Identification of a novel germline SPOP mutation in a family with hereditary prostate cancer

The Mutational and Transcriptional Landscapes of Speckle-Type POZ Protein (SPOP) and Androgen Receptor (AR) in a Single-Center pT3 Prostatectomy Cohort

Prostate cancer (PCa) is a heterogeneous disease both clinically and genetically. According to The Cancer Genome Atlas (TCGA), the speckle‑type POZ protein (SPOP) mutant form is one of the significant core subtypes of PCa. However, the prognostic value of SPOP variations remains unknown. As a critical PCa driver and an SPOP-targeted protein, androgen receptor (AR) also plays a role in PCa initiation and progression. Thus, we aimed to analyze the mutational status of SPOP and AR with their transcriptional levels in a pathological stage 3 (pT3) prostatectomy cohort consisting of 89 Turkish PCa patients. Targeted sequence analysis and RT-qPCR were performed for SPOP and AR in the benign and malign prostate tissue samples. Our results introduced the two novel pathogenic SPOP variations, C203Y and S236R, in the BTB/POZ domain and a novel pathogenic variant in the ligand-binding domain of AR, R789W. Their predicted pathogenicities and effects on protein features were evaluated by web-based in silico analysis. The overall frequency of SPOP and AR variations for pT3 patients in our population was 3.4% (3/89) and 4.5% (4/89), respectively. The mutational results represented a possible subgroup characterized by carrying the novel variants in SPOP and AR in pT3 PCa patients. In addition to the significant clinicopathological parameters, the mutational results provide a better understanding of the molecular structure of pathologically advanced PCa in the SPOP and AR aspects.

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.

SPOP in Cancer: Phenomena, Mechanisms and Its Role in Therapeutic Implications

Speckle-type POZ (pox virus and zinc finger protein) protein (SPOP) is a cullin 3-based E3 ubiquitin ligase adaptor protein that plays a crucial role in ubiquitin-mediated protein degradation. Recently, SPOP has attracted major research attention as it is frequently mutated in a range of cancers, highlighting pleiotropic tumorigenic effects and associations with treatment resistance. Structurally, SPOP contains a functionally critical N-terminal meprin and TRAF homology (MATH) domain for many SPOP substrates. SPOP has two other domains, including the internal Bric-a-brac-Tramtrack/Broad (BTB) domain, which is linked with SPOP dimerization and binding to cullin3, and a C-terminal nuclear localization sequence (NLS). The dysregulation of SPOP-mediated proteolysis is associated with the development and progression of different cancers since abnormalities in SPOP function dysregulate cellular signaling pathways by targeting oncoproteins or tumor suppressors in a tumor-specific manner. SPOP is also involved in genome stability through its role in the DNA damage response and DNA replication. More recently, studies have shown that the expression of SPOP can be modulated in various ways. In this review, we summarize the current understanding of SPOP's functions in cancer and discuss how to design a rational therapeutic target.

The diverse roles of SPOP in prostate cancer and kidney cancer

Multiple studies have confirmed that speckle-type pox virus and zinc finger (POZ) protein (SPOP) functions as a substrate adaptor of cullin 3-based E3 ligase and has a crucial role in various cellular processes via specific targeting of proteins for ubiquitination and subsequent proteasomal degradation. Dysregulation of SPOP-mediated proteolysis might be involved in the development and progression of human prostate and kidney cancers. In prostate cancer, SPOP seems to function as a tumour suppressor by targeting several proteins, including androgen receptor (AR), steroid receptor coactivator 3 (SRC3) and BRD4, for degradation, whereas it might function as an oncoprotein in kidney cancer, for example, by targeting phosphatase and tensin homologue (PTEN) for proteasomal degradation. In addition, nuclear SPOP targets AR for degradation and has a role as a tumour suppressor in prostate cancer; however, in kidney cancer, SPOP largely accumulates in the cytoplasm and fails to promote degradation of AR located in the nucleus, resulting in activation of AR-driven pathways and cancer progression. Owing to the context-dependent function of SPOP in human malignancies, further assessment of the molecular mechanisms involving SPOP in prostate and kidney cancers is needed to improve our understanding of its role in the development of these cancer types. Treatments that target SPOP might become therapeutic strategies in these malignancies in the future.

SPOP and cancer: a systematic review

The initiation and progression of cancer is dependent on the acquisition of mutations in oncogenes or tumor suppressor genes that ultimately leads to the dysregulation of key regulatory pathways. Though these mutations often occur in direct regulators of such pathways, some may confer tumorigenic potential by indirectly targeting several pathways congruently thereby exerting pleiotropic effects. In recent years, the tumor suppressor gene Speckle Type POZ Protein (SPOP) has gained a lot of attention as it has been found to be altered in a variety of different cancers. SPOP appears to exert pleiotropic tumorigenic effects as multiple different regulatory pathways become dysregulated upon SPOP alterations. SPOP has been identified as an E3 ubiquitin ligase substrate binding subunit of the proteasome complex. Since protein degradation is critical in regulating proper cellular function it is not surprising that the proteasome pathway is often found to be disrupted in cancer. Many studies have now indicated that mutations or changes in the expression of SPOP are one of several underlying reasons of proteasome pathway disruption in different cancers. Ultimately, either SPOP downregulation or mutation promotes stabilization of direct SPOP targets which subsequently promotes cancer through the dysregulation of key regulatory pathways. In this review, we will discuss the current literature on cancer-specific SPOP alterations as well the SPOP targets that are stabilized, and the pathways that are dysregulated, as a result.

Familial/inherited cancer syndrome: a focus on the highly consanguineous Arab population

The study of hereditary cancer, which accounts for ~10% of cancer cases worldwide is an important subfield of oncology. Our understanding of hereditary cancers has greatly advanced with recent advances in sequencing technology, but as with any genetic trait, gene frequencies of cancer-associated mutations vary across populations, and most studies that have located hereditary cancer genes have been conducted on European or Asian populations. There is an urgent need to trace hereditary cancer genes across the Arab world. Hereditary disease is particularly prevalent among members of consanguineous populations, and consanguineous marriages are particularly common in the Arab world. There are also cultural and educational idiosyncrasies that differentiate Arab populations from other more thoroughly studied groups with respect to cancer awareness and treatment. Therefore, a review of the literature on hereditary cancers in this understudied population was undertaken. We report that BRCA mutations are not as prevalent among Arab breast cancer patients as they are among other ethnic groups, and therefore, other genes may play a more important role. A wide variety of germline inherited mutations that are associated with cancer are discussed, with particular attention to breast, ovarian, colorectal, prostate, and brain cancers. Finally, we describe the state of the profession of familial cancer genetic counselling in the Arab world, and the clinics and societies dedicated to its advances. We describe the complexities of genetic counselling that are specific to the Arab world. Understanding hereditary cancer is heavily dependent on understanding population-specific variations in cancer-associated gene frequencies.

Hedgehog Signal and Genetic Disorders

The hedgehog (Hh) family comprises sonic hedgehog (Shh), Indian hedgehog (Ihh), and desert hedgehog (Dhh), which are versatile signaling molecules involved in a wide spectrum of biological events including cell differentiation, proliferation, and survival; establishment of the vertebrate body plan; and aging. These molecules play critical roles from embryogenesis to adult stages; therefore, alterations such as abnormal expression or mutations of the genes involved and their downstream factors cause a variety of genetic disorders at different stages. The Hh family involves many signaling mediators and functions through complex mechanisms, and achieving a comprehensive understanding of the entire signaling system is challenging. This review discusses the signaling mediators of the Hh pathway and their functions at the cellular and organismal levels. We first focus on the roles of Hh signaling mediators in signal transduction at the cellular level and the networks formed by these factors. Then, we analyze the spatiotemporal pattern of expression of Hh pathway molecules in tissues and organs, and describe the phenotypes of mutant mice. Finally, we discuss the genetic disorders caused by malfunction of Hh signaling-related molecules in humans.

Identification of novel sarcoma risk genes using a two-stage genome wide DNA sequencing strategy in cancer cluster families and population case and control cohorts

Background

Although familial clustering of cancers is relatively common, only a small proportion of familial cancer risk can be explained by known cancer predisposition genes.

Methods

In this study we employed a two-stage approach to identify candidate sarcoma risk genes. First, we conducted whole exome sequencing in three multigenerational cancer families ascertained through a sarcoma proband (n = 19) in order to prioritize candidate genes for validation in an independent case-control cohort of sarcoma patients using family-based association and segregation analysis. The second stage employed a burden analysis of rare variants within prioritized candidate genes identified from stage one in 560 sarcoma cases and 1144 healthy ageing controls, for which whole genome sequence was available.

Results

Variants from eight genes were identified in stage one. Following gene-based burden testing and after correction for multiple testing, two of these genes, ABCB5 and C16orf96, were determined to show statistically significant association with cancer. The ABCB5 gene was found to have a higher burden of putative regulatory variants (OR = 4.9, p-value = 0.007, q-value = 0.04) based on allele counts in sarcoma cases compared to controls. C16orf96, was found to have a significantly lower burden (OR = 0.58, p-value = 0.0004, q-value = 0.003) of regulatory variants in controls compared to sarcoma cases.

Conclusions

Based on these genetic association data we propose that ABCB5 and C16orf96 are novel candidate risk genes for sarcoma. Although neither of these two genes have been previously associated with sarcoma, ABCB5 has been shown to share clinical drug resistance associations with melanoma and leukaemia and C16orf96 shares regulatory elements with genes that are involved with TNF-alpha mediated apoptosis in a p53/TP53-dependent manner. Future genetic studies in other family and population cohorts will be required for further validation of these novel findings.

Electronic supplementary material

The online version of this article (10.1186/s12881-019-0808-9) contains supplementary material, which is available to authorized users.

Differential Expression of Genes for Ubiquitin Ligases in Medulloblastoma Subtypes

Using publically available datasets on gene expression in medulloblastoma (MB) subtypes, we selected genes for ubiquitin ligases and identified statistically those that best predicted each of the four major MB subgroups as separate disease entities. We identify a gene coding for an ubiquitin ligase, ZNRF3, whose overexpression alone can predict the WNT subgroup for 100% in the Pfister dataset. For the SHH subgroup, we identify a gene for a regulatory subunit of the protein phosphatase 2A (PP2A), PPP2R2C, as the major predictor among the E3 ligases genes. The ubiquitin and ubiquitin-like conjugation database (UUCD) lists PPP2R2C as coding for a Cullin Ring ubiquitin ligase adaptor. For group 3 MBs, the best ubiquitin ligase predictor was PPP2R2B, a gene which codes for another regulatory subunit of the PP2A holoenzyme. For group 4, the best E3 gene predictors were MID2, ZBTB18, and PPP2R2A, which codes for a third PP2A regulatory subunit. Heatmap analysis of the E3 gene data shows that expression of ten genes for ubiquitin ligases can be used to classify MBs into the four major consensus subgroups. This was illustrated by analysis of gene expression of ubiquitin ligases of the Pfister dataset and confirmed in the dataset of Cavalli. We conclude that genes for ubiquitin ligases can be used as genetic markers for MB subtypes and that the proteins coded for by these genes should be investigated as subtype specific therapeutic targets for MB.

Functional analysis of Cullin 3 E3 ligases in tumorigenesis

Cullin 3-RING ligases (CRL3) play pivotal roles in the regulation of various physiological and pathological processes, including neoplastic events. The substrate adaptors of CRL3 typically contain a BTB domain that mediates the interaction between Cullin 3 and target substrates to promote their ubiquitination and subsequent degradation. The biological implications of CRL3 adaptor proteins have been well described where they have been found to play a role as either an oncogene, tumor suppressor, or can mediate either of these effects in a context-dependent manner. Among the extensively studied CRL3-based E3 ligases, the role of the adaptor protein SPOP (speckle type BTB/POZ protein) in tumorigenesis appears to be tissue or cellular context dependent. Specifically, SPOP acts as a tumor suppressor via destabilizing downstream oncoproteins in many malignancies, especially in prostate cancer. However, SPOP has largely an oncogenic role in kidney cancer. Keap1, another well-characterized CRL3 adaptor protein, likely serves as a tumor suppressor within diverse malignancies, mainly due to its specific turnover of its downstream oncogenic substrate, NRF2 (nuclear factor erythroid 2-related factor 2). In accordance with the physiological role the various CRL3 adaptors exhibit, several pharmacological agents have been developed to disrupt its E3 ligase activity, therefore blocking its potential oncogenic activity to mitigate tumorigenesis.

A genomic classifier improves prediction of metastatic disease within 5 years after surgery in node-negative high-risk prostate cancer patients managed by radical prostatectomy without adjuvant therapy

BACKGROUND

Surgery is a standard first-line therapy for men with intermediate- or high-risk prostate cancer. Clinical factors such as tumor grade, stage, and prostate-specific antigen (PSA) are currently used to identify those who are at risk of recurrence and who may benefit from adjuvant therapy, but novel biomarkers that improve risk stratification and that distinguish local from systemic recurrence are needed.

OBJECTIVE

To determine whether adding the Decipher genomic classifier, a validated metastasis risk-prediction model, to standard risk-stratification tools (CAPRA-S and Stephenson nomogram) improves accuracy in predicting metastatic disease within 5 yr after surgery (rapid metastasis [RM]) in an independent cohort of men with adverse pathologic features after radical prostatectomy (RP).

DESIGN, SETTING, AND PARTICIPANTS

The study population consisted of 169 patients selected from 2641 men who underwent RP at the Cleveland Clinic between 1987 and 2008 who met the following criteria: (1) preoperative PSA>20 ng/ml, stage pT3 or margin positive, or Gleason score≥8; (2) pathologic node negative; (3) undetectable post-RP PSA; (4) no neoadjuvant or adjuvant therapy; and (5) minimum of 5-yr follow-up for controls. The final study cohort consisted of 15 RM patients and 154 patients as non-RM controls.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

The performance of Decipher was evaluated individually and in combination with clinical risk factors using concordance index (c-index), decision curve analysis, and logistic regression for prediction of RM.

RESULTS AND LIMITATIONS

RM patients developed metastasis at a median of 2.3 yr (interquartile range: 1.7-3.3). In multivariable analysis, Decipher was a significant predictor of RM (odds ratio: 1.48; p=0.018) after adjusting for clinical risk factors. Decipher had the highest c-index, 0.77, compared with the Stephenson model (c-index: 0.75) and CAPRA-S (c-index: 0.72) as well as with a panel of previously reported prostate cancer biomarkers unrelated to Decipher. Integration of Decipher into the Stephenson nomogram increased the c-index from 0.75 (95% confidence interval [CI], 0.65-0.85) to 0.79 (95% CI, 0.68-0.89).

CONCLUSIONS

Decipher was independently validated as a genomic metastasis signature for predicting metastatic disease within 5 yr after surgery in a cohort of high-risk men treated with RP and managed conservatively without any adjuvant therapy. Integration of Decipher into clinical nomograms increased prediction of RM. Decipher may allow identification of men most at risk for metastatic progression who should be considered for multimodal therapy or inclusion in clinical trials.

PATIENT SUMMARY

Use of Decipher in addition to standard clinical information more accurately identified men who developed metastatic disease within 5 yr after surgery. The results suggest that Decipher allows improved identification of the men who should consider secondary therapy from among the majority that may be managed conservatively after surgery.