Cancer Genome Research Articles

Widespread mutagenesis and chromosomal instability shape somatic genomes in systemic sclerosis

Systemic sclerosis is a connective tissue disorder characterized by excessive fibrosis that primarily affects women, and can present as a multisystem pathology. Roughly 4-22% of patients with systemic sclerosis develop cancer, which drastically worsens prognosis. However, the mechanisms underlying systemic sclerosis initiation, propagation, and cancer development are poorly understood. We hypothesize that the inflammation and immune response associated with systemic sclerosis can trigger DNA damage, leading to elevated somatic mutagenesis, a hallmark of pre-cancerous tissues. To test our hypothesis, we culture clonal lineages of fibroblasts from the lung tissues of controls and systemic sclerosis patients and compare their mutation burdens and spectra. We find an overall increase in all major mutation types in systemic sclerosis samples compared to control lung samples, from small-scale events such as single base substitutions and insertions/deletions, to chromosome-level changes, including copy-number changes and structural variants. In the genomes of patients with systemic sclerosis, we find evidence of somatic hypermutation or kategis (typically only seen in cancer genomes), we identify mutation signatures closely resembling the error-prone translesion polymerase Polη activity, and observe an activation-induced deaminase-like mutation signature, which overlaps with genomic regions displaying kataegis.

Anaplastic thyroid carcinoma: a genome-based search for new targeted therapy options

Abstract Introduction/Objective Anaplastic thyroid carcinoma (ATC) is a rare, aggressive thyroid cancer. Precision medicine, particularly gene-targeted therapy has emerged as a promising avenue in cancer treatment. However, few targeted therapies have been approved for ATC. Here, we present a genome-based search for new targeted therapy options using next-generation sequencing (NGS) data of 727 ATC cases. Methods/Case Report Deidentified NGS results in 727 ATC cases were obtained from Foundation Medicine. A search of the literature and genomic databases (TCGA, My Cancer Genome, and DGIdb) was performed to analyzed frequency of gene mutations and corresponding gene targeted drugs. Results (if a Case Study enter NA) Remarkably, 99.17% of the 727 ATC cases had at least one targeted drug option available. Among the 254 unique genes identified with pathogenic mutations, 150 (59.06%) were found to have at least 1 corresponding targeted drug. Among the top 35 most frequently mutated genes (frequency > 2.0%), 27 (80.00%) had available targeted therapies. Notably, most drug categories (70.83%) exhibited multi-gene targeting capabilities. The drug categories based on the percentage of genes targeted from highest to lowest are Serine/Threonine and Tryosine kinase inhibitors, therapeutic antibodies, MEK inhibitors, CDK inhibitors, AKT inhibitors, PI3K inhibitors and immunotherapies. There are an additional 16 drug categories that target 1 to 5 of the 35 frequently mutated genes identified. Of particular interest is MTAP, a previously unreported frequently mutated gene which is most often deleted (14.77%). Several drugs are undergoing phase 1 and/or phase 2 clinical trials for MTAP-deleted solid tumors. MTAP loss holds promise for identifying expanding therapeutic options in ATC. Conclusion Our genome-based analysis indicates that 99.17% of the 727 ATC cases have targeted drug options, targeting 59.06% of identified gene mutations. Among the 24 categories of targeted drugs 17 (70.83%) target more than one gene. The 2018 FDA approval of combination BRAF/MEK inhibitor therapy for management of BRAF V600E-positive ATC was a major first step in gene targeted therapies. Besides that, Tyrosine kinase inhibitors, mTOR inhibitor, PPAR-γ agonist, ALK inhibitor, VEGF inhibitor and several combined treatment and immunotherapeutic agents are currently being tested in ATC clinical trials. These promising findings highlight the expanding repertoire of gene-targeted therapy options in ATC and emphasizes the importance of combined strategies and identifying driver mutations.

Familial adenomatous polyposis gene MUTYH mutations are identified in anaplastic thyroid carcinoma

Abstract Introduction/Objective Anaplastic thyroid carcinoma (ATC) is a rare aggressive disease unresponsive to treatment. Next-Generation Sequencing (NGS) allows identification of targets for precision therapies, such as BRAF, with implications in treating ATC. Our prior work identified ATC clusters with characteristic gene mutations and multiple previously unreported mutations. One of these is MUTYH, which is associated with colon (CRC), ovarian, breast, bladder, and duodenal carcinomas in MUTYH-associated polyposis (MAP). Its association with ATC is not defined. Methods/Case Report Exploratory analysis of pathogenic mutations in 727 ATC cases using a 324-gene panel (FoundationOneCDx) and an interactive visualization of association rules was conducted for informative maximal frequent patterns among mutated gene combinations to identify gene clusters including genes not commonly associated with ATC. TCGA database was reviewed for frequency of MUTYH mutations. My Cancer Genome and the Drug-Gene Interaction Database were used to identify potential targeted drugs for MUTYH gene-mutated cancers. Results (if a Case Study enter NA) NGS showed MUTYH short-variant mutations in 17 cases (2.34%). Germline MUTYH variants incidence is 1.43% in normal samples. 5 cases harbored only Y165C and 7 had only G382D, with 1 case having both Y165C and G382D. The other 4 cases contained sporadic truncating events in MUTYH. All instances of Y165C and G382D were predicted to be germline. 6 patients (35%) had BRAF co-mutations, correlating with expected frequency of ATC thought to transform from papillary carcinoma (PC). One case had only MUTYH mutation while a second had MUTYH with TERT and TP53. TCGA database contained 6(0.2%) cases of PC with MUTYH mutations (total 2871 MUTYH-mutated carcinomas), but no cases of ATC or other thyroid tumors were described. Conclusion MUTYH is a DNA repair enzyme linked to CRC and other cancers. MUTYH mutations occur in 6.7% of MAP patients and 1–2.2% of sporadic CRC cases that are mutually exclusive of BRAF mutations. While MAP increases the lifetime risk of CRC by over 60%, the link of MUTYH mutations to PC has only been observed in MAP and not been described outside of it. To our knowledge this is the first description of MUTYH mutations in ATC, especially without concurrent BRAF mutation (11 cases), suggesting MUTYH may independently contribute to pathogenesis of ATC. PARP inhibitors, PD-1/PD-L1 inhibitors, and ATR inhibitors demonstrate promising results in clinical trials of MUTYH-mutated cancers, warranting further research.

PROTAC’ING CENTROSOME AMPLIfiCATION PROTEINS: TARGETED PROTEIN DEGRADATION AS A NOVEL THERAPEUTIC STRATEGY IN GLIOBLASTOMA

Abstract AIMS Glioblastomas (GBMs) are the most common and aggressive brain tumours, notoriously difficult to treat with universal treatment resistance. A key feature of cancer cells is centrosome amplification (CA), leading to chromosomal instability and worse patient outcomes, including metastasis development and treatment resistance. In this work, I identified CA proteins overexpressed in GBM and aimed to investigate how the targeted degradation of proteins associated with centrosome amplification can influence the growth and survival of GBM cells. METHOD Based on well-established literature data concerning CA-related genes, I evaluated the expression level of these targets in different types of samples from the Tumour Cancer Genome Atlas dataset of GBM patient samples. Following the identification of CA targets differentially overexpressed, to test the hypothesis that CA proteins could be involved in the survival of GBM cells and be potential therapeutic targets, I used a novel drug modality, named Proteolysis Targeting Chimeras (PROTACs) to degrade two CA proteins. PROTACs can quickly destroy specific proteins, potentially overcoming resistance to treatment. Target degradation was confirmed via immunoblotting and cell viability and cell cycle analysis were performed to evaluate the impact on GBM cells. RESULTS Both primary and recurrent GBM samples display high levels of CA gene signature when compared to noncancerous samples, and some CA genes are particularly upregulated in recurrent samples. The PROTACs were effective in degrading both CA targets in GBM cells, leading to a significant decrease in cell viability and G2 cell cycle arrest. CONCLUSION This study presents initial evidence that CA protein degradation could be a promising avenue for GBM research and therapy. Further research is needed to fully assess the translational potential of PROTACs in GBM treatment.

Analysis of SLC genes alternative splicing identifies the SLC7A6 RI isoform as a therapeutic target for colorectal cancer.

Alternative splicing (AS), a crucial mechanism in post-transcriptional regulation, has been implicated in diverse cancer processes. Several splicing variants of solute carrier (SLC) transporters reportedly play pivotal roles in tumorigenesis and tumor development. However, an in-depth analysis of AS landscapes of SLCs in colon adenocarcinoma (COAD) is lacking. Herein, we analyzed data from The Cancer Genome Atlas and identified 1215 AS events across 243 SLC genes, including 109 differentially expressed AS (DEAS) events involving 62 SLC genes in COAD. Differentially spliced SLCs were enriched in biological processes, including transmembrane transporter activity, transporter activity, ferroptosis, and choline metabolism. In patients with COAD, tumor tissues exhibited higher expression of longer mitochondrial carrier SLC25A16 isoforms than adjacent normal tissues, consistent with bioinformatics analysis. Protein-coding sequences and transmembrane helices of survival-related DEAS were predicted, revealing that shifts in splicing sites altered the number and structure of their transmembrane proteins. We developed a prognostic risk model based on the screened 6-SLC-AS (SLC7A6_RI_37208 (SLC7A6-RI), SLC11A2_AP_21724, SLC2A8_ES_87631, SLC35B1_AA_42317, SLC39A11_AD_43204, and SLC7A8_AP_26712). Knockdown of the intronic region of SLC7A6-RI isoform enhanced colon cancer cell proliferation. Invivo, knockdown of the intronic region of SLC7A6-RI isoform enhanced tumor growth in colon cancer. Mechanistically, si-SLC7A6-RI isoform exerted oncogenic effects by activating the PI3K-Akt-mTOR signaling pathway and promoting cell proliferation, evidenced by increased expression of key regulators Phosphorylated Mammalian Target of Rapamycin (p-mTOR) and a cell proliferation marker Proliferating Cell Nuclear Antigen (PCNA) using western blotting. Our study elucidated SLC-AS in COAD, highlighting its potential as a prognostic and therapeutic target and emphasizing the suppressive influence of SLC7A6-RI in colon cancer progression.

Expression and its clinical significance of cell-cycle dependent kinase 1 in malignant peripheral nerve sheath tumors

To explore the role and clinical significance of cell-cycle dependent kinase 1 (CDK1) and its upstream and downstream molecules in the development of malignant peripheral nerve sheath tumor (MPNST) through the analysis of clinical tissue samples. A total of 56 tumor samples from MPNST patients ("Tianjin" dataset) who underwent surgical resection, confirmed by histology and pathology between September 2011 and March 2020, along with 17 normal tissue samples, were selected as the research subjects. MPNST-related hub genes were identified through transcriptome sequencing, bioinformatics analysis, immunohistochemistry staining, and survival analysis, and their expression levels and prognostic associations were analyzed. Transcriptome sequencing and bioinformatics analysis revealed that upregulated genes in MPNST were predominantly enriched in cell cycle-related pathways, with CDK1 occupying a central position among all differentially expressed genes. Further differential analysis demonstrated that CDK1 mRNA expression in sarcoma tissues was significantly higher than in normal tissues [based on searching the cancer genome atlas (TCGA) dataset, P<0.05]. In MPNST tissues, CDK1 mRNA expression was not only significantly higher than in normal tissues (based on Tianjin, GSE141438 datasets, P<0.05), but also significantly higher than in neurofibromatosis (NF) and plexiform neurofibromas (PNF) (based on GSE66743 and GSE145064 datasets, P<0.05). Immunohistochemical staining results indicated that the expression rate of CDK1 protein in MPNST tissues was 40.31%. Survival analysis results demonstrated that CDK1 expression was associated with poor prognosis. The survival time of MPNST patients with high CDK1 mRNA expression was significantly lower than that of the low expression group ( P<0.05), and the overall survival trend of patients with positive CDK1 protein expression was worse than that of patients with negative CDK1 expression. Additionally, differential analysis of CDK family genes (CDK1-8) revealed that only CDK1 was significantly upregulated in MPNST, NF, and PNF. Increased expression of CDK1 is associated with poor prognosis in MPNST patients. Compared to other CDK family members, CDK1 exhibits a unique expression pattern, suggesting its potential as a therapeutic target for MPNST.

Characterizing POLE Mutation-Associated Colorectal Carcinoma: Clinical and Pathologic Insight

Abstract Introduction/Objective Colorectal carcinoma (CRC) is one of the most common cancers and a leading cause of cancer-related death in the United States. Pathogenically, colorectal carcinoma is a heterogeneous disease that develops via stepwise accumulation of well-characterized genetic and epigenetic alteration. Identification of DNA polymerase mutation leads to the characterization of a new molecular pathway of carcinogenesis named the POLE pathway. Methods/Case Report Utilizing the cBioportal platform and Cancer Genome Atlas (TCGA) Firehouse Legacy data, we identified 118 cases of CRC with mutations in the POLE gene. We evaluated the various clinical and pathologic features of POLE mutation-associated CRC. Results (if a Case Study enter NA) Within the cohort of 118 cases linked to mutations in the POLE gene, gender distribution reveals that 63 individuals, comprising 53.8% of the sample, are male, while 42 individuals, accounting for 35.9%, are female. Ethnicity breakdown showcases a predominantly White population, with 92 cases (78.6%), followed by 8 cases (6.8%) attributed to Asian-Far East/Indian Subcontinent descent, 5 cases (4.3%) categorized as Asian, and 4 cases (3.4%) each identified as Black and Black or African American. Additionally, one case (0.9%) has an unknown ethnicity, while 4 cases (3.4%) have unspecified racial backgrounds. The average age at diagnosis is recorded at 48.5 years, with ages ranging from 25 to 85, signifying a broad age spectrum within the affected population. Delving into cancer subtypes, the majority of cases, constituting 64 instances (54.2%), manifest as colon adenocarcinoma, while 38 cases (32.2%) present as rectal adenocarcinoma. Moreover, 9 cases (7.6%) are characterized as colorectal adenocarcinoma, 6 cases (5.1%) are classified as mucinous adenocarcinoma of the colon and rectum, and one case (0.8%) manifests as medullary adenocarcinoma of the colon. This detailed elucidation provides a comprehensive understanding of the demographics and clinical presentation within the cohort affected by POLE gene mutations. Conclusion In summary, our research has meticulously examined 118 instances of colorectal carcinoma (CRC) intricately linked to mutations in the POLE gene. Within this cohort, a predominant demographic emerges, with a notable prevalence among individuals of White ethnicity. Delving deeper into the pathological spectrum, colon adenocarcinoma emerges as the prevailing subtype, exemplifying the intricate interplay between genetic aberrations and cancer manifestation.

Development and Validation of a Cholesterol-related Gene Signature for Prognostic Assessment in Head and Neck Squamous Cell Carcinoma.

This study seeks to develop a prognostic risk signature for head and neck squamous cell carcinoma (HNSCC) based on cholesterol-related genes (CholRG), aiming to enhance prognostic accuracy in clinical practice. HNSCC poses significant challenges due to its aggressive behavior and limited response to standard treatments, resulting in elevated morbidity and mortality rates.In order to improve prognostic prediction in HNSCC, our study is inspired by the realization that cholesterol metabolism plays a critical role in accelerating the progression of cancer. To this end, we are developing a unique risk signature using CholRG. The aim of this study was to create a CholRG-based risk signature to predict HNSCC prognosis, aiding in clinical decision-making accurately. The TCGA HNSCC dataset, along with GSE41613 and GSE65858, was obtained from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases, respectively. A CholRG-based risk signature was then developed and validated across various independent HNSCC cohorts. Moreover, a nomogram model incorporating CholRG-based risk signature was established. Additionally, functional enrichment analysis was conducted, and the immune landscapes of the high- and low-risk groups were compared. Finally, in vitro experiments were performed using lipid-based transfection to deliver siRNAs targeting ACAT1 to SCC1 and SCC23 cell lines, further examining the effects of ACAT1 knockdown on these cells. Utilizing RNA-seq, microarray, and clinical data from public databases, we constructed and validated a CholRG-based risk signature that includes key genes such as ACAT1, CYP19A1, CYP27A1, FAXDC2, INSIG2, PRKAA2, and SEC14L2, which can effectively predict the clinical outcome of HNSCC. Additionally, our findings were reinforced by a nomogram model that integrates the risk score with clinical variables for more clinically practical prognostic assessment. In addition, patients at high risk show hypoxia and increased oncogenic pathways such as mTORC1 signaling, as well as a suppressed immune microenvironment marked by a reduction in the infiltration of important immune cells. Notably, in vitro experiments showed that ACAT1 depletion significantly suppressed the proliferation, colony formation, and invasion capabilities of HNSCC cells, confirming ACAT1's role in promoting malignancy. Collectively, our study not only underscores the importance of cholesterol metabolism in HNSCC pathogenesis but also highlights the CholRG-based risk signature as a promising tool for enhancing prognostic accuracy and personalizing therapeutic strategies.

Retinol-binding protein type 1 expression predicts poor prognosis in head and neck squamous cell carcinoma

BackgroundHead and neck squamous cell carcinoma (HNSCC) is the sixth most prevalent malignancy worldwide, with high incidence and poor survival rates. RBP1 is highly expressed in several kinds of cancer and plays a potential prognostic factor. However, the relationship between RBP1 and HNSCC were analyzed based on The Cancer Genome Atlas (TCGA) database.Materials and methodsRBP1 expression and clinical information were obtained from the Cancer Genome Atlas (TCGA) database. Tumor tissue and adjacent normal tissue of 6 HNSCC patients were collected to analyze the RBP1 mRNA expression level by quantitative PCR. Cox regression analysis was used to evaluate the prognostic values of RBP1 and clinical data in HNSCC. A nomogram was also established to predict the impact of RBP1 on prognosis based on Cox multivariate results. The methylation level of RBP1 in HNSC and its prognosis were analyzed in UALACN and MethSurv. Finally, the potential biological functions of RBP1 were investigated using gene set enrichment analysis (GSEA) and single sample GSEA (ssGSEA).ResultsThe mRNA expression levels of RBP1 were highly expressed in HNSCC tissue. The Cox analyses demonstrate that highly-expressed RBP1 is an independent prognosis marker(P < 0.05). ROC curve analysis showed that performances of RBP1 (area under the ROC curve: 0.887, sensitivity: 84.1%, specificity: 79.9%). The methylation was increased in HNSCC patients compared with normal subjects(P < 0.05) and was associated with better prognosis at sites cg06208339, cg12298268, cg12497564, cg15288618, cg20532370, cg23448348. Additionally, RBP1 expression is mildly associated with immune cell infiltration and immunological checkpoints.ConclusionRBP1 is overexpressed and associated with poor patient prognosis in head and neck squamous cell carcinoma.

Dysgerminomas: germ cell tumors exhibit high expression of PD-L1 and associated with high TILs and good prognosis

Ovarian germ cell tumors (OVGCTs) account for 28% of all diagnosed ovarian cancers, and malignant germ cell tumors specifically account for approximately 13% of diagnosed ovarian cancers in Saudi Arabia. Although most germ cell tumor patients have a high survival rate, patients who experience tumor recurrence have a poor prognosis and present with more aggressive and chemoresistant tumors. The use of immunotherapeutic agents such as PD-L1/PD-1 inhibitors for OVGCTs remains very limited because few studies have described the immunological characteristics of these tumors. This study is the first to investigate PD-L1 expression in ovarian germ cell tumors and explore the role of PD-L1 expression in tumor microenvironment cells and genetic alterations. A total of 34 ovarian germ cell tumors were collected from pathology archives. The collected tumor tissues included ten dysgerminomas, five yolk sac tumors, five immature teratomas, and one mature teratoma, and the remaining samples were mixed germ cell tumors. The tumors were analyzed using immunohistochemical analysis to determine PD-L1 expression, immune cell infiltration and cancer stem cell populations and their correlation with clinical outcome. Furthermore, the genetic alterations in different subtypes of germ cell tumors were correlated with PD-L1 expression and clinical outcome. Datasets for testicular germ cells (TGCTs) were retrieved from The Cancer Genome Atlas (TCGA) and analyzed using cBioPortal (cbioportal.org) and Gene Expression Profiling Interactive Analysis (GEPIA). Compared with yolk sac tumors, dysgerminomas highly express PD-L1 and are associated with high levels of tumor infiltrating lymphocytes (TILs) and stem cell markers. In addition, compared with PD-L1-negative yolk sac tissue, dysgerminomas/seminomas with high PD-L1 expression are associated with more genetic alterations and a better prognosis. Our findings will contribute to the knowledge about the potential benefits of ovarian cancer immunotherapy in specific subsets of germ cell tumor patients and the risk factors for resistance mediated by tumor microenvironment cells.

Association of glutaminase expression with immune-suppressive tumor microenvironment, clinicopathologic features, and clinical outcomes in endometrial cancer

ObjectiveIncreased glutamine metabolism by cancer cells via upregulation of the drug-targetable enzyme glutaminase may contribute to an immune-suppressive tumor microenvironment. Inhibiting glutamine metabolism can not only suppress tumor growth, but...

MicroRNA-34a negatively regulates Netrin1 and mediates MEK/ERK pathway to regulate chemosensitivity of gastric cancer cells.

To explore the mechanism of action of MicroRNAs-34a (miR-34a) and Eurite growth guiding factor 1 (Netrin1) in cisplatin resistance in gastric cancer (GC), providing new clues for overcoming tumor resistance and optimizing anti-tumor therapy for GC. The Cancer Genome Atlas (TCGA), Differentially Expressed MicroRNAs (miRNAs) in human cancers (dbDEMC), and Starbase online databases were used to analyze the correlation between miR-34a and Netrin-1 and prognosis in GC, and to predict and verify the targeted binding of miR-34a to Netrin-1. The experimental methods including Cell transfection, real-time polymerase chain reaction (RT-PCR), Cell-Counting-Kit-8 (CCK8) assay, flow cytometry, wound scratch assay, transwell assay, and western blotting were used to investigate the effects of miR-34a and Netrin1 on chemotherapy resistance and biological characteristics in cisplatin-resistant GC cells (HGC27/DDP), and to analyze the molecular mechanism of cisplatin resistance. miR-34a expression was downregulated in gastric cancer clinical samples and cisplatin-resistant cells, while Netrin1 was upregulated, and was related to overall survival (OS). Upregulation of miR-34a can significantly reduce the IC50 value of cisplatin(0.65 vs 1.6 ng/mL) and Multidrug Resistance 1 (MDR-1) protein level, inhibit the proliferation activity, reduce the expression levels of proliferating cell nuclear antigen (PCNA) and ki-67 protein, and induce the increase of apoptosis rate and the enhancement of cycle arrest. Upregulation of miR-34a can also significantly reduce the expression level of Matrix metalloproteinase 9 (MMP9) protein, promote the expression of E-cadherin protein, reduce the wound healing rate and invasion number to inhibit migration and invasion ability in drug-resistant gastric cancer cells. Moreover, overexpression of Netrin1 on the basis of upregulation of miR-34a can weaken the above changes caused by upregulation of miR-34a. In addition, upregulation of miR-34a can significantly inhibit the Mitogen-activated protein kinase kinase (MEK) / Extracellular regulated protein kinases (ERK) pathway, while overexpression of Netrin1 can activate the MEK/ERK pathway, and inhibition of MEK/ERK pathway can effectively counteract the protein expression of Netrin1, and reverse changes in the expression of cisplatin IC50 and MDR-1 proteins caused by co-upregulation of miR-34a/Netrin1 in HGC27/DDP, as well as changes in proliferation, apoptosis, migration and invasion. In addition, upregulation of miR-34a can significantly inhibit the MEK/ERK pathway, while overexpression of Netrin1 can activate the MEK/ERK pathway. If the MEK/ERK pathway was inhibited, it can effectively counteract the protein overexpression of Netrin1, and reverse the changes in the expression of cisplatin IC50 and MDR-1 proteins in HGC27/DDP induced by co-upregulation of miR-34a / Netrin1, as well as changes in proliferation, apoptosis, migration and invasion. miR-34a targets and negatively regulates Netrin1 to mediate the proliferation, apoptosis, apoptosis, migration, and invasion of drug-resistant gastric cancer cells via the MEK/ERK pathway, and change the chemosensitivity in GC cells. miR-34a/Netrin1/MEK/ERK axis may serve as a novel therapeutic target for chemoresistance in GC, it is of great significance for overcoming drug resistance and developing new therapeutic strategies for GC.

Effects of Differentially Methylated CpG Sites in Enhancer and Promoter Regions on the Chromatin Structures of Target LncRNAs in Breast Cancer.

Aberrant DNA methylation plays a crucial role in breast cancer progression by regulating gene expression. However, the regulatory pattern of DNA methylation in long noncoding RNAs (lncRNAs) for breast cancer remains unclear. In this study, we integrated gene expression, DNA methylation, and clinical data from breast cancer patients included in The Cancer Genome Atlas (TCGA) database. We examined DNA methylation distribution across various lncRNA categories, revealing distinct methylation characteristics. Through genome-wide correlation analysis, we identified the CpG sites located in lncRNAs and the distally associated CpG sites of lncRNAs. Functional genome enrichment analysis, conducted through the integration of ENCODE ChIP-seq data, revealed that differentially methylated CpG sites (DMCs) in lncRNAs were mostly located in promoter regions, while distally associated DMCs primarily acted on enhancer regions. By integrating Hi-C data, we found that DMCs in enhancer and promoter regions were closely associated with the changes in three-dimensional chromatin structures by affecting the formation of enhancer-promoter loops. Furthermore, through Cox regression analysis and three machine learning models, we identified 11 key methylation-driven lncRNAs (DIO3OS, ELOVL2-AS1, MIAT, LINC00536, C9orf163, AC105398.1, LINC02178, MILIP, HID1-AS1, KCNH1-IT1, and TMEM220-AS1) that were associated with the survival of breast cancer patients and constructed a prognostic risk scoring model, which demonstrated strong prognostic performance. These findings enhance our understanding of DNA methylation's role in lncRNA regulation in breast cancer and provide potential biomarkers for diagnosis.

Distinct Molecular Alterations in Hepatocellular Carcinoma (HCC) Arising in a Non-Fibrotic Liver Compared to a Cirrhotic Liver

Abstract Introduction/Objective HCC is known to more likely develop in a cirrhotic liver than a non-cirrhotic liver, irrespective of etiology, with TP53 and CTNNB1 being the most frequent driver mutations in this group. Whether there are distinctive molecular pathways for HCCs developing in the non-cirrhotic liver is not known. This study evaluated whether there is any difference in the mutational profile of HCCs arising in a non-fibrotic liver compared to a cirrhotic liver. Methods/Case Report Clinicopathologic and in-house next generation sequencing (NGS) data from HCC cases sequenced between 1/1/18-6/30/23 were reviewed. Cases from a targeted precision NGS panel were excluded. Results were correlated with publicly available data from The Cancer Genome Atlas (TCGA). Results (if a Case Study enter NA) 29 cases were available for review; 24 patients had background cirrhosis at the time of diagnosis, while 5 patients had no evidence of fibrosis. 21 of 24 patients (88%) patients in the cirrhosis group had a variant in TP53 and/or CTNNB1 that was considered to be disease associated or probably disease associated, whereas only 1 of 5 patients (20%) in the non-fibrotic group had a variant detected in one of these genes (Fisher’s exact: p &amp;lt; 0.01). BAP1 and ARID1A variants were detected in two patients in the non-fibrotic group. TP53 and CTNNB1 were generally mutually exclusive (86% of cases), however, 3 patients harbored both TP53 and CTNBB1 variants; interestingly all 3 had background cirrhosis and HCV infection. All 6 poorly differentiated tumors occurred in cirrhotic livers and were found to have TP53 variants (Figure 1). TCGA data (N = 210) similarly showed that patients with intermediate fibrosis or established cirrhosis (N = 138) were more likely than patients without background fibrosis (N = 72) to harbor TP53 or CTNNB1 variants (64% vs 42%; Chi-squared: p &amp;lt; 0.01; Figure 2). Aside from TP53 and CTNNB1, the most common variants seen in the TCGA non-fibrotic group were in TTN (22), ALB (10), FREM2 (9), LRP1B (9), and MUC16 (9). Conclusion Both in-house and TCGA data showed that TP53 and/or CTNNB1 variants were more likely to be seen in HCC cases arising in a cirrhotic liver compared to a non-fibrotic liver. This data suggests there may be unique and less-well characterized molecular pathways involved in the neoplastic progression of HCC in a non-fibrotic liver.

Feasibility of an environmental scan-based approach to collecting information about factors impacting cancer genetics services in Latin American countries.

Clinical cancer genetics services are expanding globally, but national policy and health care systems influence availability and implementation. Understanding the environmental factors within a country is required to appropriately implement, adapt, and evaluate cancer genetics service delivery models. An environmental scan (ES) is an approach used in business, public health, health care and other sectors to collect information about an environment or system for strategic decision making and program planning. An ES has been previously used to assess cancer genetics clinic-level factors to inform quality improvement efforts in the United States. We assessed the feasibility of using an ES to collect information about factors that may influence cancer genetics service delivery in the outer-most socio-ecological model environmental levels (policy, national agencies, healthcare systems, cultural considerations) in three Latin American countries. Oncology and Genetics care team members at three participating sites used publicly available sources and personal experiences to complete a data collection form (DCF) that included questions about subtopics: laws and policies, relevant agencies and regulations, health care systems and insurance, and cultural considerations. Time to complete the DCF and DCF completeness were used to measure ES feasibility. Participating sites completed the DCF in 3 months, and most questions (average, 87.0%) were answered. Questions in the cultural considerations subtopic had the fewest answers (average, 77.8%). Overall, the ES was feasible and identified a lack of published literature related to cultural considerations impacting health care and genetics services uptake in Latin America. Environmental factors impact cancer genetics services, and identification of these factors will facilitate future collaborative research and genetics service delivery dissemination efforts.

Pancancer analysis of NDUFA4L2 with focused role in tumor progression and metastasis of colon adenocarcinoma.

Colon adenocarcinoma (COAD) is a prevalent gastrointestinal malignant disease with a high mortality rate, and identification of novel prognostic biomarkers and therapeutic targets is urgently needed. Although NDUFA4L2 has high expressions in various tumors and affects tumor progression, its role in COAD remains unclear. The role of NDUFA4L2 in COAD was analyzed utilizing datasets available from public databases including The Cancer Genome Atlas, The Genotype-Tissue Expression (GTEx), Gene Expression Omnibus, Alabama Cancer Database (UALCAN), and The Human Protein Atlas databases. The prognostic value of NDUFA4L2 was determined using Kaplan-Meier analysis and Cox regression analysis. To investigate the possible mechanism underlying the role of NDUFA4L2 in COAD, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA) were employed. The correlation between NDUFA4L2 expression and immune cell infiltration levels was examined through single-sample gene set enrichment analysis (ssGSEA). The NDUFA4L2 expression levels in COAD patients and cell lines were validated through immunohistochemistry, immunofluorescence, qRT-PCR, and Western blot. Wound healing assay was also performed to evaluate the effect of NDUFA4L2 on COAD metastasis. Furthermore, the NDUFA4L2 mediated competing endogenous RNA (ceRNA) regulatory network was predicted and constructed through a variety of databases. The comprehensive pan-cancer analysis showed that NDUFA4L2 possesses diagnostic and prognostic value in many cancers, especially in COAD. GO-KEGG and GSEA analyses indicated that NDUFA4L2 was associated with multiple biological functions including epithelial-mesenchymal transition and adaptation to hypoxia. The ssGSEA analysis showed that NDUFA4L2 expression was associated with immune infiltration. In vitro experiments confirmed upregulation of NDUFA4L2 in COAD tissues and cell lines, and NDUFA4L2 overexpression significantly promoted migration of COAD cells. In addition, the C9orf139 /miR-194-3p axis was speculated as the possible upstream regulators of NDUFA4L2 in COAD. This study demonstrated that NDUFA4L2 upregulation was correlated with tumor progression, relapsed prognosis and aggressive migration of COAD, suggesting that NDUFA4L2 can act as an effective prognostic biomarker and a promising therapeutic target for COAD treatment.

FBXO family genes promotes hepatocellular carcinoma via ubiquitination of p53

FBXO protein family plays an essential role in the ubiquitination process acting as E3 ligases, which may contribute to the progression of cancers. However, the molecular functions of FBXOs in hepatocellular carcinoma (HCC) remain incompletely understood. Here, we investigated the overlapping genes between the FBXOs and differentially expressed genes (DEGs) of HCC identified by utilizing The Cancer Genome Atlas (TCGA) dataset, then, a prognostic model with effective predictive capacity was constructed based on the uni-cox and LASSO regression analyses. To elucidate the underlying mechanism of the FBXO model genes, KEGG analysis was carried out. Drug metabolism-cytochrome P450 and retinol metabolism were revealed as the potential pathway, which Increased the credibility of subsequent drug prediction research. Meanwhile, patients divided by the prognostic model showed a different immune infiltrating status and we also found FBXO model genes may ubiquitinate P53, inducing TP53 more prone to mutations, thereby promoting the occurrence and development of tumors. Consistent with these findings, the result of immunohistochemistry (IHC) validated an elevated expression of these model genes in HCC tissues than in the adjacent tissues. The primary aim of this investigation is to formulate a prognostic model while exploring the underlying mechanisms associated with FBXO genes in HCC. These findings offer initial research perspectives on the involvement of FBXO genes in HCC and contribute to the discovery of dependable biomarkers for the management, prognostication, and early detection of HCC in patients.

Identified a novel prognostic model of HCC basing on virus signature for guiding immunotherapy

Oncolytic viral immunotherapy is a cancer treatment that uses native or genetically modified viruses that selectively replicate and destroy tumor cells. In this study, we aimed to construct a virus-based prognostic model for risk assessment and prognosis prediction in patients with hepatocellular carcinoma (HCC) and determine the most appropriate virus as a candidate vector for oncolytic virus immunotherapy. Microbiome and RNA sequencing data and clinical information were obtained from The Cancer Genome Atlas, and viruses with prognostic value were identified (Deltabaculovirus, Sicinivirus, and Cytomegalovirus) to construct the prognostic model. Correlation analyses were performed to evaluate the predictive function of the viral signature. Bioinformatics analyses were conducted to explore the functional enrichment of viral expression in HCC. The risk score generated by this model could distinguish patients with different survival outcomes, have excellent reliability and accuracy, and could be used as an independent prognostic indicator. The high-risk score group showed significantly lower overall survival, and this trend was also observed in subgroups with different clinicopathological features. Furthermore, Deltabaculovirus positively correlated with amino acid metabolism, energy metabolism signaling pathways, peroxisomes, and complement coagulation cascades. In addition, Deltabaculovirus was significantly related to immune cell infiltration; therefore, patients with high Delta-baculovirus expression might respond better to HCC immunotherapy. Our study identified a promising predictive viral signature for assessing clinical prognosis and guiding immunotherapy in HCC. Deltabaculovirus might be a suitable viral vector for oncolytic virus immunotherapy.

RBM15 drives the progression of lung adenocarcinoma by regulating N6-methyladenosine-mediated LDHA mRNA stability

Abnormal N6-methyladenosine (m6A) methylation in RNA plays a pivotal role in the pathogenesis of many types of tumors by influencing mRNA metabolism, alternative splicing, translocation, stability and translation. However, the specific regulators and underlying mechanisms of m6A modification in the progression of lung adenocarcinoma are not well understood. In this study, we analyzed the RNA-seq transcriptome data downloaded from The Cancer Genome Atlas (TCGA) database, and identified “m6A writer” RNA binding motif protein 15 (RBM15) expression was significantly elevated in lung adenocarcinoma (LUAD) biopsies, and the higher RBM15 levels were correlated with the poorer overall survival (OS) of LUAD patients. Further study confirmed RBM15 was prominently expressed in LUAD tissues and cell lines. Moreover, silencing RBM15 in PC9 and H1299 cells reduced cell proliferation both in vitro and in vivo, while overexpression of RBM15 in A549 cells promoted cell growth. Mechanistically, lactate dehydrogenase A (LDHA) acted as a downstream target of RBM15. RBM15-mediated m6A modification of LDHA mRNA enhanced its stability to exert an oncogenic role in LUAD. Taken together, our findings suggest that the RBM15/LDHA axis might be a novel and promising therapeutic target for LUAD.

Knowledge and Awareness of Cancer Genome Profiling Tests among Japanese Patients with Cancer.

(1) Background: The number of patients with cancer undergoing cancer genome profiling is increasing; however, it remains unclear how accurately they understand the details of the tests and treatments. This study aimed to clarify the awareness of cancer genome profiling tests among patients with cancer who visited cancer genome medical clinics. (2) Methods: A questionnaire survey was conducted on awareness, anxiety, sources of information, and psychological states concerning cancer genome profiling tests. (3) Results: In total, 265 patients with cancer (117 men, 142 women, 6 no response, average age of 58.29 ± 11.9 years) were included in the study, of which 218 (82.3%) were aware of the term "cancer genomic medicine" and 90 (34.0%) were aware of its details. Thus, only a few respondents understood that cancer genome profiling tests facilitate the discovery of secondary findings and of genes associated with hereditary tumors. Regarding their psychological state when visiting the cancer genome clinic, the respondents were anxious about standard treatment and prognosis limits. (4) Conclusions: From the viewpoint of advance care planning, we suggest that medical professionals build a support system that links palliative care and cancer treatment and coordinates genetic counseling at an early stage.