Adjacent Non-tumor Tissues Research Articles

Study of NALT1 and CTBP1-AS1 lncRNAs expression levels in triple-negative breast cancer patients in the Iranian population

BackgroundTriple-negative breast cancer (TNBC), an aggressive subtype with a poor prognosis, is notably difficult to treat. Emerging research highlights the significant roles of long non-coding RNAs (lncRNAs) in cancer biology. LncRNAs, such as NALT1 and CTBP1-AS1 are implicated in oncogenic processes; this study hypothesizes that NALT1 and CTBP1-AS1 are overexpressed in TNBC tissues compared to adjacent non-tumor tissues and may serve as biomarkers. Methods: One hundred pairs of tumor and adjacent non-tumor tissues were obtained from female patients with triple-negative breast cancer. After extracting RNA, cDNA synthesis was carried out for all samples. Quantitative real-time PCR (qRT-PCR) was employed to assess differential gene expression. Results: The expression of NALT1 (p-value <0.0001) and CTBP1-AS1 (p-value <0.0002) lncRNAs increased in TNBC tumor tissues in comparison to adjacent non-tumor tissues. A statistically positive correlation (ρ = 0.5844, p < 0.0001) was observed between the expression levels of NALT1 and CTBP1-AS1 in breast cancer patients. The ROC analysis indicated that NALT1 (AUC = 0.718, specificity = 61 %, sensitivity = 70 %) shows moderate potential and CTBP1-AS1 (AUC = 0.648, specificity = 65 %, sensitivity = 55 %) exhibits poor potential as a diagnostic biomarker for breast cancer. Conclusion: This study shows that NALT1 and CTBP1-AS1 lncRNAs are upregulated in TNBC tissues. Additionally, a positive correlation exists between their expression levels in breast cancer. Further research is needed to understand their mechanisms as molecular biomarkers.

CTNND2 gene expression in melanoma tissues and its effects on the malignant biological functions of melanoma cells.

The catenin delta 2 (CTNND2) gene has been implicated in the progression of various cancers, but its specific role in melanoma has not yet been thoroughly investigated. This study sought to explore the expression and biological function of CTNND2 in malignant melanoma tissues to identify new targets or biomarkers for melanoma diagnosis and treatment. Immunohistochemistry was used to examine the levels of CTNND2 in melanoma and adjacent non-tumor tissues. A Western blot analysis was performed to quantify the expression levels of CTNND2 in human immortalized keratinocytes and melanoma cell lines. The Cell Counting Kit-8 (CCK-8) assay, plate colony formation assay, cell adhesion assay, scratch test, and Transwell assay were used to assess the effects of CTNND2 knockdown on the proliferation, adhesion, migration, and invasion of melanoma cells. The Harmonizome database was used to research the biological processes (BPs) involved in CTNND2. In the melanoma tissues, CTNND2 expression was substantially upregulated and its levels were closely linked with the pathological features of patients. The CTNND2 levels were notably more increased in the melanoma cell lines than the immortalized keratinocytes. The suppression of the CTNND2 gene substantially impeded the capacity of the melanoma cells to proliferate, migrate, and invade, and also significantly decreased their potential to attach to collagen I and IV, and fibronectin. The Harmonizome database results revealed a strong correlation between the BPs controlled by CTNND2 and the focal adhesion signaling pathway of the cells. The inhibition of the CTNND2 gene in melanoma cells resulted in a significant decrease in the phosphorylation of focal adhesion kinase (FAK) and the production of paxillin protein. In the melanoma cells, the reduction of CTNND2 did not have a significant effect on the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT) signaling pathway. However, it did considerably prevent the activation of mitogen-activated extracellular signal-regulated kinase 1/2 (MEK1/2) and its downstream molecule extracellular signal-regulated protein kinase 1/2 (ERK1/2). The expression of the CTNND2 gene is increased in melanoma tissues, which enhances the ability of melanoma cells to proliferate both in vivo and in vitro. Additionally, the CTNND2 gene is crucial in controlling the adhesion process of melanoma cells. This mechanism is associated with the regulation of the FAK and MEK1/2/ERK1/2 signaling pathways. Based on our findings, CTNND2 could be used as an oncogene target for melanoma and a new treatment target or diagnostic biomarker.

Prognostic significance and identification of m6A regulator genes and hub genes associated with m6A in breast cancer

This research endeavors to investigate the functions of N6-methyladenosine (m6A) regulatory genes and key genes linked to m6A modifications within the context of breast cancer (BC). The objective is to identify a promising predictive biomarker related to m6A modifications and validate its significance in BC through experimental methodologies. Utilizing data from The Cancer Genome Atlas (TCGA) database, a model for predicting prognosis was developed. Key genes connected to m6A modifications were discerned using weighted gene co-expression network analysis (WGCNA) coupled with LASSO and Cox regression analyses, which were then utilized to construct a predictive model. The influence of ZNF260 within BC was probed experimentally. The predictive model formulated using m6A regulatory genes and key m6A-associated genes demonstrated the capability to categorize BC patients into distinct risk groups effectively (all P < 0.001). Clinical sample analyses revealed notably elevated expression levels of ZNF260 in hormone receptor-positive/human epidermal growth factor receptor 2-negative (HR + /HER2−) BC tissues compared to adjacent non-tumor tissues (all P < 0.001). Reduction in ZNF260 expression was shown to inhibit the proliferation, clonogenicity, migration, and invasiveness of MCF-7 cells while concomitantly enhancing apoptosis (all P < 0.001).This investigation uniquely uncovered ZNF260 as a novel key gene, suggesting its potential utility as a predictive biomarker associated with m6A modifications specifically in HR + /HER2− BC.

MiR-3065-5p and miR-26a-5p as Clinical Biomarkers in Colorectal Cancer: A Translational Study.

Background/Objectives: The prognosis of colorectal cancer (CRC) is mainly based on the clinical stage; however, CRC is considered a complex disease due to its molecular heterogeneity. The development of novel biomarkers to improve patients' diagnosis and prognosis remains fundamental. Methods: A cohort of forty-nine CRC patients from the National Cancer Institute of Mexico was included to collect clinical and miRNA expression data. The expression of a group of miRNAs was compared between CRC and non-tumoral adjacent tissues. Prognosis assessment considering each miRNA expression was tested using Kaplan-Meier survival curves and Cox regressions. Statistical significance was defined as p ≤ 0.05. Trial registration: Retrospective study No.2021/046. Results: miR-3065-5p and miR-26a-5p expression differed between non-tumoral adjacent and tumoral tissues (p = 0.02). In terms of overall survival (OS), patients with low expression of miR-3065-5p had a median OS of 70 months, while patients with high levels did not reach the median OS (p = 0.041). Male patients with low expression of this miRNA had an OS of 70 months, whereas patients with high levels did not reach the median OS (p = 0.050). Under uni-multivariate analysis, clinical stage (HR: 1.30, CI 1.23-2.30; p: 0.001) and low levels of miR-3065-5p (HR: 1.30, CI 1.23-2.30; p: 0.001) were determined as predictor factors of OS. To this end, we designed the "Prognosis miRNAs assessment in cancer" (PROMIR-C) algorithm, which integrated clinical features with miR-3065-5p expression levels. Conclusions: These findings support the clinical utility of miR-26a-5p and miR-3065-5p in the diagnosis and prognosis of CRC. PROMIR-C is a fundamental tool for clinicians in treatment decision-making, prognosis assessment, and outcome of CRC.

The immunomodulatory role of the MAFB gene in hepatocellular carcinoma and its impact on biological activities

ObjectiveThe transcription factor MAFB is part of the MAF family and is known to promote hepatocellular carcinoma (HCC) by upregulating cyclin D1. However, its role in HCC immunity and prognosis remains unclear. This study explores the biological function, prognostic significance, and immune impact of MAFB in HCC. MethodsImmunohistochemistry was used to analyze MAFB expression in HCC and adjacent non-tumor tissues. RT-qPCR and Western blotting measured MAFB levels in HCC cell lines. Specific siRNA was used to knockdown MAFB in HCCLM3 and MHCC97H cells, followed by assays to evaluate cell proliferation, migration, and colony formation. Data from the TCGA database and online tools TIMER and TISDB were used to assess the relationship between MAFB and immune responses. A prognostic model based on MAFB-related immune genes was established, and drug sensitivity analysis was performed. ResultsMAFB was significantly overexpressed in HCC tissues. Knockdown of MAFB in HCC cell lines reduced their proliferation and migration abilities. The risk model based on MAFB-related immune genes effectively predicted patient prognosis, supported by ROC curves. Gene set enrichment analysis indicated that MAFB is involved in immune-related pathways. Several drugs were identified as potentially sensitive to MAFB expression levels. ConclusionMAFB plays a significant role in HCC development and immune regulation. The prognostic model combining MAFB-related immune genes provides valuable insights for predicting patient outcomes and identifying potential therapeutic targets.

USP7 depletion potentiates HIF2α degradation and inhibits clear cell renal cell carcinoma progression

Clear cell renal cell carcinoma (ccRCC) is characterized by Von Hippel Lindau (VHL) gene loss of function mutation, which leads to the accumulation of hypoxia-inducible factor 2α (HIF2α). HIF2α has been well-established as one of the major oncogenic drivers of ccRCC, however, its therapeutic targeting remains a challenge. Through an analysis of proteomic data from ccRCCs and adjacent non-tumor tissues, we herein revealed that Ubiquitin-Specific Peptidase 7 (USP7) was upregulated in tumor tissues, and its depletion by inhibitors or shRNAs caused significant suppression of tumor progression in vitro and in vivo. Mechanistically, USP7 expression is activated by the transcription factors FUBP1 and FUBP3, and it promotes tumor progression mainly by deubiquitinating and stabilizing HIF2α. Moreover, the combination of USP7 inhibitors and afatinib (an ERBB family inhibitor) coordinately induce cell death and tumor suppression. In mechanism, afatinib indirectly inhibits USP7 transcription and accelerates the degradation of HIF2α protein, and the combination of them caused a more profound suppression of HIF2α abundance. These findings reveal a FUBPs-USP7-HIF2α regulatory axis that underlies the progression of ccRCC and provides a rationale for therapeutic targeting of oncogenic HIF2α via combinational treatment of USP7 inhibitor and afatinib.

MMP9 gene expression alterations in gastric cancer and their role in cell migration

Background. Gastric cancer (GC) is a significant global health concern, ranking as the fifth most common malignant tumor and the fourth leading cause of cancer-related deaths worldwide. The primary treatment approach for metastatic GC is systemic chemotherapy. Matrix metalloproteinases (MMPs) are a group of zinc-dependent proteolytic enzymes that play crucial roles in various physiological processes. Among them, MMP9 is known for its complexity and its ability to degrade the components of the extracellular matrix. This study aimed to compare the expression of the MMP9 gene in cancerous and adjacent tissue of GC and evaluate its knockdown effects on GC cell line migration. Methods. In the present study, 50 tumor tissues and adjacent non-tumor control tissues were collected from patients with GC. Using a real-time polymerase chain reaction, the expression levels of the MMP9 gene were assessed in these samples. Additionally, bioinformatics methods were employed to analyze MMP9 expression in a larger cohort of GC patients. Furthermore, a data mining study was conducted to investigate the potential impact of MMP9 expression on the overall survival of GC patients. In addition, appropriate small interfering RNA (siRNA) was synthesized to suppress the MMP9 oncogene and transfected into the GC cell line, and migration was investigated eventually. Results. The results demonstrated significant upregulation of the MMP9 gene in tumor samples compared to tumor-adjacent samples, with a notable fold change of 4.6. This consistent finding was further supported by our bioinformatics analysis. Additionally, our pan-cancer analysis of TCGA data revealed that MMP9 is upregulated in various malignant tumors, indicating its potential relevance beyond GC. After MMP9 siRNA transfection, the migration rate of the cancer cells was evaluated by a wound-healing assay. The GC cell migration and invasion significantly decreased after the knockdown of MMP9 by specific siRNA. Conclusion. In general, our study showed MMP9 upregulation in GC and suggested that the transfection of MMP9 gene siRNA could reduce invasion and migration. Practical Implications. siRNAs are promising medical breakthroughs for the treatment of MMP9-related cancer invasion and migration. However, there is still a need to deepen our understanding of MMP9 gene function in tumorigenesis.

Tumor-colonized Streptococcus mutans metabolically reprograms tumor microenvironment and promotes oral squamous cell carcinoma

BackgroundOral squamous cell carcinoma (OSCC) remains a major death cause in head and neck cancers, but the exact pathogenesis mechanisms of OSCC are largely unclear.ResultsSaliva derived from OSCC patients but not healthy controls (HCs) significantly promotes OSCC development and progression in rat models, and metabolomic analyses reveal saliva of OSCC patients but not HCs and OSCC tissues but not adjacent non-tumor tissues contain higher levels of kynurenic acid (KYNA). Furthermore, large amounts of Streptococcus mutans (S. mutans) colonize in OSCC tumor tissues, and such intratumoral S. mutans mediates KYNA overproductions via utilizing its protein antigen c (PAc). KYNA shifts the cellular types in the tumor microenvironment (TME) of OSCC and predominantly expedites the expansions of S100a8highS100a9high neutrophils to produce more interleukin 1β (IL-1β), which further expands neutrophils and induces CD8 + T cell exhaustion in TME and therefore promotes OSCC. Also, KYNA compromises the therapeutic effects of programmed cell death ligand 1 (PD-L1) and IL-1β blockades in oral carcinogenesis model. Moreover, KYNA-mediated immunosuppressive program and aryl hydrocarbon receptor (AHR) expression correlate with impaired anti-tumor immunity and poorer survival of OSCC patients.ConclusionsThus, aberration of oral microbiota and intratumoral colonization of specific oral bacterium such as S. mutans may increase the production of onco-metabolites, exacerbate the oral mucosal carcinogenesis, reprogram a highly immunosuppressive TME, and promote OSCC, highlighting the potential of interfering with oral microbiota and microbial metabolism for OSCC preventions and therapeutics.5ViVJ5sCbraGF_6Zi1UXojVideo

Mitotic spindle positioning protein serves as prognostic biomarker in patients with colorectal cancer

Background Colorectal cancer (CRC) ranks among the most aggressive types of cancer globally. Currently, clinical tumor prognostic biomarkers still lack accuracy. Mitotic spindle positioning (MISP) protein connects microtubules to the actin cytoskeleton and adhesive plaques, playing a critical role in spindle positioning, orientation, and the process of cell division. MISP can regulate the malignant biological functions of pancreatic cancer and intrahepatic cholangiocarcinoma and it acts as biomarker for prognosis, but its role in CRC remains unclear. Methods This study has collected 37 CRC tissue samples and 37 corresponding adjacent nontumor tissue samples, and 57 additional CRC tissues samples. Clinical data were obtained from the patients with CRC. MISP mRNA and protein expression levels were analyzed in normal control and CRC tissues using the GEPIA and Human Protein Atlas website. MISP protein levels in the collected tissues were analyzed using immunohistochemistry. Results MISP mRNA and protein expression levels were significantly increased in CRC tissues compared to adjacent nontumor tissues. Higher MISP protein levels were associated with distant metastasis, recurrence, and lower survival rates. Kaplan–Meier analysis showed that high expression levels of MISP protein were associated with recurrence and death in CRC patients. In addition, a high expression level of MISP protein, lymph node metastasis, and distance metastasis were risk factors for recurrence and a poor prognosis in patients with CRC. Conclusion Elevated MISP protein correlated with tumor metastasis, recurrence, and lower survival rates in patients with CRC, and thus, MISP has the potential to become a prognostic marker for CRC.

The Immune Modulation HLA-G*01:01:01 Full Allele Is Associated with Gastric Adenocarcinoma Development.

The Human Leukocyte Antigen (HLA) system contains a set of genes involved at many levels in the innate and adaptive immune response. Among the non-classical HLA class I genes, HLA-G stands out for the numerous studies about its pivotal role in regulating/modulating immune responses. Also, its involvement in extravillous cytotrophoblast function, viral infections, autoimmunity, and cancer has been extensively documented. The present study explores for the first time the relationship between natural alleles of HLA-G, rather than STSs, SNPs, or partial gene polymorphisms, and the development of gastric adenocarcinoma, by analyzing the genetic profile of a cohort of 40 Spanish patients with this type of tumor using DNA extracted from paired biopsies of tumoral and adjacent non-tumoral gastric tissue. Our results reveal a significant statistical relationship between the presence of the HLA-G*01:01:01 allele and the development of gastric cancer, while other common alleles such as -G*01:04 or -G*01:05N did not demonstrate a significant correlation. Studying the involvement of HLA genes in the development of many diseases is relevant to understanding their pathophysiology. However, the absence of specific mechanisms underlying these associations suggests that investigating complete HLA natural alleles' extended haplotypes or complotypes may offer a more precise and valuable approach to elucidating the association of HLA with the pathogenesis of disease.

The branched N-glycan of PD-L1 predicts immunotherapy responses in patients with recurrent/metastatic HNSCC

Immunotherapy has revolutionized cancer treatment, but the lack of a reliable predictive biomarker for treatment response remains a challenge. Alpha-1,6-Mannosylglycoprotein 6-β-N-Acetylglucosaminyltransferase 5 (MGAT5) is a key regulator of complex N-glycan synthesis, and its dysregulation is associated with cancer progression. The lectin Phaseolus vulgaris leukoagglutinin (PHA-L) specifically binds to mature MGAT5 products. Previous studies have indicated elevated PHA-L staining in head and neck squamous cell carcinoma (HNSCC), which implies increased activity of MGAT5. However, the specific role of MGAT5 in HNSCC remains unclear. In this study, we found significantly higher PHA-L staining and MGAT5 expression in HNSCC tumors compared to adjacent non-tumor tissues. Using a mass spectrometry (MS)-based glycoproteomic approach, we identified 163 potential protein substrates of MGAT5. Functional analysis revealed that protein substrates of MGAT5 regulated pathways related to T cell proliferation and activation. We further discovered that PD-L1 was among the protein substrates of MGAT5, and the expression of MGAT5 protected tumor cells from cytotoxic T lymphocyte (CTL) killing. Treatment of nivolumab alleviated the protective effects of MGAT5 on CTL activity. Consistently, patients with MGAT5-positive tumors showed improved responses to immunotherapy compared to those with MGAT5-negative tumors. Using purified PD-L1 from HNSCC cells and a glycoproteomic approach, we further deciphered that the N35 and N200 sites carry the majority of complex N-glycans on PD-L1. Our findings highlight the critical role of MGAT5-mediated branched N-glycans on PD-L1 in modulating the interaction with the immune checkpoint receptor PD-1. Consequently, we propose that MGAT5 could serve as a biomarker to predict patients’ responses to anti-PD-1 therapy. Furthermore, targeting the branched N-glycans at N35 and N200 of PD-L1 may lead to the development of novel diagnostic and therapeutic approaches.

Value of miR-31 and miR-150-3p as diagnostic and prognostic biomarkers for breast cancer.

The most prevalent malignancy among women is breast cancer (BC). MicroRNAs (miRNAs) play a role in the initiation and progression of BC by influencing breast cancer stem cells (BCSCs) but the diagnostic and prognostic roles of those miRNAs on BC patients are still unknown. It was aimed to investigate expression profiles, diagnostic and prognostic potentials of BCSC-related miRNAs in different subtypes (Luminal A and B, HER2 + and TNBC) of BC patients. Expression analysis of 15 BCSC-related miRNAs was performed in 50 breast tumor tissues and 20 adjacent non-tumor tissues obtained from BC patients using the qRT-PCR method. The expression levels of miR-31 and miR-150-3p were significantly upregulated in the tumor tissues compared to the adjacent non-tumor tissues (p < 0.05). miR-31 expression upregulated in the Luminal A and Luminal B group compared to non-tumor tissue (p < 0.05). miR-31 expression was determined to be significantly higher in the Luminal group (Luminal A and B) compared to the aggressive group (HER2 + and TNBC) (p < 0.05). According to the ROC analysis, the area under the curve (AUC) of miR-31 and miR-150-3p were 0.66 with a sensitivity of 68% and a specificity of 70%. A significant inverse correlation was observed between miR-31 expression with metastatic carcinoma status, in situ component, and Ki67 value in tumors, and high miR-150-3p expression was correlated with p63 expression (p < 0.05). miR-31 and miR-150-3p have the potential to serve as biomarkers for guiding diagnosis, evaluating prognosis, and metastatic process in patients with BC.

BRD9 promotes the progression of gallbladder cancer via CST1 upregulation and interaction with FOXP1 through the PI3K/AKT pathway and represents a therapeutic target

Gallbladder cancer (GBC) is highly aggressive and has poor prognosis, with most patients only diagnosed at an advanced stage. Furthermore, treatment options are limited, and their effect is unsatisfactory. Bromodomain-containing protein (BRD) is an epigenetic regulator that plays a carcinogenic role in several tumors, including squamous cell lung cancer, acute myeloid leukemia, synovial sarcoma, and malignant rhabdomyosarcoma. However, the expression, biological function, and molecular mechanisms of action of BRD9 in GBC are still unknown. Kaplan–Meier analysis, qRT-PCR, and analysis of clinical features were used to assess the clinical significance of BRD9 in GBC. Cell Counting Kit-8 and colony formation assays were performed to determine the effects of BRD9 on cell growth. The functional role of BRD9 in GBC was explored using qRT-PCR, western blotting, siRNA, and CHIP-qPCR. mRNA sequencing was performed to explore the underlying mechanisms of BRD9, and a nude mouse model of GBC was established to explore the anti-tumor effects of the BRD9 inhibitor I-BRD9 in vivo. BRD9 expression was elevated in GBC tissues compared with adjacent non-tumor tissues, and high BRD9 expression was associated with poor prognosis in patients with GBC. BRD9 knockdown by siRNA significantly decreased cell growth. Targeting BRD9 with I-BRD9 inhibited the proliferation of GBC cells without significant toxic effects. Additionally, I-BRD9 treatment suppressed CST1 expression in GBC cell lines, thereby inhibiting the PI3K-AKT pathway. The transcription factor FOXP1 was found to interact with BRD9 to regulate CST1 expression. Collectively, these results suggest that BRD9 may be a promising biomarker and therapeutic target for GBC.

Abstract C101: Shared gene expression pattern among breast cancer subtypes and its association with prognostic variables in Colombian patients

Abstract Introduction: The current molecular classification of breast cancer has significantly improved treatment targeting and disease prognosis. However, the heterogeneity among subtypes also poses a limitation when proposing new targets that integrate common biological processes, hindering their applicability across the entire spectrum of the disease. In that sense, it is essential to gain a deeper understanding of the similarities and common mechanisms involved in the molecular subtypes of breast cancer. Therefore, in this study, we aimed to identify shared differentially expressed genes (DEGs) and biological processes among the different breast cancer subtypes that could potentially impact the presentation of clinically significant variables in Colombian patients diagnosed at the National Cancer Institute (NCI). Methods: We included 97 women diagnosed with breast cancer at the NCI in Colombia. From each patient, we collected tumor biopsy and adjacent non-tumoral tissue for RNA extraction and sequencing (RNA-seq). A comparative analysis of DEGs and gene set enrichment (GSE) was performed between tumor tissue and its corresponding adjacent non-tumor tissue for each subtype independently to identify common DEGs and enriched biological processes. Shared over- and under-expressed genes in at least two subtypes were tested for their association with clinically significant prognostic variables. Results: Among breast cancer subtypes, ER-/HER2+ and ER-/HER2- tumors showed the highest number of shared DEGs (22 genes), of which 19 were over-expressed and 3 under-expressed. In contrast, GSE analysis revealed a high proportion of shared biological processes (5), molecular functions (3), and cellular component classification (11) between ER+/HER2+ and ER-/HER2+ tumors, corresponding to mechanisms involved in tissue homeostasis and extracellular matrix structural constituents. Furthermore, the association with clinically significant prognostic variables was assessed for 22 over-expressed genes and 9 under-expressed genes shared in at least two subtypes. Of this set of 31 genes, 9 were significantly associated with the degree of tumor differentiation measured by the Bloom-Richardson (BR) score. Interestingly, tumor suppressor genes like ADAMTS18 showed a decline in expression as the BR score increased (fold-change (FC) in BR I: 14 vs BR II: 11; BR III: 5, p-value: 0.028). Conversely, oncogenes like EFNA4 showed the opposite trend, with an increase in expression as the BR score also increased (FC in BR I: 9 vs. BR II: 11 vs. BR III: 17, p-value: 0.019). Another identified shared over-expressed gene, JPT1, which is involved in β-catenin signaling, was found to be associated not only with higher BR scores but also with a higher proliferation index Ki67 (FC in &amp;lt;20%: 16.5 vs. ≥20%: 23; p-value: 0.05). Conclusions: Despite the high degree of molecular heterogeneity among subtypes, it is still possible to identify shared over and under-expressed genes in at least 2 subtypes with significant prognostic implications in breast cancer subtypes. Citation Format: Laura Rey-Vargas, Lina Maria Bejarano, Diego Felipe Ballen-Lozano, Silvia J. Serrano-Gomez. Shared gene expression pattern among breast cancer subtypes and its association with prognostic variables in Colombian patients [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C101.

Exploring serine-arginine rich splicing factors: potential predictive markers for dysregulation in oral cancer

BackgroundDysregulated splicing events are a common phenomenon in cancer with the Serine-arginine-rich splicing factor (SRSF) family emerging as pivotal regulators of gene expression, exerting influence over constitutive and alternative splicing processes. Although aberrations in a few SRSF family members have been implicated in various cancers, the comprehensive roles of other family constituents remain underexplored.MethodsThis study delves into the expression profile of the entire SRSF family (SRSF1-SRSF12) in 23 cancerous cell lines originating from diverse tissues using quantitative Real-Time PCR. Further, the transcript levels of the SRSF family were examined in oral cancer patient samples stratified into Pre-cancer (n = 15), Early cancer (n = 11), Late cancer (n = 14), and adjacent non-tumor tissues (n = 26) as controls. The results were corroborated by a parallel investigation utilizing the transcriptomics data of oral squamous cell carcinoma (OSCC) patients (n = 319) and controls (n = 35) available in The Cancer Genome Atlas (TCGA) database.ResultsOur investigation reveals a notable upregulation in the expression levels of key splicing factors, namely SRSF3, SRSF9, and SRSF10 in all oral cancer cell lines (SCC-4, UM-SCC-84, CAL33, SAS-H1). Conversely, no significant associations between SRSF family members and other cancer cell lines were discerned. Further, the expression profile of the SRSF family in oral cancer patient samples revealed significant upregulation of SRSF1, SRSF3, SRSF7, SRSF9, SRSF10, and SRSF11 in patients with late-stage oral cancer compared to controls. Transcriptomics data from TCGA database demonstrated remarkable upregulation of SRSF1, SRSF4, SRSF9, SRSF10, and SRSF11 in OSCC patients.ConclusionCollectively our results underscore the critical involvement of SRSF family members in the context of oral cancer, highlighting their potential as key players in the altered splicing dynamics associated with cancer progression.Graphical abstract

Telomere transcripts act as tumor suppressor and are associated with favorable prognosis in colorectal cancer with low proliferating cell nuclear antigen expression.

Telomeric repeat-containing RNAs (TERRA) and telomerase RNA component (TERC) regulate telomerase activity (TA) and thereby contribute to telomere homeostasis by influencing telomere length (TL) and the cell immortality hallmark of cancer cells. Additionally, the non-canonical functions of telomerase reverse transcriptase (TERT) and TERRA appear to be involved in the epithelial-mesenchymal transition (EMT), which is important for cancer progression. However, the relationship between TERRA and patient prognosis has not been fully characterized. In this small-scale study, 68 patients with colorectal cancer (CRC) were evaluated for correlations between telomere biology, proliferation, and EMT gene transcripts and disease outcome. The proliferating cell nuclear antigen (PCNA) and the epithelial splicing regulatory proteins 1 and 2 (ESRP1 and ESRP2) showed a positive correlation with TERRA, while TA and TERRA exhibited an inverse correlation. Consistent with previous findings, the present study revealed higher expression levels of TERT and TERC, and increased TA and TL in CRC tumor tissue compared to adjacent non-tumor tissue. In contrast, lower expression levels of TERRA were observed in tumor tissue. Patients with high TERRA expression and low PCNA levels exhibited favorable overall survival rates compared to individuals with the inverse pattern. Furthermore, TERRA suppressed CRC tumor growth in severe combined immunodeficiency disease (SCID) mice. In conclusion, our study extends previously published research on TERRA suggesting its potential therapeutic role in telomerase-positive CRC.

Construction and verification of an innovative immune-related and hallmark gene sets prognostic model for bladder cancer.

Bladder cancer (BC) is a life-threatening malignancy with high mortality rates. Current prognostic models are insufficient in accurately predicting clinical outcomes, impeding personalized treatment strategies. This study aimed to identify BC subtypes and prognostic gene sets by analyzing changes in immune and hallmark gene sets activity in tumor and adjacent non-tumor tissues to enhance patient outcomes. Utilizing data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), gene set variation analysis (GSVA) was applied to C7 immune-related and hallmark gene sets from the Molecular Signatures Database (MSigDB). The CancerSubtype R package was utilized for clustering these gene sets into three categories, from which 109 candidate sets were identified using Venn diagrams. A refined subset of seven gene sets was selected through least absolute shrinkage and selection operator (LASSO) regression for the construction of a risk model. Model validity was confirmed with receiver operating characteristic (ROC) and calibration curves, and a nomogram was constructed to integrate risk scores with clinical parameters. Finally, genes from the gene sets of the model were acquired and analyzed for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment and protein-protein interactions (PPI) via plugin Molecular Complex Detection (MCODE) and Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) in Cytoscape in both tumor and non-tumor tissues. Three BC subtypes were characterized by immunologic and hallmark gene sets, with subtype 1 patients showing worse survival. The prognostic model, based on seven gene sets, effectively stratified risk, with high-risk patients having significantly shorter survival. GO, KEGG, and PPI analyses indicated distinct influences of non-tumor and tumor tissues on the prognosis of BC patients. We constructed and validated a novel prognostic model for risk stratification in BC based on immunologic and hallmark genes sets, which presents a novel perspective on rational treatment approaches and accurate prognostic evaluations for BC by considering both tumor and adjacent non-tumor tissues. This highlights the importance of focusing on alterations in both tumor and adjacent non-tumor tissues, rather than solely on the tumor itself.

TCF4 as a potential prognostic biomarker and an anticancer target in gastric cancer.

Lymphoid enhancer-binding factor 1 (LEF1)/T cell factor (TCF) family members are key transcription factors in malignant tumors. In this study, the role of T cell factor 4 (TCF4) in the progression of gastric cancer (GC) cell migration and invasion was investigated. Fifty-five pairs of GC tissues and adjacent non-tumor tissues were collected for evaluating the expression of LEF1/TCF family members, which were also evaluated by the Gene Expression Profiling Interactive Analysis (GEPIA) database, an online analysis platform based on The Cancer Genome Atlas and Genotype-Tissue Expression databases. Through GEPIA online analysis and our experimental specimens, we found that TCF4 messenger RNA (mRNA) expression was significantly upregulated in GC tissues compared with normal non-tumor tissues. The findings from protein-protein interaction (PPI) analysis suggested that myocyte enhancer factor 2C (MEF2C) may function as a regulatory gene for TCF4 and play a role in the progression of GC. A significant increase in TCF4 mRNA expression was observed in the GC cell lines. Silencing of TCF4 led to significant inhibition of the proliferation, migration, and invasion of the MGC-803 and SGC-7901 cells. TdT-mediated dUTP nick end labeling (TUNEL)-positive staining cells were significantly increased after transfection with TCF4 small interfering (si)-RNA into GC cells. In addition, patients with GC with high TCF4 expression were associated with poor T stage, pathologic stages, histologic grade, overall survival, and recurrence-free survival, indicating that TCF4 may be a potential prognostic marker of GC. TCF4 potentially exerts a carcinogenic role in the progression of GC. TCF4 may serve as a prognostic indicator and therapeutic target for GC.

GATA4 downregulation enhances CCL20-mediated immunosuppression in hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is a deadly cancer with a high global mortality rate, and the downregulation of GATA binding protein 4 (GATA4) has been implicated in HCC progression. In this study, we investigated the role of GATA4 in shaping the immune landscape of HCC. HCC tumor samples were classified into "low" or "normal/high" based on GATA4 RNA expression relative to adjacent non-tumor liver tissues. The immune landscapes of GATA4-low and GATA4-normal/high tumors were analyzed using cytometry by time-of-flight, bulk/spatial transcriptomic analyses and validated by multiplex immunofluorescence. GATA4-low tumors displayed enrichment in exhausted programmed cell death protein 1+ T cells, immunosuppressive regulatory T cells, myeloid-derived suppressor cells, and macrophages, highlighting the impact of GATA4 downregulation on immunosuppression. Spatial and bulk transcriptomic analyses revealed a negative correlation between GATA4 and C-C Motif Chemokine Ligand 20 (CCL20) expression in HCC. Overexpressing GATA4 confirmed CCL20 as a downstream target, contributing to an immunosuppressive tumor microenvironment, as evidenced by increased regulatory T cells and myeloid-derived suppressor cells in CCL20-high tumors. Lastly, the reduced expression of GATA4 and higher expression of CCL20 were associated with poorer overall survival in patients with HCC, implicating their roles in tumor progression. Our study reveals that GATA4 downregulation contributes to an immunosuppressive microenvironment, driven by CCL20-mediated enrichment of regulatory T cells and myeloid-derived suppressor cells in HCC. These findings underscore the critical role of GATA4 reduction in promoting immunosuppression and HCC progression.

A novel m6A reader RBFOX2 expression is increased in oral squamous cell carcinoma and promotes tumorigenesis

Background and ObjectiveOral squamous cell carcinoma (OSCC) is a significant global health concern due to its aggressive nature and poor prognosis. Recent research has highlighted the important role of RNA modifications in cancer biology, especially N6-methyladenosine (m6A) modifications, which are controlled by a complex interplay of m6A regulators. This study specifically investigates RBFOX2, a new m6A reader, and its involvement in OSCC. MethodsOur study primarily utilized OSCC tissue, adjacent normal tissue samples, OSCC cell lines, and normal healthy oral keratinocytes to validate RBFOX2 mRNA expression. Additionally, we used the TCGA-HNSCC dataset for large cohort analysis and clinicopathological characterization. Furthermore, we visualized the RBFOX2 network to identify the primary functions of the protein. ResultsOur research shows a noticeable increase in RBFOX2 expression in OSCC tissues compared to adjacent non-tumorous tissues, as determined by quantitative PCR and immunohistochemistry analyses. Functional pathway enrichment analysis revealed that RBFOX2 is involved in the receptor tyrosine kinase signaling pathway and the Hippo signaling pathway, which plays a critical role in oral cancer development and progression. Clinically, elevated RBFOX2 expression correlated with advanced tumor stages and poorer patient outcomes, demonstrating its prognostic value. These findings indicate that RBFOX2 acts as an oncogenic driver in OSCC as an m6A reader, facilitating the expression of m6A-modified oncogenes. ConclusionOur study identifies RBFOX2 as a critical player in OSCC pathogenesis and opens avenues for novel therapeutic strategies targeting the m6A regulatory machinery in this malignancy.