Analysis Of The Cancer Genome Atlas Data Research Articles

A novel amino acid metabolism-related gene signature to predict the overall survival of esophageal squamous cell carcinoma patients.

Esophageal squamous cell carcinoma (ESCC) has a poor early detection rate, prognosis, and survival rate. Effective prognostic markers are urgently needed to assist in the prediction of ESCC treatment outcomes. There is accumulating evidence of a strong relationship between cancer cell growth and amino acid metabolism. This study aims to determine the relationship between amino acid metabolism and ESCC prognosis. This study comprehensively evaluates the association between amino acid metabolism-related gene (AAMRG) expression profiles and the prognosis of ESCC patients based on data from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases. Real-time quantitative polymerase chain reaction (RT-qPCR) was used to verify the expression of prognosis-related genes. A univariate Cox regression analysis of TCGA data identified 18 prognosis-related AAMRGs. The gene expression profiles of 90 ESCC tumor and normal tissues were obtained from the GSE20347 and GSE67269 datasets. Two differently expressed genes (DEGs) were considered as ESCC prognosis-related genes; and they were branched-chain amino acid transaminase 1 (BCAT1) and methylmalonic aciduria and homocystinuria type C protein (MMACHC). These two AAMRGs were used to develop a novel AAMRG-related gene signature to predict 1- and 2-year prognostic risk in ESCC patients. Both BCAT1 and MMACHC expression were verified by RT-qPCR. A prognostic nomogram that incorporated clinical factors and BCAT1 and MMACHC gene expression was constructed, and the calibration plots showed that it had good prognostic performance. The AAMRG signature established in our study is efficient and could be used in clinical settings to predict the early prognosis of ESCC patients.

Overexpression of ZNF169 promotes the growth and proliferation of colorectal cancer cells via the upregulation of ANKZF1.

Colorectal cancer (CRC) is one of the most common malignancies worldwide. The 5‑year survival rate of patients diagnosed with the early stages of the disease is markedly higher than that of patients in the advanced stages. Therefore, identifying novel biomarkers and drug targets for CRC is critical for clinical practice. Zinc finger protein 169 (ZNF169) is a crucial transcription factor, and its role in CRC remains to be explored. The present study aimed to investigate the clinical relevance, function and underlying mechanisms of ZNF169 in CRC growth and proliferation. The Cancer Genome Atlas (TCGA) database was utilized to analyze the clinical relevance of ZNF169 in patients with CRC. Immunohistochemical staining was performed on tissue samples from patients with CRC to detect the expression of ZNF169. The HCT‑116, HT‑29 and RKO cell lines were employed for in vitro experiments. The overexpression and knockdown of ZNF169 were achieved by transfecting the cells with lentivirus and small interfering RNAs, respectively. Cell Counting Kit‑8, colony formation and EdU staining assays were applied to investigate the function of ZNF169 in CRC cells. Dual luciferase activity and chromatin immunoprecipitation (ChIP)‑quantitative PCR (qPCR) assays were performed to identify the regulatory effects of ZNF169 on the ankyrin repeat and zinc‑finger domain‑containing 1 (ANKZF1; also known as ZNF744) gene. Reverse transcription‑quantitative PCR and western blot analysis were performed to measure mRNA and protein expression, respectively. The analysis of TCGA data revealed a positive correlation between ZNF169 and ANKZF1, with the overexpression of ANKZF1 being associated with a poor prognosis of patients with CRC. The experimental results demonstrated that ZNF169 was expression upregulated in CRC tissue compared with that in normal colon tissue. Gain‑of‑function and loss‑of‑function experiments revealed that ZNF169 enhanced the intensity of EdU staining, promoting the growth and proliferation of CRC cells. Furthermore, the overexpression of ZNF169 potentiated the transcriptional activity of the ANKZF1 gene, while the knockdown of ZNF169 produced the opposite results. ChIP‑qPCR confirmed the interaction between ZNF169 and the promoter sequence of ANKZF1. Rescue experiments revealed that ZNF169 accelerated CRC cell growth and proliferation through the upregulation of ANKZF1. Furthermore, there was a positive correlation identified between ZNF169 and ANKZF1, and upregulation of ANKZF1 expression was associated with the poor prognosis of patients with CRC. On the whole, the present study demonstrates that ZNF169 contributes to CRC malignancy by potentiating the expression of ANKZF1. Thus, the regulation of ZNF169 and/or ANKZF1 expression may represent a viable strategy for the treatment patients with CRC with a high expression of ZNF169.

Prognostic significance of connective tissue growth factor expression in stromal cells in patients with diffuse‑type gastric cancer.

Connective tissue growth factor (CTGF) is a target gene of the Hippo signaling pathway. Its differential role in the histological types of gastric cancer (GC) remains unknown; therefore, the present study aimed to confirm the clinical significance of CTGF expression in cancer and stromal cells in patients with GC depending on the histological type. The present study enrolled 589 patients with GC. Immunohistochemistry was used to analyze CTGF expression in cancer and stromal cells. CTGF mRNA expression data and the corresponding clinical information of GC samples were collected from The Cancer Genome Atlas (TCGA) database. Subsequently, the associations between CTGF expression and several clinicopathological factors were investigated. In the present study, CTGF expression was mainly observed in the cytoplasm of cancer and stromal cells. CTGF expression in stromal cells was significantly associated with CTGF expression in cancer cells (P<0.001). CTGF positivity in stromal cells was also significantly associated with intestinal type, non-scirrhous type, tumor depth (T1-2), lymph node metastasis (negative), lymphatic invasion (negative) and tumor size (<5 cm). Low CTGF expression in stromal cells was independently associated with worse overall survival (OS). Furthermore, the OS of patients with low CTGF expression in stromal cells, especially in patients with diffuse-type GC, was significantly worse than patients with high CTGF expression (P=0.022). This trend was similar to that revealed by TCGA data analysis. In conclusion, low CTGF expression was associated with a significantly worse OS in patients with diffuse-type GC. These data indicated that CTGF, and its control by the Hippo pathway, may be considered potential treatment targets in diffuse-type GC.

ZNF26-Associated Genes as Prognostic Signatures in Colorectal Cancer with Broad Therapeutic Implications.

The identification of biomarkers correlated with colorectal cancer (CRC) prognosis holds substantial importance from both clinical and scientific perspectives. Zinc finger protein 26 (ZNF26) has not been previously investigated or documented in solid tumors; thus, further research is necessary to ascertain its prognostic value in CRC. Gene expression profiles and clinicopathological data were acquired from The Cancer Genome Atlas (TCGA) database. Subsequently, expression correlation was assessed utilizing the TCGA CRC cohort. The prognostic value of ZNF26 was evaluated through Kaplan-Meier (KM) and ROC curve analyses. Following this, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted to perform enrichment analysis between high- and low-ZNF26 expression groups. The association between immune cells, immune checkpoint genes, and ZNF26 expression levels was examined. Lastly, the research findings were further validated using CRC tissue samples. The results revealed that, in comparison to healthy controls, CRC significantly reduced ZNF26 expression. Elevated ZNF26 expression was associated with poorer overall survival in CRC patients. Additionally, high ZNF26 expression exhibited an inverse relationship with the immunological score and immune checkpoint gene expression in CRC patients. The findings from the TCGA data analysis were corroborated by the PCR results obtained from CRC tissue samples. ZNF26 is markedly upregulated in colorectal cancer tissues, potentially serving as a biomarker for CRC.

Abstract 3500: Refining diagnosis of renal cell carcinoma subtypes through single-cell resolution transcriptomic signatures

Abstract A remaining challenge in the field of renal cell carcinoma (RCC) is diagnosis of rare or mixed subtypes, which hampers the delivery of the most effective healthcare to patients. While a new classification scheme, integrating molecular characteristics of tumors, is emerging, it requires a deep understanding of the tumor heterogeneity and etiopathogenesis of each subtype. We have generated and analyzed single-cell transcriptome profiles of 38 human RCCs and normal kidneys 16 RCCs with diverse histological subtypes and established gene signatures specific to each cell type. We have applied these gene signatures to bulk RNA-sequencing data of 1000 RCC tumors with different histological subtypes and normal kidneys from The Cancer Genome Atlas (TCGA) to characterize different cancer types and cellular origins. Unsupervised clustering analysis of TCGA data shows diagnostic discrepancies for 9.3% cases and subclassifies each major subtype (clear cell, papillary and chromophobe) into clusters with differential clinical outcomes.[KM1]. The pathological marker expression in misdiagnosed tumors is consistent with clustering-based classification, not their original diagnosis. Notably, using unique and subtype-specific gene signature patterns, we identified clear cell papillary renal cell tumor (ccpRCT), which is a newly classified benign entity and the main tumor type representing the mis-diagnosed tumors. These observations have further been confirmed by reviewing histological images of the tumors by an experienced genitourinary pathologist. Interestingly, our gene signatures reveal that ccpRCT does not originate from proximal tubule cells unlike clear cell and papillary RCCs. Taken together, our approach suggests a potential new classification method connected to clinical behaviors and drug responses based on overall transcriptomic differences. Citation Format: Minjun Kim, Ariel Madrigal, Zohreh Mehrjoo, Kate I. Glennon, Madeleine Arseneault, Morag Park, Fadi Brimo, Simon Tanguay, Hamed S. Najafabadi, Yasser Riazalhosseini. Refining diagnosis of renal cell carcinoma subtypes through single-cell resolution transcriptomic signatures [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3500.

Downregulation of long noncoding RNA B4GALT1-AS1 is associated with breast cancer development

The misregulation of long non-coding RNAs (lncRNAs) is related to the progressive evolution of various human cancers, such as Breast cancer (BC). The role of lncRNA B4GALT1-AS1 has been investigated in some human cancers. Therefore, studying B4GALT1-AS1 expression was aimed for the first time in the tumor and marginal tissues of BC in this study. The cancer genome atlas (TCGA) database was utilized to evaluate the relative expression of B4GALT1-AS1 in BC and other cancers. RNA was extracted from twenty-eight paired BC and marginal tissues, and cDNA was synthesized. The quantitative expression level of B4GALT1-AS1 was evaluated using real-time PCR. The bioinformatics analyses were performed to identify co-expression genes and related pathways. B4GALT1-AS1 was significantly downregulated in BC specimens compared to tumor marginal samples. The TCGA data analysis confirmed the downregulation of B4GALT1-AS1 in BC. The bioinformatics analysis discovered the correlation between 700 genes and B4GALT1-AS1 and identified GNAI1 as the high degree gene which was positively correlated with B4GALT1-AS1 expression. It seems B4GALT1-AS1 provides its function, at least partly, in association with one of the hippo pathway components, YAP, in other cancers. This protein has the opposite role in BC and its loss of function can result in poor survival in BC. Further research is needed to investigate the interaction between B4GALT1‐AS1 and YAP in various subtypes of BC.

Integrated analysis of TCGA data identifies endoplasmic reticulum stress-related lncRNA signature in stomach adenocarcinoma

Abstract Objectives To investigaed the role of endoplasmic reticulum stress (ERS)-related long non-coding RNAs (lncRNAs) in stomach adenocarcinoma (STAD) using TCGA data. Methods This study integrated clinical, transcriptomic, and tumor data from the Cancer Genome Atlas (TCGA). The expression of ERS genes was evaluated, alongside their association with identified lncRNAs. Gene set enrichment analysis and immune cell infiltration analysis were performed to elucidate the biological pathways influenced by these lncRNAs. Results The study identified five lncRNAs – AC012055.1, LINC01235, LINC00571, LINC02073, and CFAP61-AS1 – strongly correlated with ERS pathways and cancer prognosis. A prognostic model based on these lncRNAs was developed and validated across low- and high-risk groups. Potential biological pathways associated with these lncRNAs were uncovered through immune cell infiltration and GSEA. Additionally, screening identified drugs potentially effective against STAD, highlighting co-expressed genes as probable therapeutic targets. Conclusions This research offers detailed insights into the molecular mechanisms of STAD, enhancing understanding of potential therapeutic targets and showing promise for clinical applications.

CA9 and PRELID2; hypoxia-responsive potential therapeutic targets for pancreatic ductal adenocarcinoma as per bioinformatics analyses

A strong hypoxic environment has been observed in pancreatic ductal adenocarcinoma (PDAC) cells, which contributes to drug resistance, tumor progression, and metastasis. Therefore, we performed bioinformatics analyses to investigate potential targets for the treatment of PDAC. To identify potential genes as effective PDAC treatment targets, we selected all genes whose expression level was related to worse overall survival (OS) in The Cancer Genome Atlas (TCGA) database and selected only the genes that matched with the genes upregulated due to hypoxia in pancreatic cancer cells in the dataset obtained from the Gene Expression Omnibus (GEO) database. Although the extracted 107 hypoxia-responsive genes included the genes that were slightly enriched in angiogenic factors, TCGA data analysis revealed that the expression level of endothelial cell (EC) markers did not affect OS. Finally, we selected CA9 and PRELID2 as potential targets for PDAC treatment and elucidated that a CA9 inhibitor, U-104, suppressed pancreatic cancer cell growth more effectively than 5-fluorouracil (5-FU) and PRELID2 siRNA treatment suppressed the cell growth stronger than CA9 siRNA treatment. Thus, we elucidated that specific inhibition of PRELID2 as well as CA9, extracted via exhaustive bioinformatic analyses of clinical datasets, could be a more effective strategy for PDAC treatment.

Prognostic and immunological potential of PPM1G in lung adenocarcinoma.

Lung cancer is one of the most common types of cancer worldwide, with the highest incidence and mortality rates. Protein phosphatase, Mg2+/Mn2+ dependent 1G (PPM1G) is a serine/threonine phosphatase, which is involved in the proliferation, invasion and metastasis of tumor cells. However, there are few reports on the role of PPM1G in lung adenocarcinoma (LUAD). The present study used publicly available data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus databases to evaluate the expression of PPM1G in LUAD, and to assess the relationship between PPM1G expression and the prognosis of patients with LUAD. Protein expression data of PPM1G obtained by immunohistochemical staining were collected from the Human Protein Atlas database. The correlation between PPM1G and immune cell infiltration and immune checkpoints was analyzed by single‑sample gene set enrichment analysis of TCGA data. The Kaplan‑Meier method was used for survival analysis, and univariate and multivariate Cox regression were used to analyze the effect of PPM1G on prognosis with data from TCGA database. The results showed that PPM1G was highly expressed in LUAD cancer tissues. The high expression of PPM1G was associated with poor clinical stage, T stage, N stage and overall survival in LUAD. The present study screened 29 genes related to PPM1G and closely related to the cell cycle in patients with LUAD. The expression of PPM1G was positively correlated with γδ‑Τ cells, T helper 2 cells and natural killer CD56dim cells, and was negatively correlated with B cells, mast cells, plasmacytoid dendritic cells, T helper cells, macrophages, T cells, CD8 T cells, central memory T cells, effector memory T cells, neutrophils and T follicular helper cells. In addition, PPM1G was positively correlated with immune detection points. In conclusion, PPM1G may be involved in the control of the lung cancer cell cycle, and could be associated with prognosis and immune infiltration in patients with LUAD.

Reduced YAP1 and FOLR1 in gliomas predict better response to chemotherapeutics

Gliomas harbouring mutations in IDH1 (isocitrate dehydrogenase 1) are characterized by greater sensitivity to chemotherapeutics. These mutants also exhibit diminished levels of transcriptional coactivator YAP1 (yes-associated protein 1). Enhanced DNA damage in IDH1 mutant cells, as evidenced by γH2AX formation (phosphorylation of histone variant H2A.X) and ATM (serine/threonine kinase; ataxia telangiectasia mutated) phosphorylation, was accompanied by reduced FOLR1 (folate receptor 1) expression. Diminished FOLR1, concomitant with heightened γH2AX levels, was also observed in patient-derived IDH1 mutant glioma tissues. Chromatin immunoprecipitation, overexpression of mutant YAP1, and treatment with YAP1-TEAD (TEA domain transcription factors) complex inhibitor verteporfin demonstrated regulation of FOLR1 expression by YAP1 and its partner transcription factor TEAD2. TCGA (The Cancer Genome Atlas) data analysis demonstrated better patient survival with reduced FOLR1 expression. Depletion of FOLR1 rendered IDH1 wild-type gliomas more susceptible to temozolomide-mediated death. Despite heightened DNA damage, IDH1 mutants exhibited reduced levels of IL6 (interleukin 6) and IL8 (interleukin 8) – pro-inflammatory cytokines known to be associated with persistent DNA damage. While both FOLR1 and YAP1 influenced DNA damage, only YAP1 was involved in regulating IL6 and IL8. ESTIMATE and CIBERSORTx analyses revealed the association between YAP1 expression and immune cell infiltration in gliomas. By identifying the influence of YAP1-FOLR1 link in DNA damage, our findings suggest that simultaneous depletion of both could amplify the potency of DNA damaging agents, while concomitantly reducing the release of inflammatory mediators and potentially affecting immune modulation. This study also highlights the novel role of FOLR1 as a probable prognostic marker in gliomas, predicting responsiveness to temozolomide and other DNA damaging agents.

Abstract 5572: A COX-2-based pro-tumourigenic inflammatory signature predicts poor outcome in early-stage non-small cell lung cancer

Abstract Lung cancer is the most common cause of cancer-related deaths with Non-Small Cell Lung Cancer (NSCLC) accounting for ~85% of cases. Patients with early-stage NSCLC (stages I-IIIA) undergo surgery with curative intent but up to 30% relapse. Identification of biomarkers that predict outcome at the point of surgery could inform patient management. Here, we explored whether a COX-2-based pro-tumourigenic inflammatory gene signature (PTI), measured in surgically resected samples from early-stage NSCLC patients, can predict patient outcome. Gene expression analysis was performed on 30 formalin fixed paraffin embedded surgical tumour samples from early-stage NSCLC patients with 36-63 months follow-up, using a custom code-set on the NanoString nCounter® platform. Additionally, in silico analysis of early-stage NSCLC data from The Cancer Genome Atlas (TCGA) was undertaken. The PTI gene signature and a published signature associated with T cell-inflamed tumours measuring IFNγ activity (IFNG)1 were assessed in both datasets and correlated with patient outcome. NanoString gene expression data was robust, displaying good correlations with immunohistochemistry (IHC) expression for key proteins such as CD8 and COX-2, R=0.88, p&amp;lt;1 × 10−6 and R=0.83, p&amp;lt;1 × 10−6, respectively. The IFNG signature score, widely reported to associate with response to checkpoint inhibitors2, did not correlate with outcome and consistent with this observation neither did CD8 protein expression (by IHC). In contrast, patients with LUSC (n=16) with the highest (upper quartile) PTI score showed significantly worse overall survival (p&amp;lt;0.01). Median overall survival for these PTIhigh patients was &amp;lt;6 months vs 4.5 years for LUSC patients with PTIlow scores. Analysis of TCGA data from stage I-IIIA LUAD/LUSC cases confirmed these contrasting findings for the PTI compared with the IFNG signature. A multiplexed IHC panel for immune contexture analysis was successfully transferred from the Coussens Laboratory Oregon to CRUK Manchester3 and with inclusion of COX-2 in this panel and adaptation of the pipeline for use with the HALO image analysis platform, analysis of the immune contexture in PTI high versus low tumours is underway. Transcriptional profiling of early-stage NSCLC samples revealed that COX-2-associated inflammation predicts patient outcome following surgery. These data highlight the importance of pro-tumourigenic inflammation in early-stage NSCLC. Findings are under validation in a larger cohort, including early-stage NSCLC samples from Manchester’s early-detection screening studies and mapping of the immune contexture of PTI high versus low tumours is underway. 1: Ayers, M., et al., J Clin Invest., 2017 2: Danaher, P., et al., J Immunother Cancer., 2018 3: Banik, G., et al., Methods Enzymol., 2020 Citation Format: Victoria Fife, Matthew Roberts, Christian P. Bromley, Derrick Morgan, Sophie Atkinson, Cong Zhou, Anshuman Chaturvedi, Steven Bagley, Garry Ashton, Lisa M. Coussens, Philip A. Crosbie, Caroline Dive, Elaine Kilgour, Santiago Zelenay. A COX-2-based pro-tumourigenic inflammatory signature predicts poor outcome in early-stage non-small cell lung cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5572.

Abstract 4396: TROP2 expression in non-small cell lung cancer

Abstract Introduction: Non-small cell lung cancer (NSCLC) is a major cause of cancer-related deaths globally with high unmet need. A variety of novel therapeutic strategies are being explored to improve patient outcomes including the use of antibody drug conjugates (ADCs) to deliver highly potent, cytotoxic payloads to tumors. Trophoblast cell-surface antigen 2 (TROP2), also known as tumor-associated calcium signal transducer 2 (TACSTD2), has emerged as an attractive target for ADCs. Sacituzumab govitecan-hziy is a novel ADC composed of a TROP2 antibody coupled to SN-38 and is being evaluated in NSCLC. High TROP2 mRNA expression is observed in many tumor types, however, TROP2 protein expression in NSCLC is not well-established. Here we characterized TROP2 expression across three independent datasets to explore the TROP2 relationship to baseline characteristics, molecular features of interest, and its prognostic value in NSCLC. Methods: We analyzed three independent datasets: (1) The Cancer Genome Atlas (TCGA) NSCLC adenocarcinoma (LUAD, N=660) and squamous cell carcinoma (LUSC, N=484) mRNA expression data, (2) a NSCLC adenocarcinoma FFPE tumor sample set (“Translational data set”; N=107), (3) an independent clinical NSCLC adenocarcinoma (N=103) and squamous cell carcinoma (N=37) data set. TROP2 IHC was performed on tumor sample sets (2) and (3) using the SP295 antibody (Robust Prototype Assay, Ventana) with H-Score and assessment of the percentage of membrane-positive tumor cells as readouts. Wilcoxon rank-sum and Kruskal-Wallis tests (continuous variables), Kaplan-Meier method (survival probability curves) and log-rank test (time to event outcome) were used (GraphPad Prism 8.1.2 and R version 4.0.5). Results: TROP2 mRNA was highly expressed in NSCLC and expression was similar in adenocarcinoma and squamous cell carcinoma in the TCGA data set. TROP2 expression did not vary with patient’s age, gender, race or tumor stage. Furthermore, TROP2 expression was not associated with TP53, KRAS or driver mutation status (including EGFR, ALK, ROS, RET, MET). TROP2 expression in the Translational sample set was consistent with the findings from the TCGA data analysis: TROP2 mRNA and protein expression were high and independent of patient baseline demographics, tumor stage and TP53 and KRAS mutation status. Finally, in an independent clinical NSCLC dataset, TROP2 protein was highly expressed and there was no relationship between TROP2 and baseline demographics including gender and age. TROP2 membrane H-scores and percentage of membrane-positive tumor cells also highly correlated in the two independent datasets. Conclusions: Three large independent datasets confirmed high expression of TROP2 in NSCLC both, as mRNA and protein. TROP2 expression in tumors did not differ between histological subtypes, baseline characteristics or clinically relevant driver alterations. Based on the TCGA data set, TROP2 expression was not prognostic for survival. Citation Format: Peiwen Kuo, Emon Elboudwarej, Lauri Diehl, Jilpa Patel, Sabeen Mekan, Juliane M. Jürgensmeier. TROP2 expression in non-small cell lung cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4396.

Abstract 3701: Targeting wild-type IDH1 enhances chemosensitivity in pancreatic cancer

Abstract Introduction: Pancreatic ductal adenocarcinoma (PDAC) is a leading cause of cancer mortality in the United States. The poor prognosis is in part due to development of chemotherapy resistance, despite improvements in multiagent regimens. Our previous work demonstrated that oxidative stress plays an important role in drug resistance. Wild-type isocitrate dehydrogenase 1 (IDH1) is an important enzyme that generates cytosolic NADPH to maintain redox homeostasis and protect cancer cells from oxidative damage. Additionally, we demonstrated that ivosidenib (AG-120), an FDA-approved mutant IDH1 inhibitor, is actually a potent inhibitor of wild-type IDH1, under low magnesium and nutrient levels that are present in the tumor microenvironment. Methods: We evaluated IDH1 expression in PDAC using The Cancer Genome Atlas (TCGA). Cell viability was assessed by Trypan blue and PicoGreen in drug combination assays. Cellular reactive oxygen species (ROS) levels were determined by the DCFDA method. To further assess the therapeutic potential of AG-120 in combination with chemotherapy, tumor volume analyses were performed using patient-derived xenografts (PDX) in athymic nude mice, and survival studies were performed in C57BL/6J mice transplanted with orthotopic murine pancreatic cancer. Results: Analysis of TCGA data indicated that IDH1 is overexpressed in pancreatic cancer tumors. Treatment of MiaPaca2 and Panc1 cancer cells with 5- fluorouracil (5-FU) induced expression of wild-type IDH1 in vitro. Short-term cell viability data demonstrated that targeting IDH1 with AG-120 when combined with DNA-damaging agents (5-FU, oxaliplatin) had a synergistic effect with a positive synergy score and Bliss score greater than 1. Additionally, we assessed long-term cell survival using colony formation assays, which yielded a dramatic reduction in cell survival for both Panc1 and MiaPaCa-2 cells when 5-FU was combined with AG-120, as compared to single-agent controls. Inhibiting IDH1 impairs the ability of pancreatic cancer cells to scavenge ROS levels, enhances chemotherapy-induced apoptosis in pancreatic cancer cells via ROS-mediated damage in vitro. Both PDX tumor volume studies and overall survival analyses revealed that the combination of these AG-120 and chemotherapy synergistically enhanced anti-tumor activity and doubled the survival benefits as compared to single-agent alone. Conclusion: IDH1 plays a critical role in tumorigenesis and chemoresistance in pancreatic cancer. Our data demonstrate that IDH1 inhibition with AG-120 may enhance chemotherapy efficacy and represents an important area for future investigation in the form of clinical trials. Citation Format: Mehrdad Zarei, Omid Hajihassani, Jonathan J. Hue, Hallie J. Graor, Arian Hajihassani, Alexander W. Loftus, Luke D. Rothermel, Jordan M. Winter. Targeting wild-type IDH1 enhances chemosensitivity in pancreatic cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3701.

Abstract 3602: The metastasis-suppressive function of intracellular galectin-3 in melanoma

Abstract Melanoma is a relatively rare skin cancer. However, it accounts for most of all skin cancer-related deaths worldwide. Once melanoma spreads to distant sites, it confers a poor prognosis characterized by resistance to therapy and high mortality rate. Hence, a favorable clinical outcome is strongly correlated with early diagnosis. Despite the ongoing research to identify novel diagnostic, prognostic, and therapeutic targets for metastatic melanoma (MM), a reliable serum marker to predict whether melanoma is vulnerable to metastasize or has already metastasized is still lacking. Galectin-3 (Gal-3), a ß-galactoside-binding protein, is widely expressed by many human epithelial and immune cells. High extracellular Gal-3 expression levels have been reported to be positively correlated with late-stage disease in melanoma patients, where it is theorized to bind surface glycosylated proteins to promote melanoma cell invasion and metastasis. Gal-3 is also expressed intracellularly where it participates in the regulation of many biological processes. However, intrinsic Gal-3 levels within the melanoma cell and its relationship to melanoma progression is still poorly understood. Using The Cancer Genome Atlas (TCGA) database, we analyzed the Gal-3 expression profiles of 471 tumor samples obtained from melanoma patients. To our surprise, TCGA data analysis has shown significantly higher expression of Gal-3 in primary melanoma samples compared to metastatic melanoma. We hypothesize that intracellular Gal-3 potentially negatively regulates primary melanoma progression to metastatic disease. Using several human melanoma cell lines silenced for Gal-3 expression, we investigated the corresponding malignancy-associated activities of these cells. Our results revealed that Gal-3 silencing in melanoma cells potentiated melanoma migration, invasion, and colony formation, compared with mock controls, suggesting that intracellular Gal-3 could interfere with melanoma metastatic activity. Moreover, loss of Gal-3 boosted the activation of the PI3K/AKT and MAPK signaling pathways and upregulated nuclear factor of activated T cells (NFAT1) expression and its pro-metastatic downstream target genes. Importantly, this study illuminates the apparent opposing roles of Gal-3 in melanoma progression, with intracellular Gal-3 potentially serving as a metastasis-suppressive molecule. Moreover, these studies reveal the potential of analyzing melanoma cell-intrinsic levels of Gal-3 to better predict metastatic potential and clinical outcome in melanoma patients. Citation Format: Norhan B. B. Mohammed, Charles J. Dimitroff. The metastasis-suppressive function of intracellular galectin-3 in melanoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3602.

CPT1C-mediated fatty acid oxidation facilitates colorectal cancer cell proliferation and metastasis.

Fatty acid oxidation (FAO) has been proven to be an accomplice in tumor progression. Carnitine palmitoyltransferase 1C (CPT1C), a rate-limiting enzyme in FAO, mainly functions to catalyze fatty acid carnitinylation and guarantee subsequent entry into the mitochondria for FAO in colorectal cancer (CRC). Gene expression data and clinical information extracted from The Cancer Genome Atlas (TCGA) database show significantly higher expression of CPT1C in patients with metastatic CRC ( P=0.005). Moreover, overexpression of CPT1C is correlated with worse relapse-free survival in CRC (HR 2.1, P=0.0006), while no statistical significance is indicated for CPT1A and CPT1B. Further experiments demonstrate that downregulation of CPT1C expression leads to a decrease in the FAO rate, suppression of cell proliferation, cell cycle arrest and repression of cell migration in CRC, whereas opposite results are obtained when CPT1C is overexpressed. Furthermore, an FAO inhibitor almost completely reverses the enhanced cell proliferation and migration induced by CPT1C overexpression. In addition, analysis of TCGA data illustrates a positive association between CPT1C expression and HIF1α level, suggesting that CPT1C is a transcriptional target of HIF1α. In conclusion, CPT1C overexpression indicates poor relapse-free survival of patients with CRC, and CPT1C is transcriptionally activated by HIF1α, thereby promoting the proliferation and migration of CRC cells.

Assessment of the prognostic and clinicopathological significance of HOXA-AS2 in human cancers: a systematic review and meta-analysis.

Numerous studies have reported that abnormally HOXA cluster antisense RNA 2 (HOXA-AS2) expression plays a critical role in various cancers. Thus, we performed this meta-analysis to comprehensively evaluate the prognostic value of HOXA-AS2 in human cancers. Databases, including PubMed, Web of Science, Embase, China National Knowledge Infrastructure, and Wanfang Data, were searched to retrieve articles on HOXA-AS2 and the prognosis of cancer patients, which were then screened. The association between HOXA-AS2 and overall survival (OS) and the clinicopathological characteristics of patients with cancers were assessed using hazard ratios (HRs) and odds ratios (ORs) combined with 95% confidence intervals (CIs). A subgroup analysis and the Begg test were used to assess the risk of bias of the included studies. Data from The Cancer Genome Atlas (TCGA) were analyzed to verify the results, and the potential regulation mechanism of HOXA-AS2 in cancers was revealed by an immune analysis. A total of 17 articles, comprising 1,176 patients, were included in this meta-analysis. The results showed that high HOXA-AS2 expression was associated with worse OS, advanced tumor node metastasis (TNM) stage, larger tumor size, lymph node metastasis, and distant metastasis in cancer patients but was not related to age, sex, or poor histological grade. The results of the analysis of TCGA data further supported our findings. Additionally, the immune analysis revealed that the expression of HOXA-AS2 was associated with immune cell infiltration and various immune checkpoints. In summary, our results suggest that the high expression of HOXA-AS2 is associated with poor prognosis and the clinicopathological characteristics of cancer patients; thus, it could serve as a prognosis biomarker and therapeutic target for various cancers. However, the small sample size of this study and the inclusion of participants of a single race might have affected the generalizability of our findings. Thus, large-sample, multicenter studies need to be conducted to further evaluate the prognostic role of HOXA-AS2.

MicroRNAs affecting the susceptibility of melanoma cells to CD8+ T cell-mediated cytolysis.

The regulatory functions of microRNAs (miRNAs) in anti-tumour immunity have been mainly described in immune effector cells. Since little is known about miRNA effects on the susceptibility of target cells during T cell-target cell interaction, this study focused on the identification of miRNAs expressed in tumour cells controlling their susceptibility to CD8+ T cell-mediated cytotoxicity. Luciferase expressing B16F10 melanoma (B16F10 Luci+ ) cells transfected with individual miRNAs covering a comprehensive murine miRNA library were screened for their susceptibility to lysis by an established cytotoxic T lymphocyte (CTL) line (5a, clone Nβ) specific for the melanoma-associated antigen tyrosinase-related protein 2. miRNAs with the most pronounced effects on T cell-mediated lysis were validated and stably expressed in B16F10 cells. In silico analyses identified common targets of miRNA sets determined by the screen, which were further confirmed by small interfering RNA (siRNA)-mediated silencing experiments modulating immune surveillance. The Ingenuity Pathway Analysis (IPA) software and RNA sequencing (RNA-seq) data from miRNA-overexpressing cell lines were applied to investigate the underlying mechanisms. The Cancer Genome Atlas (TCGA)-derived miRNA sequencing data were used to assess the correlation of miRNA expression with melanoma patients' survival. The miRNA screen resulted in the selection of seven miRNAs enhancing CTL-mediated melanoma cell killing in vitro. Upon stable overexpression of selected miRNAs, hsa-miR-320a-3p, mmu-miR-7037-5p and mmu-miR-666-3p were determined as most effective in enhancing susceptibility to CTL lysis. In silico analyses and subsequent siRNA-mediated silencing experiments identified Psmc3 and Ndufa1 as common miRNA targets possibly involved in the functional effects observed. The analyses of RNA-seq data with IPA showed pathways, networks, biological functions and key molecules potentially involved in the miRNA-mediated functional effects. Finally, based on TCGA data analysis, a positive correlation of the conserved miRNAs among the panel of the seven identified miRNAs with overall survival of melanoma patients was determined. For the first time, this study uncovered miRNA species that affect the susceptibility of melanoma cells to T cell-mediated killing. These miRNAs might represent attractive candidates for novel therapy approaches against melanoma and other tumour entities.

Expression of CD22 in Triple-Negative Breast Cancer: A Novel Prognostic Biomarker and Potential Target for CAR Therapy.

Triple-negative breast cancer (TNBC) accounts for 15-20% of all breast cancer cases. Due to the lack of expression of well-known molecular targets [estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2)], there is a need for more alternative treatment approaches in TNBC. Chimeric antigen receptor (CAR)-T cell-based immunotherapy treatment is one of the latest treatment technologies with outstanding therapeutic advances in the past decade, especially in the treatment of hematologic malignancies, but the therapeutic effects of CAR-T cells against solid tumors have not yet shown significant clinical benefits. Identification of highly specific CAR-T targets in solid tumors is also crucial for its successful treatment. CD22 is reported to be a multifunctional receptor that is mainly expressed on the surface of mature B-cells (lymphocytes) and is also highly expressed in most B-cell malignancies. This study aimed to investigate the expression of CD22 in TNBC. Bioinformatic analysis was performed to evaluate the expression of CD22 in breast carcinoma and normal tissues. RNA-seq data of normal and breast carcinoma patients were downloaded from The Cancer Genome Atlas (TCGA), and differential gene expression was performed using R language. Additionally, online bioinformatics web tools (GEPIA and TNM plot) were used to evaluate the expression of CD22 in breast carcinoma and normal tissues. Western blot (WB) analysis and immunofluorescence (IF) were performed to characterize the expression of CD22 in TNBC cell lines. Immunohistochemical (IHC) staining was performed on tumor specimens from 97 TNBC patients for CD22 expression. Moreover, statistical analysis was performed to analyze the association of clinical pathological parameters with CD22 expression. Correlation analysis between overall survival data of TNBC patients and CD22 expression was also performed. Differential gene expression analysis of TCGA data revealed that CD22 is among the upregulated differentially expressed genes (DEGs) with high expression in breast cancer, as compared to normal breast tissues. WB and IF analysis revealed high expression of CD22 in TNBC cell lines. IHC results also showed that approximately 62.89% (61/97) of TNBC specimens were stained positive for CD22. Cell membrane expression of CD22 was evident in 23.71% (23/97) of TNBC specimens, and 39.18% (38/97) of TNBC specimens showed cytoplasmic/membrane expression, while 37.11% (36/97) specimens were negative for CD22. Furthermore, significant associations were found between the size of tumors in TNBC patients and CD22 expression, which unveils its potential as a prognostic biomarker. No significant correlation was found between the overall survival of TNBC patients and CD22 expression. In conclusion, we demonstrated for the first time that CD22 is highly expressed in TNBC. Based on our findings, we anticipated that CD22 could be used as a prognostic biomarker in TNBC, and it might be a potential CAR-T target in TNBC for whom few therapeutic options exist. However, more large-scale studies and clinical trials will ensure its potential usefulness as a CAR-T target in TNBC.

Expression analysis of human glioma susceptibility gene and P53 in human glioma and its clinical significance based on bioinformatics.

The exact mechanism of glioblastoma multiforme (GBM) remains unclear. This study was to clarify the expression of P53 in glioma and its molecular mechanism, and to explore the possibility of P53 as a potential therapeutic target of glioma and its clinical application value, so as to provide a new theoretical basis for the treatment of glioma. Firstly, a dataset was established to analyze the expression of P53 in different stages of glioma and its relationship with prognosis by using The Cancer Genome Atlas (TCGA) database, RNA-seq data, and survival data of glioma and normal control samples in gene expression profiling and interactive analysis (GEPIA). The genes co-expressed with P53 were screened out, their differential expression between glioma and normal control group was analyzed, and their functions were analyzed by enrichment analysis. The TGGA database was used for data verification and analysis. The correlation between P53 expression and clinicopathological parameters was analyzed. Kaplan-Meier survival analysis was used to analyze the relationship between P53 expression and overall survival (OS) and progression-free survival (PFS) of glioma patients, and Cox regression analysis was used to analyze the independent factors affecting OS and PFS of glioma patients. The results of TCGA data analysis were as follows: The expression level of P53 was different from that of different stages of glioma, namely, the expression level of P53 between grade II and grade III, grade III and grade IV, and grade II and grade IV were significantly different (P<0.05). The results of P53 gene-related survival analysis showed that KNL1 high expression and low expression were significantly different in OS, and the high expression group was associated with poor prognosis (P<0.05). The P53 expression can be an effective biological indicator of poor prognosis of glioma.

Protooncogenic Role of ARHGAP11A and ARHGAP11B in Invasive Ductal Carcinoma: Two Promising Breast Cancer Biomarkers.

Invasive duct carcinoma (IDC) is one of the most common types of breast cancer (BC) in women worldwide, with a high risk of malignancy, metastasis, recurrence, and death. So far, molecular patterns among IDC cases have not been fully defined. However, extensive evidence has shown that dysregulated Rho family small GTPases (Rho GTPases) including Rho GTPase activating proteins (RhoGAPs) have important roles in the invasive features of IDCs. In the current study, we analyzed the expression levels of two RhoGAP genes, ARHGAP11A and ARHGAP11B, in The Cancer Genome Atlas (TCGA) breast cancer (BRCA) and also our 51 IDC tumors compared to their matched normal tissues using quantitative polymerase chain reaction (qPCR). Our TCGA data analysis revealed higher expression of ARHGAP11A and ARHGAP11B in various cancers comprising BCs. Also, we found correlations between these genes and other genes in TCGA-BRCA. Moreover, our methylation analysis showed that their promotor methylation had a negative correlation with their overexpression. QPCR revealed their significant upregulation in our tumor samples. Furthermore, we found that the expression level of ARHGAP11A was considerably lower in women who were breastfeeding. Moreover, it had overexpression in cases who had regular menstrual cycles and early age (younger than 14) at menarche. However, ARHGAP11B had a higher expression in HER2-positive tumors versus HER2-positive and ER-positive tumors. Our study found possible protooncogenic roles for these genes and their involvement in IDC pathogenesis and malignancy. Therefore, they can be considered novel prognostic and diagnostic biomarkers for IDC.