Cancer Genome Research Articles

Translating potential germline findings from tumour profiling into routine clinical care.

105 Background: Tumor molecular profiling (TMP) provides an opportunity to identify heritable cancer predisposition. Molecular Screening and Therapeutics Study (MoST) (8000 patients, 2016-23) and Cancer Screening Program (CaSP) (23000 patients, 2023-25) are Australian research programs providing TMP for therapy matching in advanced cancer. Matched germline testing is resource-inefficient and is not performed . An integrated approach between TMP and cancer genetics is needed to improve familial cancer outcomes through prevention and early detection. Methods: In MoST, potential germline variants (PGV) in actionable cancer genes were investigated in blood DNA in a research setting. Positive cases were informed, and a genetics review for clinical testing recommended. In CaSP, germline follow-up recommendations are included in the Molecular Oncology Board (MOB) Report based on decision algorithms to inform clinicians of PGV needing clinical assessment. Cancer genetics clinics in Australia were surveyed regarding preferences for the return of genetic information from tumor profiling. A centralised precision care clinic was launched in March 2024 to investigate the implementation of returning PGV information from tumor-only profiling. Results: In MoST, 38% (140/367) of PGVs tested were positive in blood DNA. Of these, 44% were identified in the highest actionability genes: BRCA1, BRCA2, PALB2, Lynch Syndrome. The validation and return of results process was unsatisfactory; it was resource-heavy, timeframes were extended, DNA was sometimes unavailable, and communicating information to non-participating relatives of deceased participants was challenging due to a lack of established pathways. The systems design in CaSP has allowed the study to manage higher volume without a net increase in germline workforce. To date, 2372 patients have completed profiling with 173 MOB recommendations for PGV validations. Fifty-four cancer genetics staff nationally responded to the survey. Many (61%) were concerned about the increased uptake of TMP without a workforce to match germline testing demand (97%) and lack of funding assigned in a universal healthcare system (70%) being main concerns. Most (82%) supported a centralised service anticipating improved efficiency gain (71%), equity of access (77%) and streamlining of processes (71%). The stakeholders voiced a consistently high (>50%) demand for information regarding PGV in lower actionability genes. MOB recommendations were adapted to reflect 3 tiers of actionability The centralised clinic has reviewed 21 patients nationally to test 23 highest actionability variants. The average referral to review time is 2 weeks. Conclusions: Precision oncology can play a role in familial cancer prevention. Deliberate collaboration and integration between precision research and relevant specialised care can lead to resource-optimised, equitable delivery of quality care.

Bitter taste receptors as prognostic markers in adrenocortical carcinoma.

230 Background: Adrenocortical carcinoma (ACC) is a rare malignant neoplasm of the adrenal gland. Progressive forms of this cancer carry a dismal prognosis with 5-year survival rates < 40%. As such, predictors of stage progression and prognostic biomarkers are a must. Taste 2 receptors (TAS2Rs) are localized on the surface of bitter receptor cells. Recent evidence has shown their role as prognostic biomarkers in multiple cancers, such as breast, prostate, and head and neck squamous cell carcinoma. The aim of this study was to elucidate the role of TAS2Rs in ACC. Methods: Differentially expressed genes (DEGs) based on high and low expression groups of TAS2R genes were identified through the 'DESeq2' package on R. Subsequent Gene Set Enrichment Analysis (GSEA) was performed using the 'TCGAbiolinks' package on R and Enrichr online tool. Immune infiltration analysis was conducted using TIMER2.0 and CIBERSORT. Survival analysis with an optimal expression cutoff for overall survival (OS) and a median cutoff for disease-free survival (DFS) based on The Cancer Genome Atlas Adrenocortical carcinoma (TCGA-ACC) data was executed using the 'survival' and 'survminer' R packages and GEPIA2 online tool. Results: Analysis of the TCGA-ACC cohort revealed OS estimates that indicated worse survival in patients with higher TAS2R14, TAS2R19, TAS2R20, and TAS2R30 expression (Table). Further analysis produced consistent results, demonstrating that elevated expressions of TAS2R14 and TAS2R19 are correlated with decreased DFS, with Hazard Ratios (HR) of 2.60 (p = 0.0046) and 2.20 (p = 0.022), respectively. Furthermore, the F-test and stage plots have shown consistent upregulation of selected TAS2R genes across stages I–IV (p < 0.05). RNA-seq analysis revealed 1170 common (579 downregulated, 591 upregulated) DEGs between high and low TAS2R14 and TAS2R19 expression groups. GSEA showed upregulated genes in high expressers have relations to hedgehog signaling, epithelial to mesenchymal transition, TGF-B signaling, and organization of the extracellular matrix. On the other hand, down-regulated genes showed functions in metabolic reprogramming, chemokine receptor binding, MHC protein complex, and chemokine-mediated inflammation. GSEA on co-expressed genes showed pathways related to ferroptosis, autolysosome activity, and iron homeostasis and metabolism. Immune infiltration analysis revealed significantly increased CD4+, naïve and plasma B cell infiltration with higher TAS2R14 and TAS2R19 expression (Rho > 0.25, p < 0.05), in addition to increased M1 macrophage infiltration with higher TAS2R19 expression (Rho = 0.28, p < 0.05). Conclusions: TAS2R genes are potentially involved in modulating carcinogenic processes, including stage progression, metastasis and invasion, immune regulation, and metabolic processes. This modulation may explain the poorer prognostic outcomes in ACC patients with elevated TAS2R expression. Further validation in external cohorts is necessary to confirm these results. [Table: see text]

The role of ALDH1A1 in glioblastoma proliferation and invasion

High-grade gliomas, including glioblastoma multiforme (GBM), continue to be a leading aggressive brain tumor in adults, marked by its rapid growth and invasive nature. Aldehyde dehydrogenase 1 family, member A1 (ALDH1A1), an enzyme, plays a significant role in tumor progression, yet its function in high-grade gliomas is still poorly investigated. In this study, we evaluated ALDH1A1 levels in clinical samples of GBM. We also assessed the prognostic significance of ALDH1A1 expression in GBM and LGG (low grade glioma) patients using TCGA (The Cancer Genome Atlas) database analysis. The MTT and transwell assays were utilized to examine cell growth and the invasive capability of U87 cells, respectively. We quantitatively examined markers for cell proliferation (Ki-67 and cyclin D1) and invasion (MMP2 and 9). A Western blot test was conducted to determine the downstream signaling of ALDH1A1. We found a notable increase in ALDH1A1 expression in high-grade gliomas compared to their low-grade counterparts. U87 cells that overexpressed ALDH1A1 showed increased cell growth and invasion. We found that ALDH1A1 promotes the phosphorylation of AKT, and inhibiting AKT phosphorylation mitigates the ALDH1A1's effects on tumor growth and migration. In summary, our findings suggest ALDH1A1 as a potential therapeutic target for GBM treatment.

The impact of HRD mutation on survival in patients with KRAS-mutated advanced pancreatic cancer: A real-world database study.

221 Background: Advanced pancreatic ductal adenocarcinoma (PDAC) is associated with a poor prognosis. Prior studies indicate that homologous repair deficient (HRD+ve) PDAC patients (pts) have improved survival and greater response to platinum agents, but the optimal treatment for these population is still unclear. Here, we evaluate the survival impact of HRD mutations in KRAS-mutated PDAC, which represent 90% of cases, in a real-world setting. Methods: We retrospectively reviewed all pts diagnosed with KRAS-mutated PDAC from Jun 2019 to Dec 2021, who were registered in the Center for Cancer Genomics and Advanced Therapeutics (C-CAT), the cancer registry with comprehensive genomic profiling (CGP) data. Pts were stratified with the presence or absence of HRD mutations identified through Foundation One, including ATM, ATR, BRCA1, BRCA2, BRIP1, CHEK2, FANCA, PALB2, and RAD51. We analyzed the prevalence of co-alterations and the impact of HRD status on survival. Pts with a history of systemic therapy for curative intent were excluded from the survival analysis. Results: In 2251 PDAC cases (HRD+ve 232pts, HRD-ve 2019pts) enrolled, we found that HRD+ve PDAC had a significantly lower incidence of TP53 mutation (p<0.001), CDKN2A mutation (p<0.046), and CDKN2A loss (p<0.046). Survival analysis was performed in 823 pts (HRD+ve 92pts, HRD-ve 731pts). HRD+ve pts had significantly longer overall survival (OS, 28.8m vs 23.5m, P=0.030). In the first line setting, HRD+ve pts had exhibited a markedly extended time-to-treatment failure (TTF; [HRD+ve, 19pts vs. HRD-ve, 177pts]; 7.6m vs. 5.4m; p=0.026) and OS ([HRD+ve, 30pts vs. HRD-ve, 239pts]; 28.8m vs. 23.5m; p=0.019) when treated with mFOLFIRINOX (mFFX), but not when treated with gemcitabine plus nab-paclitaxel (GA; [HRD+ve, 34pts vs. HRD-ve 276pts]; OS, 29.3m vs 26.3m; p=0.34; TTF, 5.2m vs. 5.2m; p=0.80). In the second line setting, there were no differences in TTF between HRD+ve and HRD-ve irrespective of these regimens. Among HRD+ve PDAC pts, pts who having received mFFX tend to have better survival compared to those who did not (46pts vs. 46pts; OS, 31.7m vs 26.3m; p=0.09). Conclusions: Our analysis has identified a unique profile in HRD+ve PDAC, underscoring the importance of platinum-based chemotherapy in the initial treatment to enhance survival, which highlights the practical clinical benefits of routine CGP for pts with KRAS-mutated PDAC.

ExpOmics: a comprehensive web platform empowering biologists with robust multi-omics data analysis capabilities.

High-throughput technologies yield a broad spectrum of multi-omics datasets, which offer unparalleled insights into complex biological systems. However, effectively analyzing this diverse array of data presents challenges, considering factors such as species diversity, data types, costs, and limitations of the available tools. Herein, we present ExpOmics, a comprehensive web platform featuring 7 applications and 4 toolkits, with 28 customizable analysis functions spanning various analyses of differential expression, co-expression, Weighted Gene Co-expression Network Analysis (WGCNA), feature selection, and functional enrichment. ExpOmics allows users to upload and explore multi-omics data without organism restrictions, supporting various expression data, including genes, mRNAs, lncRNAs, miRNAs, circRNAs, piRNAs, and proteins and is compatible with diverse gene nomenclatures and expression values. Moreover, ExpOmics enables users to analyze 22427 transcriptomic datasets of 196 cancer subtypes sourced from 63 projects of The Cancer Genome Atlas Program (TCGA) to identify cancer biomarkers. The analysis results from ExpOmics are presented in high-quality graphical formats suitable for publication and are available for free download. A case study using ExpOmics identified two potential oncogenes, SERPINE1 and SLC43A1, that may regulate colorectal cancer through distinct biological processes. In summary, ExpOmics can serves as a robust platform for global researchers to explore multi-omics data, gain biological insights, and formulate testable hypotheses. ExpOmics is available at http://www.biomedical-web.com/expomics.

MUL1 identified as mitochondria-linked biomarker promoting cisplatin resistance in OC cells

Ovarian cancer (OC) ranks among the prevalent tumors affecting the female reproductive system. The aim of this study was to evaluate mitochondria-associated platinum resistance genes using organoid models. Univariate Cox regression, LASSO and multivariate Cox regression analyses were performed on The Cancer Genome Atlas (TCGA) database to construct 2-gene prognostic signature (MUL1 and SSBP1), and GSE26712 dataset was used for external validation. In addition, the relationship between MUL1 and platinum resistance was examined by organoid culture, lentiviral transduction, CCK8 assay, and Western blot. The results showed that patients in the high-risk group exhibited significantly worse OS (P = 0.002, P = 0.017). Drug sensitivity analysis revealed that platinum resistance increased with the upregulation of MUL1 expression (Cor = 0.5154, P = 0.02). Our experimental findings demonstrated that knockout of the MUL1 gene significantly increased apoptosis and enhanced the sensitivity of the OC cell line A2780 to cisplatin. Through this study, we have provided strong evidence for further research on prognostic risk factors and individualized treatment in OC patients, and provided new insights into addressing platinum resistance in OC.

Cancer genetics and deep learning applications for diagnosis, prognosis, and categorization

Cancer genetics and deep learning applications for diagnosis, prognosis, and categorization

Genomic landscape of hepatocellular carcinoma in Egyptian patients by whole exome sequencing

BackgroundHepatocellular carcinoma (HCC) is the most common primary liver cancer. Chronic hepatitis and liver cirrhosis lead to accumulation of genetic alterations driving HCC pathogenesis. This study is designed to explore genomic landscape of HCC in Egyptian patients by whole exome sequencing.MethodsWhole exome sequencing using Ion Torrent was done on 13 HCC patients, who underwent surgical intervention (7 patients underwent living donor liver transplantation (LDLT) and 6 patients had surgical resection}.ResultsMutational signature was mostly S1, S5, S6, and S12 in HCC. Analysis of highly mutated genes in both HCC and Non-HCC revealed the presence of highly mutated genes in HCC (AHNAK2, MUC6, MUC16, TTN, ZNF17, FLG, MUC12, OBSCN, PDE4DIP, MUC5b, and HYDIN). Among the 26 significantly mutated HCC genes—identified across 10 genome sequencing studies—in addition to TCGA, APOB and RP1L1 showed the highest number of mutations in both HCC and Non-HCC tissues. Tier 1, Tier 2 variants in TCGA SMGs in HCC and Non-HCC (TP53, PIK3CA, CDKN2A, and BAP1). Cancer Genome Landscape analysis revealed Tier 1 and Tier 2 variants in HCC (MSH2) and in Non-HCC (KMT2D and ATM). For KEGG analysis, the significantly annotated clusters in HCC were Notch signaling, Wnt signaling, PI3K-AKT pathway, Hippo signaling, Apelin signaling, Hedgehog (Hh) signaling, and MAPK signaling, in addition to ECM-receptor interaction, focal adhesion, and calcium signaling. Tier 1 and Tier 2 variants KIT, KMT2D, NOTCH1, KMT2C, PIK3CA, KIT, SMARCA4, ATM, PTEN, MSH2, and PTCH1 were low frequency variants in both HCC and Non-HCC.ConclusionOur results are in accordance with previous studies in HCC regarding highly mutated genes, TCGA and specifically enriched pathways in HCC. Analysis for clinical interpretation of variants revealed the presence of Tier 1 and Tier 2 variants that represent potential clinically actionable targets. The use of sequencing techniques to detect structural variants and novel techniques as single cell sequencing together with multiomics transcriptomics, metagenomics will integrate the molecular pathogenesis of HCC in Egyptian patients.

Genetic Analysis of Melanoma Types Using Japanese Genomic Database.

The purpose of this study is to compare genetic mutations, tumor mutation burden (TMB), and the effects of molecular targeted drugs and immune checkpoint inhibitors (ICIs) in head and neck mucosal melanoma (HNMUM) with those in skin melanoma (SKM) and ocular melanoma (OM). Data were analyzed for 72 consecutive patients with HNMUM, including 366 with SKM and 31 with OM, registered at the Japan National Cancer Center, Center for Cancer Genomics and Advanced Therapeutics (C-CAT) between June 2019 and October 2023. Genetic alterations and TMB were determined by FoundationOne CDx next-generation sequencing. The top 10 mutations in HNMUM were RAD21 (47.2%), NBN (45.8%), MYC (40.3%), LYN (31.9%), NRAS (29.1%), IRF4 (23.6%), DAXX (22.2%), KIT (22.2%), NOTCH3 (20.8%), and DDR1 (19.4%), with 16.6 ± 0.8 (mean ± SEM) mutations/individual. In SKM, BRAF (p = 0.04) mutation was associated with a significantly better prognosis. The TMB values were 5.7 ± 2.1 (mean ± SEM) in HNMUM, 4.1 ± 0.2 in SKM, and 3.4 ± 0.9 in OM, with no significant differences among the three groups. The median survival time for patients with distant metastases was 803 (95% confidence interval: 539-NA) days for HNMUM, 1413 (831-2172) days for SKM, and 1138 (438-NA) days for OM. The top 10 mutations in HNMUM are closer to those in OM than those in SKM. There was no significant difference in TMB values or survival rates with regard to the therapeutic effect of ICIs among the diseases, which suggests that current treatment of HNMUM with ICIs is appropriate. 3 Laryngoscope, 2024.

Decreased sirtuin 4 levels promote cellular proliferation and invasion in papillary thyroid carcinoma.

This study examined the effect of sirtuin 4 (SIRT4), a NAD+-dependent deacetylase, on the proliferation and progression of papillary thyroid carcinoma (PTC). Data from The Cancer Genome Atlas (TCGA) were analyzed to identify SIRT4 expression in thyroid cancer. Subsequently, the correlation between SIRT4 expression and clinical characteristics was examined in 205 PTC tissue samples. In vitro assays using three human thyroid cancer cell lines (B-CPAP, TPC-1, and SNU-790) were conducted to assess the effects of regulated SIRT4 expression on cell growth, apoptosis, invasion, and migration. Furthermore, in vivo experiments were performed in a xenograft mouse model. Gene Expression Omnibus (GEO) and TCGA data indicated that SIRT4 expression is lower in thyroid cancer and SIRT4 downregulation is associated with poor overall survival. In PTC tissues, positive SIRT4 expression was associated with decreased extracapsular extension. In in vitro experiments using three human thyroid cancer cell lines, overexpression of SIRT4 decreased cell survival, clonogenic potential, and invasion and migratory capabilities, as well as inducing apoptosis and increasing reactive oxygen species levels. SIRT4 overexpression upregulated E-cadherin and downregulated N-cadherin, suggesting its potential involvement in the regulation of epithelial-mesenchymal transition. These findings were confirmed in vivo using a xenograft mouse model. This study provides novel insight into the potential contribution of SIRT4 to the regulation of the pathological progression of PTC. The data suggest that SIRT4 plays a tumor-suppressive role in PTC by inhibiting growth, survival, and invasive potential. Future research should investigate the molecular mechanisms underlying these effects of SIRT4.

Molecular and Clinicopathologic Impact of GNAS Variants Across Solid Tumors.

The molecular drivers underlying mucinous tumor pathogenicity are poorly understood. GNAS mutations predict metastatic burden and treatment resistance in mucinous appendiceal adenocarcinoma. We investigated the pan-cancer clinicopathologic relevance of GNAS variants. We assessed 58,043 patients with Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (IMPACT)-sequenced solid tumors to identify oncogenic variants, including GNAS, associated with mucinous tumor phenotype. We then performed comprehensive molecular analyses to compare GNAS-mutant (mut) and wild-type tumors across cancers. Gene expression patterns associated with GNAS-mut tumors were assessed in a The Cancer Genome Atlas cohort. Associations between GNAS variant status and peritoneal metastasis, first-line systemic therapy response, progression-free survival (PFS), and overall survival (OS) were determined using a propensity-matched subcohort of patients with metastatic disease. Mucinous tumors were enriched for oncogenic GNAS variants. GNAS was mutated in >1% of small bowel, cervical, colorectal, pancreatic, esophagogastric, hepatobiliary, and GI neuroendocrine cancers. Across these cancers, GNAS-mut tumors exhibited a generally conserved C-to-T mutation-high, aneuploidy-low molecular profile with co-occurring prevalent KRAS variants (65% of GNAS-mut tumors) and fewer TP53 alterations. GNAS-mut tumors exhibited recurrently comutated alternative tumor suppressors (RBM10, INPPL1) and upregulation of MAPK and cell surface modulators. GNAS-mut tumors demonstrate an increased prevalence of peritoneal metastases (odds ratio [OR], 1.7 [95% CI, 1.1 to 2.5]; P = .006), worse response to first-line systemic therapy (OR, 2.2 [95% CI, 1.3 to 3.8]; P = .003), and shorter PFS (median, 5.6 v 7.0 months; P = .047). In a multivariable analysis, GNAS mutated status was independently prognostic of worse OS (hazard ratio, 1.25 [95% CI, 1.01 to 1.56]; adjusted P = .04). Across the assessed cancers, GNAS-mut tumors exhibit a conserved molecular and clinical phenotype defined by mucinous tumor status, increased peritoneal metastasis, poor response to first-line systemic therapy, and worse survival.

Loss of Lkb1 cooperates with BrafV600E and ultraviolet radiation, increasing melanoma multiplicity and neural-like dedifferentiation.

The mechanisms that work alongside BRAFV600E oncogene in melanoma development, in addition to ultraviolet (UV) radiation (UVR), are of great interest. Analysis of human melanoma tumors [data from The Cancer Genome Atlas (TCGA)] revealed that 50% or more of the samples expressed no or low amounts of serine/threonine protein kinase STK11 (also known as LKB1) protein. Here, we report that, in a mouse model, concomitant neonatal BrafV600E activation and Lkb1 tumor suppressor ablation in melanocytes led to full melanoma development. A single postnatal dose of UVB radiation had no effect on melanoma onset in Lkb1-depleted mice compared with BrafV600E-irradiated mice, but increased tumor multiplicity. In concordance with these findings and previous reports, Lkb1-null irradiated mice exhibited deficient DNA damage repair (DDR). Histologically, tumors lacking Lkb1 were enriched in neural-like tumor morphology. Genetic profiling and gene set enrichment analyses of tumor sample mutated genes indicated that loss of Lkb1 promoted the selection of altered genes associated with neural differentiation processes. Thus, these results suggest that the loss of Lkb1 cooperates with BrafV600E and UVR, impairing the DDR and increasing melanoma multiplicity and neural-like dedifferentiation.

A metabolic reprogramming-related gene signature correlates with prognosis and proliferation of BLCA

Bladder cancer (BLCA) is one of the most frequent urothelium carcinoma, but with poor prognosis due to lack of reliable predictive biomarkers. Metabolic reprogramming involving in various nutrients, and is reported to be closely associated with malignant progression in BLCA. With the use of transcriptome sequencing data profiles of 349 patients from The Cancer Genome Atlas, we established a three-gene glycolysis-related signature to predict the prognosis of BLCA patients. Our signature constructed on the basis of AK3, GALK1 and NUP205 expression, detail features and interactions between these three genes were further explored. We established a nomogram by integrating clinical variables and the risk score. Glycolytic level and proliferation ability were detected to study the role and mechanisms of NUP205 on BLCA. The connections between three genes in our signature were independent. We found our signature gains more value for patients with highly malignant stage. The established nomogram also confirmed that the signature had a eligible clinically predict capacity. After inhibited NUP205 expression, we found the glycolysis level of BLCA cells decreased and proliferation ability suppressed, mainly through AMPK signaling pathway inactivation. Collectively, our study explored a three-gene glycolysis-related signature that predict the prognosis of patients with BLCA, and highlights NUP205 as a potential therapeutic target for inhibiting glycolytic processes and proliferation in BLCA cells.

Identification of RBM15 as a prognostic biomarker in prostate cancer involving the regulation of prognostic m6A-related lncRNAs

BackgroundLong noncoding RNAs (lncRNAs) and N6-methyladenosine (m6A) modification of RNA play pivotal roles in tumorigenesis and cancer progression. However, knowledge regarding the expression patterns of m6A-related lncRNAs and their corresponding m6A regulators in prostate cancer (PCa) is limited. This study aimed to delineate the landscape of m6A-related lncRNAs, develop a predictive model, and identify the critical m6A regulators of prognostic lncRNAs in PCa.MethodsClinical and transcriptome data of PCa patients were downloaded from The Cancer Genome Atlas (TCGA) database. Prognostic m6A-related lncRNAs were subsequently identified through Pearson correlation and univariate Cox regression analyses. The prognostic lncRNAs were clustered into two groups by consensus clustering analysis, and a risk signature model was constructed using least absolute shrinkage and selection operator (LASSO) regression analysis of the lncRNAs. This model was evaluated using survival, clinicopathological, and immunological analyses. Furthermore, based on the constructed lncRNA-m6A regulatory network and RT-qPCR results, RBM15 was identified as a critical regulator of m6A-related lncRNAs. The biological roles of RBM15 in PCa were explored through bioinformatics analysis and biological experiments.ResultsThirty-four prognostic m6A-related lncRNAs were identified and categorized into two clusters with different expression patterns and survival outcomes in PCa patients. Seven m6A lncRNAs (AC105345.1, AL354989.1, AC138028.4, AC022211.1, AC020558.2, AC004076.2, and LINC02666) were selected to construct a risk signature with robust predictive ability for overall survival and were correlated with clinicopathological characteristics and the immune microenvironment of PCa patients. Among them, LINC02666 and AC022211.1 were regulated by RBM15. In addition, RBM15 expression correlated with PCa progression, survival, and the immune response. Patients with elevated RBM15 expression were more susceptible to the drug AMG-232. Moreover, silencing RBM15 decreased the viability of PCa cells and promoted apoptosis.ConclusionRBM15 is involved in the regulation of prognostic lncRNAs in the risk signature and has a robust predictive ability for PCa, making it a promising biomarker in PCa.

Glycolysis-related genes predict prognosis and indicate immune microenvironment features in gastric cancer.

Gastric cancer (GC) is a major contributor to cancer-related mortality. Glycolysis plays a pivotal role in tumor microenvironment (TME) reprogramming. In this research, the functions of glycolysis-associated genes (GRGs) were evaluated to predict the outcome and reveal the characteristics of the immune microenvironment in individuals with stomach cancer. The Cancer Genome Atlas (TCGA)-stomach adenocarcinoma (STAD) cohort provided gene expression and clinical data for gastric cancer (GC) patients, which were further authenticated using datasets sourced from the Gene Expression Omnibus (GEO). By referencing the Molecular Signatures Database (MSigDB), a total of 326 GRGs were pinpointed. The various subtypes of GC were outlined through consensus clustering, derived from the expression patterns of these GRGs. Utilizing multivariate Cox regression analysis, a multigene risk score model was formulated. Both the CIBERSORT and ESTIMATE algorithms played a pivotal role in assessing the immune microenvironment. To delve into the biological functions of the key genes, wound healing, transwell invasion, and MTT assays were conducted. Based on the expression patterns of GRGs, patients were categorized into two distinct groups: the metabolic subtype, designated as cluster A, and the immune subtype, labeled as cluster B. Patients belonging to cluster B exhibited a poorer prognosis. A prognostic risk score model, formulated upon the expression levels of six key GRGs - ME1, PLOD2, NUP50, CXCR4, SLC35A3, and SRD35A3 - emerged as a viable tool for predicting patient outcomes. The downregulation of CXCR4 notably diminished the glycolytic capacity of gastric cancer (GC) cells, alongside their migratory, invasive, and proliferative capabilities. Intriguingly, despite the adverse prognostic implications associated with both the immune subtype (cluster B) and the high-risk cohort, these groups exhibited a favorable immune microenvironment coupled with elevated expression of immune checkpoint genes. Our investigations revealed a positive correlation between high CXCR4 expression and low ME1 expression with the infiltration of CD8+ T cells, as well as an enhanced responsiveness to treatment with an anti-PD-1 immune checkpoint inhibitor. In this study, we discovered that the expression profiles of GRGs hold the potential to forecast the prognosis of gastric cancer (GC) patients, thereby possibly aiding in clinical treatment decision-making.

Late-onset tumors in rhabdoid tumor predisposition syndrome type-1 (RTPS1) and implications for surveillance.

Rhabdoid tumor predisposition syndrome type-1 (RTPS1) is characterized by germline pathogenic variants in SMARCB1 and development of INI1-deficient rhabdoid tumors in early childhood. Due to its poor prognosis, the risk of subsequent tumor development and the impact of surveillance at later ages are poorly understood. We retrospectively reviewed individuals referred to the Cancer Genetics Program at The Hospital for Sick Children for SMARCB1 genetic testing and/or surveillance for RTPS1. In addition, to explore characteristics of late-onset tumors in RTPS1, a literature review was conducted. Of eighty-three individuals (55 probands and 28 family members), 12 probands and 4 family members were genetically confirmed with RTPS1. Four pediatric probands with RTPS1 underwent surveillance. An additional three individuals, including one patient with 22q11.2 distal deletion without history of tumor, one patient with negative genetic testing results but clinically diagnosed with RTPS1, and one sibling identified through cascade testing, underwent surveillance. Three patients with RTPS1 developed tumors between the ages of 9 and 17, including malignant rhabdoid tumors (N = 3), schwannomas (N = 4), and epithelioid malignant peripheral nerve sheath tumor (N = 1). Three of these lesions were asymptomatically detected by surveillance. A literature review revealed 17 individuals with RTPS1 who developed INI1-deficient tumors after age five. Individuals with RTPS1 remain at elevated risk for developing INI1-deficient tumors after the peak age of rhabdoid tumor in early childhood. Extension of surveillance beyond 5 years of age could lead to improved survival and reduced morbidity for these patients, and prospective evaluation of revised approaches will be important.

Prognostic genome and transcriptome signatures in colorectal cancers

Colorectal cancer is caused by a sequence of somatic genomic alterations affecting driver genes in core cancer pathways1. Here, to understand the functional and prognostic impact of cancer-causing somatic mutations, we analysed the whole genomes and transcriptomes of 1,063 primary colorectal cancers in a population-based cohort with long-term follow-up. From the 96 mutated driver genes, 9 were not previously implicated in colorectal cancer and 24 had not been linked to any cancer. Two distinct patterns of pathway co-mutations were observed, timing analyses identified nine early and three late driver gene mutations, and several signatures of colorectal-cancer-specific mutational processes were identified. Mutations in WNT, EGFR and TGFβ pathway genes, the mitochondrial CYB gene and 3 regulatory elements along with 21 copy-number variations and the COSMIC SBS44 signature correlated with survival. Gene expression classification yielded five prognostic subtypes with distinct molecular features, in part explained by underlying genomic alterations. Microsatellite-instable tumours divided into two classes with different levels of hypoxia and infiltration of immune and stromal cells. To our knowledge, this study constitutes the largest integrated genome and transcriptome analysis of colorectal cancer, and interlinks mutations, gene expression and patient outcomes. The identification of prognostic mutations and expression subtypes can guide future efforts to individualize colorectal cancer therapy.

ExomiRHub: A comprehensive database for hosting and analyzing human disease-related extracellular microRNA transcriptomics data

Extracellular microRNA (miRNA) expression data generated by different laboratories exhibit heterogeneity, which poses challenges for biologists without bioinformatics expertise. To address this, we introduce ExomiRHub (http://www.biomedical-web.com/exomirhub/), a user-friendly database designed for biologists. This database incorporates 191 human extracellular miRNA expression datasets associated with 112 disease phenotypes, 62 treatments, and 24 genotypes, encompassing 29,198 and 23 sample types. ExomiRHub also integrates 16,012 miRNA transcriptomes of 156 cancer subtypes from The Cancer Genome Atlas. All the data in ExomiRHub were further standardized and curated with annotations. The platform offers 25 analytical functions, including differential expression, co-expression, Weighted Gene Co-Expression Network Analysis (WGCNA), feature selection, and functional enrichment, enabling users to select samples, define groups, and customize parameters for analyses. Moreover, ExomiRHub provides a web service that allows biologists to analyze their uploaded miRNA expression data. Four additional tools were developed to evaluate the functions and targets of miRNAs and miRNA variations. Through ExomiRHub, we identified extracellular miRNA biomarkers associated with angiogenesis for monitoring glioma progression, demonstrating its potential to significantly accelerate the discovery of extracellular miRNA biomarkers.

Discovery of an 8-oxoguanine regulator PCBP1 inhibitor by virtual screening and its synergistic effects with ROS-modulating agents in pancreatic cancer.

Introduction: Drugs that target reactive oxygen species (ROS) metabolism have progressed the treatment of pancreatic cancer treatment, yet their efficacy remains poor because of the adaptation of cancer cells to high concentration of ROS. Cells cope with ROS by recognizing 8-oxoguanine residues and processing severely oxidized RNA, which make it feasible to improve the efficacy of ROS-modulating drugs in pancreatic cancer by targeting 8-oxoguanine regulators. Methods: Poly(rC)-binding protein 1 (PCBP1) was identified as a potential oncogene in pancreatic cancer through datasets of The Cancer Genome Atlas (TCGA) project and Gene Expression Omnibus (GEO). High-throughput virtual screening was used to screen out potential inhibitors for PCBP1. Computational molecular dynamics simulations was used to verify the stable interaction between the two compounds and PCBP1 and their structure-activity relationships. In vitro experiments were performed for functional validation of silychristin. Results: In this study, we identified PCBP1 as a potential oncogene in pancreatic cancer. By applying high-throughput virtual screening, we identified Compound 102 and Compound 934 (silychristin) as potential PCBP1 inhibitors. Computational molecular dynamics simulations and virtual alanine mutagenesis verified the structure-activity correlation between PCBP1 and the two identified compounds. These two compounds interfere with the PCBP1-RNA interaction and impair the ability of PCBP1 to process RNA, leading to intracellular R loop accumulation. Compound 934 synergized with ROS agent hydrogen peroxide to strongly improve induced cell death in pancreatic cancer cells. Discussion: Our results provide valuable insights into the development of drugs that target PCBP1 and identified promising synergistic agents for ROS-modulating drugs in pancreatic cancer.

Association of Inflammation and Immune Cell Infiltration with Estrogen Receptor Alpha in an Estrogen and Ionizing Radiation-Induced Breast Cancer Model.

Breast cancer is the most diagnosed cancer in the world, and it is the primary cause of cancer death for women. The risk of breast cancer is increased by endogenous factors like hormones and exogenous factors like radiation exposure that causes damage to the mammary epithelial cells leading to an inflammatory response. Chronic inflammation creates a microenvironment composed of, among other factors, chemokines, and interleukins, which promote cancer. The gene expression of the interleukin 1 receptor type 1, the interleukin 1 receptor antagonist, the Interleukin 1 Receptor Accessory Protein, the interleukin 6 cytokine family signal transducer, the C-X-C motif chemokine ligand 3, the C-X-C motif chemokine ligand 5, and the C-X-C motif chemokine ligand 6 were analyzed in an estrogen and radiation experimental breast cancer model. Furthermore, the expression of these genes was correlated with immune cell infiltration, estrogen receptor expression, and their clinical relevance in breast cancer patients based on data provided by The Cancer Genome Atlas database online. Results given by the experimental breast cancer model showed that all genes related to inflammation respond to ionizing radiation alone or in combination with estrogen. On the other hand, the immune response depended on the breast cancer type and on the expression of the gene that encoded the estrogen receptor. Finally, the importance of the expression of these genes in breast cancer is such that high IL1R1 or IL1RAP is strongly related to patient survival. These findings may help to improve the understanding of the role of immune molecules in carcinogenesis and enhance therapeutic approaches.