Mapping of the chromosomal amplification 1p21-22 in bladder cancer

Background The aim of the study was to characterize a recurrent amplification at chromosomal region 1p21-22 in bladder cancer. Methods ArrayCGH (aCGH) was performed to identify DNA copy number variations in 7 clinical samples and 6 bladder cancer cell lines. FISH was used to map the amplicon at 1p21-22 in the cell lines. Gene expression microarrays and qRT-PCR were used to study the expression of putative target genes in the region. Results aCGH identified an amplification at 1p21-22 in 10/13 (77%) samples. The minimal region of the amplification was mapped to a region of about 1 Mb in size, containing a total of 11 known genes. The highest amplification was found in SCaBER squamous cell carcinoma cell line. Four genes, TMED5, DR1, RPL5 and EVI5, showed significant overexpression in the SCaBER cell line compared to all the other samples tested. Oncomine database analysis revealed upregulation of DR1 in superficial and infiltrating bladder cancer samples, compared to normal bladder. Conclusions In conclusions, we have identified and mapped chromosomal amplification at 1p21-22 in bladder cancer as well as studied the expression of the genes in the region. DR1 was found to be significantly overexpressed in the SCaBER, which is a model of squamous cell carcinoma. However, the overexpression was found also in a published clinical sample cohort of superficial and infiltrating bladder cancers. Further studies with more clinical material are needed to investigate the role of the amplification at 1p21-22.BioMed Central open acces

Recurrent SKIL-activating rearrangements in ETS-negative prostate cancer

Prostate cancer is the third most common cause of male cancer death in developed countries, and one of the most comprehensively characterized human cancers. Roughly 60% of prostate cancers harbor gene fusions that juxtapose ETS-family transcription factors with androgen regulated promoters. A second subtype, characterized by SPINK1 overexpression, accounts for 15% of prostate cancers. Here we report the discovery of a new prostate cancer subtype characterized by rearrangements juxtaposing the SMAD inhibitor SKIL with androgen regulated promoters, leading to increased SKIL expression. SKIL fusions were found in 6 of 540 (1.1%) prostate cancers and 1 of 27 (3.7%) cell lines and xenografts. 6 of 7 SKIL-positive cancers were negative for ETS overexpression, suggesting mutual exclusivity with ETS fusions. SKIL knockdown led to growth arrest in PC-3 and LNCaP cell line models of prostate cancer, and its overexpression led to increased invasiveness in RWPE-1 cells. The role of SKIL as a prostate cancer oncogene lends support to recent studies on the role of TGF-β signaling as a rate-limiting step in prostate cancer progression. Our findings highlight SKIL as an oncogene and potential therapeutic target in 1-2% of prostate cancers, amounting to an estimated 10,000 cancer diagnoses per year worldwide.This article has supplementary files, which can be found here:http://dx.doi.org/10.18632/oncotarget.335

Gene copy number alterations in prostate cancer

Eturauhassyöpä on yleisin miesten syöpä Suomessa ja kolmannes kaikista miehillä diagnosoiduista syövistä on eturauhasesta lähtöisin. Vuosittain diagnosoidaan yli 4200 eturauhassyöpätapausta ja yli 740 miestä kuolee tautiin. Paikallisen eturauhassyövän hoitona on eturauhasen poisto, mutta levinnyttä syöpää hoidetaan hormonaalisella hoidolla. Hoito kuitenkin pettää lopulta yli 80%:ssa tapauksista ja syöpä muuttuu ns. hormonirefraktoriseksi, minkä jälkeen tehokasta hoitoa ei ole. Hormonirefraktorisista eturauhassyövistä löytyy usein kromosomialueiden monistumia, joiden kohdegeenejä ei yleensä tunneta. Syövän varhaisemmassa vaiheessa ilmaantuvat geenimonistumat saattavat puolestaan olla merkittäviä syövän aggressiivisuuden ilmaisijoita. Monistumien kohdegeenien tunnistaminen voisi johtaa uusien diagnostisten ja prognostisten menetelmien, sekä uusien hoitojen kehitykseen. Väitöskirjatutkimuksessa selvitettiin neljän (EIF3S3, MYC, HIF-1A ja EZH2) geenin kopiolukumuutoksia ja ennusteellista merkitystä eturauhassyövässä. HIF-1A-geenin kopiolukumuutokset olivat vähäisiä. Muiden geenien ylimääräisiä kopioita oli huomattavasti enemmän pitkälle edenneissä syövissä, jopa yli 50%:ssa hormonihoidon jälkeen uusiutuneista eturauhassyövistä. Lisäksi EIF3S3- ja EZH2- geenien monistumilla oli heikko yhteys lyhyempään tautivapaaseen aikaan leikkauksella hoidetuilla potilailla. EZH2-proteiinin ilmentyminen oli voimakkaampaa edenneissä syövissä, erityisesti sellaisissa, joissa oli geenin monistuma. EIF3S3-geenin monistuma näyttäisi myös olevan ennusteellinen tekijä sattumalta löydetyissä eturauhassyövissä. Näitä geenejä voidaan pitää kromosomialueidensa kopiolukumuutosten mahdollisina kohdegeeneinä. Tutkimustarkoituksiin kehitetyistä eturauhassyöpämalleista (n=18) seulottiin koko genomin kattavasti geenien kopioluku- ja ilmentymismuutoksia cDNA-mikrosirujen avulla. Havaitut kopiolukumuutokset olivat enimmäkseen yhteneväisiä aikaisempien tutkimusten kanssa, mutta joidenkin muuttuneiden kromosomialueiden voitiin osoittaa olevan pienempiä tai koostuvan useasta erillisestä muutoksesta. Lisäksi löydettiin aiemmin tuntemattomia yleisiä kopiolukumuutoksia, kuten alueiden 1q21.2-23.1, 9p13-q21 ja 16p monistumat. Näillä alueilla sijaitsee useita geenejä, joiden ilmentymiseen kopioluvun muutoksella näyttäisi olevan vaikutusta ja niitä voidaankin pitää mahdollisina kohdegeeneinä, joiden tutkimuksia tulisi jatkaa. Yleisellä tasolla (koko genomin kattavasti) vähäinenkin kopioluvun muutos (+1-2 kopiota tai -1 kopio) näyttäisi vaikuttavan geenien ilmentymiseen merkittävästi.Chromosomal aberrations, including deletions, gains and amplifications are thought to be a mechanism for the development and progression of cancer. Many frequent alterations have been described in prostate cancer, but only a few definitive target genes have been identified. The identification of target genes could lead to the development of diagnostic and/or prognostic markers as well as new targets for therapy. According to comparative genomic hybridisation (CGH), the HIF1A locus (14q23.2) is amplified in the prostate cancer cell line PC-3, and the EZH2 locus (7q36.1) in the prostate cancer xenograft LuCaP41. The locus of EIF3S3 (8q23.3­24.11) is gained in up to 80% of advanced prostate cancers. In order to determine whether these genes could be the target genes of the amplifications, fluorescence in situ hybridisation (FISH) was used to assess their amplification frequencies. In addition, the expression of EZH2 was studied by quantitative real-time reverse transcription polymerase chain reaction (Q-RT-PCR) and immunohistochemistry (IHC). No amplifications of HIF1A were found in clinical prostate cancer samples. Only PC-3 had an amplification of the gene, indicating that the generally observed overexpression of the protein in prostate cancer is not due to gene amplification. The frequencies of EIF3S3 and EZH2 gains/amplifications were significantly higher in advanced disease, reaching over 50% in hormone-refractory prostate cancer. The alterations were weakly associated with poor progression-free survival in prostatectomy-treated patients. The expression of EZH2 was higher in advanced disease and especially in samples with high-level amplification of the gene (p Finally, array comparative genomic hybridisation (aCGH) and cDNA microarrays were used to screen prostate cancer cell lines and xenografts for genome wide copy number and expression alterations. The copy number alterations (CNAs) and their frequencies were generally consistent with earlier data obtained by CGH of the same samples, although due to the better resolution some aberrations were narrowed down or shown to consist of several smaller aberrations interrupted by regions of normal copy number. Previously unreported frequent copy number alterations were also found, for example, gains in 1q21.2­23.1, 9p13­q21 and 16p. The amplicon in 9p13 was verified by FISH. cDNA microarrays showed that even a modest increase in copy number significantly affects the expression of the altered genes, indicating that simple gains may have a larger impact in prostate cancer than previously thought. Several putative target genes for copy number aberrations were also identified by cDNA microarray analysis, including POGZ (gain 1q21.3), ITGA4 (loss 2q31.3), FZD6 (gain 8q22.3), UBE2R2 (gain 9p13.3), and RBBP6 (gain 16p13.3). In conclusion, EIF3S3 and EZH2 may be considered putative target genes of the amplifications at 8q23­24 and 7q36.1, respectively. In addition, EIF3S3 could be used as prognostic marker. Array-CGH (aCGH) detects smaller regions of copy number alterations than CGH and may be used to narrow down known alterations and detect novel CNAs. When it is used together with expression arrays, putative target genes of the CNAs may be directly identified. Even a low-level copy number alteration appears to affect the expression of the altered genes

Gene copy number alterations in prostate cancer

Eturauhassyöpä on yleisin miesten syöpä Suomessa ja kolmannes kaikista miehillä diagnosoiduista syövistä on eturauhasesta lähtöisin. Vuosittain diagnosoidaan yli 4200 eturauhassyöpätapausta ja yli 740 miestä kuolee tautiin. Paikallisen eturauhassyövän hoitona on eturauhasen poisto, mutta levinnyttä syöpää hoidetaan hormonaalisella hoidolla. Hoito kuitenkin pettää lopulta yli 80%:ssa tapauksista ja syöpä muuttuu ns. hormonirefraktoriseksi, minkä jälkeen tehokasta hoitoa ei ole. Hormonirefraktorisista eturauhassyövistä löytyy usein kromosomialueiden monistumia, joiden kohdegeenejä ei yleensä tunneta. Syövän varhaisemmassa vaiheessa ilmaantuvat geenimonistumat saattavat puolestaan olla merkittäviä syövän aggressiivisuuden ilmaisijoita. Monistumien kohdegeenien tunnistaminen voisi johtaa uusien diagnostisten ja prognostisten menetelmien, sekä uusien hoitojen kehitykseen. Väitöskirjatutkimuksessa selvitettiin neljän (EIF3S3, MYC, HIF-1A ja EZH2) geenin kopiolukumuutoksia ja ennusteellista merkitystä eturauhassyövässä. HIF-1A-geenin kopiolukumuutokset olivat vähäisiä. Muiden geenien ylimääräisiä kopioita oli huomattavasti enemmän pitkälle edenneissä syövissä, jopa yli 50%:ssa hormonihoidon jälkeen uusiutuneista eturauhassyövistä. Lisäksi EIF3S3- ja EZH2- geenien monistumilla oli heikko yhteys lyhyempään tautivapaaseen aikaan leikkauksella hoidetuilla potilailla. EZH2-proteiinin ilmentyminen oli voimakkaampaa edenneissä syövissä, erityisesti sellaisissa, joissa oli geenin monistuma. EIF3S3-geenin monistuma näyttäisi myös olevan ennusteellinen tekijä sattumalta löydetyissä eturauhassyövissä. Näitä geenejä voidaan pitää kromosomialueidensa kopiolukumuutosten mahdollisina kohdegeeneinä. Tutkimustarkoituksiin kehitetyistä eturauhassyöpämalleista (n=18) seulottiin koko genomin kattavasti geenien kopioluku- ja ilmentymismuutoksia cDNA-mikrosirujen avulla. Havaitut kopiolukumuutokset olivat enimmäkseen yhteneväisiä aikaisempien tutkimusten kanssa, mutta joidenkin muuttuneiden kromosomialueiden voitiin osoittaa olevan pienempiä tai koostuvan useasta erillisestä muutoksesta. Lisäksi löydettiin aiemmin tuntemattomia yleisiä kopiolukumuutoksia, kuten alueiden 1q21.2-23.1, 9p13-q21 ja 16p monistumat. Näillä alueilla sijaitsee useita geenejä, joiden ilmentymiseen kopioluvun muutoksella näyttäisi olevan vaikutusta ja niitä voidaankin pitää mahdollisina kohdegeeneinä, joiden tutkimuksia tulisi jatkaa. Yleisellä tasolla (koko genomin kattavasti) vähäinenkin kopioluvun muutos (+1-2 kopiota tai -1 kopio) näyttäisi vaikuttavan geenien ilmentymiseen merkittävästi.Chromosomal aberrations, including deletions, gains and amplifications are thought to be a mechanism for the development and progression of cancer. Many frequent alterations have been described in prostate cancer, but only a few definitive target genes have been identified. The identification of target genes could lead to the development of diagnostic and/or prognostic markers as well as new targets for therapy. According to comparative genomic hybridisation (CGH), the HIF1A locus (14q23.2) is amplified in the prostate cancer cell line PC-3, and the EZH2 locus (7q36.1) in the prostate cancer xenograft LuCaP41. The locus of EIF3S3 (8q23.3­24.11) is gained in up to 80% of advanced prostate cancers. In order to determine whether these genes could be the target genes of the amplifications, fluorescence in situ hybridisation (FISH) was used to assess their amplification frequencies. In addition, the expression of EZH2 was studied by quantitative real-time reverse transcription polymerase chain reaction (Q-RT-PCR) and immunohistochemistry (IHC). No amplifications of HIF1A were found in clinical prostate cancer samples. Only PC-3 had an amplification of the gene, indicating that the generally observed overexpression of the protein in prostate cancer is not due to gene amplification. The frequencies of EIF3S3 and EZH2 gains/amplifications were significantly higher in advanced disease, reaching over 50% in hormone-refractory prostate cancer. The alterations were weakly associated with poor progression-free survival in prostatectomy-treated patients. The expression of EZH2 was higher in advanced disease and especially in samples with high-level amplification of the gene (p Finally, array comparative genomic hybridisation (aCGH) and cDNA microarrays were used to screen prostate cancer cell lines and xenografts for genome wide copy number and expression alterations. The copy number alterations (CNAs) and their frequencies were generally consistent with earlier data obtained by CGH of the same samples, although due to the better resolution some aberrations were narrowed down or shown to consist of several smaller aberrations interrupted by regions of normal copy number. Previously unreported frequent copy number alterations were also found, for example, gains in 1q21.2­23.1, 9p13­q21 and 16p. The amplicon in 9p13 was verified by FISH. cDNA microarrays showed that even a modest increase in copy number significantly affects the expression of the altered genes, indicating that simple gains may have a larger impact in prostate cancer than previously thought. Several putative target genes for copy number aberrations were also identified by cDNA microarray analysis, including POGZ (gain 1q21.3), ITGA4 (loss 2q31.3), FZD6 (gain 8q22.3), UBE2R2 (gain 9p13.3), and RBBP6 (gain 16p13.3). In conclusion, EIF3S3 and EZH2 may be considered putative target genes of the amplifications at 8q23­24 and 7q36.1, respectively. In addition, EIF3S3 could be used as prognostic marker. Array-CGH (aCGH) detects smaller regions of copy number alterations than CGH and may be used to narrow down known alterations and detect novel CNAs. When it is used together with expression arrays, putative target genes of the CNAs may be directly identified. Even a low-level copy number alteration appears to affect the expression of the altered genes

Prevalence and prognostic significance of TMPRSS2-ERG gene fusion in lymph node positive prostate cancers.

BACKGROUND TMPRSS2-ERG gene fusion is the most frequent genetic alteration in prostate cancer. However, information about its distribution in lymph node positive prostate cancers and the prognostic significance in these advanced tumors is unknown. METHODS Gene fusion status was determined by fluorescence in situ hybridization on a tissue-microarray constructed from 119 hormone-naïve nodal positive, surgically treated prostate cancers containing samples from the primary tumors and corresponding lymph node metastases. Data were correlated with various tumor features (Gleason score, stage, cancer volume, nodal tumor burden) and biochemical recurrence-free, disease-specific, and overall survival. RESULTS TMPRSS2-ERG fusion was detected in 43.5% of the primary tumors. Conversely, only 29.9% of the metastasizing components showed the fusion. Concordance in TMPRSS2-ERG status between primary tumors and metastases was 70.9% (Kappa 0.39); 20.9% and 8.1% of the patients showed the mutation solely in their primary tumors and metastases, respectively. TMPRSS2-ERG fusion was not correlated with specific histopathological tumor features but predicted favorable biochemical recurrence-free, disease-specific and overall survival independently when present in the primary tumor (P < 0.05 each). CONCLUSION TMPRSS2-ERG fusion is more frequent in primary prostate cancer than in corresponding metastases suggesting no selection of fusion-positive cells in the metastatic process. The gene fusion in primary tumors independently predicts favorable outcome

Microseminoprotein-Beta Expression in Different Stages of Prostate Cancer

Microseminoprotein-beta (MSMB, MSMB) is an abundant secretory protein contributed by the prostate, and is implicated as a prostate cancer (PC) biomarker based on observations of its lower expression in cancerous cells compared with benign prostate epithelium. However, as the current literature on MSMB is inconsistent, we assessed the expression of MSMB at the protein and mRNA levels in a comprehensive set of different clinical stages of PC. Immunohistochemistry using monoclonal and polyclonal antibodies against MSMB was used to study protein expression in tissue specimens representing prostatectomies (n = 261) and in diagnostic needle biopsies from patients treated with androgen deprivation therapy (ADT) (n = 100), and in locally recurrent castration-resistant PC (CRPC) (n = 105) and CRPC metastases (n = 113). The transcript levels of MSMB, nuclear receptor co-activator 4 (NCOA4) and MSMB-NCOA4 fusion were examined by qRT-PCR in prostatectomy samples and by RNA-sequencing in benign prostatic hyperplasia, PC, and CRPC samples. We also measured serum MSMB levels and genotyped the single nucleotide polymorphism rs10993994 using DNA from the blood of 369 PC patients and 903 controls. MSMB expression in PC (29% of prostatectomies and 21% of needle biopsies) was more frequent than in CRPC (9% of locally recurrent CRPCs and 9% of CRPC metastases) (p<0.0001). Detection of MSMB protein was inversely correlated with the Gleason score in prostatectomy specimens (p = 0.024). The read-through MSMB-NCOA4 transcript was detected at very low levels in PC. MSMB levels in serum were similar in cases of PC and controls but were significantly associated with PC risk when adjusted for age at diagnosis and levels of free or total PSA (p<0.001). Serum levels of MSMB in both PC patients and controls were significantly associated with the rs10993994 genotype (p<0.0001). In conclusion, decreased expression of MSMB parallels the clinical progression of PC and adjusted serum MSMB levels are associated with PC risk.Public Library of Science open acces

CIP2A is a candidate therapeutic target in clinically challenging prostate cancer cell populations

Residual androgen receptor (AR)-signaling and presence of cancer stem-like cells (SCs) are the two emerging paradigms for clinically challenging castration-resistant prostate cancer (CRPC). Therefore, identification of AR-target proteins that are also overexpressed in the cancer SC population would be an attractive therapeutic approach. Our analysis of over three hundred clinical samples and patient-derived prostate epithelial cultures (PPECs), revealed Cancerous inhibitor of protein phosphatase 2A (CIP2A) as one such target. CIP2A is significantly overexpressed in both hormone-naïve prostate cancer (HN-PC) and CRPC patients . CIP2A is also overexpressed, by 3- and 30-fold, in HN-PC and CRPC SCs respectively. In vivo binding of the AR to the intronic region of CIP2A and its functionality in the AR-moderate and AR-high expressing LNCaP cell-model systems is also demonstrated. Further, we show that AR positively regulates CIP2A expression, both at the mRNA and protein level. Finally, CIP2A depletion reduced cell viability and colony forming efficiency of AR-independent PPECs as well as AR-responsive LNCaP cells, in which anchorage-independent growth is also impaired. These findings identify CIP2A as a common denominator for AR-signaling and cancer SC functionality, highlighting its potential therapeutic significance in the most clinically challenging prostate pathology: castration-resistant prostate cancer