A novel hotspot and rare somatic mutation p.A138V, at TP53 is associated with poor survival of pancreatic ductal and periampullary adenocarcinoma patients

Identification of KCNJ5 gene an adverse prognosis associated novel onco-ionchannel in Indian pancreatic cancer cohort

BACKGROUND

Pancreatic cancer (PanCa) is one of the most lethal cancers (survival ~ 12%). As the conventional therapeutic interventions are mostly futile, a deep understanding of the disease pathophysiology is an urgent need. Ion channels, located on cell membrane, contribute significantly to cancer hallmarks, through dysregulation of various ion translocation; however, the fundamental mechanisms remain uncertain.

METHODS

To identify these oncochannels in Indian cohort of PanCa, we utilized 450 K data, published in our previous study, and identified potential pathways involved. Their expressions were evaluated using TCGA data and an independent Indian paired patient cohort (n = 20). The top genes were further validated using GEO and ScRNA seq dataset. Potential target ability of KCNJ5 was identified through molecular dynamic based drug designing.

RESULTS

A set of 7 differentially methylated and differentially expressed genes of ion-channel proteins namely KCNJ5, CACNB2, KCNA3, KCNA6, RASA3, GABBR2 and CLIC5 were identified in Indian PanCa cohort only. KCNJ5 was significantly upregulated and associated with worse survival in Indian cohort, whereas downregulated in TCGA and other Caucasians patient populations. Two TFs controlling the KCNJ5 expression are POU2F1 and POU3F1. Few predicted small molecules targeting Kcnj5 are, Amiloride, Vernakalant hydrochloride, Dalfampridine, Glyburide and Levcromakalim. It also showed notable interactions with a steroidal anticancer agent, protodioscin.

CONCLUSION

An onco-channel gene, KCNJ5 significantly upregulated, and showing adverse survival in highly expressed KCNJ5 group in Indian cohort of PanCa, can be targeted with Amiloride, Vernakalant hydrochloride, Dalfampridine, Glyburide Levcromakalim and protodioscin. This understanding can lead to novel target identification for PanCa therapy development.

From experimental studies to computational approaches: recent trends in designing novel therapeutics for amyloidogenesis

Amyloidosis is a condition marked by misfolded proteins that build up in tissues and eventually destroy organs. It has been connected to a number of fatal illnesses, including non-neuropathic and neurodegenerative conditions, which in turn have a significant influence on the worldwide health sector. The inability to identify the underlying etiology of amyloidosis has hampered efforts to find a treatment for the condition. Despite the identification of a multitude of putative pathogenic variables that may operate independently or in combination, the molecular mechanisms responsible for the development and progression of the disease remain unclear. A thorough investigation into protein aggregation and the impacts of toxic aggregated species will help to clarify the cytotoxicity of aggregation-mediated cellular apoptosis and lay the groundwork for future studies aimed at creating effective treatments and medications. This review article provides a thorough summary of the combination of various experimental and computational approaches to modulate amyloid aggregation. Further, an overview of the latest developments of novel therapeutic agents is given, along with a discussion of the possible obstacles and viewpoints on this developing field. We believe that the information provided by this review will help scientists create innovative treatment strategies that affect the way proteins aggregate.

Utility of Polygenic Risk Scores (PRSs) in Predicting Pancreatic Cancer: A Systematic Review and Meta-Analysis of Common-Variant and Mixed Scores with Insights into Rare Variant Analysis

Pancreatic adenocarcinoma is the most common histological subtype of pancreatic cancer, representing approximately 85% of all cases [...].

Mutant Pattern of p53 as a Feasible Predictor of Distant Metastasis Following Curative Gastrectomy for Advanced-stage Gastric Cancer

Objective: The TP53 mutation is a poor prognostic factor for malignant tumors in a number of organs. The present study primarily aimed to clarify the impact of the mutant pattern of p53 on the prognosis and recurrence of gastric cancer. Methods: For this purpose, 519 patients who underwent radical gastrectomy for cancer were enrolled in the present study. Immunohistochemistry (IHC) was used to examine p53 expression in tissues and a three-stage classification system was used to divide the patient tissues into three groups according to the expression of p53: Heterogeneous (wild-type), absent and overexpression (mutant). Results: After 5 years of follow-up, recurrence and metastasis occurred in 38.7% of patients with stomach cancer, with a p53 mutant pattern in 48.4% of these patients. Patients with a p53 mutant pattern had lower recurrence-free and overall survival rates at 5 years compared with those who were p53 wild-type (P<0.001). It was found that the p53 pattern differed significantly (P<0.001) between the wild-type and mutant patterns, including the pN0 and pN+ gastric cancer subgroups (P<0.001 and P=0.014, respectively). The p53 mutant pattern was also significant in the determination of the recurrence-free survival of patients with progressive stomach cancer (P<0.0001). The 5-year overall survival rates were 71.7 and 36.2%, and the recurrence-free survival rates were 71.2 and 35.2% in the pN0 and pN+ groups, respectively (P<0.001). The mutant pattern of p53 was a significant prognostic factor for both distant metastasis [relative risk (RR)=2.881, P<0.001] and overall survival (RR=2.809, P<0.001) in the univariate Cox regression analysis. In the multivariate analysis, distant metastasis (RR=2.767, P<0.001) remained significant in the mutant pattern of p53 staining. After propensity score matching, 189 patients with a p53 wild-type and 189 patients with a p53 mutant pattern were extracted for analysis. The 5-year overall survival rate in patients with the p53 mutant pattern (n = 189) was worse than that in the patients with p53 wild-type (n = 189) and with significant differences (log-rank P<0.01). The study was statistically significant after Cox univariate and multivariate regression analysis, which revealed that the mutant pattern of p53 is an independent prognostic factor impacting distant metastases following curative gastrectomy for advanced-stage gastric cancer (p = 0.48).

Oncometabolites in pancreatic cancer: Strategies and its implications

Pancreatic cancer (PanCa) is a catastrophic disease, being third lethal in both the genders around the globe. The possible reasons are extreme disease invasiveness, highly fibrotic and desmoplastic stroma, dearth of confirmatory diagnostic approaches and resistance to chemotherapeutics. This inimitable tumor microenvironment (TME) or desmoplasia with excessive extracellular matrix accumulation, create an extremely hypovascular, hypoxic and nutrient-deficient zone inside the tumor. To survive, grow and proliferate in such tough TME, pancreatic tumor and stromal cells transform their metabolism. Transformed glucose, glutamine, fat, nucleotide metabolism and inter-metabolite communication between tumor and TME in synergism, impart therapy resistance, and immunosuppression in PanCa. Thus, a finer knowledge of altered metabolism would uncover its metabolic susceptibilities. These unique metabolic targets may help to device novel diagnostic/prognostic markers and therapeutic strategies for better management of PanCa. In this review, we sum up reshaped metabolic pathways in PanCa to formulate detection and remedial strategies of this devastating disease.

Combining evolution and protein language models for an interpretable cancer driver mutation prediction with D2Deep

The mutations driving cancer are being increasingly exposed through tumor-specific genomic data. However, differentiating between cancer-causing driver mutations and random passenger mutations remains challenging. State-of-the-art homology-based predictors contain built-in biases and are often ill-suited to the intricacies of cancer biology. Protein language models have successfully addressed various biological problems but have not yet been tested on the challenging task of cancer driver mutation prediction at a large scale. Additionally, they often fail to offer result interpretation, hindering their effective use in clinical settings. The AI-based D2Deep method we introduce here addresses these challenges by combining two powerful elements: (i) a nonspecialized protein language model that captures the makeup of all protein sequences and (ii) protein-specific evolutionary information that encompasses functional requirements for a particular protein. D2Deep relies exclusively on sequence information, outperforms state-of-the-art predictors, and captures intricate epistatic changes throughout the protein caused by mutations. These epistatic changes correlate with known mutations in the clinical setting and can be used for the interpretation of results. The model is trained on a balanced, somatic training set and so effectively mitigates biases related to hotspot mutations compared to state-of-the-art techniques. The versatility of D2Deep is illustrated by its performance on non-cancer mutation prediction, where most variants still lack known consequences. D2Deep predictions and confidence scores are available via https://tumorscope.be/d2deep to help with clinical interpretation and mutation prioritization.

Understanding the Genetic Landscape of Pancreatic Ductal Adenocarcinoma to Support Personalized Medicine: A Systematic Review

Pancreatic ductal adenocarcinoma (PDAC) is one of the most fatal malignancies worldwide. While population-wide screening recommendations for PDAC in asymptomatic individuals are not achievable due to its relatively low incidence, pancreatic cancer surveillance programs are recommended for patients with germline causative variants in PDAC susceptibility genes or a strong family history. In this study, we sought to determine the prevalence and significance of germline alterations in major genes (ATM, BRCA1, BRCA2, CDKN2A, EPCAM, MLH1, MSH2, MSH6, PALB2, PMS2, STK11, TP53) involved in PDAC susceptibility. We performed a systematic review of PubMed publications reporting germline variants identified in these genes in PDAC patients. Overall, the retrieved articles included 1493 PDAC patients. A high proportion of these patients (n = 1225/1493, 82%) were found to harbor alterations in genes (ATM, BRCA1, BRCA2, PALB2) involved in the homologous recombination repair (HRR) pathway. Specifically, the remaining PDAC patients were reported to carry alterations in genes playing a role in other cancer pathways (CDKN2A, STK11, TP53; n = 181/1493, 12.1%) or in the mismatch repair (MMR) pathway (MLH1, MSH2, MSH6, PMS2; n = 87/1493, 5.8%). Our findings highlight the importance of germline genetic characterization in PDAC patients for better personalized targeted therapies, clinical management, and surveillance.

Loss of fragile WWOX gene leads to senescence escape and genome instability

Induction of DNA damage response (DDR) to ensure accurate duplication of genetic information is crucial for maintaining genome integrity during DNA replication. Cellular senescence is a DDR mechanism that prevents the proliferation of cells with damaged DNA to avoid mitotic anomalies and inheritance of the damage over cell generations. Human WWOX gene resides within a common fragile site FRA16D that is preferentially prone to form breaks on metaphase chromosome upon replication stress. We report here that primary Wwox knockout (Wwox-/-) mouse embryonic fibroblasts (MEFs) and WWOX-knockdown human dermal fibroblasts failed to undergo replication-induced cellular senescence after multiple passages in vitro. Strikingly, by greater than 20 passages, accelerated cell cycle progression and increased apoptosis occurred in these late-passage Wwox-/- MEFs. These cells exhibited γH2AX upregulation and microsatellite instability, indicating massive accumulation of nuclear DNA lesions. Ultraviolet radiation-induced premature senescence was also blocked by WWOX knockdown in human HEK293T cells. Mechanistically, overproduction of cytosolic reactive oxygen species caused p16Ink4a promoter hypermethylation, aberrant p53/p21Cip1/Waf1 signaling axis and accelerated p27Kip1 protein degradation, thereby leading to the failure of senescence induction in Wwox-deficient cells after serial passage in culture. We determined that significantly reduced protein stability or loss-of-function A135P/V213G mutations in the DNA-binding domain of p53 caused defective induction of p21Cip1/Waf1 in late-passage Wwox-/- MEFs. Treatment of N-acetyl-L-cysteine prevented downregulation of cyclin-dependent kinase inhibitors and induced senescence in Wwox-/- MEFs. Our findings support an important role for fragile WWOX gene in inducing cellular senescence for maintaining genome integrity during DDR through alleviating oxidative stress.

Deoxyribonucleic acid methylation driven aberrations in pancreatic cancer-related pathways

Pancreatic cancer (PanCa) presents a catastrophic disease with poor overall survival at advanced stages, with immediate requirement of new and effective treatment options. Besides genetic mutations, epigenetic dysregulation of signaling pathway-associated enriched genes are considered as novel therapeutic target. Mechanisms beneath the deoxyribonucleic acid methylation and its utility in developing of epi-drugs in PanCa are under trails. Combinations of epigenetic medicines with conventional cytotoxic treatments or targeted therapy are promising options to improving the dismal response and survival rate of PanCa patients. Recent studies have identified potentially valid pathways that support the prediction that future PanCa clinical trials will include vigorous testing of epigenomic therapies. Epigenetics thus promises to generate a significant amount of new knowledge of biological and medical importance. Our review could identify various components of epigenetic mechanisms known to be involved in the initiation and development of pancreatic ductal adenocarcinoma and related precancerous lesions, and novel pharmacological strategies that target these components could potentially lead to breakthroughs. We aim to highlight the possibilities that exist and the potential therapeutic interventions.

Emerging role of non-invasive and liquid biopsy biomarkers in pancreatic cancer

A global increase in the incidence of pancreatic cancer (PanCa) presents a major concern and health burden. The traditional tissue-based diagnostic techniques provided a major way forward for molecular diagnostics; however, they face limitations based on diagnosis-associated difficulties and concerns surrounding tissue availability in the clinical setting. Late disease development with asymptomatic behavior is a drawback in the case of existing diagnostic procedures. The capability of cell free markers in discriminating PanCa from autoimmune pancreatitis and chronic pancreatitis along with other precancerous lesions can be a boon to clinicians. Early-stage diagnosis of PanCa can be achieved only if these biomarkers specifically discriminate the non-carcinogenic disease stage from malignancy with respect to tumor stages. In this review, we comprehensively described the non-invasive disease detection approaches and why these approaches are gaining popularity for their early-stage diagnostic capability and associated clinical feasibility.

Molecular pathways in periampullary cancer: An overview

Molecular alterations in oncogenes and tumor suppressors in various signaling pathways are basis for personalized therapy in cancer. Periampullary carcinoma behaves differently from pancreatic carcinoma both in prognosis and outcome, therefore it needs special attention. Pancreatic cancer have higher incidence of nodal spread and perineural &lymphovascular invasion suggesting it biologically more aggressive tumor compared to periampullary cancer. Since PAC tumors consist of heterogenous tissue of origin, they might contain different mutations in tumor associated genes and other changes in tissue composition among different subgroups clubbed together. Significant progress has been made in understanding the molecular nature of PAC in the previous two decades, and a large number of mutations and other genetic changes have been identified as being responsible for the disease. This review article targets to collate and discuss the molecular evolution of PAC and their implication in its outcome. As per literature, mitogen-activated protein kinase (MAPK), phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K), and Wnt signaling are the most common pathways involved in PAC. Mutations in KRAS, TP53, CTNNB1, SMAD4 and APC genes were the most frequently reported. I-subtype resembles colorectal cancer while the morphology of PB-type shows close resemblance to pancreatic tumors. The frequency of driver gene mutations is higher in I-type compared to PB-type of PAC indicating I-type to be genetically more unstable. The genetic landscape of PAC obtained from WES data highlighted PI3/AKT pathway to be a primary target in I-type and RAS/RAF in PB-type.

DNA methylome in pancreatic cancer identified novel promoter hyper-methylation in NPY and FAIM2 genes associated with poor prognosis in Indian patient cohort

BACKGROUND

Pancreatic ductal adenocarcinoma (PDAC) is one of the leading cancers worldwide and has a poor survival, with a 5-year survival rate of only 8.5%. In this study we investigated altered DNA methylation associated with PDAC severity and prognosis.

METHODS

Methylome data, generated using 450 K bead array, was compared between paired PDAC and normal samples in the TCGA cohort (n = 9) and our Indian cohort (n = 7). The total Indian Cohort (n = 75) was split into cohort 1 (n = 7), cohort 2 (n = 22), cohort 3 (n = 26) and cohort 4 (n = 20).Validation of differential methylation (6 selected CpG loci) and associated gene expression for differentially methylated genes (10 selected gDMs) were carried out in separate validation cohorts, using MSP, RT-PCR and IHC correlations between methylation and gene expression were observed in TCGA, GTEx cohorts and in validation cohorts. Kaplan-Meier survival analysis was done to study differential prognosis, during 2-5 years of follow-up.

RESULTS

We identified 156 DMPs, mapped to 91 genes (gDMs), in PDAC; 68 (43.5%) DMPs were found to be differentially methylated both in TCGA cohort and our cohort, with significant concordance at hypo- and hyper-methylated loci. Enrichments of "regulation of ion transport", "Interferon alpha/beta signalling", "morphogenesis and development" and "transcriptional dysregulation" pathways were observed among 91 gDMs. Hyper-methylation of NPY and FAIM2 genes with down-regulated expression in PDAC, were significantly associated with poor prognosis in the Indian patient cohort.

CONCLUSIONS

Ethnic variations among populations may determine the altered epigenetic landscape in the PDAC patients of the Indian cohort. Our study identified novel differentially methylated genes (mainly NPY and FAIM2) and also validated the previously identified differentially methylated CpG sites associated with PDAC cancer patient's survival. Comparative analysis of our data with TCGA and CPTAC cohorts showed that both NPY and FAIM2 hyper-methylation and down-regulations can be novel epigenetically regulated genes in the Indian patient population, statistically significantly associated with poor survival and advanced tumour stages.