8q24 genetic variation and comprehensive haplotypes altering familial risk of prostate cancer

Prenatal diagnosis and genetic counseling of a paternally inherited chromosome 8q24.22q24.23 microdeletion in a Chinese family

BACKGROUND

Copy number variants (CNVs) are an important source of normal and pathogenic genome variations. Especially CNVs identified in prenatal cases need careful considerations and correct interpretation if those are harmless or harmful variants from the norm. The literature on 8q24.22q24.23 microdeletion is rare, which is a challenge for genetic counselling.

CASE PRESENTATION

We have performed prenatal diagnosis and genetic counseling of a paternally inherited 8q24.22q24.23 microdeletion. In this family, father with normal phenotype and fetus with abnormal phenotype have the same microdeletion.

CONCLUSION

Chromosomal microdeletions and microduplications are difficult to detect by conventional cytogenetics, combination of prenatal ultrasound, karyotype analysis, copy number variation sequencing (CNV-seq), whole-exome sequencing (WES) and genetic counseling is helpful for the prenatal diagnosis of chromosomal microdeletions/microduplications.

Coding Variants of the Genitourinary Development Gene WNT9B Carry High Risk for Prostate Cancer

PURPOSE

Considerable genetic heterogeneity is currently thought to underlie hereditary prostate cancer (HPC). Most families meeting criteria for HPC cannot be attributed to currently known pathogenic variants.

METHODS

To discover pathogenic variants predisposing to prostate cancer, we conducted a familial case-control association study using both genome-wide single-allele and identity-by-descent analytic approaches. Sequence of high-risk haplotype carriers was used for variant detection. Candidate pathogenic variants were tested for association with prostate cancer across independent biobanks for replication of observations.

RESULTS

Pathogenic variants within WNT9B were associated with familial prostate cancer and observations replicated within four of four independent biobanks. WNT9B E152K carried 2.5-fold risk and reached genome-wide significance under meta-analysis, collectively encompassing a half million patients. WNT9B Q47R was also associated with prostate cancer with genome-wide significance among Finns, for which identity-by-descent analyses confirmed a founder effect. WNT9B shares an unexpected commonality with the previously established prostate cancer risk genes HOXB13 and HNF1B: they are each required for embryonic prostate development. With this recognition, we further evaluated two additional genes known to cause Mendelian genitourinary developmental defects, KMT2D and DHCR7. These too were nominally associated with prostate cancer under meta-analyses.

CONCLUSION

WNT9B and additional genes that are required for early genitourinary development are also involved in the later development of prostate cancer.

Causal association of peripheral immune cell counts with risk of prostate cancer: insights from bidirectional Mendelian randomization

Objectives

This study aimed to examine the causal relationships between peripheral immune cell counts and prostate cancer, adhering to Mendelian Randomization reporting guidelines for transparency and reproducibility.

Methods

In this study, bidirectional Mendelian randomization (MR) analysis, which includes MR-Egger, weighted median, weighted mode, and inverse variance weighted (IVW) approaches, was utilized to evaluate the bidirectional causal relationship between peripheral immune cell counts and the risk of PCa.

Results

The primary analysis using the IVW method suggests a potential causal association between basophil counts and the risk of prostate cancer (PCa), with an odds ratio (OR) of 1.111 and a 95% confidence interval (CI) of 1.011-1.222 (P = 0.028). Conversely, non-causal associations have been observed between other peripheral immune cell types, such as white blood cells, neutrophils, lymphocytes, eosinophils, or monocytes, and the incidence of PCa (P values > 0.05). Furthermore, although reverse analysis indicated a causal link between PCa and the counts of leukocytes and neutrophils (OR = 1.013; 95% CI = 1.002-1.225; P = 0.018 and OR = 1.013; 95% CI = 1.002-1.025; P = 0.019), no causal association was detected between PCa and basophil count (P value > 0.050).

Conclusion

This study suggests a potential bidirectional link between peripheral immune cells and prostate cancer, but inconsistencies in Mendelian Randomization methods mean these findings are preliminary and require further investigation.

Germline sequence variation in cancer genes in Rwandan breast and prostate cancer cases

Cancer genetic data from Sub-Saharan African (SSA) are limited. Patients with female breast (fBC), male breast (mBC), and prostate cancer (PC) in Rwanda underwent germline genetic testing and counseling. Demographic and disease-specific information was collected. A multi-cancer gene panel was used to identify germline Pathogenic Variants (PV) and Variants of Uncertain Significance (VUS). 400 patients (201 with BC and 199 with PC) were consented and recruited to the study. Data was available for 342 patients: 180 with BC (175 women and 5 men) and 162 men with PC. PV were observed in 18.3% fBC, 4.3% PC, and 20% mBC. BRCA2 was the most common PV. Among non-PV carriers, 65% had ≥1 VUS: 31.8% in PC and 33.6% in BC (female and male). Our findings highlight the need for germline genetic testing and counseling in cancer management in SSA.

A New Era of Data-Driven Cancer Research and Care: Opportunities and Challenges

People diagnosed with cancer and their formal and informal caregivers are increasingly faced with a deluge of complex information, thanks to rapid advancements in the type and volume of diagnostic, prognostic, and treatment data. This commentary discusses the opportunities and challenges that the society faces as we integrate large volumes of data into regular cancer care.

Leveraging Random Effects in Cistrome-Wide Association Studies for Decoding the Genetic Determinants of Prostate Cancer

Cistrome-wide association studies (CWAS) are pivotal for identifying genetic determinants of diseases by correlating genetically regulated cistrome states with phenotypes. Traditional CWAS typically develops a model based on cistrome and genotype data to associate predicted cistrome states with phenotypes. The random effect cistrome-wide association study (RECWAS), reevaluates the necessity of cistrome state prediction in CWAS. RECWAS utilizes either a linear model or marginal effect for initial feature selection, followed by kernel-based feature aggregation for association testing is introduced. Through simulations and analysis of prostate cancer data, a thorough evaluation of CWAS and RECWAS is conducted. The results suggest that RECWAS offers improved power compared to traditional CWAS, identifying additional genomic regions associated with prostate cancer. CWAS identified 102 significant regions, while RECWAS found 50 additional significant regions compared to CWAS, many of which are validated. Validation encompassed a range of biological evidence, including risk signals from the GWAS catalog, susceptibility genes from the DisGeNET database, and enhancer-domain scores. RECWAS consistently demonstrated improved performance over traditional CWAS in identifying genomic regions associated with prostate cancer. These findings demonstrate the benefits of incorporating kernel methods into CWAS and provide new insights for genetic discovery in complex diseases.

Aligning germline and somatic mutations in prostate cancer. Are genetics changing practice?

OBJECTIVE

To review the current status of germline and somatic (tumour) genetic testing for prostate cancer (PCa), and its relevance for clinical practice.

METHODS

A narrative synthesis of various molecular profiles related to their clinical context was carried out. Current guidelines for genetic testing and its feasibility in clinical practice were analysed. We report the main identified genetic sequencing results or functional genomic scores for PCa published in the literature or obtained from the French PROGENE study.

RESULTS

The molecular alterations observed in PCa are mostly linked to disruption of the androgen receptor (AR) pathway or DNA repair deficiency. The main known germline mutations affect the BReast CAncer gene 2 (BRCA2) and homeobox B13 (HOXB13) genes, whereas AR and tumour protein p53 (TP53) are the genes with most frequent somatic alterations in tumours from men with metastatic PCa. Molecular tests are now available for detecting some of these germline or somatic alterations and sometimes recommended by guidelines, but their utilisation must combine rationality and feasibility. They can guide specific therapies, notably for the management of metastatic disease. Indeed, following androgen deprivation, targeted therapies for PCa currently include poly-(ADP-ribose)-polymerase (PARP) inhibitors, immune checkpoint inhibitors, and prostate-specific membrane antigen (PSMA)-guided radiotherapy. The genetic tests currently approved for targeted therapies remain limited to the detection of BRCA1 and BRCA2 mutation and DNA mismatch repair deficiency, while large panels are recommended for germline analyses, not only for inherited cancer predisposing syndrome, but also for metastatic PCa.

CONCLUSIONS

Further consensus aligning germline with somatic molecular analysis in metastatic PCa is required, including genomics scars, emergent immunohistochemistry, or functional pre-screen imaging. With rapid advances in knowledge and technology in the field, continuous updating of guidelines to help the clinical management of these individuals, and well-conducted studies to evaluate the benefits of genetic testing are needed.

Clinical performance of magnetic resonance imaging and biomarkers for prostate cancer diagnosis in men at high genetic risk

OBJECTIVES

To evaluate different scenarios for the management of early diagnosis of cancer (PCa) in men at high genetic risk, using recently developed blood and urinary molecular biomarkers in combination with clinical information alongside multiparametric magnetic resonance imaging (mpMRI).

PATIENTS AND METHODS

A total of 322 patients with a high genetic risk (familial or personal history of cancers or a predisposing germline variant) were included in this study. The primary outcome was the detection rates of PCa (positive biopsy) or clinically significant PCa (biopsy with International Society of Urological Pathology [ISUP] grade >1). Clinical parameters included age, body mass index, ancestry, and germline mutational status, mpMRI, prostate-specific antigen density (PSAD), Prostate Health Index and urinary markers (Prostate Cancer Associated 3, SelectMdx™ and T2:ERG score) were assessed. Sensitivity (Se) and specificity (Sp) for each marker at their recommended cut-off for clinical practice were calculated. Comparison between diagnoses accuracy of each procedure and scenario was computed using mutual information based and direct effect contribution using a supervised Bayesian network approach.

RESULTS

A mpMRI Prostate Imaging-Reporting and Data System (PI-RADS) score ≥3 showed higher Se than mpMRI PI-RADS score ≥4 for detection of PCa (82% vs 61%) and for the detection of ISUP grade >1 lesions (96% vs 80%). mpMRI PI-RADS score ≥3 performed better than a PSA level of ≥3 ng/mL (Se 96%, Sp 53% vs Se 91%, Sp 8%) for detection of clinically significant PCa. In case of negative mpMRI results, the supervised Bayesian network approach showed that urinary markers (with the same accuracy for all) and PSAD of ≥0.10 ng/mL/mL were the most useful indicators of decision to biopsy.

CONCLUSIONS

We found that screening men at high genetic risk of PCa must be based on mpMRI without pre-screening based on a PSA level of >3 ng/mL, to avoid missing too many ISUP grade >1 tumours and to significantly reduce the number of unnecessary biopsies. However, urinary markers or a PSAD of ≥0.10 ng/mL/mL when mpMRI was negative increased the detection of ISUP grade >1 cancers. We suggest that a baseline mpMRI be discussed for men at high genetic risk from the age of 40 years.

Ancestry: How researchers use it and what they mean by it

Background: Ancestry is often viewed as a more objective and less objectionable population descriptor than race or ethnicity. Perhaps reflecting this, usage of the term "ancestry" is rapidly growing in genetics research, with ancestry groups referenced in many situations. The appropriate usage of population descriptors in genetics research is an ongoing source of debate. Sound normative guidance should rest on an empirical understanding of current usage; in the case of ancestry, questions about how researchers use the concept, and what they mean by it, remain unanswered. Methods: Systematic literature analysis of 205 articles at least tangentially related to human health from diverse disciplines that use the concept of ancestry, and semi-structured interviews with 44 lead authors of some of those articles. Results: Ancestry is relied on to structure research questions and key methodological approaches. Yet researchers struggle to define it, and/or offer diverse definitions. For some ancestry is a genetic concept, but for many-including geneticists-ancestry is only tangentially related to genetics. For some interviewees, ancestry is explicitly equated to ethnicity; for others it is explicitly distanced from it. Ancestry is operationalized using multiple data types (including genetic variation and self-reported identities), though for a large fraction of articles (26%) it is impossible to tell which data types were used. Across the literature and interviews there is no consistent understanding of how ancestry relates to genetic concepts (including genetic ancestry and population structure), nor how these genetic concepts relate to each other. Beyond this conceptual confusion, practices related to summarizing patterns of genetic variation often rest on uninterrogated conventions. Continental labels are by far the most common type of label applied to ancestry groups. We observed many instances of slippage between reference to ancestry groups and racial groups. Conclusion: Ancestry is in practice a highly ambiguous concept, and far from an objective counterpart to race or ethnicity. It is not uniquely a "biological" construct, and it does not represent a "safe haven" for researchers seeking to avoid evoking race or ethnicity in their work. Distinguishing genetic ancestry from ancestry more broadly will be a necessary part of providing conceptual clarity.

FAM84B promotes the proliferation of glioma cells through the cell cycle pathways

Background

This study aimed to investigate FAM84B expression in glioma tissues and explore the role of FAM84B in promoting the proliferation of glioma cells and the mechanism of regulating the cell cycle pathways.

Methods

The TCGA database was adopted to analyze FAM84B expression in glioma tissues. The FAM84B expression was detected by qRT-PCR in patients with glioma, especially that in glioma cells, U251, LN-229, U98, and U87. Two glioma cell lines U87 and T98 were selected for siRNA transfection, which were divided into si-NC si-FAM84B-1 and si-FAM84B-2 groups. The effect of FAM84B on the proliferation of glioma cells was detected with the MTT experiment and that on the glioma cell cycle was detected with the flow cytometry. The signaling pathways potentially regulated by FAM84B in glioma were analyzed through the bioinformatics analysis. The expression of proteins, Cyclin D1, CDK4, Cdk6, and p21, in the cell cycle-related pathways in cells of each group was detected by the Western blot.

Results

TCGA database results showed a significantly higher FAM84B expression in glioma tissues than that in paracancerous tissues. According to the detection of qRT-PCR, FAM84B expressed the highest in the glioma cell line U87 (P < 0.05). Compared with the serum of healthy controls, FAM84B mRNA expression significantly increased in patients with gliomas. And compared with the si-NC group, the proliferation ability of U87 and T98 cells decreased and the cell cycle was blocked in the G0/G1 phase in both si-FAM84B transfection groups (P < 0.05). According to the bioinformatics analysis, FAM84B regulated the cell cycle pathways in glioma. FAM84B siRNA inhibited the expression of key proteins, Cyclin D1, CDK2, CDK4, and Cdk6, of the cell cycle pathways in glioma cells and promoted the expression of P53 and P21 proteins.

Conclusions

In conclusion, FAM84B may inhibit the proliferation of glioma cells by regulating the cell cycle pathways.

1. FAM84B expressed highly in glioma tissues and cells.

2. Knockdown of FAM84B expression significantly inhibited the proliferation of glioma cells.

3. Knockdown of FAM84B inhibited the proliferation of glioma cells by regulating the cell cycle signaling pathways.

The Spontaneous Remission of Recurrent Lymph Node Metastatic Prostate Cancer With Lowering Serum Prostate-Specific Antigen Level

The incidence rate of spontaneous remission of malignant cancer is very low. Reports on spontaneous remission in advanced prostate cancer are extremely limited. Our patient was treated with androgen deprivation therapy, local radiotherapy, and surgical castration at the initial diagnosis. Approximately nine years after treatment, he experienced a rise in serum prostate-specific antigen level and relapse of obturator lymph node adenopathy. Initially, androgen deprivation therapy was reinitiated, which resulted in castration-resistant prostate cancer. Although androgen deprivation therapy was discontinued, spontaneous remission of recurrent lymph node and spontaneous reduction in serum prostate-specific antigen level was seen. There was no sign of radiological recurrence for over eight years without prostate cancer treatment.

The promising role and prognostic value of miR-198 in human diseases

The importance of microRNAs (miRNAs or miRs) has attracted more and more attention. MiRNA is an approximately 22-nucleotide, single-stranded, non-coding RNA molecule that affects the expression of downstream target genes. MiRNAs regulate the occurrence and development of human diseases. The objective of this article is to explore the abnormal expression of miR-198 in a variety of human diseases. The relationships between abnormally expressed miR-198 and clinicopathological characteristics are also summarized. Its roles in various diseases and potential molecular mechanisms include involvement in many biological processes, such as cell cycle regulation, proliferation, invasion, migration, apoptosis, and drug resistance. The potential value of miR-198 for disease diagnosis, treatment, and especially, prognosis, are discussed. More in-depth research on miRNA will support the conversion from basic research to clinical applications of this molecule.

Prediction of clinically significant prostate cancer using polygenic risk models in Asians

Purpose

To develop and evaluate the performance of a polygenic risk score (PRS) constructed in a Korean male population to predict clinically significant prostate cancer (csPCa).

Materials and Methods

Total 2,702 PCa samples and 7,485 controls were used to discover csPCa susceptible single nucleotide polymorphisms (SNPs). Males with biopsy-proven or post-radical prostatectomy Gleason score 7 or higher were included for analysis. After genotype imputation for quality control, logistic regression models were applied to test association and calculate effect size. Extracted candidate SNPs were further tested to compare predictive performance according to number of SNPs included in the PRS. The best-fit model was validated in an independent cohort of 311 cases and 822 controls.

Results

Of the 83 candidate SNPs with significant PCa association reported in previous literature, rs72725879 located in PRNCR1 showed the highest significance for PCa risk (odds ratio, 0.597; 95% confidence interval [CI], 0.555–0.641; p=4.3×10^-45). Thirty-two SNPs within 26 distinct loci were further selected for PRS construction. Best performance was found with the top 29 SNPs, with AUC found to be 0.700 (95% CI, 0.667–0.734). Males with very-high PRS (above the 95th percentile) had a 4.92-fold increased risk for csPCa.

Conclusions

Ethnic-specific PRS was developed and validated in Korean males to predict csPCa susceptibility using the largest csPCa sample size in Asia. PRS can be a potential biomarker to predict individual risk. Future multi-ethnic trials are required to further validate our results.

Prostate cancer risk variants of the HOXB genetic locus

The G84E germline mutation of HOXB13 predisposes to prostate cancer and is clinically tested for familial cancer care. We investigated the HOXB locus to define a potentially broader contribution to prostate cancer heritability. We sought HOXB locus germline variants altering prostate cancer risk in three European-ancestry case-control study populations (combined 7812 cases and 5047 controls): the International Consortium for Prostate Cancer Genetics Study; the Nashville Familial Prostate Cancer Study; and the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial. Multiple rare genetic variants had concordant and strong risk effects in these study populations and exceeded genome-wide significance. Independent risk signals were best detected by sentinel variants rs559612720 within SKAP1 (OR = 8.1, P = 2E-9) and rs138213197 (G84E) within HOXB13 (OR = 5.6, P = 2E-11), separated by 567 kb. Half of carriers inherited both risk alleles, while others inherited either alone. Under mutual adjustment, the variants separately carried 3.6- and 3.1-fold risk, respectively, while joint inheritance carried 11.3-fold risk. These risks were further accentuated among men meeting criteria for hereditary prostate cancer, and further still for those with early-onset or aggressive disease. Among hereditary prostate cancer cases diagnosed under age 60 and with aggressive disease, joint inheritance carried a risk of OR = 27.7 relative to controls, P = 2E-8. The HOXB sentinel variant pair more fully captured genetic risk for prostate cancer within the study populations than either variant alone.

[Familial prostate cancer and genetic predisposition]

BACKGROUND

Twenty percent of all prostate cancer patients have a positive family history (at least 1 first-degree relative with prostate cancer) and a part of these patients have a genetic predisposition.

OBJECTIVES

A literature search and analysis of studies investigating incidence, diagnosis, and clinical course of familial compared to sporadic prostate cancer as well as genetic predisposition was performed using PubMed and Embase.

RESULTS

Risk of prostate cancer depends on number, degree of relationship, and age of onset of affected men in the family. The incidence of familial prostate cancer is higher and the age of diagnosis lower compared to sporadic cases. The clinical course of the disease is comparable, but in individuals with a germline mutation, more intensive therapy is needed due to a more aggressive disease.

CONCLUSIONS

Crucial for risk assessment is a detailed family history, including creation of a pedigree with cancer family history if necessary. In high-risk families, genetic counselling and annual prostate-specific antigen (PSA) screening beginning at the age of 40 should be performed. Verification of a germline mutation requires more intensive therapy due to more aggressive disease.

Identification of Germline Genetic Variants that Increase Prostate Cancer Risk and Influence Development of Aggressive Disease

Prostate cancer (PrCa) is a heterogeneous disease, which presents in individual patients across a diverse phenotypic spectrum ranging from indolent to fatal forms. No robust biomarkers are currently available to enable routine screening for PrCa or to distinguish clinically significant forms, therefore late stage identification of advanced disease and overdiagnosis plus overtreatment of insignificant disease both remain areas of concern in healthcare provision. PrCa has a substantial heritable component, and technological advances since the completion of the Human Genome Project have facilitated improved identification of inherited genetic factors influencing susceptibility to development of the disease within families and populations. These genetic markers hold promise to enable improved understanding of the biological mechanisms underpinning PrCa development, facilitate genetically informed PrCa screening programmes and guide appropriate treatment provision. However, insight remains largely lacking regarding many aspects of their manifestation; especially in relation to genes associated with aggressive phenotypes, risk factors in non-European populations and appropriate approaches to enable accurate stratification of higher and lower risk individuals. This review discusses the methodology used in the elucidation of genetic loci, genes and individual causal variants responsible for modulating PrCa susceptibility; the current state of understanding of the allelic spectrum contributing to PrCa risk; and prospective future translational applications of these discoveries in the developing eras of genomics and personalised medicine.