A genetic study and meta-analysis of the genetic predisposition of prostate cancer in a Chinese population

Polygenic Risk Scores in Prostate Cancer Risk Assessment and Screening

More than 40% of the risk of developing prostate cancer (PCa) is from genetic factors. Genome-wide association studies have led to the discovery of more than 140 variants associated with PCa risk. Polygenic risk scores (PRS) generated using these variants show promise in identifying individuals at much higher (and lower) lifetime risk than the average man. PCa PRS also improve the predictive value of prostate-specific antigen screening, may inform the age for starting PCa screening, and are informative for development of more aggressive tumors. Despite the promise, few clinical trials have evaluated the benefit of PCa PRS for clinical care.

The interplay between host genetics and the gut microbiome reveals common and distinct microbiome features for complex human diseases

BACKGROUND

Interest in the interplay between host genetics and the gut microbiome in complex human diseases is increasing, with prior evidence mainly being derived from animal models. In addition, the shared and distinct microbiome features among complex human diseases remain largely unclear.

RESULTS

This analysis was based on a Chinese population with 1475 participants. We estimated the SNP-based heritability, which suggested that Desulfovibrionaceae and Odoribacter had significant heritability estimates (0.456 and 0.476, respectively). We performed a microbiome genome-wide association study to identify host genetic variants associated with the gut microbiome. We then conducted bidirectional Mendelian randomization analyses to examine the potential causal associations between the gut microbiome and complex human diseases. We found that Saccharibacteria could potentially decrease the concentration of serum creatinine and increase the estimated glomerular filtration rate. On the other hand, atrial fibrillation, chronic kidney disease and prostate cancer, as predicted by host genetics, had potential causal effects on the abundance of some specific gut microbiota. For example, atrial fibrillation increased the abundance of Burkholderiales and Alcaligenaceae and decreased the abundance of Lachnobacterium, Bacteroides coprophilus, Barnesiellaceae, an undefined genus in the family Veillonellaceae and Mitsuokella. Further disease-microbiome feature analysis suggested that systemic lupus erythematosus and chronic myeloid leukaemia shared common gut microbiome features.

CONCLUSIONS

These results suggest that different complex human diseases share common and distinct gut microbiome features, which may help reshape our understanding of disease aetiology in humans. Video Abstract.

Clinical Experience of Steroid Switch from Prednisone to Dexamethasone in Patients with Metastatic Castration-Resistant Prostate Cancer Treated with Abiraterone Acetate

OBJECTIVE

To evaluate the therapeutic efficacy of a steroid switch from prednisone to dexamethasone in Asians with metastatic castration-resistant prostate cancer (mCRPC) that progressed after docetaxel chemotherapy.

METHODS

This study included postdocetaxel patients with mCRPC treated with abiraterone acetate combined with prednisone (AA + P) who had experienced prostate-specific antigen (PSA) progression. All patients underwent a steroid switch from prednisone (10 mg/day) to dexamethasone (1 mg/day). The PSA level and clinical symptoms were recorded. Moreover, follow-up was conducted until patients were either lost to follow-up or death.

RESULTS

This study included 11 patients from a single center in Taiwan. The median follow-up time starting from AA + P treatment was 19.47 months. Seven patients (63.64%) had >30% PSA decline, and 6 patients (54.55%) had >50% PSA decline. The median percentage of PSA decline was 83.6%. The median time until PSA progression after the steroid switch was 11.38 months. No adverse events greater than grade 3 were noted.

CONCLUSIONS

Steroid switching is a feasible and effective therapy in docetaxel-treated Asian patients with mCRPC.

Active monitoring, radical prostatectomy and radical radiotherapy in PSA-detected clinically localised prostate cancer: the ProtecT three-arm RCT

BACKGROUND

Prostate cancer is the most common cancer among men in the UK. Prostate-specific antigen testing followed by biopsy leads to overdetection, overtreatment as well as undertreatment of the disease. Evidence of treatment effectiveness has lacked because of the paucity of randomised controlled trials comparing conventional treatments.

OBJECTIVES

To evaluate the effectiveness of conventional treatments for localised prostate cancer (active monitoring, radical prostatectomy and radical radiotherapy) in men aged 50-69 years.

DESIGN

A prospective, multicentre prostate-specific antigen testing programme followed by a randomised trial of treatment, with a comprehensive cohort follow-up.

SETTING

Prostate-specific antigen testing in primary care and treatment in nine urology departments in the UK.

PARTICIPANTS

Between 2001 and 2009, 228,966 men aged 50-69 years received an invitation to attend an appointment for information about the Prostate testing for cancer and Treatment (ProtecT) study and a prostate-specific antigen test; 82,429 men were tested, 2664 were diagnosed with localised prostate cancer, 1643 agreed to randomisation to active monitoring (n = 545), radical prostatectomy (n = 553) or radical radiotherapy (n = 545) and 997 chose a treatment.

INTERVENTIONS

The interventions were active monitoring, radical prostatectomy and radical radiotherapy.

TRIAL PRIMARY OUTCOME MEASURE

Definite or probable disease-specific mortality at the 10-year median follow-up in randomised participants.

SECONDARY OUTCOME MEASURES

Overall mortality, metastases, disease progression, treatment complications, resource utilisation and patient-reported outcomes.

RESULTS

There were no statistically significant differences between the groups for 17 prostate cancer-specific (p = 0.48) and 169 all-cause (p = 0.87) deaths. Eight men died of prostate cancer in the active monitoring group (1.5 per 1000 person-years, 95% confidence interval 0.7 to 3.0); five died of prostate cancer in the radical prostatectomy group (0.9 per 1000 person-years, 95% confidence interval 0.4 to 2.2 per 1000 person years) and four died of prostate cancer in the radical radiotherapy group (0.7 per 1000 person-years, 95% confidence interval 0.3 to 2.0 per 1000 person years). More men developed metastases in the active monitoring group than in the radical prostatectomy and radical radiotherapy groups: active monitoring, n = 33 (6.3 per 1000 person-years, 95% confidence interval 4.5 to 8.8); radical prostatectomy, n = 13 (2.4 per 1000 person-years, 95% confidence interval 1.4 to 4.2 per 1000 person years); and radical radiotherapy, n = 16 (3.0 per 1000 person-years, 95% confidence interval 1.9 to 4.9 per 1000 person-years; p = 0.004). There were higher rates of disease progression in the active monitoring group than in the radical prostatectomy and radical radiotherapy groups: active monitoring (n = 112; 22.9 per 1000 person-years, 95% confidence interval 19.0 to 27.5 per 1000 person years); radical prostatectomy (n = 46; 8.9 per 1000 person-years, 95% confidence interval 6.7 to 11.9 per 1000 person-years); and radical radiotherapy (n = 46; 9.0 per 1000 person-years, 95% confidence interval 6.7 to 12.0 per 1000 person years; p < 0.001). Radical prostatectomy had the greatest impact on sexual function/urinary continence and remained worse than radical radiotherapy and active monitoring. Radical radiotherapy's impact on sexual function was greatest at 6 months, but recovered somewhat in the majority of participants. Sexual and urinary function gradually declined in the active monitoring group. Bowel function was worse with radical radiotherapy at 6 months, but it recovered with the exception of bloody stools. Urinary voiding and nocturia worsened in the radical radiotherapy group at 6 months but recovered. Condition-specific quality-of-life effects mirrored functional changes. No differences in anxiety/depression or generic or cancer-related quality of life were found. At the National Institute for Health and Care Excellence threshold of £20,000 per quality-adjusted life-year, the probabilities that each arm was the most cost-effective option were 58% (radical radiotherapy), 32% (active monitoring) and 10% (radical prostatectomy).

LIMITATIONS

A single prostate-specific antigen test and transrectal ultrasound biopsies were used. There were very few non-white men in the trial. The majority of men had low- and intermediate-risk disease. Longer follow-up is needed.

CONCLUSIONS

At a median follow-up point of 10 years, prostate cancer-specific mortality was low, irrespective of the assigned treatment. Radical prostatectomy and radical radiotherapy reduced disease progression and metastases, but with side effects. Further work is needed to follow up participants at a median of 15 years.

TRIAL REGISTRATION

Current Controlled Trials ISRCTN20141297.

FUNDING

This project was funded by the National Institute for Health Research Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 24, No. 37. See the National Institute for Health Research Journals Library website for further project information.

Hereditary Predisposition to Prostate Cancer: From Genetics to Clinical Implications

Prostate cancer (PrCa) ranks among the top five cancers for both incidence and mortality worldwide. A significant proportion of PrCa susceptibility has been attributed to inherited predisposition, with 10-20% of cases expected to occur in a hereditary/familial context. Advances in DNA sequencing technologies have uncovered several moderate- to high-penetrance PrCa susceptibility genes, most of which have previously been related to known hereditary cancer syndromes, namely the hereditary breast and ovarian cancer (BRCA1, BRCA2, ATM, CHEK2, and PALB2) and Lynch syndrome (MLH1, MSH2, MSH6, and PMS2) genes. Additional candidate genes have also been suggested, but further evidence is needed to include them in routine genetic testing. Recommendations based on clinical features, family history, and ethnicity have been established for more cost-efficient genetic testing of patients and families who may be at an increased risk of developing PrCa. The identification of alterations in PrCa predisposing genes may help to inform screening strategies, as well as treatment options, in the metastatic setting. This review provides an overview of the genetic basis underlying hereditary predisposition to PrCa, the current genetic screening recommendations, and the implications for clinical management of the disease.

Pathway Analysis of Genes Identified through Post-GWAS to Underpin Prostate Cancer Aetiology

Understanding the functional role of risk regions identified by genome-wide association studies (GWAS) has made considerable recent progress and is referred to as the post-GWAS era. Annotation of functional variants to the genes, including cis or trans and understanding their biological pathway/gene network enrichments, is expected to give rich dividends by elucidating the mechanisms underlying prostate cancer. To this aim, we compiled and analysed currently available post-GWAS data that is validated through further studies in prostate cancer, to investigate molecular biological pathways enriched for assigned functional genes. In total, about 100 canonical pathways were significantly, at false discovery rate (FDR) < 0.05), enriched in assigned genes using different algorithms. The results have highlighted some well-known cancer signalling pathways, antigen presentation processes and enrichment in cell growth and development gene networks, suggesting risk loci may exert their functional effect on prostate cancer by acting through multiple gene sets and pathways. Additional upstream analysis of the involved genes identified critical transcription factors such as HDAC1 and STAT5A. We also investigated the common genes between post-GWAS and three well-annotated gene expression datasets to endeavour to uncover the main genes involved in prostate cancer development/progression. Post-GWAS generated knowledge of gene networks and pathways, although continuously evolving, if analysed further and targeted appropriately, will have an important impact on clinical management of the disease.

Targeted next-generation sequencing for locally advanced prostate cancer in the Korean population

Purpose

This study aimed to evaluate the feasibility of pan-cancer panel analysis for locally advanced prostate cancer in the Korean population.

Materials and Methods

We analyzed 20 patients with locally advanced prostate cancer who underwent radical prostatectomy. A pan-cancer panel (1.9 Mbp) developed by Seoul National University Hospital (SNUH), composed of 183 target genes, 23 fusion genes, and 45 drug target regions was used for this analysis. We compared the SNUH pan-cancer panel results with The Cancer Genome Atlas (TCGA) database to search for different mutations in the Korean population. Clinical data were analyzed with univariate and multivariate analysis, and p-values <0.05 were considered statistically significant. Kaplan–Meier curve and log-rank tests were performed to evaluate survival.

Results

The average age of the patients and initial prostate-specific antigen values were 69.3±7.8 years and 66.3±16.9 ng/dL, respectively. Average sequencing depth was 574.5±304.1×. Ninety-nine genetic mutations and 5 fusions were detected. SPOP (25%), KMT2D (20%), and BRAF (15%) were frequently detected. ERG fusions were recurrently detected in 20% of the patients, with SLMAP and SETD4 as novel fusion partners. BRAF mutation was frequently detected in this study, but not in the TCGA database. Multivariate analysis showed BRAF mutation as an independent prognostic factor for biochemical recurrence (hazard ratio, 9.84; p=0.03).

Conclusions

The pan-cancer panel comprising genes related to prostate cancer is a useful tool for evaluating genetic alterations in locally advanced prostate cancers. Our results suggest that the BRAF mutation is associated with biochemical recurrence in the Korean population.

Cross-population analysis for functional characterization of type II diabetes variants

BACKGROUND

As Genome-Wide Association Studies (GWAS) have been increasingly used with data from various populations, it has been observed that data from different populations reveal different sets of Single Nucleotide Polymorphisms (SNPs) that are associated with the same disease. Using Type II Diabetes (T2D) as a test case, we develop measures and methods to characterize the functional overlap of SNPs associated with the same disease across populations.

RESULTS

We introduce the notion of an Overlap Matrix as a general means of characterizing the functional overlap between different SNP sets at different genomic and functional granularities. Using SNP-to-gene mapping, functional annotation databases, and functional association networks, we assess the degree of functional overlap across nine populations from Asian and European ethnic origins. We further assess the generalizability of the method by applying it to a dataset for another complex disease - Prostate Cancer. Our results show that more overlap is captured as more functional data is incorporated as we go through the pipeline, starting from SNPs and ending at network overlap analyses. We hypothesize that these observed differences in the functional mechanisms of T2D across populations can also explain the common use of different prescription drugs in different populations. We show that this hypothesis is concordant with the literature on the functional mechanisms of prescription drugs.

CONCLUSION

Our results show that although the etiology of a complex disease can be associated with distinct processes that are affected in different populations, network-based annotations can capture more functional overlap across populations. These results support the notion that it can be useful to take ethnicity into account in making personalized treatment decisions for complex diseases.

A Review of Prostate Cancer Genome-Wide Association Studies (GWAS)

Prostate cancer is the most common cancer in men in Europe and the United States. The genetic heritability of prostate cancer is contributed to by both rarely occurring genetic variants with higher penetrance and moderate to commonly occurring variants conferring lower risks. The number of identified variants belonging to the latter category has increased dramatically in the last 10 years with the development of the genome-wide association study (GWAS) and the collaboration of international consortia that have led to the sharing of large-scale genotyping data. Over 40 prostate cancer GWAS have been reported, with approximately 170 common variants now identified. Clinical utility of these variants could include strategies for population-based risk stratification to target prostate cancer screening to men with an increased genetic risk of disease development, while for those who develop prostate cancer, identifying genetic variants could allow treatment to be tailored based on a genetic profile in the early disease setting. Functional studies of identified variants are needed to fully understand underlying mechanisms of disease and identify novel targets for treatment. This review will outline the GWAS carried out in prostate cancer and the common variants identified so far, and how these may be utilized clinically in the screening for and management of prostate cancer. Cancer Epidemiol Biomarkers Prev; 27(8); 845-57. ©2018 AACR.

Prostate Cancer Genomics: Recent Advances and the Prevailing Underrepresentation from Racial and Ethnic Minorities

Prostate cancer (CaP) is the most commonly diagnosed non-cutaneous cancer and the second leading cause of male cancer deaths in the United States. Among African American (AA) men, CaP is the most prevalent malignancy, with disproportionately higher incidence and mortality rates. Even after discounting the influence of socioeconomic factors, the effect of molecular and genetic factors on racial disparity of CaP is evident. Earlier studies on the molecular basis for CaP disparity have focused on the influence of heritable mutations and single-nucleotide polymorphisms (SNPs). Most CaP susceptibility alleles identified based on genome-wide association studies (GWAS) were common, low-penetrance variants. Germline CaP-associated mutations that are highly penetrant, such as those found in HOXB13 and BRCA2, are usually rare. More recently, genomic studies enabled by Next-Gen Sequencing (NGS) technologies have focused on the identification of somatic mutations that contribute to CaP tumorigenesis. These studies confirmed the high prevalence of ERG gene fusions and PTEN deletions among Caucasian Americans and identified novel somatic alterations in SPOP and FOXA1 genes in early stages of CaP. Individuals with African ancestry and other minorities are often underrepresented in these large-scale genomic studies, which are performed primarily using tumors from men of European ancestry. The insufficient number of specimens from AA men and other minority populations, together with the heterogeneity in the molecular etiology of CaP across populations, challenge the generalizability of findings from these projects. Efforts to close this gap by sequencing larger numbers of tumor specimens from more diverse populations, although still at an early stage, have discovered distinct genomic alterations. These research findings can have a direct impact on the diagnosis of CaP, the stratification of patients for treatment, and can help to address the disparity in incidence and mortality of CaP. This review examines the progress of understanding in CaP genetics and genomics and highlight the need to increase the representation from minority populations.

Association of genetic polymorphisms in immune-related lncRNA with osteoarthritis susceptibility in Chinese Han population

Aim: Immune-related lncRNA may influence osteoarthritis (OA) susceptibility. We conducted this study to assess whether the genetic variants in several immune-related lncRNA influence OA susceptibility. Methods: The current research genotyped four SNPs in 306 OA patients and 316 healthy controls, including PRNCR1 rs7463708, PRNCR1 rs1456315, PRNCR1 rs16901946 and KIF13B1 rs643472, to investigate their associations with OA susceptibility. Results: We identified that PRNCR1 rs1456315 was associated with OA susceptibility in Chinese Han population (recessive model: odds ratio = 2.24; 95% CI: 1.05–4.81; additive model: odds ratio = 1.36; 95% CI: 1.03–1.80). Conclusion: Individuals with PRNCR1 rs1456315 mutant G allele were more likely to suffer from OA in Chinese Han population.

Stanniocalcin 1 promotes cell proliferation via cyclin E1/cyclin‑dependent kinase 2 in human prostate carcinoma

Stanniocalcin 1 (STC1) is a glycoprotein hormone that is involved in calcium/phosphate homeostasis. Increasing evidence suggests that STC1 is involved in carcinogenesis; however, few studies have defined the mechanisms and functional roles of STC1 activity in prostate carcinogenesis. In the present study, MTT, flow cytometry and colony formation assays, and small interfering RNA (siRNA) and overexpression in multiple cell lines were used to investigate the function of STC1 in prostate carcinoma in vivo and in vivo. Knockdown of endogenous STC1 using a siRNA decreased the proliferation of DU145 and LNCaP2 cells. These results were consistent with the changes in the protein levels of cyclin E1 and cyclin‑dependent kinase 2. By contrast, increased expression of STC1 in RWPE-1 cells led to increased cell proliferation, suggesting that STC1 promotes prostate carcinoma cell proliferation. In summary, the present study investigated the impact of STC1 on the proliferation and growth of prostate cancer in an effort to evaluate STC1 as a predictive biomarker and as a potential target for therapy.

Genetic predisposition to prostate cancer

INTRODUCTION

Prostate cancer (PrCa) is the commonest non-cutaneous cancer in men in the UK. Epidemiological evidence as well as twin studies points towards a genetic component contributing to aetiology.

SOURCES OF DATA

Key recently published literature.

AREAS OF AGREEMENT

A family history of PrCa doubles the risk of disease development in first-degree relatives. Linkage and genetic sequencing studies identified rare moderate-high-risk gene loci, which predispose to PrCa development when altered by mutation. Genome-wide association studies have identified common single-nucleotide polypmorphisms (SNPs), which confer a cumulative risk of PrCa development with increasing number of risk alleles. There are emerging data that castrate-resistant disease is associated with mutations in DNA repair genes.

AREAS OF CONTROVERSY

Linkage studies investigating possible high-risk loci leading to PrCa development identified possible loci on several chromosomes, but most have not been consistently replicated by subsequent studies. Germline SNPs related to prostate specific antigen (PSA) levels and to normal tissue radiosensitivity have also been identified though not all have been validated in subsequent studies.

GROWING POINTS

Utilizing germline SNP profiles as well as identifying high-risk genetic variants could target screening to high-risk groups, avoiding the drawbacks of PSA screening.

AREAS TIMELY FOR DEVELOPING RESEARCH

Incorporating genetics into PrCa screening is being investigated currently using both common SNP profiles and higher risk rare variants. Knowledge of germline genetic defects will allow the development of targeted screening programs, preventive strategies and the personalized treatment of PrCa.

Association of Family History of Type 2 Diabetes with Prostate Cancer: A National Cohort Study

Background

Personal history of type 2 diabetes mellitus (T2DM) is associated with a lower incidence of prostate cancer, but the underlying mechanisms are largely unknown. We hypothesized that genetic factors that are involved in the development of T2DM might protect against prostate cancer.

Methods

We used a few Swedish registers, including the Swedish Multigeneration Register and the Cancer Register, to examine the risk of prostate cancer among men with a family history of T2DM. Standardized incidence ratios were used to calculate the relative risk.

Results

The overall risk of prostate cancer among men with a familial history of T2DM was 0.87 (95% CI: 0.86–0.89) as compared to matched controls. The risk was even lower for those multiple affected relatives with T2DM, and it was 0.86 for those with two affected relatives and 0.67 for those with three and more affected relatives.

Conclusion

Family history of T2DM was associated with a lower incidence of prostate cancer, and the risk was even lower for those with more than one affected relative. Our study strongly suggests that genetic factors or shared familial factors, such as obesity, that contributed to T2DM may protect against prostate cancer.

Association between LAPTM4B gene polymorphism and prostate cancer susceptibility in an Iranian population

Lysosome associated protein transmembrane 4 β (LAPTM4B) is an oncogene associated with many human cancers. In the present study we aimed to examine the possible association between LAPTM4B polymorphism and risk of prostate cancer (PCa) in an Iranian population. This case control study was performed on 168 patients with PCa and 176 controls with benign prostatic hyperplasia (BPH). Genomic DNA was extracted from whole blood and LAPTM4B genotypes were identified by polymerase chain reaction. The distributions of LAPTM4B genotypes were significantly different between PCa patients (60.7% for *1/1, 32.8% for *1/2, and 6.5% for *2/2) and controls (44.9% for *1/1, 49.4% for *1/2, and 5.7% for *2/2). Both the *1/2 and *1/2+*2/2 genotypes significantly decreased the risk of PCa compared with the *1/1 genotype (OR = 49, 95% CI = 0.31-0.77, p = 0.002 and OR = 0.53, 95% CI = 0.34-0.81, p = 0.004, respectively). The minor allele (LAPTM4B*2) was associated with a decreased risk of PCa compared with the LAPTM4B*1 allele (OR = 0.68, 95% CI = 0.48-0.96, p = 0.031). Moreover, LAPTM4B polymorphism was not associated with clinicopathological characteristics of PCa patients. The results of this study showed that LAPTM4B*2 was associated with a decreased risk of PCa but the clinicopathological characteristics of PCa were not linked to LAPTM4B polymorphism. Further studies with larger sample sizes and different ethnicities are needed to confirm our findings.