scholarly journals A comparative study of PCS and PAM50 prostate cancer classification schemes

2021 ◽  
Author(s):  
Junhee Yoon ◽  
Minhyung Kim ◽  
Edwin M. Posadas ◽  
Stephen J. Freedland ◽  
Yang Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Clinical Outcomes ◽  
Marker Gene ◽  
Classification Systems ◽  
Luminal B ◽  
Cellular Processes ◽  
Basal Marker ◽  
Pam50 Subtypes ◽  
Prostate Cancer Classification

Abstract Background Two prostate cancer (PC) classification methods based on transcriptome profiles, a de novo method referred to as the “Prostate Cancer Classification System” (PCS) and a variation of the established PAM50 breast cancer algorithm, were recently proposed. Both studies concluded that most human PC can be assigned to one of three tumor subtypes, two categorized as luminal and one as basal, suggesting the two methods reflect consistency in underlying biology. Despite the similarity, differences and commonalities between the two classification methods have not yet been reported. Methods Here, we describe a comparison of the PCS and PAM50 classification systems. PCS and PAM50 signatures consisting of 37 (PCS37) and 50 genes, respectively, were used to categorize 9,947 PC patients into PCS and PAM50 classes. Enrichment of hallmark gene sets and luminal and basal marker gene expression were assessed in the same datasets. Finally, survival analysis was performed to compare PCS and PAM50 subtypes in terms of clinical outcomes. Results PCS and PAM50 subtypes show clear differential expression of PCS37 and PAM50 genes. While only three genes are shared in common between the two systems, there is some consensus between three subtype pairs (PCS1 versus Luminal B, PCS2 versus Luminal A, and PCS3 versus Basal) with respect to gene expression, cellular processes, and clinical outcomes. PCS categories displayed better separation of cellular processes and luminal and basal marker gene expression compared to PAM50. Although both PCS1 and Luminal B tumors exhibited the worst clinical outcomes, outcomes between aggressive and less aggressive subtypes were better defined in the PCS system, based on larger hazard ratios observed. Conclusion The PCS and PAM50 classification systems are similar in terms of molecular profiles and clinical outcomes. However, the PCS system exhibits greater separation in multiple clinical outcomes and provides better separation of prostate luminal and basal characteristics.

Gene expression associated with lymphovascular invasion and genomic risk in early-stage breast cancer.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. 559-559
Author(s):  
Nina D'Abreo ◽  
Abhinav Rohatgi ◽  
Douglas Kanter Marks ◽  
Heather Kling ◽  
Josien Haan ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Cell Adhesion ◽  
Clinical Outcomes ◽  
Lymphovascular Invasion ◽  
Group Analysis ◽  
Enrichment Analysis ◽  
Functional Enrichment ◽  
Tumor Type ◽  
Luminal B

559 Background: Lymphovascular invasion (LVI), the passage of carcinoma cells through lymphatic and blood vessels, is an important early step in metastasis; however, LVI is excluded from most breast cancer (BC) clinical risk assessments. Previous studies assessed the prognostic value of LVI to estimate clinical outcomes. To gain understanding of the molecular basis of LVI, we evaluated differentially expressed genes (DEGs) between tumors with LVI versus those without LVI, stratified by the 70-gene signature (MammaPrint/MP) and 80-gene molecular subtyping signature (BluePrint/BP). Methods: The prospective, observational FLEX Study (NCT03053193) includes stage I-III BC patients who receive MP/BP testing and consent to full transcriptome and clinical data collection. Patients with LVI (n=581) and without LVI (n=600, randomly selected), enrolled from 2017 to present, were included. LVI was assessed by local pathology laboratories. Differential gene expression analysis of 44k Agilent microarray data was performed with R limma package. DEGs were compared within all samples, BP Luminal subtype, MP risk groups (Low Risk [LR]/Luminal A and High Risk [HR]/Luminal B), and by lymph node (LN) status. DEGs with FDR<0.05 were considered significant. Results: Of tumors with LVI (LVI+), 66% were MP HR; notably, 51% of tumors without LVI (LVI-) were MP HR. LVI was associated with larger T stage, LN involvement, high grade, negative ER status by IHC, and younger patient age (LVI+ vs. LVI-, p<0.05 for all comparisons). Patient ethnicity, obesity, and tumor type did not differ by LVI status; however, prevalence of type 2 diabetes trended higher in patients with LVI+ HR tumors (21%), compared with LVI- HR (15%, p=0.09) and LVI+ LR (11%, p=0.004). There were significant transcriptomic differences between LVI+ and LVI, with most DEGs evident in the Luminal B subset. DEGs in LVI+, LN-negative (LN-) tumors overlapped substantially with the overall Luminal group analysis. Functional enrichment analysis showed dysregulation of cell cycle, extracellular matrix (ECM) organization, cell adhesion, and cytokine receptor pathways. Gene sets related to insulin growth factor pathways were also enriched in LVI+ tumors. Conclusions: DEGs associated with LVI were primarily found in MP HR Luminal, LN-negative tumors; enrichment analysis suggested dysregulation of ECM organization and cell adhesion pathways, consistent with previous reports. DEGs were not associated with LVI presence in LN+ tumors, suggesting that LVI assessment may be less relevant in LN+ breast cancer. Future studies will assess clinical outcomes, as well as LVI-associated gene expression in BP Basal- and HER2-type tumors. However, the current analysis indicates few DEGs in LVI+ MP LR tumors; thus, the potential prognostic information gained from LVI-associated gene expression is likely already captured by the MP and BP signatures. Clinical trial information: NCT03053193.

Characterization of PSMA and 18F-fluciclovine transporter gene expression in localized prostate cancer.

2020 ◽  
Vol 38 (6_suppl) ◽  
pp. 295-295
Author(s):  
Carissa Chu ◽  
Mohammed Alshalalfa ◽  
Martin Sjöström ◽  
Shuang Zhao ◽  
Annika Herlemann ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Clinical Outcomes ◽  
Molecular Subtypes ◽  
Localized Prostate Cancer ◽  
Transporter Gene ◽  
Psma Pet ◽  
Pet Ct ◽  
Genomic Risk ◽  
Psma Expression

295 Background: While 18F-fluciclovine PET/CT is approved in the US and recommended by the NCCN, prostate-specific membrane antigen (PSMA) PET/CT is more common in Europe/Australia and recommended by the EAU. Less is known about the biology of lesions detected by either modality. 18F-fluciclovine PET relies on radiotracer uptake by amino acid transporters LAT1-4 and ASCT1-2. PSMA PET is dependent on surface expression of PSMA. We compared relative expression of PSMA and fluciclovine transporter genes in radical prostatectomy (RP) samples to determine their distribution across subtypes and correlation with outcomes. Methods: Gene expression data of 19,102 RP samples were analyzed using the Affymetrix Human Exon 1.0 ST microarray. 1,135 patients had long term follow up. Associations between expression of PSMA and fluciclovine transporter genes (LAT1-4 and ASCT1-2) and pathologic variables, molecular subtypes, and clinical outcomes were conducted. Results: All fluciclovine transporter genes (LAT 1-4, ASCT1-2) were expressed at lower levels than PSMA (p <0.0001). PSMA expression was positively correlated with genomic risk score and pathologic Gleason score (p<0.0001), but LAT2-3 and ASCT2 were inversely correlated with genomic risk in primary tumors (p<0.0001) and less expressed in GS 9-10 tumors (p<0.0001). PSMA expression was associated with worse metastasis-free survival (MFS) (HR 1.45, p=0.001) and lymph node involvement (HR 2.14, p<0.0001). Expression of LAT2, LAT3, ASCT2 expression was associated with better MFS (HR 0.85, 0.63, 0.74, p<0.0001-0.04). After multivariable adjustment, PSMA expression remained independently prognostic of poorer MFS (HR 1.3, p=0.028). Luminal B subtype was notable for PSMA overexpression; Luminal A was enriched in ASCT2 and LAT2 (p<0.0001). PSMA expression did not correlate with ERG fusion prostate cancers, but LAT2, ASCT1, and ASCT2 were overexpressed in ERG fusion negative tumors (p<0.0001). Conclusions: PSMA expression is associated with more aggressive disease and poorer clinical outcomes than fluciclovine transporter genes in localized prostate cancer. Molecular subtypes of prostate cancer vary in PSMA and fluciclovine transporter gene expression.

scholarly journals IL1B loss is associated with increased AR activity in castration-resistant prostate cancer

2021 ◽  
Author(s):  
Wisam N. Awadallah ◽  
Jagpreet S. Nanda ◽  
Sarah E. Kohrt ◽  
Magdalena M Grabowska
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Cancer Cells ◽  
Marker Gene ◽  
Neuroendocrine Differentiation ◽  
Castration Resistant Prostate Cancer ◽  
Prostate Cancer Cells ◽  
Castration Resistant ◽  
Expression And Activity

Castration-resistant prostate cancer represents a continuum of phenotypes, including tumors with high levels of androgen receptor (AR) expression and activity and those which do not express AR and rely on alternative pathways for survival. The process by which AR-positive prostate cancer cells and tumors lose AR expression and acquire neuroendocrine features is referred to as neuroendocrine differentiation. Numerous therapies and exposures have been demonstrated to induce neuroendocrine differentiation in vitro, including the pro-inflammatory cytokine, interleukin 1 beta (IL-1β), encoded by the gene IL1B. The purpose of our studies was to determine the relationship between the expression and activity of AR in relationship to IL-1β and IL1B in prostate cancer. We performed analysis of de-identified human clinical data and generated prostate cancer cell lines with overexpression or knockout of IL1B. In primary prostate cancer, higher expression of IL1B predicts longer time to biochemical recurrence. In metastatic castration-resistant prostate cancer, IL1B expression is decreased and inversely correlates with AR and AR-target gene expression and AR activity, while positively correlating with the neuroendocrine prostate cancer (NEPC) score and neuroendocrine marker gene expression. In vitro, we report that AR-positive castration-resistant prostate cancer cells (C4-2B, 22Rv1) secrete IL-1β, and knockout of IL1B in these cells results in increased AR activity, in the presence and absence of dihydrotestosterone (DHT). Importantly, knockout of IL1B prevented AR attrition during androgen-deprivation. Taken together, our studies demonstrate that loss of IL1B in AR-positive castration-resistant prostate cancer cells can increase and maintain AR activity in the absence of androgens, suggesting another potential mechanism of high AR activity in castration-resistant prostate cancer.

A genomic blood test (NETest) identifies neuroendocrine transformation of prostate cancer.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e17511-e17511
Author(s):  
Kambiz Rahbar ◽  
Mark S. Kidd ◽  
Ignat A. Drozdov ◽  
Anna Malczewska ◽  
Lisa Bodei ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Marker Gene ◽  
Castration Resistant Prostate Cancer ◽  
Tissue Samples ◽  
Blood Gene Expression ◽  
Castration Resistant ◽  
Hormone Sensitive ◽  
Sensitivity Specificity ◽  
Real Time Information

e17511 Background: Neuroendocrine-like differentiation (NELD) and an aggressive phenotype are key features of castration-resistant prostate cancer (CRPC). Current blood-based biomarkers cannot detect these treatment-refractory variants. Our aim was to evaluate the NETest, a blood-based 51-marker gene neuroendocrine detection tool, as a CRPC-diagnostic versus prostate cancer (PCA). Methods: In silico evaluation: NETest gene identification in the TCGA-PRAD ( n= 500 PCA) and CRPC RNAseq datasets (cBIOPortal: dbGap-phs000909.v.p1, tissue samples: n= 47, including 15 CRPC). Blood gene expression: PCA: n= 50, CRPC: n= 40, hormone-sensitive PCA: n= 75 and benign prostatic hyperplasia (BPH: n= 41). NETest assay: Normalized gene expression, algorithmically assessed and scored: 0-100. Cut-off 20. PSA: ECLIA diagnostic assay: cut-off 4ng/L, > 10ng/ml = actionable value. Statistics: ANOVA, AUROC analyses and sensitivity/specificity metrics. Data is mean±SEM. Results: RNAseq: Two (4%) of the 51 NETest genes were identified in TCGA-PCA. In contrast, all 51 NETest genes (100%) were identified in CRPC tumors. Thirty-three (65%) were detected as upregulated (1.09-1425-fold vs. normal tissue). Blood-PCR: 49/51 (96%) NETest genes detected in CRPC blood. NELD-gene expression was significantly upregulated ( > 2-fold, p< 0.01) in CRPC vs. PCA ( TPH1, PNMA2, SSTR etc). NETest scores were elevated in CRPC (79±2.8) (ANOVA, p< 0.0001) vs. PCA (22±2) and BPH (23±3). The AUC differentiating CRPC from PCA was 0.93 ( p< 0.0001). NETest was elevated in 94% of CRPC vs. 13% PCA and 15% BPH (both p< 0.001). The diagnostic sensitivities and specificities were 94% and 87%, respectively. PSA: PSA was elevated in CRPC (220±372ng/ml). This was different to PCA (14±20ng/ml, p< 0.0001) and BPH (10.3±5.7ng/ml, p< 0.003). The AUC for CRPC vs. PCA/BPH was 0.70 ( p= 0.10). PSA > 10ng/ml occurred in 70% of CRPC, 60% of PCA ( p= NS) and 39% of BPH ( p< 0.05). The AUC for NETest (0.93) was significantly better than PSA (z-statistic: 4.63, p< 0.0001). Conclusions: The NETest is a liquid biopsy that detects neuroendocrine neoplasia genes in the blood and accurately identifies NELD in castration-resistant prostate cancer. We anticipate that the NETest could be used to provide real-time information relevant to the evolving neuroendocrine status of a PCA during therapy.

Luminal B subtype as a predictive biomarker of docetaxel benefit for newly diagnosed metastatic hormone sensitive prostate cancer (mHSPC): A correlative study of E3805 CHAARTED.

2020 ◽  
Vol 38 (6_suppl) ◽  
pp. 162-162 ◽  
Author(s):  
Anis Hamid ◽  
Xin Victoria Wang ◽  
Yu-Hui Chen ◽  
Felix Y Feng ◽  
Robert Benjamin Den ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
De Novo ◽  
Local Therapy ◽  
Microarray Platform ◽  
High Volume ◽  
Predictive Biomarker ◽  
Luminal A ◽  
Luminal B ◽  
Basal Subtype

162 Background: Through gene expression profiling (GEP), the PAM50 classifier demonstrates prognostic value in localized prostate cancer (PCa). Pre-clinical drug response models predict increased taxane sensitivity in luminal subtypes compared to basal subtype. Men with mHSPC and high-risk features have greatest benefit from androgen deprivation therapy (ADT) plus docetaxel (D) vs ADT alone. We therefore sought to test the prognostic and predictive value of PAM50 in pre-ADT specimens from E3805 CHAARTED. Methods: Whole transcriptomic profiling of formalin-fixed, paraffin-embedded primary PCa biopsies from pts enrolled in the E3805 CHAARTED trial of ADT vs ADT+D was performed using the Human Exon 1.0 ST microarray platform (Decipher Biosciences). Normalized gene expression was used to classify subjects as luminal A, luminal B or basal subtype. Multivariable analyses (MVA) adjusted for ECOG status, de novo metastasis vs prior local therapy and volume of disease. The primary endpoint was overall survival (OS). Secondary endpoint was time to castration resistant PCa (TTCRPC). Results: Successful GEP was completed in 160 of 198 pts with available specimens. Eighty (50%), 77 (48%) and 3 (2%) pts were classified as luminal B, basal and luminal A, respectively. High volume disease was similarly present in luminal B (79%) and basal (78%) subtypes. In the ADT arm, luminal B subtype was associated with shorter OS vs basal (HR 1.75, p=0.05); consistent in MVA. Pts with luminal B subtype treated with ADT+D showed significant improvement in TTCRPC and OS (Table). By contrast, basal subtype showed no OS benefit from ADT+D even in pts with high volume disease. Conclusions: We demonstrate that GEP identifies tumor subtypes associated with differential benefit from chemohormonal therapy for mHSPC. Luminal B subtype is associated with poorer OS with ADT alone and benefits from addition of D. Basal subtype shows a lack of OS benefit from upfront ADT+D. We plan to validate these findings in independent trial cohorts.[Table: see text]

The relationship between proangiogenic gene expression levels in prostate cancer and their prognostic value for clinical outcomes

The Prostate ◽  
2010 ◽  
Vol 70 (15) ◽  
pp. 1692-1700 ◽  
Author(s):  
Ryutaro Mori ◽  
Tanya B. Dorff ◽  
Shigang Xiong ◽  
Chad J. Tarabolous ◽  
Wei Ye ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Clinical Outcomes ◽  
Prognostic Value ◽  
Expression Levels ◽  
The Relationship ◽  
Gene Expression Levels

Luminal and basal subtyping of metastatic castration-resistant prostate cancer (mCRPC) and its clinical implications.

2018 ◽  
Vol 36 (6_suppl) ◽  
pp. 197-197 ◽  
Author(s):  
Won Kim ◽  
Eric Jay Small ◽  
Rahul Raj Aggarwal ◽  
Robert Benjamin Den ◽  
Jonathan Lehrer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Drug Response ◽  
Metastatic Tumor ◽  
Localized Prostate Cancer ◽  
Patient Specific ◽  
Expression Data ◽  
Castration Resistant Prostate Cancer ◽  
Luminal A ◽  
Luminal B

197 Background: The PAM50 gene expression classifier (PAM50) identifies luminal and basal subtypes and predicts response to androgen deprivation therapy in localized prostate cancer. The clinical utility of using PAM50 to molecularly subtype mCRPC was evaluated. Methods: PAM50 was applied to RNA expression data from 86 metastatic tumor biopsies from the SU2C-AACR-PCF West Coast Prostate Cancer Dream Team (WCDT; NCT02432001). Overall survival (OS) differences between luminal A (LuA), luminal B (LuB), or basal patients (pts) were determined using Kaplan-Meier analyses. PAM50 was also applied to 15,136 prospectively collected radical prostatectomy (RP) samples from the Decipher GRiD database (NCT02609269). Drug response signatures (DRS) for 89 drugs were derived using publicly available data from the NCI60 cell line panel, and applied to gene expression data from the RP samples to predict patient-specific drug sensitivities. Differences in DRS as a function of PAM50 subtype were assessed using the Pearson’s chi-squared test. Results: The application of PAM50 to mCRPC transcriptional data segregated pts into LuA, LuB, and basal populations (43%, 14%, and 43%, respectively). The median OS for LuA, LuB, and basal pts was 20.6 months, 9.5 months, and 10.4 months, respectively (p=0.04), which was consistent with localized prostate cancer where LuB pts have the worst prognosis. DRS analyses revealed statistically significant differences in drug sensitivities, with LuA and LuB pts predicted to be markedly more sensitive to docetaxel than basal pts (p<0.00001), and basal pts predicted to be markedly more sensitive to platinums and etoposide than LuA and LuB pts (p<0.00001). Conclusions: PAM50 subtyping is prognostic in mCRPC, with LuA pts demonstrating the longest OS. Luminal and basal subtypes have distinct in silico drug response profiles that may be associated with response to mCRPC therapies. Prospective testing of DRS as a biomarker to guide treatment in mCRPC is warranted. Clinical trial information: NCT02432001, NCT02609269.

Enhancer of zeste-homolog 2 (EZH2) expression and clinical outcomes in metastatic castrate resistant prostate cancer (mCRPC).

2018 ◽  
Vol 36 (6_suppl) ◽  
pp. 350-350
Author(s):  
Karthik Giridhar ◽  
Brian Addis Costello ◽  
Carlos Sosa ◽  
Haojie Huang ◽  
Manish Kohli
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Clinical Outcomes ◽  
Prognostic Significance ◽  
Disease Recurrence ◽  
Abiraterone Acetate ◽  
Rna Seq ◽  
Exact Test ◽  
P Gene ◽  
Ezh2 Expression

350 Background: In prostate cancer, overexpression of EZH2 is associated with disease recurrence, androgen independent growth, cell invasion, and metastases. We evaluated the prognostic significance of EZH2 gene expression in metastatic biopsies from men with CRPC. Methods: EZH2 (RNA) expression was evaluated in two serial metastatic site biopsies in patients (pts) prior to treatment with abiraterone acetate and prednisone (pre-AA/P) and after 12 weeks of treatment (post-AA/P). All pts were enrolled and prospectively followed for clinical outcomes. The primary endpoint was overall survival (OS), defined as the time from CRPC to death or last follow-up. Cox proportional hazard regression analysis was performed on EZH2 expression using normalized fragments per kilobase million (FPKM) > 1 for association with OS and time to treatment failure (TTF). Results: Of 92 enrolled pts, 59 pts had (pre-AA/P) gene expression using RNA-seq, 45 had paired pre and post-AA/P RNA-seq available for analysis. In pre-AA/P samples, the median EZH2 expression was 4.82 FPKMs (range 1.05-38.8). Elevated expression of EZH2 was associated with shorter OS [hazard ratio (HR) 2.58, p = 0.016]. Radiographic progression at 12 weeks was more frequent in high EZH2 tumors compared to low EZH2 tumors (48% vs 20%, p = 0.03, Fisher’s exact test) No statistically significant associations were identified between EZH2 expression and TTF. In paired post-AA/P biopsies, EZH2 expression increased in 13/45 tumors and decreased in 32/45 tumors. The median log2 fold change in EZH2 expression was -1.38 (range -6.7 to 3.1). In post-AA/P biopsies, no associations were identified between an increase in EZH2 expression and OS or TTF. Conclusions: EZH2 expression represents a potential novel prognostic biomarker in mCRPC and warrants further exploration. Clinical trial information: 01953640.

402: CPG Methylation at Promoter Site -140 Inactivates TGF- β Receptor Type II Gene Expression in Prostate Cancer

2005 ◽  
Vol 173 (4S) ◽  
pp. 110-110
Author(s):  
Kirsten L. Greene ◽  
Hong Zhao ◽  
Hiroaki Shiina ◽  
Long-Cheng Li ◽  
Yuichiro Tanaka ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Cpg Methylation ◽  
Receptor Type ◽  
Type Ii ◽  
Β Receptor
Sign in / Sign up

Export Citation Format

Share Document