Single nucleotide polymorphisms as prognostic and predictive biomarkers in renal cell carcinoma

Role of polymorphisms on the Recurrent Pregnancy Loss: A systematic review, Meta-analysis and bioinformatic analysis

Recurrent miscarriage (RM) is a major reproductive health issue. RM is a multi-factorial disease, and is affected by environmental, genetic, and epigenetic factors. Genetics has a common role in recurrent miscarriage occurrence. It seems that molecular genetics has a great role in RSA incidence. So, in these years, RM has become for a major subject of genetics research. There are many genes that are involved in each phase for successful reproduction. This research aimed to evaluate the effect of all studied polymorphisms in studies on RSA that have not been included in any meta-analysis. PubMed, Scopus, and Web of Science databases were recruited to investigate the related articles. The systematic review results identified 143 studies worldwide. Thirteen genes have been included in assessing the case-control studies. Sixty-four SNPs were recruited to assess the association between genetic factors and RSA susceptibility. Ninety-two studies containing twenty two SNPs (from 10 genes) were included in the quantitative analysis. Bioinformatic analysis indicated that rs12722482 showed "Damaging Status" by double servers, and rs315952 and rs854560 had "Possibly damaging" status in the PolyPhen-2 server. MethPrimer server indicated that there is "CpG Island" in the rs10895068, rs1130355, and rs41557518 variants, and rs10895068-G allele makes a CpG dinucleotide which can change the gene methylation and result in altering the gene expression. So, further studies on rs12722482 and rs10895068 can demonstrate valuable results. To the best of our knowledge, this systematic review has covered the all studied polymorphisms of HLA-C, HLA-G, PON1, AGTR1, TAFI, FAS, FAS-L, ESR1, PGR, CTLA-4, MMP-2, MMP-3, MMP-9, and IL1RN for the first time. Also, we did a novel meta-analysis for AGTR1 rs5186, TAFI rs1926447, rs3742264, HLA-G rs1063320, rs1233334, rs1736936, rs2249863, PON1 rs662, rs854560, FAS rs2234767, rs1800682, FAS-L rs763110, ESR1, rs9340799, rs3798759, PGR rs1042838, CTLA4 rs4553808, rs5742909, rs231775, rs3087243, and MMP-2 rs243865 and updated statistical finding for rs2234693 and rs371194629. Rs2234693, rs9340799, rs231775, and rs371194629 demonstrated a significant association with RSA risk. Some variations showed significant association, while further studies are suggested to confirm the results. Finally, Rs4553808 and rs5742909 revealed no significant deviation in the results. It is suggested that these SNPs may be excluded from subsequent case-control studies or other analyses.

Single-nucleotide polymorphism associations with efficacy and toxicity in metastatic castration-resistant prostate cancer treated with cabazitaxel

Background: The aim of this study was to evaluate the impact of certain single-nucleotide polymorphisms (SNPs) in cabazitaxel activity and toxicity in patients with metastatic castration-resistant prostate cancer (mCRPC). Patients & methods: 56 SNPs in five genes (CYP3A4, CYP3A5, ABCB1, TUBB1 and CYP2C8) were genotyped in 67 mCRPC patients and their correlation with outcomes analyzed. Results: TUBB1-rs151352 (hazard ratio: 0.52) and CYP2C8-rs1341164 (hazard ratio: 0.53) were associated with better overall survival, and CYP2C8-rs1058932 with biochemical progression (odds ratio: 6.60) in multivariate analysis. ABCB1-rs17327624 correlated with severe toxicity ≥ grade 3 (odds ratio: 8.56) and CYP2C8-rs11572093 with asthenia (odds ratio: 8.12). Conclusion: Genetic variants in mCRPC patients could explain different outcomes with cabazitaxel. Nonetheless, the small sample size and the high number of SNPs analyzed mean that the results are only hypothesis-generating and require further validation.

Synonymous Variants: Necessary Nuance in our Understanding of Cancer Drivers and Treatment Outcomes

Once called "silent mutations" and assumed to have no effect on protein structure and function, synonymous variants are now recognized to be drivers for some cancers. There have been significant advances in our understanding of the numerous mechanisms by which synonymous single nucleotide variants (sSNVs) can affect protein structure and function by affecting pre-mRNA splicing, mRNA expression, stability, folding, miRNA binding, translation kinetics, and co-translational folding. This review highlights the need for considering sSNVs in cancer biology to gain a better understanding of the genetic determinants of human cancers and to improve their diagnosis and treatment. We surveyed the literature for reports of sSNVs in cancer and found numerous studies on the consequences of sSNVs on gene function with supporting in vitro evidence. We also found reports of sSNVs that have statistically significant associations with specific cancer types but for which in vitro studies are lacking to support the reported associations. Additionally, we found reports of germline and somatic sSNVs that were observed in numerous clinical studies and for which in silico analysis predicts possible effects on gene function. We provide a review of these investigations and discuss necessary future studies to elucidate the mechanisms by which sSNVs disrupt protein function and are play a role in tumorigeneses, cancer progression, and treatment efficacy. As splicing dysregulation is one of the most well recognized mechanisms by which sSNVs impact protein function, we also include our own in silico analysis for predicting which sSNVs may disrupt pre-mRNA splicing.

Germline Variants in Angiogenesis-Related Genes Contribute to Clinical Outcome in Head and Neck Squamous Cell Carcinoma

Simple Summary

A high risk of relapse and treatment resistance are among the major challenges in locally advanced head and neck squamous cell carcinoma (HNSCC). Data show that common germline alterations in genes regulating angiogenesis may modulate treatment sensitivity, cancer progression, and prognosis, but relatively little is known about their role in HNSCC. Thus, our goal was to examine the effect of variation in these genes on survival outcomes in HNSCC patients receiving radiotherapy and cisplatin-based chemoradiotherapy. We identified genetic variants significantly affecting therapy results, constituting independent prognostic factors in these patients. Our results suggest that some polymorphisms in angiogenesis genes may be determinants of treatment efficacy and tumor aggressiveness in HNSCC, which may be of importance in standard therapy. These findings emphasize the potential value of the host genetic profile related to angiogenesis in assessing the risk of treatment failure.

Abstract

Fibroblast growth factor (FGF)/FGF receptor (FGFR), and platelet-derived growth factor (PDGF)/PDGF receptor (PDGFR) systems, as well as some matrix metalloproteinases (MMPs) and their tissue inhibitors (TIMPs), are involved in various steps of angiogenesis. Data indicate that common germline variations in angiogenesis-regulating genes may modulate therapy results and cancer progression. However, whether these variants affect clinical outcome in head and neck squamous cell carcinoma (HNSCC) is unclear. Hence, we assessed the relationship between FGF/FGFR, PDGF/PDGFR, MMP, and TIMP genetic variants and treatment outcomes in HNSCC patients receiving radiotherapy (RT) alone or combined with cisplatin-based chemotherapy. In multivariate analysis, FGF2 rs1048201 CC homozygotes showed a higher risk of death (p = 0.039), while PDGFRA rs2228230 T was strongly associated with an increased risk of locoregional relapse (HR 2.49, p = 0.001) in the combination treatment subgroup. In the RT alone subset, MMP2 rs243865 TT carriers had a higher risk of locoregional recurrence (HR 2.92, p = 0.019), whereas PDGFRB rs246395 CC homozygotes were at increased risk of metastasis (HR 3.06, p = 0.041). The MMP2 rs7201 C and TIMP2 rs7501477 T were associated with a risk of locoregional failure in the entire cohort (p = 0.032 and 0.045, respectively). Furthermore, rs1048201, rs2228230, rs246395, rs243865, rs7201, and rs7201/rs7501477 were independent indicators of an unfavorable outcome. This study demonstrates that the FGF2, PDGFRA, PDGFRB, MMP2, and TIMP2 variants may contribute to treatment failure and poor prognosis in HNSCC.

Computational and structural based approach to identify malignant nonsynonymous single nucleotide polymorphisms associated with CDK4 gene

Cycline-dependent kinase 4 (CDK4), an enzyme of the cycline dependent or Ser/Thr protein kinase family, plays a role in cell cycle progression (G1 phase) by phosphorylating a tumor suppressor protein called pRB. Alteration of this enzyme due to missense mutation/ nonsynonymous single nucleotide polymorphisms (nsSNPs) are responsible for various types of cancer progression, e.g. melanoma, lung cancer, and breast cancer. Hence, this study is designed to identify the malignant missense mutation of CDK4 from the single nucleotide polymorphism database (dbSNP) by incorporating computational algorithms. Out of 239 nsSNPs; G15S, D140Y and D140H were predicted to be highly malignant variants which may have a devastating impact on protein structure or function. We also found defective binding motif of these three mutants with the CDK4 inhibitor ribociclib and ATP. However, by incorporating molecular dynamic simulation, our study concludes that the superiority of G15S than the other two mutants (D140Y and D140H) in destabilizing proteins nature.

Nanodiagnostics: A review of the medical capabilities of nanopores

Modern diagnostics strive to be accurate, fast, and inexpensive in addition to properly identifying the presence of a disease, infection, or illness. Early diagnosis is key; catching a disease in its early stages can be the difference between fatality and treatment. The challenge with many diseases is that detectability of the disease scales with disease progression. Since single molecule sensors, e.g., nanopores, can sense biomolecules at low concentrations, they have the potential to become clinically relevant in many of today's medical settings. With nanopore-based sensing, lower volumes and concentrations are required for detection, enabling it to be clinically beneficial. Other advantages to using nanopores include that they are tunable to an enormous variety of molecules and boast low costs, and fabrication is scalable for manufacturing. We discuss previous reports and the potential for incorporating nanopores into the medical field for early diagnostics, therapeutic monitoring, and identifying relapse/recurrence.

PP1, PKA and DARPP-32 in breast cancer: A retrospective assessment of protein and mRNA expression

Cyclic AMP–dependent protein kinase A (PKA) and protein phosphatase 1 (PP1) are proteins involved in numerous essential signalling pathways that modulate physiological and pathological functions. Both PP1 and PKA can be inhibited by dopamine‐ and cAMP‐regulated phosphoprotein 32 kD (DARPP‐32). Using immunohistochemistry, PKA and PP1 expression was determined in a large primary breast tumour cohort to evaluate associations between clinical outcome and clinicopathological criteria (n > 1100). In addition, mRNA expression of PKA and PP1 subunits was assessed in the METABRIC data set (n = 1980). Low protein expression of PKA was significantly associated with adverse survival of breast cancer patients; interestingly, this relationship was stronger in ER‐positive breast cancer patients. PP1 protein expression was not associated with patient survival. PKA and PP1 subunit mRNA was also assessed; PPP1CA, PRKACG and PRKAR1B were associated with breast cancer–specific survival. In patients with high expression of DARPP‐32, low expression of PP1 was associated with adverse survival when compared to high expression in the same group. PKA expression and PP1 expression are of significant interest in cancer as they are involved in a wide array of cellular processes, and these data indicate PKA and PP1 may play an important role in patient outcome.

Implementation of computational approaches to explore the deleterious effects of non-synonymous SNPs on pRB protein

Retinoblastoma 1 (RB1) is the first discovered tumor suppressor gene and recognized as the simple model system whose encoded defective protein can cause a pediatric cancer retinoblastoma. It functions as a negative regulator of the cell cycle through the interactions with members of the E2F transcription factors family. The protein of the RB1 gene (pRB) is engaged in various cell cycle processes including apoptosis, cell cycle arrest and chromatin remodeling. Recent studies on Retinoblastoma also exhibited multiple sets of point mutation in the associated protein due to its large polymorphic information in the local database. In this study, we identified the list of disease associated non-synonymous single nucleotide polymorphisms (nsSNPs) in RB1 by incorporating different computational algorithms, web servers, modeling of the mutants and finally superimposing it. Out of 826 nsSNPs, W516G and W563G were predicted to be highly deleterious variants in the conserved regions and found to have an impact on protein structure and protein-protein interaction. Moreover, our study concludes the effect of W516G variant was more detrimental in destabilizing protein's nature as compared to W563G variant. We also found defective binding of pRB having W516G mutation with E2F2 protein. Findings of this study will aid in shortening of the expensive experimental cost of identifying disease associated SNPs in retinoblastoma for which specialized personalized treatment or therapy can be formulated.Communicated by Ramaswamy H. Sarma.

Dysregulated PDGFR alpha expression and novel somatic mutations in colorectal cancer: association to RAS wild type status and tumor size

Background

Platelet derived growth factor receptor alpha (PDGFRα) has been considered as a relevant factor in tumor proliferation, angiogenesis and metastatic dissemination. It was a target of tyrosine kinase (TK) inhibitors emerged in the therapy of diverse cancers. In colorectal cancer, the commonly used therapy is anti-epithelial growth factor receptor (EGFR). However, both RAS mutated and a subgroup of RAS wild type patients resist to such therapy. The aim of this study is to investigate PDGFRα protein expression and mutational status in colorectal adenocarcinoma and their association with clinicopathological features and molecular RAS status to provide useful information for the identification of an effective biomarker that might be implicated in prognosis and treatment prediction.

Methods

Our study enrolled 103 formalin fixed paraffin-embedded (FFPE) colorectal adenocarcinoma. PDGFRα expression was investigated by immunohistochemistry (IHC). Hotspot exon 18 of PDGFRA was studied by PCR followed by Sanger sequencing and RAS status was determined by real time quantitative PCR. Thirteen normal colon tissues were used as negative controls.

Results

PDGFRα staining was detected in the cytoplasm of all tissues. Low expression was observed in all normal colon mucosa. In adenocarcinoma, 45% (45/100) of cases showed PDGFRα overexpression. This overexpression was significantly associated with mutations in exon 18 (P = 0.024), RAS wild type status (P < 10^–3), tumor diameter (P = 0.048), whereas there was no association with tumor side (P = 0.13) and other clinicopathological features.

Conclusion

Overexpression of PDGFRα in adenocarcinoma suggests its potential role in tumor cells growth and invasion. The association between PDGFRα overexpression in both tumor and stromal adenocarcinoma cells with RAS wild type status suggests its potential role in anti-EGFR therapy resistance and the relevance of using it as specific or adjuvant therapeutic target.

Validation of the Correlation Between Single Nucleotide Polymorphism rs307826 in VEGFR3 and Outcome in Metastatic Clear-Cell Renal Cell Carcinoma Patients Treated with Sunitinib

BACKGROUND: Previously, we have shown a correlation between single nucleotide polymorphism (SNP) rs307826 in vascular endothelial growth factor receptor-3 (VEGFR3) and outcome in metastatic clear-cell renal cell carcinoma (m-ccRCC) patients treated with sunitinib. OBJECTIVE: We aimed to validate this finding in an independent patient series. METHODS: m-ccRCC patients receiving sunitinib as first-line targeted therapy were included in a validation cohort. Endpoints were response rate (RR), progression-free survival (PFS) and overall survival (OS). We also updated survival data of our discovery cohort as described previously. RESULTS: Eighty-four patients were included in the validation cohort. rs307826 AG/GG-carriers had a shorter PFS (8 versus 12 months, p = 0.04) and a trend towards a shorter OS (18 versus 27 months, p = 0.22) compared to AA-carriers. In the total series of 168 patients (from the discovery cohort, as described previously, and the validation cohort), rs307826 AG/GG-carriers had a poorer RR (29% versus 53%, p = 0.008), PFS (8 versus 15 months, p = 0.0002) and OS (22 versus 31 months, p = 0.004) compared to AA-carriers. rs307826 was independently associated with PFS and OS on multivariate analysis. CONCLUSION: VEGFR3 rs307826 seems to be associated with outcome on sunitinib in m-ccRCC. Its impact highlights the role of VEGFR3 in ccRCC pathogenesis and as a target of sunitinib.

Whole-genome sequence association analysis of blood proteins in a longitudinal wellness cohort

BACKGROUND

The human plasma proteome is important for many biological processes and targets for diagnostics and therapy. It is therefore of great interest to understand the interplay of genetic and environmental factors to determine the specific protein levels in individuals and to gain a deeper insight of the importance of genetic architecture related to the individual variability of plasma levels of proteins during adult life.

METHODS

We have combined whole-genome sequencing, multiplex plasma protein profiling, and extensive clinical phenotyping in a longitudinal 2-year wellness study of 101 healthy individuals with repeated sampling. Analyses of genetic and non-genetic associations related to the variability of blood levels of proteins in these individuals were performed.

RESULTS

The analyses showed that each individual has a unique protein profile, and we report on the intra-individual as well as inter-individual variation for 794 plasma proteins. A genome-wide association study (GWAS) using 7.3 million genetic variants identified by whole-genome sequencing revealed 144 independent variants across 107 proteins that showed strong association (P < 6 × 10-11) between genetics and the inter-individual variability on protein levels. Many proteins not reported before were identified (67 out of 107) with individual plasma level affected by genetics. Our longitudinal analysis further demonstrates that these levels are stable during the 2-year study period. The variability of protein profiles as a consequence of environmental factors was also analyzed with focus on the effects of weight loss and infections.

CONCLUSIONS

We show that the adult blood levels of many proteins are determined at birth by genetics, which is important for efforts aimed to understand the relationship between plasma proteome profiles and human biology and disease.

A Functional Synonymous Variant in PDGFRA Is Associated with Better Survival in Acral Melanoma

Purpose: Polymorphisms of genes in the platelet-derived growth factor (PDGF) signaling pathway have been found to predict cutaneous melanoma (CM) survival, but their clinical effects in acral melanoma (AM) patients have not been explored. The aim of this study was to characterize the functional effect of the tag single-nucleotide polymorphism (SNP) rs2228230:C>T and assess its association with clinical outcomes in AM patients.

Methods: The effect of rs2228230:C>T on mRNA structures and codon usage values were evaluated using in silico analyses. PDGF receptor alpha (PDGFRA) expression vectors with the rs2228230:C or rs2228230:T allele were constructed to evaluate the expression and signaling activity of PDGFRA. The expression of PDGFRA in AM samples was measured using in situ RNAscope hybridization and immunohistochemical staining. The association of the rs2228230 genotype with survival was analyzed in two independent AM cohorts.

Results: In silico analyses indicated that the rs2228230:T allele increases the minimum free energy and reduces synonymous codon usage. The rs2228230:T allele decreased the expression of PDGFRA by reducing the stability of its mRNA and protein as well as the signaling activity of the MAPK and PI3K/AKT pathways. PDGFRA mRNA and protein expression was significantly reduced in AM tissues with the rs2228230:T allele. The progression-free survival and overall survival of AM patients with the rs2228230:T allele were significantly longer than those of patients with the CC genotype.

Conclusion: Our study indicated that rs2228230:T can reduce the expression of PDGFRA and downstream signaling activity and is associated with better survival in AM patients.

Genetic interactions between ANLN and KDR are prognostic for breast cancer survival

Single nucleotide polymorphisms (SNPs) are the most common genetic variation in mammalian cells with prognostic potential. Anillin-actin binding protein (ANLN) has been identified as being involved in PI3K/PTEN signaling, which is critical in cell life/death control, and kinase insert domain receptor (KDR) encodes a key receptor mediating the cancer angiogenesis/metastasis switch. Knowledge of the intrinsic connections between PI3K/PTEN and KDR signaling, which represent two critical transitions in carcinogenesis, led the present study to investigate the effects of the potential synergy between ANLN and KDR on breast cancer outcome and identify relevant SNPs driving such a synergy at the genetic level. The survival associations of SNPs from KDR and ANLN were assessed through pairwise interaction survival analysis, quantitative trait loci analysis, pathway enrichment analysis and network construction, and the interactions between ANLN and KDR were validated in vitro. It was found that both rare homozygotes in the ANLN:rs12535394 and KDR:rs11133360 SNP pair are prognostic of favorable breast cancer survival and underpin the prominent roles of the immune response in cancer state control. This study contributes to breast cancer prognosis and therapeutic design by providing genetic evidence of interactions between ANLN and KDR, and suggesting the prominent role of the immune response in driving the synergies between the cancer cell life/death and angiogenesis/metastasis transitions during carcinogenesis.

The evolving role of cytoreductive nephrectomy: incorporating genomics of metastatic renal cell carcinoma into treatment decisions

PURPOSE OF REVIEW

Recent publications evaluating cytoreductive nephrectomy in the era of targeted therapy emphasize the importance of patient selection. We reviewed the predictive role of genetic alterations in patients with metastatic renal cell carcinoma (mRCC) undergoing cytoreductive nephrectomy.

RECENT FINDINGS

Studies evaluating the association between genetic alterations and outcomes following systemic treatment for mRCC include mainly patients after cytoreductive nephrectomy. Expression of proangiogenic genes, single nucleotide polymorphisms involving genes of the vascular-endothelial growth factor (VEGF) pathway and somatic mutations of chromatin remodeling genes were associated with response to VEGF-targeted therapy. Outcomes following treatment with mammalian target of rapamycin (mTOR) inhibitors were initially associated with mTOR/TSC1/TSC2 mutations; however, subsequent studies did not validate these findings but rather found an association between loss of PTEN expression and PBRM1 mutations and improved outcomes. Loss of PBRM1 was initially linked to response to immunotherapy; however, larger studies question this association and showed high expression of T-effector gene signature predicted improved outcome. Primary tumors with low intratumor heterogeneity but elevated somatic copy-number alterations were associated with rapid progression at multiple sites.

SUMMARY

Genetic alterations may help select patients for cytoreductive nephrectomy and optimize timing of treatment. Intratumor heterogeneity and genetic discordance between primary and metastatic tumors may limit clinical applicability. Future studies should evaluate approaches to overcome these limitations.