference: Prostate Cancer: Advances in Basic, Translational, and Clinical Research; 2017 Dec 2-5; Orlando, Florida. Philadelphia (PA): AACR; Cancer Res 2018;78(16 Suppl):Abstract nr IA03.
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Affiliation(s)
- Christopher McNair
- 1Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA,
| | - Kexin Xu
- 2Department of Molecular Medicine/Institute of Biotechnology, The University of Texas Health Science Center at San Antonio, San Antonio, TX,
| | - Amy C. Mandigo
- 1Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA,
| | - Matteo Benelli
- 3Centre for Integrative Biology, University of Trento, Trento, Italy,
| | - Benjamin Leiby
- 1Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA,
| | - Daniel Rodrigues
- 4Division of Cancer Therapeutics and Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom,
| | - Johan Lindberg
- 5Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden,
| | - Henrik Gronberg
- 5Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden,
| | - Bram De Laere
- 6Centre for Oncological Research, University of Antwerp, Antwerp, Belgium,
| | - Luc Dirix
- 6Centre for Oncological Research, University of Antwerp, Antwerp, Belgium,
- 7Department of Oncology, GZA Hospitals Sint-Augustinus, Antwerp, Belgium,
| | - Tapio Visakorpi
- 8BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland,
| | - Fugen Li
- 9Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA,
| | - Felix Y. Feng
- 10Department of Radiation Oncology, Urology, and Medicine and Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA,
| | - Johann de Bono
- 4Division of Cancer Therapeutics and Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom,
| | - Francesca Demichelis
- 3Centre for Integrative Biology, University of Trento, Trento, Italy,
- 11Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian Hospital, New York, NY,
| | - Mark A Rubin
- 11Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian Hospital, New York, NY,
- 12Sandra and Edward Meyer Cancer Center at Weill Cornell Medicine, New York, NY,
| | - Myles Brown
- 9Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA,
- 13Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Karen E. Knudsen
- 1Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA,
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Kallio HML, Hieta R, Latonen L, Brofeldt A, Annala M, Kivinummi K, Tammela TL, Nykter M, Isaacs WB, Lilja HG, Bova GS, Visakorpi T. Constitutively active androgen receptor splice variants AR-V3, AR-V7 and AR-V9 are co-expressed in castration-resistant prostate cancer metastases. Br J Cancer 2018; 119:347-356. [PMID: 29988112 PMCID: PMC6070921 DOI: 10.1038/s41416-018-0172-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 06/08/2018] [Accepted: 06/13/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND A significant subset of prostate cancer (PC) patients with a castration-resistant form of the disease (CRPC) show primary resistance to androgen receptor (AR)-targeting drugs developed against CRPC. As one explanation could be the expression of constitutively active androgen receptor splice variants (AR-Vs), our current objectives were to study AR-Vs and other AR aberrations to better understand the emergence of CRPC. METHODS We analysed specimens from different stages of prostate cancer by next-generation sequencing and immunohistochemistry. RESULTS AR mutations and copy number variations were detected only in CRPC specimens. Genomic structural rearrangements of AR were observed in 5/30 metastatic CRPC patients, but they were not associated with expression of previously known AR-Vs. The predominant AR-Vs detected were AR-V3, AR-V7 and AR-V9, with the expression levels being significantly higher in CRPC cases compared to prostatectomy samples. Out of 25 CRPC metastases that expressed any AR variant, 17 cases harboured expression of all three of these AR-Vs. AR-V7 protein expression was highly heterogeneous and higher in CRPC compared to hormone-naïve tumours. CONCLUSIONS AR-V3, AR-V7 and AR-V9 are co-expressed in CRPC metastases highlighting the fact that inhibiting AR function via regions common to all AR-Vs is likely to provide additional benefit to patients with CRPC.
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Affiliation(s)
- Heini M L Kallio
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, Finland.
| | - Reija Hieta
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, Finland
| | - Leena Latonen
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, Finland
| | - Anniina Brofeldt
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, Finland
| | - Matti Annala
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, Finland
| | - Kati Kivinummi
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, Finland
| | - Teuvo L Tammela
- Department of Urology, University of Tampere, Tampere University Hospital, Tampere, Finland
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, Finland
| | - William B Isaacs
- The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hans G Lilja
- Departments of Surgery (Urology), Laboratory Medicine and Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.,Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK.,Department of Translational Medicine, Lund University, Malmö, Sweden.,Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, Finland
| | - G Steven Bova
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, Finland
| | - Tapio Visakorpi
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, Finland.,Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
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Granberg KJ, Annala M, Lehtinen B, Kesseli J, Haapasalo J, Ruusuvuori P, Yli-Harja O, Visakorpi T, Haapasalo H, Nykter M, Zhang W. Strong FGFR3 staining is a marker for FGFR3 fusions in diffuse gliomas. Neuro Oncol 2018; 19:1206-1216. [PMID: 28379477 PMCID: PMC5570261 DOI: 10.1093/neuonc/nox028] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Background Inhibitors of fibroblast growth factor receptors (FGFRs) have recently arisen as a promising treatment option for patients with FGFR alterations. Gene fusions involving FGFR3 and transforming acidic coiled-coil protein 3 (TACC3) have been detected in diffuse gliomas and other malignancies, and fusion-positive cases have responded well to FGFR inhibition. As high FGFR3 expression has been detected in fusion-positive tumors, we sought to determine the clinical significance of FGFR3 protein expression level as well as its potential for indicating FGFR3 fusions. Methods We performed FGFR3 immunohistochemistry on tissue microarrays containing 676 grades II-IV astrocytomas and 116 grades II-III oligodendroglial tumor specimens. Fifty-one cases were further analyzed using targeted sequencing. Results Moderate to strong FGFR3 staining was detected in gliomas of all grades, was more common in females, and was associated with poor survival in diffuse astrocytomas. Targeted sequencing identified FGFR3-TACC3 fusions and an FGFR3-CAMK2A fusion in 10 of 15 strongly stained cases, whereas no fusions were found in 36 negatively to moderately stained cases. Fusion-positive cases were predominantly female and negative for IDH and EGFR/PDGFRA/MET alterations. These and moderately stained cases show lower MIB-1 proliferation index than negatively to weakly stained cases. Furthermore, stronger FGFR3 expression was commonly observed in malignant tissue regions of lower cellularity in fusion-negative cases. Importantly, subregional negative FGFR3 staining was also observed in a few fusion-positive cases. Conclusions Strong FGFR3 protein expression is indicative of FGFR3 fusions and may serve as a clinically applicable predictive marker for treatment regimens based on FGFR inhibitors.
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Affiliation(s)
- Kirsi J Granberg
- BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland; Department of Signal Processing, Tampere University of Technology, Tampere, Finland; Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas; Science Center, Tampere University Hospital, Tampere, Finland; Fimlab Laboratories Ltd., Tampere University Hospital, Tampere, Finland; Unit of Neurosurgery, Tampere University Hospital, Tampere, Finland; Pori unit, Tampere University of Technology, Pori, Finland; Department of Pathology, University of Tampere, Tampere, Finland; Department of Cancer Biology, Comprehensive Cancer Center of Wake Forest Baptist Medical Center, Winston-Salem, North Carolina
| | - Matti Annala
- BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland; Department of Signal Processing, Tampere University of Technology, Tampere, Finland; Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas; Science Center, Tampere University Hospital, Tampere, Finland; Fimlab Laboratories Ltd., Tampere University Hospital, Tampere, Finland; Unit of Neurosurgery, Tampere University Hospital, Tampere, Finland; Pori unit, Tampere University of Technology, Pori, Finland; Department of Pathology, University of Tampere, Tampere, Finland; Department of Cancer Biology, Comprehensive Cancer Center of Wake Forest Baptist Medical Center, Winston-Salem, North Carolina
| | - Birgitta Lehtinen
- BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland; Department of Signal Processing, Tampere University of Technology, Tampere, Finland; Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas; Science Center, Tampere University Hospital, Tampere, Finland; Fimlab Laboratories Ltd., Tampere University Hospital, Tampere, Finland; Unit of Neurosurgery, Tampere University Hospital, Tampere, Finland; Pori unit, Tampere University of Technology, Pori, Finland; Department of Pathology, University of Tampere, Tampere, Finland; Department of Cancer Biology, Comprehensive Cancer Center of Wake Forest Baptist Medical Center, Winston-Salem, North Carolina
| | - Juha Kesseli
- BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland; Department of Signal Processing, Tampere University of Technology, Tampere, Finland; Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas; Science Center, Tampere University Hospital, Tampere, Finland; Fimlab Laboratories Ltd., Tampere University Hospital, Tampere, Finland; Unit of Neurosurgery, Tampere University Hospital, Tampere, Finland; Pori unit, Tampere University of Technology, Pori, Finland; Department of Pathology, University of Tampere, Tampere, Finland; Department of Cancer Biology, Comprehensive Cancer Center of Wake Forest Baptist Medical Center, Winston-Salem, North Carolina
| | - Joonas Haapasalo
- BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland; Department of Signal Processing, Tampere University of Technology, Tampere, Finland; Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas; Science Center, Tampere University Hospital, Tampere, Finland; Fimlab Laboratories Ltd., Tampere University Hospital, Tampere, Finland; Unit of Neurosurgery, Tampere University Hospital, Tampere, Finland; Pori unit, Tampere University of Technology, Pori, Finland; Department of Pathology, University of Tampere, Tampere, Finland; Department of Cancer Biology, Comprehensive Cancer Center of Wake Forest Baptist Medical Center, Winston-Salem, North Carolina
| | - Pekka Ruusuvuori
- BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland; Department of Signal Processing, Tampere University of Technology, Tampere, Finland; Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas; Science Center, Tampere University Hospital, Tampere, Finland; Fimlab Laboratories Ltd., Tampere University Hospital, Tampere, Finland; Unit of Neurosurgery, Tampere University Hospital, Tampere, Finland; Pori unit, Tampere University of Technology, Pori, Finland; Department of Pathology, University of Tampere, Tampere, Finland; Department of Cancer Biology, Comprehensive Cancer Center of Wake Forest Baptist Medical Center, Winston-Salem, North Carolina
| | - Olli Yli-Harja
- BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland; Department of Signal Processing, Tampere University of Technology, Tampere, Finland; Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas; Science Center, Tampere University Hospital, Tampere, Finland; Fimlab Laboratories Ltd., Tampere University Hospital, Tampere, Finland; Unit of Neurosurgery, Tampere University Hospital, Tampere, Finland; Pori unit, Tampere University of Technology, Pori, Finland; Department of Pathology, University of Tampere, Tampere, Finland; Department of Cancer Biology, Comprehensive Cancer Center of Wake Forest Baptist Medical Center, Winston-Salem, North Carolina
| | - Tapio Visakorpi
- BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland; Department of Signal Processing, Tampere University of Technology, Tampere, Finland; Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas; Science Center, Tampere University Hospital, Tampere, Finland; Fimlab Laboratories Ltd., Tampere University Hospital, Tampere, Finland; Unit of Neurosurgery, Tampere University Hospital, Tampere, Finland; Pori unit, Tampere University of Technology, Pori, Finland; Department of Pathology, University of Tampere, Tampere, Finland; Department of Cancer Biology, Comprehensive Cancer Center of Wake Forest Baptist Medical Center, Winston-Salem, North Carolina
| | - Hannu Haapasalo
- BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland; Department of Signal Processing, Tampere University of Technology, Tampere, Finland; Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas; Science Center, Tampere University Hospital, Tampere, Finland; Fimlab Laboratories Ltd., Tampere University Hospital, Tampere, Finland; Unit of Neurosurgery, Tampere University Hospital, Tampere, Finland; Pori unit, Tampere University of Technology, Pori, Finland; Department of Pathology, University of Tampere, Tampere, Finland; Department of Cancer Biology, Comprehensive Cancer Center of Wake Forest Baptist Medical Center, Winston-Salem, North Carolina
| | - Matti Nykter
- BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland; Department of Signal Processing, Tampere University of Technology, Tampere, Finland; Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas; Science Center, Tampere University Hospital, Tampere, Finland; Fimlab Laboratories Ltd., Tampere University Hospital, Tampere, Finland; Unit of Neurosurgery, Tampere University Hospital, Tampere, Finland; Pori unit, Tampere University of Technology, Pori, Finland; Department of Pathology, University of Tampere, Tampere, Finland; Department of Cancer Biology, Comprehensive Cancer Center of Wake Forest Baptist Medical Center, Winston-Salem, North Carolina
| | - Wei Zhang
- BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland; Department of Signal Processing, Tampere University of Technology, Tampere, Finland; Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas; Science Center, Tampere University Hospital, Tampere, Finland; Fimlab Laboratories Ltd., Tampere University Hospital, Tampere, Finland; Unit of Neurosurgery, Tampere University Hospital, Tampere, Finland; Pori unit, Tampere University of Technology, Pori, Finland; Department of Pathology, University of Tampere, Tampere, Finland; Department of Cancer Biology, Comprehensive Cancer Center of Wake Forest Baptist Medical Center, Winston-Salem, North Carolina
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Kohvakka A, Shcherban A, Kivinummi KK, Annala M, Urbanucci A, Nykter M, Visakorpi T. Abstract 2476: Discovery of an androgen-responsive long noncoding RNA that associates with progression of ERG-overexpressing prostate cancers. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-2476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Androgen receptor (AR) signaling pathway has an important role in the growth and development of normal prostate, but also in tumorigenesis and progression of prostate cancer (PC). Although the mechanisms of AR signaling have been widely studied and utilized for treatment in advanced PC, the exact role of AR in development of primary PC is unclear. Former studies have found that AR cistrome is reprogrammed during tumorigenesis to bind novel genomic loci by master regulators, including the ETS family transcription factor ERG. While many AR-induced target genes are known, the effect of AR signaling on regulation of long noncoding RNAs (lncRNAs) is poorly understood, especially in the context of PC progression. Previously, we discovered multiple novel PC-associated transcripts (PCATs) to be aberrantly expressed in PC. Here, we evaluated the expression of 39 Tampere PCATs (TPCATs) in 87 radical prostatectomy specimens using high-throughput real-time PCR, and studied their association with time to PSA progression after prostatectomy. Six TPCATs were significantly associated with time to PSA progression, and four of them also associated with extracapsular extension. In addition, we assessed the expression of TPCATs in the TCGA prostate adenocarcinoma cohort, and found many to be correlated with ERG expression. Moreover, publicly available AR ChIP-seq data from PC tumors indicated that several ERG-associated TPCATs had AR-binding sites on their promoters, some of which overlapped with ERG binding sites. Most notably, we found one progression-associated TPCAT that was regulated by AR in an androgen-sensitive manner according to AR siRNA knockdown and DHT stimulation experiments in vitro. The same TPCAT was also highly associated with overexpression of ERG, and further validated to be a highly PC-specific lncRNA that was abundantly expressed in primary PCs. Taken together, these findings give more insight into the role of AR cistrome in the regulation of lncRNAs in primary PC, and introduce a potential novel prognostic marker to be used in early detection of aggressive PC.
Citation Format: Annika Kohvakka, Anastasia Shcherban, Kati K. Kivinummi, Matti Annala, Alfonso Urbanucci, Matti Nykter, Tapio Visakorpi. Discovery of an androgen-responsive long noncoding RNA that associates with progression of ERG-overexpressing prostate cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2476.
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Kallio HM, Hieta R, Brofeldt A, Annala M, Kivinummi K, Tammela TL, Nykter M, Isaacs WB, Lilja HG, Bova GS, Visakorpi T. Abstract 1802: Constitutively active androgen receptor splice variants AR-V3, AR-V7 and AR-V9 are co-expressed in castration-resistant prostate cancer metastases. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-1802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Prostate cancer (PC) is the most commonly diagnosed male cancer both in the United States and in Europe. Approximately 20-25% of cases will develop metastatic disease, which eventually progresses to lethal castration-resistant form of the disease (CRPC). Even though the exact mechanism by which CRPC develops remains to be fully understood, several mechanisms of castration resistance have been identified. Importantly, androgen signaling remains active even in the CRPC stage. This has led to the clinical development of second-generation AR-targeting drugs enzalutamide and abiraterone that target the ligand-binding domain of AR directly and indirectly, respectively. Unfortunately, a significant subset of patients show primary resistance to these agents. One potential explanation for this is the presence of AR splice variants (AR-Vs). AR-Vs are alternatively spliced isoforms of the AR mRNA usually resulting in truncated AR protein product. Even though AR-Vs lack variable portions of the AR COOH-terminal domain including the ligand-binding domain (LBD), they are constitutively active as transcription factors. The aim of this work was to study AR-Vs and also AR rearrangements, mutations and copy number variations (CNVs) to better understand the emergence of CRPC. This was done by analyzing specimens from different stages of prostate cancer by next-generation sequencing methods. Our sample cohorts included hormone-naïve PCs and lymph node metastases as well as locally recurrent and metastatic CRPCs. AR mutations and CNVs were detected only in CRPC specimens. Genomic structural rearrangements of AR (AR-GSRs) were observed in 5/30 metastatic CRPC patients but they were not associated with the expression of previously known AR-Vs, and their variant allele fractions were low. The main AR-Vs detected were AR-V3, AR-V7 and AR-V9, whose expression levels were higher in CRPC cases in comparison to prostatectomy samples. The differences were statistically significant for either variant alone or when their expression fractions were combined (p=0.0006). In addition, metastatic CRPC cases expressed significantly more AR-V3, AR-V7 and AR-V9 when compared to non-androgen deprived pelvic lymph node metastases (p=0.0282). The expression of these AR-Vs was strongly associated with the levels of full-length AR. Out of 25 CRPC metastases that expressed any AR variant, 17 cases harbored expression of all three of these AR-Vs. In conclusion, AR-V3, AR-V7 and AR-V9 tend to be co-expressed in metastatic CRPC highlighting the fact that targeting of the AR ligand-binding domain might not be sufficient to achieve a treatment response in certain patients. Consequently, targeting of AR via regions common to all AR-Vs is likely to provide additional benefit to patients suffering from CRPC.
Citation Format: Heini M. Kallio, Reija Hieta, Anniina Brofeldt, Matti Annala, Kati Kivinummi, Teuvo L. Tammela, Matti Nykter, William B. Isaacs, Hans G. Lilja, G Steven Bova, Tapio Visakorpi. Constitutively active androgen receptor splice variants AR-V3, AR-V7 and AR-V9 are co-expressed in castration-resistant prostate cancer metastases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1802.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Hans G. Lilja
- 4Memorial Sloan-Kettering Cancer Center, New York, NY
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Latonen L, Nykter M, Visakorpi T. Proteomics of prostate cancer - revealing how cancer cells master their messy genomes. Oncoscience 2018; 5:216-217. [PMID: 30234142 PMCID: PMC6142899 DOI: 10.18632/oncoscience.453] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 06/19/2018] [Indexed: 01/21/2023] Open
Affiliation(s)
- Leena Latonen
- Leena Latonen: Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, Finland; FimLab laboratories, Tampere University Hospital, Tampere, Finland
| | - Matti Nykter
- Leena Latonen: Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, Finland; FimLab laboratories, Tampere University Hospital, Tampere, Finland
| | - Tapio Visakorpi
- Leena Latonen: Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, Finland; FimLab laboratories, Tampere University Hospital, Tampere, Finland
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36
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Wedge DC, Gundem G, Mitchell T, Woodcock DJ, Martincorena I, Ghori M, Zamora J, Butler A, Whitaker H, Kote-Jarai Z, Alexandrov LB, Van Loo P, Massie CE, Dentro S, Warren AY, Verrill C, Berney DM, Dennis N, Merson S, Hawkins S, Howat W, Lu YJ, Lambert A, Kay J, Kremeyer B, Karaszi K, Luxton H, Camacho N, Marsden L, Edwards S, Matthews L, Bo V, Leongamornlert D, McLaren S, Ng A, Yu Y, Zhang H, Dadaev T, Thomas S, Easton DF, Ahmed M, Bancroft E, Fisher C, Livni N, Nicol D, Tavaré S, Gill P, Greenman C, Khoo V, Van As N, Kumar P, Ogden C, Cahill D, Thompson A, Mayer E, Rowe E, Dudderidge T, Gnanapragasam V, Shah NC, Raine K, Jones D, Menzies A, Stebbings L, Teague J, Hazell S, Corbishley C, de Bono J, Attard G, Isaacs W, Visakorpi T, Fraser M, Boutros PC, Bristow RG, Workman P, Sander C, Hamdy FC, Futreal A, McDermott U, Al-Lazikani B, Lynch AG, Bova GS, Foster CS, Brewer DS, Neal DE, Cooper CS, Eeles RA. Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets. Nat Genet 2018; 50:682-692. [PMID: 29662167 PMCID: PMC6372064 DOI: 10.1038/s41588-018-0086-z] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 02/22/2018] [Indexed: 12/18/2022]
Abstract
Prostate cancer represents a substantial clinical challenge because it is difficult to predict outcome and advanced disease is often fatal. We sequenced the whole genomes of 112 primary and metastatic prostate cancer samples. From joint analysis of these cancers with those from previous studies (930 cancers in total), we found evidence for 22 previously unidentified putative driver genes harboring coding mutations, as well as evidence for NEAT1 and FOXA1 acting as drivers through noncoding mutations. Through the temporal dissection of aberrations, we identified driver mutations specifically associated with steps in the progression of prostate cancer, establishing, for example, loss of CHD1 and BRCA2 as early events in cancer development of ETS fusion-negative cancers. Computational chemogenomic (canSAR) analysis of prostate cancer mutations identified 11 targets of approved drugs, 7 targets of investigational drugs, and 62 targets of compounds that may be active and should be considered candidates for future clinical trials.
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Affiliation(s)
- David C Wedge
- Oxford Big Data Institute, University of Oxford, Oxford, UK.
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK.
- Oxford NIHR Biomedical Research Centre, Oxford, UK.
| | - Gunes Gundem
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Thomas Mitchell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Urology, Addenbrooke's Hospital, Cambridge, UK
- Uro-Oncology Research Group, Cancer Research UK, Cambridge Institute, Cambridge, UK
| | - Dan J Woodcock
- Oxford Big Data Institute, University of Oxford, Oxford, UK
| | | | - Mohammed Ghori
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Jorge Zamora
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Adam Butler
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Hayley Whitaker
- Molecular Diagnostics and Therapeutics Group, University College London, London, UK
| | | | | | - Peter Van Loo
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Cancer Genomics, The Francis Crick Institute, London, UK
| | - Charlie E Massie
- Uro-Oncology Research Group, Cancer Research UK, Cambridge Institute, Cambridge, UK
- Early Detection Programme, Cancer Research UK Cambridge Centre, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Stefan Dentro
- Oxford Big Data Institute, University of Oxford, Oxford, UK
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Cancer Genomics, The Francis Crick Institute, London, UK
| | - Anne Y Warren
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Clare Verrill
- Oxford NIHR Biomedical Research Centre, Oxford, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Dan M Berney
- Centre for Molecular Oncology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Nening Dennis
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Sue Merson
- The Institute of Cancer Research, London, UK
| | - Steve Hawkins
- Uro-Oncology Research Group, Cancer Research UK, Cambridge Institute, Cambridge, UK
| | - William Howat
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Yong-Jie Lu
- Centre for Molecular Oncology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Adam Lambert
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Jonathan Kay
- Molecular Diagnostics and Therapeutics Group, University College London, London, UK
| | - Barbara Kremeyer
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Katalin Karaszi
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Hayley Luxton
- Molecular Diagnostics and Therapeutics Group, University College London, London, UK
| | - Niedzica Camacho
- Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- The Institute of Cancer Research, London, UK
| | - Luke Marsden
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | | | - Lucy Matthews
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Valeria Bo
- Statistics and Computational Biology Laboratory, Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Daniel Leongamornlert
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- The Institute of Cancer Research, London, UK
| | - Stuart McLaren
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Anthony Ng
- The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Yongwei Yu
- Second Military Medical University, Shanghai, China
| | | | | | - Sarah Thomas
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | | | - Elizabeth Bancroft
- The Institute of Cancer Research, London, UK
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Cyril Fisher
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Naomi Livni
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - David Nicol
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Simon Tavaré
- Statistics and Computational Biology Laboratory, Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Pelvender Gill
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | | | - Vincent Khoo
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | | | - Pardeep Kumar
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | | | - Declan Cahill
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Alan Thompson
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Erik Mayer
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Edward Rowe
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Tim Dudderidge
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Vincent Gnanapragasam
- Department of Urology, Addenbrooke's Hospital, Cambridge, UK
- Department of Surgical Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Nimish C Shah
- Department of Urology, Addenbrooke's Hospital, Cambridge, UK
| | - Keiran Raine
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - David Jones
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Andrew Menzies
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Lucy Stebbings
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Jon Teague
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Steven Hazell
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | | | | | | | | | - Tapio Visakorpi
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Michael Fraser
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Paul C Boutros
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Robert G Bristow
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | | | - Chris Sander
- cBio Center, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA, USA
| | - Freddie C Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Andrew Futreal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Ultan McDermott
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Andrew G Lynch
- Statistics and Computational Biology Laboratory, Cancer Research UK Cambridge Institute, Cambridge, UK
- School of Mathematics and Statistics/School of Medicine, University of St. Andrews, Fife, UK
| | - G Steven Bova
- Johns Hopkins School of Medicine, Baltimore, MD, USA
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | | | - Daniel S Brewer
- The Institute of Cancer Research, London, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
- Earlham Institute, Norwich, UK
| | - David E Neal
- Uro-Oncology Research Group, Cancer Research UK, Cambridge Institute, Cambridge, UK
- Department of Surgical Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Colin S Cooper
- The Institute of Cancer Research, London, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Rosalind A Eeles
- The Institute of Cancer Research, London, UK.
- Royal Marsden NHS Foundation Trust, London and Sutton, UK.
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37
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Sainio M, Visakorpi T, Tolonen T, Ilvesaro J, Bova GS. Expression of neuroendocrine differentiation markers in lethal metastatic castration-resistant prostate cancer. Pathol Res Pract 2018; 214:848-856. [PMID: 29728311 DOI: 10.1016/j.prp.2018.04.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 04/09/2018] [Accepted: 04/20/2018] [Indexed: 12/31/2022]
Abstract
Neuroendocrine differentiation (NED) is a common phenomenon in prostate cancer, and it has been associated with poor prognosis in some studies of primary prostate cancer. Incidence and patterns of NED in metastatic prostate cancer sites have not been examined widely. In this study, we studied expression of three commonly used markers of NED (chromogranin A, neuron specific enolase and synaptophysin) in 89 metastases from 31 men that died of castration-resistant prostate cancer and underwent rapid autopsy, and in 89 hormone-naïve primary tumors removed by radical prostatectomy. In addition, we examined NED association with androgen receptor, ERG and Ki-67 expression in metastatic tumor sites. Morphologically, 1 of 31 cases was classified as small cell carcinoma, and the remaining 30 were classified as usual prostate adenocarcinoma using a recently proposed classification of prostate cancers with NED. Metastases showed more expression of neuron specific enolase and synaptophysin compared to prostatectomies (6.3% of cells vs. 1.0%, p < 0.001 and 4.0% vs. 0.4%, p < 0.001, respectively). At least focal expression of one of the markers was seen in 78% of metastases. Strong expression was relatively uncommon, seen in 3/89 (chromogranin A), 8/89 (neuron specific enolase), and 5/89 (synaptophysin) metastases. Expression of chromogranin A and synaptophysin correlated with each other (r = 0.64, p < 0.001), but expression of neuron specific enolase did not correlate with the two other markers. Extent of NED varied significantly between different metastatic sites in individual patients. Absent androgen receptor expression was associated with strong expression of chromogranin A (p = .02) and neuron specific enolase (p = .02), but not with focal expression of any marker. No clear association was found between expression of NE markers and ERG or Ki-67. In conclusion, NED is a common and heterogeneous phenomenon in metastatic, castration-resistant prostate cancer. NED is more often present in castration-resistant prostate cancer compared to hormone-naïve disease, and it is associated with androgen receptor negativity. More research is needed to understand significance of NED in the progression of prostate cancer.
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Affiliation(s)
- Miika Sainio
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, FI-33014, Finland.
| | - Tapio Visakorpi
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, FI-33014, Finland.
| | - Teemu Tolonen
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, FI-33014, Finland; Department of Pathology, Tampere University Hospital, Fimlab Laboratories, Tampere, Finland.
| | - Joanna Ilvesaro
- Department of Pathology, Tampere University Hospital, Fimlab Laboratories, Tampere, Finland.
| | - G Steven Bova
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, FI-33014, Finland.
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38
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Latonen L, Afyounian E, Jylhä A, Nättinen J, Aapola U, Annala M, Kivinummi KK, Tammela TTL, Beuerman RW, Uusitalo H, Nykter M, Visakorpi T. Integrative proteomics in prostate cancer uncovers robustness against genomic and transcriptomic aberrations during disease progression. Nat Commun 2018; 9:1176. [PMID: 29563510 PMCID: PMC5862881 DOI: 10.1038/s41467-018-03573-6] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 02/21/2018] [Indexed: 01/23/2023] Open
Abstract
To understand functional consequences of genetic and transcriptional aberrations in prostate cancer, the proteomic changes during disease formation and progression need to be revealed. Here we report high-throughput mass spectrometry on clinical tissue samples of benign prostatic hyperplasia (BPH), untreated primary prostate cancer (PC) and castration resistant prostate cancer (CRPC). Each sample group shows a distinct protein profile. By integrative analysis we show that, especially in CRPC, gene copy number, DNA methylation, and RNA expression levels do not reliably predict proteomic changes. Instead, we uncover previously unrecognized molecular and pathway events, for example, several miRNA target correlations present at protein but not at mRNA level. Notably, we identify two metabolic shifts in the citric acid cycle (TCA cycle) during prostate cancer development and progression. Our proteogenomic analysis uncovers robustness against genomic and transcriptomic aberrations during prostate cancer progression, and significantly extends understanding of prostate cancer disease mechanisms. Understanding of molecular events in cancer requires proteome-level characterisation. Here, proteome profiling of patient samples representing primary and progressed prostate cancer enables the authors to identify pathway alterations that are not reflected at the genomic and transcriptomic levels.
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Affiliation(s)
- Leena Latonen
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, 33014, Finland.,FimLab Laboratories, Tampere University Hospital, Tampere, 33101, Finland
| | - Ebrahim Afyounian
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, 33014, Finland
| | - Antti Jylhä
- Department of Ophthalmology, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, 33014, Finland
| | - Janika Nättinen
- Department of Ophthalmology, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, 33014, Finland
| | - Ulla Aapola
- Department of Ophthalmology, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, 33014, Finland
| | - Matti Annala
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, 33014, Finland
| | - Kati K Kivinummi
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, 33014, Finland
| | - Teuvo T L Tammela
- Department of Urology, University of Tampere and Tampere University Hospital, Tampere, 33521, Finland
| | - Roger W Beuerman
- Department of Ophthalmology, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, 33014, Finland.,Singapore Eye Research Institute, Singapore, 169856, Singapore.,Duke-NUS Neuroscience, Singapore, 169857, Singapore.,Duke-NUS Medical School Ophthalmology and Visual Sciences Academic Clinical Program, Singapore, 169857, Singapore.,Ophthalmology, Yong Loo Lin Medical School, National University of Singapore, Singapore, 119228, Singapore
| | - Hannu Uusitalo
- Department of Ophthalmology, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, 33014, Finland.,Tays Eye Centre, Tampere University Hospital, Tampere, 33521, Finland
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, 33014, Finland. .,Science Center, Tampere University Hospital, Tampere, 33521, Finland.
| | - Tapio Visakorpi
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere, Tampere, 33014, Finland. .,FimLab Laboratories, Tampere University Hospital, Tampere, 33101, Finland.
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39
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Urbanucci A, Barfeld SJ, Kytölä V, Itkonen HM, Coleman IM, Vodák D, Sjöblom L, Sheng X, Tolonen T, Minner S, Burdelski C, Kivinummi KK, Kohvakka A, Kregel S, Takhar M, Alshalalfa M, Davicioni E, Erho N, Lloyd P, Karnes RJ, Ross AE, Schaeffer EM, Vander Griend DJ, Knapp S, Corey E, Feng FY, Nelson PS, Saatcioglu F, Knudsen KE, Tammela TLJ, Sauter G, Schlomm T, Nykter M, Visakorpi T, Mills IG. Androgen Receptor Deregulation Drives Bromodomain-Mediated Chromatin Alterations in Prostate Cancer. Cell Rep 2018; 19:2045-2059. [PMID: 28591577 DOI: 10.1016/j.celrep.2017.05.049] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Revised: 04/01/2017] [Accepted: 05/12/2017] [Indexed: 12/17/2022] Open
Abstract
Global changes in chromatin accessibility may drive cancer progression by reprogramming transcription factor (TF) binding. In addition, histone acetylation readers such as bromodomain-containing protein 4 (BRD4) have been shown to associate with these TFs and contribute to aggressive cancers including prostate cancer (PC). Here, we show that chromatin accessibility defines castration-resistant prostate cancer (CRPC). We show that the deregulation of androgen receptor (AR) expression is a driver of chromatin relaxation and that AR/androgen-regulated bromodomain-containing proteins (BRDs) mediate this effect. We also report that BRDs are overexpressed in CRPCs and that ATAD2 and BRD2 have prognostic value. Finally, we developed gene stratification signature (BROMO-10) for bromodomain response and PC prognostication, to inform current and future trials with drugs targeting these processes. Our findings provide a compelling rational for combination therapy targeting bromodomains in selected patients in which BRD-mediated TF binding is enhanced or modified as cancer progresses.
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Affiliation(s)
- Alfonso Urbanucci
- Centre for Molecular Medicine Norway, Nordic European Molecular Biology Laboratory Partnership, Forskningsparken, University of Oslo, 21 0349 Oslo, Norway; Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway.
| | - Stefan J Barfeld
- Centre for Molecular Medicine Norway, Nordic European Molecular Biology Laboratory Partnership, Forskningsparken, University of Oslo, 21 0349 Oslo, Norway
| | - Ville Kytölä
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology (BioMediTech), University of Tampere and Tampere University of Technology, 33520 Tampere, Finland
| | - Harri M Itkonen
- Centre for Molecular Medicine Norway, Nordic European Molecular Biology Laboratory Partnership, Forskningsparken, University of Oslo, 21 0349 Oslo, Norway
| | - Ilsa M Coleman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Daniel Vodák
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, 0424 Oslo, Norway
| | - Liisa Sjöblom
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology (BioMediTech), University of Tampere and Fimlab Laboratories, Tampere University Hospital, 33520 Tampere, Finland
| | - Xia Sheng
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Teemu Tolonen
- Department of Pathology, Fimlab Laboratories, Tampere University Hospital, 33520 Tampere, Finland
| | - Sarah Minner
- University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Christoph Burdelski
- General, Visceral and Thoracic Surgery Department and Clinic, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Kati K Kivinummi
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology (BioMediTech), University of Tampere and Tampere University of Technology, 33520 Tampere, Finland
| | - Annika Kohvakka
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology (BioMediTech), University of Tampere and Fimlab Laboratories, Tampere University Hospital, 33520 Tampere, Finland
| | - Steven Kregel
- Department of Surgery - Section of Urology, University of Chicago, Chicago, IL 60637, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109-0940, USA
| | - Mandeep Takhar
- Research and Development, GenomeDx Biosciences, Vancouver, BC V6B 1B8, Canada
| | - Mohammed Alshalalfa
- Research and Development, GenomeDx Biosciences, Vancouver, BC V6B 1B8, Canada
| | - Elai Davicioni
- Research and Development, GenomeDx Biosciences, Vancouver, BC V6B 1B8, Canada
| | - Nicholas Erho
- Research and Development, GenomeDx Biosciences, Vancouver, BC V6B 1B8, Canada
| | - Paul Lloyd
- Department of Medicine, University of California at San Francisco, San Francisco, CA 94143-0410, USA; Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA 94143-0981, USA
| | | | - Ashley E Ross
- Brady Urological Institute, Johns Hopkins Medical Institute, Baltimore, MD 21287, USA
| | - Edward M Schaeffer
- Department of Urology, Northwestern University, Feinberg School of Medicine, 303 East Chicago Avenue, Tarry 16-703, Chicago, IL 60611-3008, USA
| | - Donald J Vander Griend
- Department of Surgery - Section of Urology, University of Chicago, Chicago, IL 60637, USA
| | - Stefan Knapp
- Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK; Institute for Pharmaceutical Chemistry, Goethe-University Frankfurt, Campus Riedberg, Max-von Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, WA 98195, USA
| | - Felix Y Feng
- Department of Medicine, University of California at San Francisco, San Francisco, CA 94143-0410, USA; Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA 94143-0981, USA; Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Peter S Nelson
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Urology, University of Washington, Seattle, WA 98195, USA; Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Fahri Saatcioglu
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway; Institute for Cancer Genetics and Informatics, Oslo University Hospital, 0424 Oslo, Norway
| | - Karen E Knudsen
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Teuvo L J Tammela
- Prostate Cancer Research Center and Department of Urology, University of Tampere and Tampere University Hospital, 33014 Tampere, Finland
| | - Guido Sauter
- University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Thorsten Schlomm
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg 20095, Germany
| | - Matti Nykter
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology (BioMediTech), University of Tampere and Tampere University of Technology, 33520 Tampere, Finland
| | - Tapio Visakorpi
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology (BioMediTech), University of Tampere and Fimlab Laboratories, Tampere University Hospital, 33520 Tampere, Finland
| | - Ian G Mills
- Centre for Molecular Medicine Norway, Nordic European Molecular Biology Laboratory Partnership, Forskningsparken, University of Oslo, 21 0349 Oslo, Norway; Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway; PCUK Movember Centre of Excellence, CCRCB, Queen's University, Belfast BT7 1NN, Northern Ireland, UK.
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40
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Affiliation(s)
- Frank Claessens
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, Campus GHB ON1, Herestraat 49, 6000, Leuven, Belgium.
| | - Tapio Visakorpi
- Prostate Cancer Research Center, Institute for Biomedical Technology, FI-33014 University of Tampere, Biokatu, 6-8 33520, Tampere, Finland
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41
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Rane JK, Erb HHH, Nappo G, Mann VM, Simms MS, Collins AT, Visakorpi T, Maitland NJ. Inhibition of the glucocorticoid receptor results in an enhanced miR-99a/100-mediated radiation response in stem-like cells from human prostate cancers. Oncotarget 2018; 7:51965-51980. [PMID: 27340920 PMCID: PMC5239528 DOI: 10.18632/oncotarget.10207] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 06/09/2016] [Indexed: 12/21/2022] Open
Abstract
Radiation therapy is a major primary treatment option for both localized early stage prostate cancer, and for advanced, regionally un-resectable, cancer. However, around 30% of patients still experience biochemical recurrence after radiation therapy within 10 years. Thus, identification of better biomarkers and new targets are urgently required to improve current therapeutic strategies. The miR-99 family has been shown to play an important role in the regulation of the DNA damage response, via targeting of the SWI/SNF chromatin remodeling factors, SMARCA5 and SMARCD1 in cell line models. In the present study, we have demonstrated that low expression of miR-99a and miR-100 is present in cell populations which are relatively radiation insensitive, for example in prostate cancer stem cells and in castration-resistant prostate cancer. Additionally, treatment of cells with the synthetic glucocorticoid, Dexamethasone resulted in decreased miR-99a and 100 expression, suggesting a new mechanism of miR-99a and 100 regulation in androgen-independent prostate cells. Strikingly, treatment of prostate cells with the glucocorticoid receptor inhibitor, Mifepristone was found to sensitize prostate cells to radiation by increasing the levels of miR-99a and miR-100. These results qualify the miR99 family as markers of radiation sensitivity and as potential therapeutic targets to improve efficiency of radiotherapy.
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Affiliation(s)
- Jayant K Rane
- The Cancer Research Unit, Department of Biology, University of York, York, North Yorkshire, YO10 5DD, UK.,Leukaemia and Stem Cell Biology Group, Department of Haematological Medicine, King's College London, Rayne Institute, London, SE5 9NU, UK
| | - Holger H H Erb
- The Cancer Research Unit, Department of Biology, University of York, York, North Yorkshire, YO10 5DD, UK
| | - Giovanna Nappo
- The Cancer Research Unit, Department of Biology, University of York, York, North Yorkshire, YO10 5DD, UK.,Laboratory of Molecular Haematopoiesis and Stem Cell Biology, Department of Experimental and Clinical Medicine, Magna Græcia University, 88100, Catanzaro, Italy
| | - Vincent M Mann
- Hull York Medical School, University of Hull, Hull, East Yorkshire, HU6 7RX, UK.,Department of Urology, Castle Hill Hospital, Cottingham, East Yorkshire, HU16 5JQ, UK
| | - Matthew S Simms
- Hull York Medical School, University of Hull, Hull, East Yorkshire, HU6 7RX, UK.,Department of Urology, Castle Hill Hospital, Cottingham, East Yorkshire, HU16 5JQ, UK
| | - Anne T Collins
- The Cancer Research Unit, Department of Biology, University of York, York, North Yorkshire, YO10 5DD, UK
| | - Tapio Visakorpi
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology - BioMediTech, University of Tampere and Tampere University Hospital, Tampere, 33520 Finland
| | - Norman J Maitland
- The Cancer Research Unit, Department of Biology, University of York, York, North Yorkshire, YO10 5DD, UK.,Hull York Medical School, University of Hull, Hull, East Yorkshire, HU6 7RX, UK
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42
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Högnäs G, Kivinummi K, Kallio HML, Hieta R, Ruusuvuori P, Koskenalho A, Kesseli J, Tammela TLJ, Riikonen J, Ilvesaro J, Kares S, Hirvikoski PP, Laurila M, Mirtti T, Nykter M, Kujala PM, Visakorpi T, Tolonen T, Bova GS. Feasibility of Prostate PAXgene Fixation for Molecular Research and Diagnostic Surgical Pathology: Comparison of Matched Fresh Frozen, FFPE, and PFPE Tissues. Am J Surg Pathol 2017; 42:103-115. [PMID: 28984675 DOI: 10.1097/pas.0000000000000961] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Advances in prostate cancer biology and diagnostics are dependent upon high-fidelity integration of clinical, histomorphologic, and molecular phenotypic findings. In this study, we compared fresh frozen, formalin-fixed paraffin-embedded (FFPE), and PAXgene-fixed paraffin-embedded (PFPE) tissue preparation methods in radical prostatectomy prostate tissue from 36 patients and performed a preliminary test of feasibility of using PFPE tissue in routine prostate surgical pathology diagnostic assessment. In addition to comparing histology, immunohistochemistry, and general measures of DNA and RNA integrity in each fixation method, we performed functional tests of DNA and RNA quality, including targeted Miseq RNA and DNA sequencing, and implemented methods to relate DNA and RNA yield and quality to quantified DNA and RNA picogram nuclear content in each tissue volume studied. Our results suggest that it is feasible to use PFPE tissue for routine robot-assisted laparoscopic prostatectomy surgical pathology diagnostics and immunohistochemistry, with the benefit of significantly improvedDNA and RNA quality and RNA picogram yield per nucleus as compared with FFPE tissue. For fresh frozen, FFPE, and PFPE tissues, respectively, the average Genomic Quality Numbers were 7.9, 3.2, and 6.2, average RNA Quality Numbers were 8.7, 2.6, and 6.3, average DNA picogram yields per nucleus were 0.41, 0.69, and 0.78, and average RNA picogram yields per nucleus were 1.40, 0.94, and 2.24. These findings suggest that where DNA and/or RNA analysis of tissue is required, and when tissue size is small, PFPE may provide important advantages over FFPE. The results also suggest several interesting nuances including potential avenues to improve RNA quality in FFPE tissues and confirm recent suggestions that some DNA sequence artifacts associated with FFPE can be avoided.
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Affiliation(s)
- Gunilla Högnäs
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute
| | - Kati Kivinummi
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute
| | - Heini M L Kallio
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute
| | - Reija Hieta
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute
| | - Pekka Ruusuvuori
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute.,Signal Processing Laboratory, Tampere University of Technology, Pori
| | - Antti Koskenalho
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute
| | - Juha Kesseli
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute
| | - Teuvo L J Tammela
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute.,Department of Urology, University of Tampere
| | | | - Joanna Ilvesaro
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere
| | - Saara Kares
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere
| | | | - Marita Laurila
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere
| | - Tuomas Mirtti
- Institute for Molecular Medicine Finland, University of Helsinki.,Department of Pathology, HUSLAB, Helsinki University Hospital, Helsinki, Finland
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute
| | - Paula M Kujala
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere
| | - Tapio Visakorpi
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute.,Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere
| | - Teemu Tolonen
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere
| | - G Steven Bova
- Prostate Cancer Research Center, Faculty of Medicine and Life Sciences and BioMediTech Institute
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43
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Olvedy M, Scaravilli M, Hoogstrate Y, Visakorpi T, Jenster G, Martens-Uzunova ES. A comprehensive repertoire of tRNA-derived fragments in prostate cancer. Oncotarget 2017; 7:24766-77. [PMID: 27015120 PMCID: PMC5029740 DOI: 10.18632/oncotarget.8293] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 03/02/2016] [Indexed: 12/20/2022] Open
Abstract
Prostate cancer (PCa) is the most common cancer among men in developed countries. Although its genetic background is thoroughly investigated, rather little is known about the role of small non-coding RNAs (sncRNA) in this disease. tRNA-derived fragments (tRFs) represent a new class of sncRNAs, which are present in a broad range of species and have been reported to play a role in several cellular processes. Here, we analyzed the expression of tRFs in fresh frozen patient samples derived from normal adjacent prostate and different stages of PCa by RNA-sequencing. We identified 598 unique tRFs, many of which are deregulated in cancer samples when compared to normal adjacent tissue. Most of the identified tRFs are derived from the 5’- and 3’-ends of mature cytosolic tRNAs, but we also found tRFs produced from other parts of tRNAs, including pre-tRNA trailers and leaders, as well as tRFs from mitochondrial tRNAs. The 5’-derived tRFs comprise the most abundant class of tRFs in general and represent the major class among upregulated tRFs. The 3’-derived tRFs types are dominant among downregulated tRFs in PCa. We validated the expression of three tRFs using qPCR. The ratio of tRFs derived from tRNALysCTT and tRNAPheGAA emerged as a good indicator of progression-free survival and a candidate prognostic marker. This study provides a systematic catalogue of tRFs and their dysregulation in PCa and can serve as the basis for further research on the biomarker potential and functional roles of tRFs in this disease.
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Affiliation(s)
- Michael Olvedy
- Department of Urology, Erasmus MC, Rotterdam, The Netherlands.,Current address: VIB Center for the Biology of Disease, KU Leuven, Leuven, Belgium.,Current address: Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Mauro Scaravilli
- Institute of Biosciences and Medical Technology-BioMediTech, University of Tampere, Tampere, Finland.,Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | | | - Tapio Visakorpi
- Institute of Biosciences and Medical Technology-BioMediTech, University of Tampere, Tampere, Finland.,Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Guido Jenster
- Department of Urology, Erasmus MC, Rotterdam, The Netherlands
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44
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Kivinummi K, Urbanucci A, Leinonen K, Tammela TLJ, Annala M, Isaacs WB, Bova GS, Nykter M, Visakorpi T. The expression of AURKA is androgen regulated in castration-resistant prostate cancer. Sci Rep 2017; 7:17978. [PMID: 29269934 PMCID: PMC5740165 DOI: 10.1038/s41598-017-18210-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 12/06/2017] [Indexed: 11/13/2022] Open
Abstract
Although second generation endocrine therapies have significantly improved survival, castration-resistant prostate cancer (CRPC) cells are eventually able to escape available hormonal treatments due to reactivation of androgen receptor (AR) signaling. Identification of novel, non-classical and druggable AR-target genes may provide new approaches to treat CRPC. Our previous analyses suggested that Aurora kinase A (AURKA) is regulated by androgens in prostate cancer cells that express high levels of AR. Here, we provide further evidence that AURKA is significantly overexpressed in AR-positive CRPC samples carrying amplification of AR gene and/or expressing AR in high levels. We also demonstrate androgen-induced AR binding in the intronic region of AURKA. The expression of AURKA is increased upon androgen stimulation in LNCaP-ARhi cells that express high levels of AR. The growth of the cells was also significantly inhibited by an AURKA specific inhibitor, alisertib (MLN8237). Together, these findings suggest that the expression of AURKA is regulated by androgen in prostate cancer cells that highly express AR, emphasizing its potential as a therapeutic target in patients with CRPC.
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Affiliation(s)
- Kati Kivinummi
- BioMediTech Institute, Faculty of Medicine and Life Sciences, University of Tampere, Fimlab Laboratories, Tampere University Hospital, Tampere, Finland.
| | - Alfonso Urbanucci
- BioMediTech Institute, Faculty of Medicine and Life Sciences, University of Tampere, Fimlab Laboratories, Tampere University Hospital, Tampere, Finland.,Centre for Molecular Medicine Norway, Nordic European Molecular Biology Laboratory Partnership, Forksningsparken, University of Oslo, Oslo, Norway.,Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Inflammation Research Centre, University of Oslo, Oslo, Norway
| | - Katri Leinonen
- BioMediTech Institute, Faculty of Medicine and Life Sciences, University of Tampere, Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Teuvo L J Tammela
- Department of Urology, Tampere University Hospital and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Matti Annala
- BioMediTech Institute, Faculty of Medicine and Life Sciences, University of Tampere, Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - William B Isaacs
- The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21287, USA
| | - G Steven Bova
- BioMediTech Institute, Faculty of Medicine and Life Sciences, University of Tampere, Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Matti Nykter
- BioMediTech Institute, Faculty of Medicine and Life Sciences, University of Tampere, Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Tapio Visakorpi
- BioMediTech Institute, Faculty of Medicine and Life Sciences, University of Tampere, Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
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45
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McNair C, Xu K, Mandigo AC, Benelli M, Leiby B, Rodrigues D, Lindberg J, Gronberg H, Crespo M, De Laere B, Dirix L, Visakorpi T, Li F, Feng FY, de Bono J, Demichelis F, Rubin MA, Brown M, Knudsen KE. Differential impact of RB status on E2F1 reprogramming in human cancer. J Clin Invest 2017; 128:341-358. [PMID: 29202480 DOI: 10.1172/jci93566] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 10/24/2017] [Indexed: 01/03/2023] Open
Abstract
The tumor suppressor protein retinoblastoma (RB) is mechanistically linked to suppression of transcription factor E2F1-mediated cell cycle regulation. For multiple tumor types, loss of RB function is associated with poor clinical outcome. RB action is abrogated either by direct depletion or through inactivation of RB function; however, the basis for this selectivity is unknown. Here, analysis of tumor samples and cell-free DNA from patients with advanced prostate cancer showed that direct RB loss was the preferred pathway of disruption in human disease. While RB loss was associated with lethal disease, RB-deficient tumors had no proliferative advantage and exhibited downstream effects distinct from cell cycle control. Mechanistically, RB loss led to E2F1 cistrome expansion and different binding specificity, alterations distinct from those observed after functional RB inactivation. Additionally, identification of protumorigenic transcriptional networks specific to RB loss that were validated in clinical samples demonstrated the ability of RB loss to differentially reprogram E2F1 in human cancers. Together, these findings not only identify tumor-suppressive functions of RB that are distinct from cell cycle control, but also demonstrate that the molecular consequence of RB loss is distinct from RB inactivation. Thus, these studies provide insight into how RB loss promotes disease progression, and identify new nodes for therapeutic intervention.
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Affiliation(s)
- Christopher McNair
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Kexin Xu
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Amy C Mandigo
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Matteo Benelli
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Benjamin Leiby
- Department of Pharmacology and Experimental Therapeutics, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Daniel Rodrigues
- Division of Cancer Therapeutics and Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Johan Lindberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Gronberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mateus Crespo
- Division of Cancer Therapeutics and Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Bram De Laere
- Centre for Oncological Research, University of Antwerp, Antwerp, Belgium
| | - Luc Dirix
- Centre for Oncological Research, University of Antwerp, Antwerp, Belgium.,Department of Oncology, GZA Hospitals Sint-Augustinus, Antwerp, Belgium
| | - Tapio Visakorpi
- BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Fugen Li
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Felix Y Feng
- Department of Radiation Oncology, Urology, and Medicine and Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
| | - Johann de Bono
- Division of Cancer Therapeutics and Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Francesca Demichelis
- Centre for Integrative Biology, University of Trento, Trento, Italy.,Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian Hospital, New York, New York, USA
| | - Mark A Rubin
- Englander Institute for Precision Medicine, Weill Cornell Medicine and New York Presbyterian Hospital, New York, New York, USA.,Sandra and Edward Meyer Cancer Center at Weill Cornell Medicine, New York, New York, USA
| | - Myles Brown
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Karen E Knudsen
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
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46
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Assel M, Sjöblom L, Murtola TJ, Talala K, Kujala P, Stenman UH, Taari K, Auvinen A, Vickers A, Visakorpi T, Tammela TL, Lilja H. A Four-kallikrein Panel and β-Microseminoprotein in Predicting High-grade Prostate Cancer on Biopsy: An Independent Replication from the Finnish Section of the European Randomized Study of Screening for Prostate Cancer. Eur Urol Focus 2017; 5:561-567. [PMID: 29137895 DOI: 10.1016/j.euf.2017.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/05/2017] [Indexed: 12/25/2022]
Abstract
BACKGROUND A panel of four kallikrein markers (total, free, and intact prostate-specific antigen [PSA] and human kallikrein-related peptidase 2 [hK2]) improves predictive accuracy for Gleason score ≥7 (high-grade) prostate cancer among men biopsied for elevated PSA. A four-kallikrein panel model was originally developed and validated by the Dutch center of the European Randomized Study of Screening for Prostate Cancer (ERSPC). The kallikrein panel is now commercially available as 4Kscore™. OBJECTIVE To assess whether these findings could be replicated among participants in the Finnish section of ERSPC (FinRSPC) and whether β-microseminoprotein (MSP), a candidate prostate cancer biomarker, adds predictive value. DESIGN, SETTING, AND PARTICIPANTS Among 4861 biopsied screening-positive participants in the first three screening rounds of FinRSPC, a case-control subset was selected that included 1632 biopsy-positive cases matched by age at biopsy to biopsy-negative controls. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS The predictive accuracy of prespecified prediction models was compared with biopsy outcomes. RESULTS AND LIMITATIONS Among men with PSA of 4.0-25ng/ml, 1111 had prostate cancer, 318 of whom had high-grade disease. Total PSA and age predicted high-grade cancer with an area under the curve of 0.648 (95% confidence interval [CI] 0.614-0.681) and the four-kallikrein panel increased discrimination to 0.746 (95% CI 0.717-0.774). Adding MSP to the four-kallikrein panel led to a significant (Wald test; p=0.015) but small increase (0.003) in discrimination. Limitations include a risk of verification bias among men with PSA of 3.0-3.99ng/ml and the absence of digital rectal examination results. CONCLUSIONS These findings provide additional evidence that kallikrein markers can be used to inform biopsy decision-making. Further studies are needed to define the role of MSP. PATIENT SUMMARY Four kallikrein markers and β-microseminoprotein in blood improve discrimination of high-grade prostate cancer at biopsy in men with elevated prostate-specific antigen.
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Affiliation(s)
- Melissa Assel
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Liisa Sjöblom
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology, University of Tampere, Tampere, Finland; Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Teemu J Murtola
- Prostate Cancer Research Center, School of Health Sciences, University of Tampere, Tampere, Finland; Department of Urology, Tampere University Hospital, Tampere, Finland
| | | | - Paula Kujala
- Fimlab Laboratories, Tampere University Hospital, Tampere, Finland; Department of Pathology, Tampere University Hospital, Tampere, Finland
| | - Ulf-Håkan Stenman
- Department of Clinical Chemistry, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Kimmo Taari
- Department of Urology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Anssi Auvinen
- Prostate Cancer Research Center, School of Health Sciences, University of Tampere, Tampere, Finland
| | - Andrew Vickers
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tapio Visakorpi
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology, University of Tampere, Tampere, Finland; Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Teuvo L Tammela
- Prostate Cancer Research Center, School of Health Sciences, University of Tampere, Tampere, Finland; Department of Urology, Tampere University Hospital, Tampere, Finland
| | - Hans Lilja
- Prostate Cancer Research Center, Institute of Biosciences and Medical Technology, University of Tampere, Tampere, Finland; Departments of Laboratory Medicine, Surgery, and Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK; Department of Translational Medicine, Lund University, Malmö, Sweden.
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47
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Camacho N, Van Loo P, Edwards S, Kay JD, Matthews L, Haase K, Clark J, Dennis N, Thomas S, Kremeyer B, Zamora J, Butler AP, Gundem G, Merson S, Luxton H, Hawkins S, Ghori M, Marsden L, Lambert A, Karaszi K, Pelvender G, Massie CE, Kote-Jarai Z, Raine K, Jones D, Howat WJ, Hazell S, Livni N, Fisher C, Ogden C, Kumar P, Thompson A, Nicol D, Mayer E, Dudderidge T, Yu Y, Zhang H, Shah NC, Gnanapragasam VJ, Isaacs W, Visakorpi T, Hamdy F, Berney D, Verrill C, Warren AY, Wedge DC, Lynch AG, Foster CS, Lu YJ, Bova GS, Whitaker HC, McDermott U, Neal DE, Eeles R, Cooper CS, Brewer DS. Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data. PLoS Genet 2017; 13:e1007001. [PMID: 28945760 PMCID: PMC5628936 DOI: 10.1371/journal.pgen.1007001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 10/05/2017] [Accepted: 08/28/2017] [Indexed: 12/13/2022] Open
Abstract
A variety of models have been proposed to explain regions of recurrent somatic copy number alteration (SCNA) in human cancer. Our study employs Whole Genome DNA Sequence (WGS) data from tumor samples (n = 103) to comprehensively assess the role of the Knudson two hit genetic model in SCNA generation in prostate cancer. 64 recurrent regions of loss and gain were detected, of which 28 were novel, including regions of loss with more than 15% frequency at Chr4p15.2-p15.1 (15.53%), Chr6q27 (16.50%) and Chr18q12.3 (17.48%). Comprehensive mutation screens of genes, lincRNA encoding sequences, control regions and conserved domains within SCNAs demonstrated that a two-hit genetic model was supported in only a minor proportion of recurrent SCNA losses examined (15/40). We found that recurrent breakpoints and regions of inversion often occur within Knudson model SCNAs, leading to the identification of ZNF292 as a target gene for the deletion at 6q14.3-q15 and NKX3.1 as a two-hit target at 8p21.3-p21.2. The importance of alterations of lincRNA sequences was illustrated by the identification of a novel mutational hotspot at the KCCAT42, FENDRR, CAT1886 and STCAT2 loci at the 16q23.1-q24.3 loss. Our data confirm that the burden of SCNAs is predictive of biochemical recurrence, define nine individual regions that are associated with relapse, and highlight the possible importance of ion channel and G-protein coupled-receptor (GPCR) pathways in cancer development. We concluded that a two-hit genetic model accounts for about one third of SCNA indicating that mechanisms, such haploinsufficiency and epigenetic inactivation, account for the remaining SCNA losses.
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Affiliation(s)
- Niedzica Camacho
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, United Kingdom
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, London, United Kingdom
- Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Sandra Edwards
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, United Kingdom
| | - Jonathan D. Kay
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, Cambridgeshire, United Kingdom
- Molecular Diagnostics and Therapeutics Group, University College London, London, United Kingdom
| | - Lucy Matthews
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, United Kingdom
| | - Kerstin Haase
- Cancer Genomics Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Jeremy Clark
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, United Kingdom
| | - Nening Dennis
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Sarah Thomas
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Barbara Kremeyer
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Jorge Zamora
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Adam P. Butler
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Gunes Gundem
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
- Epidemiology & Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Sue Merson
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, United Kingdom
| | - Hayley Luxton
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, Cambridgeshire, United Kingdom
- Molecular Diagnostics and Therapeutics Group, University College London, London, United Kingdom
| | - Steve Hawkins
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, Cambridgeshire, United Kingdom
| | - Mohammed Ghori
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Luke Marsden
- Department of Physiology, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Adam Lambert
- Department of Oncology, CRUK/MRC Oxford Institute for Radiation Oncology, Oxford, Oxfordshire, United Kingdom
| | - Katalin Karaszi
- Department of Oncology, CRUK/MRC Oxford Institute for Radiation Oncology, Oxford, Oxfordshire, United Kingdom
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Gill Pelvender
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Charlie E. Massie
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, Cambridgeshire, United Kingdom
- CRUK Cambridge Centre, Early Detection Programme, Urological Malignancies Programme, Hutchison-MRC Research Centre, Cambridge, Cambridgeshire, United Kingdom
| | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, United Kingdom
| | - Keiran Raine
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - David Jones
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - William J. Howat
- Histopathology and in situ hybridization Research Group, Cancer Research UK Cambridge Institute, Cambridge, Cambridgeshire, United Kingdom
| | - Steven Hazell
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Naomi Livni
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Cyril Fisher
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Christopher Ogden
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Pardeep Kumar
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Alan Thompson
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - David Nicol
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Erik Mayer
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Tim Dudderidge
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Yongwei Yu
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Hongwei Zhang
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Nimish C. Shah
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, Cambridgeshire, United Kingdom
| | - Vincent J. Gnanapragasam
- Academic Urology Group, Department of Surgery, University of Cambridge, Cambridge, Cambridgeshire, United Kingdom
| | | | - William Isaacs
- School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Tapio Visakorpi
- Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Freddie Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Dan Berney
- Centre for Molecular Oncology, Barts Cancer Institute, The Barts and London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Clare Verrill
- Department of Cellular Pathology and Oxford Biomedical Research Centre, Oxford University Hospitals NHS Trust, Oxford, Oxfordshire, United Kingdom
| | - Anne Y. Warren
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, Cambridgeshire, United Kingdom
| | - David C. Wedge
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
- Oxford Big Data Institute & Oxford Centre for Cancer Gene Research, Wellcome Trust Centre for Human Genetics, Oxford, Oxfordshire, United Kingdom
| | - Andrew G. Lynch
- Statistics and Computational Biology Laboratory, Cancer Research UK Cambridge Institute, Cambridge, Cambridgeshire, United Kingdom
- School of Mathematics and Statistics/School of Medicine, University of St Andrews, St Andrews, Fife, Scotland
| | | | - Yong Jie Lu
- Centre for Molecular Oncology, Barts Cancer Institute, The Barts and London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - G. Steven Bova
- Faculty of Medicine and Life Sciences and BioMediTech Institute, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Hayley C. Whitaker
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, Cambridgeshire, United Kingdom
- Molecular Diagnostics and Therapeutics Group, University College London, London, United Kingdom
| | - Ultan McDermott
- Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - David E. Neal
- Uro-Oncology Research Group, Cancer Research UK Cambridge Institute, Cambridge, Cambridgeshire, United Kingdom
- Academic Urology Group, Department of Surgery, University of Cambridge, Cambridge, Cambridgeshire, United Kingdom
| | - Rosalind Eeles
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, United Kingdom
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Colin S. Cooper
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, United Kingdom
| | - Daniel S. Brewer
- Norwich Medical School, University of East Anglia, Norwich, Norfolk, United Kingdom
- Organisms and Ecosystems, The Earlham Institute, Norwich, Norfolk, United Kingdom
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48
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Schiewer MJ, Mandigo AC, Gordon N, Huang F, Gaur S, Zhao S, Evans J, Han S, Parsons T, Birbe R, McCue P, Visakorpi T, Raj G, Rubin M, Bono JD, Lallas C, Trabulsi E, Gomella LG, Dicker AP, Kelly K, Knudsen B, Feng F, Knudsen KE. Abstract LB-086: PARP-1 controls the DNA damage response by regulating E2F1 transcriptional activity. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-lb-086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
PARP-1 holds two major functions on chromatin, DNA damage repair and transcriptional regulation, both of which are relevant in the context of cancer. Notably, PARP-1 has been found to be a key modulator of androgen receptor (AR) function and AR-dependent phenotypes, which is a driving factor in prostate cancer (PCa) biology and therapeutic management. Recent studies indicate an unanticipated prevalence of DNA repair alterations in advanced PCa and showed that PARP-1 inhibitors (PARPi) can effectively manage of a subset of these tumors. Despite the functions of PARP-1 in DNA repair having been exploited as a therapeutic target for tumors with BRCA1/2 aberrations, factors beyond DNA repair alterations clearly play a role in the response to PARPi. Notably, in the TO-PARP trial, not all patients with DNA repair aberrations responded to PARPi; conversely, tumors lacking BRCA1/2 or other DNA repair alterations show objective response to PARPi in PCa and other tumor types. These clinical data suggest that the genetic (e.g. BRCA-ness) and pharmacologic interplay is complex in the context of PARPi. Given the preclinical and clinical data, pursuing a deeper understanding of the molecular underpinnings of PARPi action in PCa may yield significant benefit. Genome-wide transcriptional profiling in response to PARPi was performed and the PARP-1-regulated transcriptome was identified. Human tissue microarrays were utilized to quantify PARP-1 levels and activity as a function of PCa progression. Both the PARP-1-regulated transcriptome, as well as PARP-1 enzymatic activity, were found to be elevated as a function of PCa progression. Further interrogation of the PARP-1-regulated transcriptome revealed a major impact on E2F1-regulated genes, and chromatin immunoprecipitation analyses indicated that PARP-1 functions to regulate the chromatin architecture and E2F1 occupancy at E2F1 target gene loci. Most prominent among the E2F1-regulated genes responsive to PARPi were genes associated with DNA damage repair, with a particular enrichment for genes involved in homologous recombination (HR). In sum, these data indicate PARP-1 regulates the function of key oncogenic transcription factors (AR and E2F1) in PCa, and part of the effect of PARPi may be through down-regulation of DNA repair factors.
Citation Format: Matthew J. Schiewer, Amy C. Mandigo, Nicolas Gordon, Fangjin Huang, Sanchaika Gaur, Shuang Zhao, Joseph Evans, Sumin Han, Theodore Parsons, Ruth Birbe, Peter McCue, Tapio Visakorpi, Ganesh Raj, Mark Rubin, Johann de Bono, Costas Lallas, Edouard Trabulsi, Leonard G. Gomella, Adam P. Dicker, Kevin Kelly, Beatrice Knudsen, Felix Feng, Karen E. Knudsen. PARP-1 controls the DNA damage response by regulating E2F1 transcriptional activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-086. doi:10.1158/1538-7445.AM2017-LB-086
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Affiliation(s)
| | - Amy C. Mandigo
- 1Thomas Jefferson University, Sidney Kimmel Cancer Center, Philadelphia, PA
| | - Nicolas Gordon
- 1Thomas Jefferson University, Sidney Kimmel Cancer Center, Philadelphia, PA
| | | | | | | | | | - Sumin Han
- 3University of Michigan, Ann Arbor, MI
| | - Theodore Parsons
- 1Thomas Jefferson University, Sidney Kimmel Cancer Center, Philadelphia, PA
| | - Ruth Birbe
- 1Thomas Jefferson University, Sidney Kimmel Cancer Center, Philadelphia, PA
| | - Peter McCue
- 1Thomas Jefferson University, Sidney Kimmel Cancer Center, Philadelphia, PA
| | | | | | - Mark Rubin
- 6Weill Cornell Medical College, New York, NY
| | - Johann de Bono
- 7Institute for Cancer Research, Royal Marsden, London, United Kingdom
| | - Costas Lallas
- 1Thomas Jefferson University, Sidney Kimmel Cancer Center, Philadelphia, PA
| | - Edouard Trabulsi
- 1Thomas Jefferson University, Sidney Kimmel Cancer Center, Philadelphia, PA
| | - Leonard G. Gomella
- 1Thomas Jefferson University, Sidney Kimmel Cancer Center, Philadelphia, PA
| | - Adam P. Dicker
- 1Thomas Jefferson University, Sidney Kimmel Cancer Center, Philadelphia, PA
| | - Kevin Kelly
- 1Thomas Jefferson University, Sidney Kimmel Cancer Center, Philadelphia, PA
| | | | - Felix Feng
- 8University of California, San Francisco, San Francisco, CA
| | - Karen E. Knudsen
- 1Thomas Jefferson University, Sidney Kimmel Cancer Center, Philadelphia, PA
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49
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McNair C, Xu K, Mandigo A, Benelli M, Leiby B, Rodrigues D, Lindberg J, Gronberg H, Visakorpi T, Li F, Bono JD, Demichelis F, Rubin M, Brown M, Knudsen KE. Abstract LB-085: RB loss-induced genome wide E2F1 reprogramming drive advanced prostate cancer. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-lb-085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Prostate adenocarcinoma (PCa) is the most highly diagnosed non-cutaneous malignancy in the United States and the third most lethal among men in this category. First line therapies targeting disruption of the androgen receptor (AR) signaling axis are initially effective, however within 2-3 years patients commonly relapse, due in part to reactivation of the receptor, and progress to the ultimately fatal form of the disease (castrate resistant prostate cancer, CRPC). Interestingly, recent examination of CRPC identified a major mechanism of progression as loss of the retinoblastoma (RB) protein. Along with its critical role in controlling cell cycle progression, RB is known to have important tumor suppressor functions, and has been shown in PCa to be lost exclusively in late stage disease. Additionally, loss of RB has been shown to correlate with increases in both AR and E2F1 expression, via E2F dependent mechanisms. Despite the vital role RB loss has been shown to play in this fatal stage of disease, the molecular underpinnings remain undefined. Thus, in order to elucidate these CRPC specific alterations, the current study utilizes isogenic models of RB loss in combination with genome wide binding and transcriptional studies. Data presented herein demonstrate that loss of RB is frequent in CRPC, however this phenomenon is not correlated with changes in proliferative indices, suggested a role for RB loss outside of cell cycle control. Further, RB loss induces genome wide transcriptional changes in PCa cells in castrate conditions, including up-regulation in Myc, E2F, and DNA-repair related pathways. Additionally, RB loss significantly expands E2F1 binding capacity, while maintaining the majority of the RB-intact E2F1 cistrome. Strikingly, while the current RB/E2F1 paradigm suggests that E2F1 exclusively occupies promoter regions of DNA in order to regulate transcriptional changes, RB loss induces sweeping reprogramming of E2F1 occupied regions, with a marked increase in enhancer-bound E2F1. Further, motif analyses suggest divergence away from canonical E2F1 binding motifs after RB loss specifically in regions of expanded E2F1 binding, and additionally suggest likely interaction of novel E2F1 co-factors under RB loss conditions. Finally, interrogation of a CRPC patient tumor cohort showed predictive capacity for RB-loss induced E2F1 binding and differentially expressed gene signature to select for RB loss in patient samples, indicating a novel E2F1 driven set of targets vital for CRPC transition in human disease. Together, these data present the first insight into E2F1 activity resulting from RB loss, and the role these changes play in progression to CRPC.
Citation Format: Christopher McNair, Kexin Xu, Amy Mandigo, Matteo Benelli, Benjamin Leiby, Daniel Rodrigues, Johan Lindberg, Henrik Gronberg, Tapio Visakorpi, Fugen Li, Johann De Bono, Francesca Demichelis, Mark Rubin, Myles Brown, Karen E. Knudsen. RB loss-induced genome wide E2F1 reprogramming drive advanced prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-085. doi:10.1158/1538-7445.AM2017-LB-085
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Affiliation(s)
- Christopher McNair
- 1Thomas Jefferson University, Sidney Kimmel Cancer Center, Philadelphia, PA
| | - Kexin Xu
- 2University of Texas, Southwestern, Dallas, TX
| | - Amy Mandigo
- 1Thomas Jefferson University, Sidney Kimmel Cancer Center, Philadelphia, PA
| | | | - Benjamin Leiby
- 1Thomas Jefferson University, Sidney Kimmel Cancer Center, Philadelphia, PA
| | | | | | | | | | - Fugen Li
- 7Dana Farber Cancer Institute, Boston, MA
| | - Johann De Bono
- 4The Institute of Cancer Research, London, United Kingdom
| | | | - Mark Rubin
- 8Weill Cornell Medical College, New York, NY
| | | | - Karen E. Knudsen
- 1Thomas Jefferson University, Sidney Kimmel Cancer Center, Philadelphia, PA
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Lehtinen B, Raita A, Kesseli J, Annala M, Nordfors K, Yli-Harja O, Zhang W, Visakorpi T, Nykter M, Haapasalo H, Granberg KJ. Clinical association analysis of ependymomas and pilocytic astrocytomas reveals elevated FGFR3 and FGFR1 expression in aggressive ependymomas. BMC Cancer 2017; 17:310. [PMID: 28468611 PMCID: PMC5415775 DOI: 10.1186/s12885-017-3274-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 04/07/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Fibroblast growth factor receptors (FGFRs) are well-known proto-oncogenes in several human malignancies and are currently therapeutically targeted in clinical trials. Among glioma subtypes, activating FGFR1 alterations have been observed in a subpopulation of pilocytic astrocytomas while FGFR3 fusions occur in IDH wild-type diffuse gliomas, resulting in high FGFR3 protein expression. The purpose of this study was to associate FGFR1 and FGFR3 protein levels with clinical features and genetic alterations in ependymoma and pilocytic astrocytoma. METHODS FGFR1 and FGFR3 expression levels were detected in ependymoma and pilocytic astrocytoma tissues using immunohistochemistry. Selected cases were further analyzed using targeted sequencing. RESULTS Expression of both FGFR1 and FGFR3 varied within all tumor types. In ependymomas, increased FGFR3 or FGFR1 expression was associated with high tumor grade, cerebral location, young patient age, and poor prognosis. Moderate-to-strong expression of FGFR1 and/or FGFR3 was observed in 76% of cerebral ependymomas. Cases with moderate-to-strong expression of both proteins had poor clinical prognosis. In pilocytic astrocytomas, moderate-to-strong FGFR3 expression was detected predominantly in non-pediatric patients. Targeted sequencing of 12 tumors found no protein-altering mutations or fusions in FGFR1 or FGFR3. CONCLUSIONS Elevated FGFR3 and FGFR1 protein expression is common in aggressive ependymomas but likely not driven by genetic alterations. Further studies are warranted to evaluate whether ependymoma patients with high FGFR3 and/or FGFR1 expression could benefit from treatment with FGFR inhibitor based therapeutic approaches currently under evaluation in clinical trials.
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Affiliation(s)
- Birgitta Lehtinen
- BioMediTech Institute and Faculty of Medicine and Life Sciences, Biokatu 8, 33520, Tampere, Finland
| | - Annina Raita
- Fimlab Laboratories Ltd., Tampere University Hospital, Biokatu 4, 33520, Tampere, Finland.,Department of Pathology, University of Tampere, 33014, Tampere, Finland
| | - Juha Kesseli
- BioMediTech Institute and Faculty of Medicine and Life Sciences, Biokatu 8, 33520, Tampere, Finland
| | - Matti Annala
- BioMediTech Institute and Faculty of Medicine and Life Sciences, Biokatu 8, 33520, Tampere, Finland
| | - Kristiina Nordfors
- Fimlab Laboratories Ltd., Tampere University Hospital, Biokatu 4, 33520, Tampere, Finland.,Department of Pediatrics, Tampere University Hospital; Tampere Center for Child Health Research, University of Tampere, 33014, Tampere, Finland
| | - Olli Yli-Harja
- Department of Signal Processing, Tampere University of Technology, Korkeakoulunkatu 10, 33720, Tampere, Finland
| | - Wei Zhang
- Department of Signal Processing, Tampere University of Technology, Korkeakoulunkatu 10, 33720, Tampere, Finland.,Department of Cancer Biology, Comprehensive Cancer Center of Wake Forest Baptist Medical Center, 1 Medical Center Blvd, Winston-Salem, NC, 27157, USA
| | - Tapio Visakorpi
- BioMediTech Institute and Faculty of Medicine and Life Sciences, Biokatu 8, 33520, Tampere, Finland.,Fimlab Laboratories Ltd., Tampere University Hospital, Biokatu 4, 33520, Tampere, Finland
| | - Matti Nykter
- BioMediTech Institute and Faculty of Medicine and Life Sciences, Biokatu 8, 33520, Tampere, Finland.,Science Center, Tampere University Hospital, Biokatu 6, 33520, Tampere, Finland
| | - Hannu Haapasalo
- Fimlab Laboratories Ltd., Tampere University Hospital, Biokatu 4, 33520, Tampere, Finland. .,Department of Pathology, University of Tampere, 33014, Tampere, Finland.
| | - Kirsi J Granberg
- BioMediTech Institute and Faculty of Medicine and Life Sciences, Biokatu 8, 33520, Tampere, Finland. .,Department of Signal Processing, Tampere University of Technology, Korkeakoulunkatu 10, 33720, Tampere, Finland. .,Science Center, Tampere University Hospital, Biokatu 6, 33520, Tampere, Finland.
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