Adjacent Normal Mucosa Tissues Research Articles

Long non-coding RNA H19 as a prognostic biomarker for oral squamous cell carcinoma.

H19, a 2.3 kb lncRNA, has been linked to tumor metastasis and progression, but its significance in oral squamous cell carcinoma (OSCC) remains unclear. H19 was initially thought to have a tumor-suppressive function, but recent studies have shown that it possesses both tumor-promoting and suppressive functions. The variation in H19 expression may be due to the influence of tobacco or low basal expression levels. However, there are limited studies available on the association between H19 and its role in the prognosis of OSCC. The present study analyzes the expression of H19 correlated with clinicopathological parameters, tobacco habit, loco-regional recurrence, and overall survival. A longitudinal study was undertaken using 96 formalin-fixed paraffin-embedded (FFPE) OSCC tissues and 30 FFPE adjacent normal mucosa (NM) tissues from patients who had surgery between 2015 and 2018. The tissues were subjected to quantitative reverse-transcription PCR (qRT-PCR) to determine H19 expression. The differential expression levels of H19 in OSCC were compared to clinicopathological variables and risk habits using the t-test and ANOVA. H19 expression correlated overall survival was analyzed by drawing the Kaplan-Meier curve followed by the log-rank test. A multivariate Cox proportional hazards regression analysis was performed to determine the ability of H19 to independently predict loco-regional recurrence and overall survival for OSCC. H19 was significantly underexpressed in OSCC compared to NM in both the study cases and the TCGA OSCC database. The lower expression of H19 was significantly associated with the tobacco smoking habit and was not associated with any clinical or pathological features. Multivariate Cox's proportional hazards regression analysis indicated that low H19 expression and positive lymph node metastasis were independent predictors of overall survival for OSCC. Higher age, higher TNM staging, and low H19 expression were independent predictors of loco-regional recurrence. The findings in the present study indicate that H19 is a novel prognostic marker and may provide a therapeutic strategy for the targeted treatment of OSCC, and tobacco may play a role in the expression of H19.

Methionine restriction promotes cisplatin sensitivity of gastric cancer resistant cells by down-regulating circ-CDK13 level

BackgroundMethionine restriction (MR) is a research direction in the treatment of gastric cancer (GC). The aim of this study was to investigate the molecular mechanism of MR on enhancing cisplatin (DDP) sensitivity of drug-resistant GC cells. MethodsTwenty pairs of GC tissues and adjacent normal gastric mucosa tissues were collected. DDP-resistant cell lines (KATO/DDP and MKN45/DDP), mouse model of GC and GC patient-derived organoid (PDO) models were established. Lentivirus-mediated METase overexpression was used for MR. Cell viability and apoptosis were detected by MTT assay and flow cytometry. Western blotting was used to detect multi-drug resistance-1 (MDR1), MDR-associated protein 1 (MRP1) eukaryotic initiation factor 4A-Ⅲ (EIF4A3), and METase protein expressions. The levels of circRNAs were detected by qRT-PCR. Tumor volume and weight were measured. The proliferation of tumor cells was detected by immunohistochemical staining. ResultsThe differentially expressed circRNAs of GC were screened in Gene Expression Omnibus database. MR in KATO/DDP and MKN45/DDP cells significantly down-regulated circ-CDK13 level. Overexpression of circ-CDK13 significantly inhibited apoptosis of sensitive cells (KATO III and MKN45). Interference with circ-CDK13 significantly promoted apoptosis of drug-resistant cells (KATO/DDP and MKN45/DDP). MR enhanced the DDP sensitivity of GC resistant cells, GC PDO and GC mice by down-regulating circ-CDK13. EIF4A3 binds to the downstream flanking sequence of circ-CDK13, and interference with EIF4A3 reduces circ-CDK13 levels, but does not affect CDK13. The expressions of circ-CDK13 and EIF4A3 in GC clinical samples were increased and positively correlated. Simultaneously overexpression of METase and EIF4A3 in resistant cells inhibited apoptosis, and further interference with circ-CDK13 reversed this effect. ConclusionMR inhibits circ-CDK13 level by down-regulating EIF4A3, thereby increasing the sensitivity of GC drug-resistant cells to DDP.

Abstract 6992: Profilin 2 (PFN2) promotes the proliferation, migration, invasion and epithelial-to-mesenchymal transition of oral squamous cell carcinoma

Abstract Background:Oral squamous cell carcinoma (OSCC) stands as a prevalent malignancy worldwide. Profilin 2 (PFN2), an actin-binding protein regulating actin polymerization dynamics and associated with cell motility, has recently gained attention as a significant regulator in various cancers. However, the clinical significance and biological function of PFN2 in OSCC remain debatable. This study aims to elucidate the role of PFN2 in OSCC. Methods:We assessed PFN2 expression in OSCC and adjacent normal oral mucosa tissues through Q-RT-PCR and immunohistochemistry analysis. Associations between PFN2 expression, clinicopathological features, and OSCC prognosis were analyzed. Cell proliferation, invasion, and migration effects were examined via MTT and Transwell assays. Western blotting assessed the protein expression related to epithelial–mesenchymal transition (EMT). Additionally, we established OSCC xenografts to determine tumorigenicity in vivo using female Nude mice. Results:PFN2 RNA and protein expression were significantly increased in OSCC compared to normal oral mucosa. PFN2 expression positively correlated with lymphovascular invasion and cervical lymph node metastasis. MTT and Transwell assays demonstrated that PFN2 promoted OSCC cell proliferation, migration, invasion, and endothelial invasion. Downregulation of PFN2 induced an EMT phenotype, including an increase in the expression of the epithelial marker E-cadherin and a decrease in the expression of mesenchymal markers Vimentin, Snail, and Slug in OSCC cells in vitro. Similarly, OSCC cells with reduced PFN2 expression exhibited weaker tumorigenicity in vivo. Conclusions:Our findings unveil a novel role for PFN2 in promoting OSCC progression and metastasis, suggesting its potential as an early biomarker for high-risk populations. Targeting PFN2 may offer a promising therapeutic strategy for OSCC treatment. Citation Format: Chung Ji LIu, Li-Han Lin, Kuo-Wei Chang, Hui-Wen Cheng. Profilin 2 (PFN2) promotes the proliferation, migration, invasion and epithelial-to-mesenchymal transition of oral squamous cell carcinoma [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 6992.

Function of hsa_circ_0006646 as a competing endogenous RNA to promote progression in gastric cancer by regulating the miR-665-HMGB1 axis.

Mounting evidences indicate that circular RNAs (circRNAs) are a novel class of non-coding RNAs and play vital roles in the tumorigenesis and aggressiveness including gastric cancer (GC). Nevertheless, the precise functions and underlying mechanisms of circRNAs in GC remain largely unknown. The Gene Expression Omnibus (GEO) data set GSE163416 was analyzed to screen the key circRNAs in GC. hsa_circ_0006646 was chosen for further study. GC tissues and matched adjacent normal gastric mucosal epithelial tissues were obtained from the Fourth Hospital of Hebei Medical University. The expressions of hsa_circ_0006646 was detected using quantitative real-time polymerase chain reaction (qRT-PCR). hsa_circ_0006646 was knocked down to identify its effects on GC cells. Bioinformatics algorithms were analyzed to predict the microRNA (miRNAs) potentially sponged by hsa_circ_0006646 and its target genes. Fluorescence in situ hybridization (FISH) was conducted to determine the subcellular location of hsa_circ_0006646 and the predicted miRNA. Then, qRT-PCR, luciferase reporter assay, radioimmunoprecipitation assay, Western blotting, and miRNA rescue experiments were used to confirm the hsa_circ_0006646-related regulatory axis in GC. Cell Counting Kit-8 (CCK-8), colony formation, wound healing, and Transwell experiments were performed to determine the effect of the hsa_circ_0006646-related regulatory axis on GC cells' malignant behaviors in vitro. The xenograft tumor mouse model was established to evaluate the effect of hsa_circ_0006646 in vivo. hsa_circ_0006646 exhibited a high expression in GC tissues as compared to corresponding adjacent normal gastric mucosal epithelial tissues and its high expression was positively correlated with TNM stage, lymph node invasion and poor prognosis (P<0.05). Knockdown of hsa_circ_0006646 suppressed the proliferation, colony formation, migration, and invasion in GC cells (all P<0.05). hsa_circ_0006646 upregulated high mobility group box 1 (HMGB1) by sponging miR-665 in GC cells (P<0.05). The hsa_circ_0006646-miR-665-HMGB1 axis promoted malignant behaviors and epithelial-mesenchymal transition (EMT) in GC cells by activating the Wnt/β-catenin pathway (P<0.05). The existence of hsa_circ_0006646-miR-665-HMGB1 axis was confirmed in GC specimens (P<0.05). Consequently, down-regulated hsa_circ_0006646 inhibited the progression and EMT of GC cells in vivo (P<0.05). For the first time, we demonstrated that hsa_circ_0006646-miR-665-HMGB1 axis exerted its tumor-promoting effects in GC, which suggested that hsa_circ_0006646 could be potentially targeted for GC treatment.

Identification of a seven-lncRNAs panel that serves as a prognosis predictor and contributes to the malignant progression of laryngeal squamous cell carcinoma.

Laryngeal squamous cell carcinoma (LSCC) is one of the most frequent head and neck cancers worldwide. Long non-coding RNAs (lncRNAs) play a critical role in tumorigenesis. However, the clinical significance of lncRNAs in LSCC remains largely unknown. In this study, transcriptome sequencing was performed on 107 LSCC and paired adjacent normal mucosa (ANM) tissues. Furthermore, RNA expression and clinical data of 111 LSCC samples were obtained from The Cancer Genome Atlas (TCGA) database. Bioinformatics analysis were performed to construct a model for predicting the overall survival (OS) of LSCC patients. Moreover, we investigated the roles of lncRNAs in LSCC cells through loss-of-function experiments. A seven-lncRNAs panel including ENSG00000233397, BARX1-DT, LSAMP-AS1, HOXB-AS4, MNX1-AS1, LINC01385, and LINC02893 was identified. The Kaplan-Meier analysis demonstrated that the seven-lncRNAs panel was significantly associated with OS (HR:6.21 [3.27-11.81], p-value<0.0001), disease-specific survival (DSS) (HR:4.34 [1.83-10.26], p-value=0.0008), and progression-free interval (PFI) (HR:3.78 [1.92-7.43], p-value=0.0001). ROC curves showed the seven-lncRNAs panel predicts OS with good specificity and sensitivity. Separately silencing the seven lncRNAs inhibited the proliferation, migration, and invasion capacity of LSCC cells. Collectively, this seven-lncRNAs panel is a promising signature for predicting the prognosis of LSCC patients, and these lncRNAs could serve as potential targets for LSCC treatment.

Biological function and clinical significance of long non-coding RNA LINC00342 in head and neck squamous carcinoma

Objective: To investigate the relationship between the long-non-coding RNA LINC00342 expression and the clinicopathological parameters of head and neck squamous cell carcinoma (HNSCC) and the biological function of LINC00342 in HNSCC cells. Methods: The expression level of LINC00342 in the HNSCC was analyzed using transcriptome sequencing data from TCGA (The Cancer Genome Atlas) database, and the expressions of LINC00342 in laryngeal squamous cell carcinoma tissues (LSCC) of 27 patients in the First Hospital of Shanxi Medical University were detected by transcriptome sequencing. The expression levels of LINC00342 in human embryonic lung diploid cells 2BS, HNSCC cell lines FD-LSC-1, CAL-27 and Detroit562 were determined by real-time quantitative polymerase chain reaction (qPCR). RNAi (RNA interference) was used for LINC00342 knockdown in HNSCC cell lines, and the changes of malignant phenotype in the tumor cells after LINC00342 knockdown were examined by cell counting kit-8 (CCK-8), colony formation, flow cytometry, transwell invasion and migration assays. Bioinformatics analysis was performed to construct a LINC00342-centered competing endogenous RNA (ceRNA) regulatory network, and GO (Gene Ontology) enrichment analysis was performed. Statistical analysis and graphing were performed using SPSS 25.0 software and GraphPad Prism 6 software. Results: Mean LINC00342 levels in HNSCC tissues and TCGA database were higher than that in normal control tissues, but with no significantly statistical difference (P=0.522). LINC00342 expression levels were positively correlated with cervical lymph node metastasis and pathological grade in patients with HNSCC, with higher expression in male patients than in female patients (P<0.05). Transcriptome sequencing analysis showed that mean expression level of LINC00342 in LSCC tissues of 27 patients was significantly higher than that in the paired adjacent normal mucosa tissues (t=1.56, P=0.036). LINC00342 expression was significantly upregulated in HNSCC cell lines FD-LSC-1, CAL-27 and Detroit562 (t-values of -12.17, -23.26 and -388.57, respectively; all P<0.001). Knockdown of LINC00342 by transfecting si-LINC00342-1 and si-LINC00342-2 inhibited HNSCC cell proliferation (t-values of 8.95 and 4.84, 2.70 and 5.55, 2.02 and 3.70, respectively), colony formation (t-values of 6.66 and 6.17, 7.38 and 11.65, 4.90 and 5.79, respectively), migration (t-values of 8.21 and 7.19, 5.76 and 6.46, 6.28 and 9.92, respectively) and invasion abilities (t-values of 9.29 and 10.25, 11.30 and 11.36, 8.02 and 8.66, respectively), but promoting apoptosis in cell lines FD-LSC-1 and CAL-27 (t-values of -2.21 and -5.83, -3.05 and -5.25 respectively) (all P-values<0.05). The LINC00342-centered ceRNA network consists of 10 downregulated microRNA and 647 upregulated mRNA nodes. GO analysis results indicated that LINC00342-regulated mRNAs were enriched in 22 biological processes, 32 molecular functions, and 12 cellular components. Conclusion: High level of LINC00342 is associated with the malignant progression of HNSCC. LINC00342 promotes the proliferation, migration, invasion, and antagonizes apoptosis of HNSCC cells, which serves as a potential molecular marker in HNSCC.

Prognostic and predictive value of a lncRNA signature in patients with stage II colon cancer

The current staging method is inadequate to identify high-risk recurrence patients with stage II colon cancer (CC). Using a systematic and comprehensive-biomarker discovery and validation method, we aimed to construct a lncRNA-based signature to improve the prognostic prediction of stage II CC. We identified 1,377 differently expressed lncRNAs by analyzing 16 paired stage II CC tumor tissue and adjacent normal mucosal tissue from the TCGA dataset. Subsequently, using a univariable and step multivariable Cox regression model, we trained an 11-lncRNA signature in the training cohort (n = 141), which could divide patients into high-risk and low-risk groups (AUC at 3 years = 0.801, 95% CI: 0.724–0.877; AUC at 5 years = 0.801, 95% CI: 0.718–0.885). Significantly, patients in the high-risk group had poorer recurrence-free survival (RFS) compared with the low-risk group (log-rank test, P < 0.001 in the training cohort). This lncRNA-based signature was further confirmed in the validation cohort (P < 0.001). Multivariate Cox regression and stratified survival analyses showed that the prognostic value of this signature was independent of other clinicopathological risk factors (CEA, T stage, and chemotherapy). Time-dependent receiver operating characteristic (ROC) analysis demonstrated that this signature had better prognostic ability than any other clinical risk factors or single lncRNAs (all P < 0.05). A nomogram was constructed for clinical use, which integrated both the lncRNA-based signature and clinical risk factors (CEA and T stage) and performed well in the calibration plots. Altogether, our lncRNA-based signature was an independent prognostic factor and possessed a stronger predictive power compared with the currently used clinicopathological risk factors when predicting the recurrence of patients with stage II CC. Collectively, this lncRNA-based signature might facilitate individualized treatment decisions and postoperative counseling, ultimately contributing to improved survival.

Identification and validation of crucial lnc-TRIM28-14 and hub genes promoting gastric cancer peritoneal metastasis

BackgroundGastric cancer peritoneal metastasis (GCPM) is an important cause of cancer-related deaths worldwide. Long non-coding RNAs (lncRNAs) play a key role in the regulation of GCPM, but the underlying mechanisms have not been elucidated.MethodsHigh-throughput RNA sequencing (RNA-seq) was performed on four groups of clinical specimens (non-metastatic gastric cancer primary tumor, adjacent normal gastric mucosal tissue, gastric cancer primary tumor with peritoneal metastasis and adjacent normal gastric mucosal tissue). After sequencing, many lncRNAs and mRNAs were screened for further Weighted Gene Co-expression Network Analysis (WGCNA). GCPM-related hub lncRNAs and genes were identified by cytoHubba and validated by Quantitative real-time PCR (qRT-PCR), Receiver operating characteristic curve (ROC) analysis and Kaplan-Meier survival analysis. GO, KEGG and GSEA showed GCPM-related pathways. Correlation analysis revealed the potential relationship between hub lncRNAs and genes.ResultsBy analyzing lncRNA expression data by WGCNA, we found that blue module was highly correlated with GCPM (r = 0.44, p = 0.04) and six lncRNAs involved in this module (DNM3OS, lnc-MFAP2-53, lnc-PPIAL4C-4, lnc-RFNG-1, lnc-TRIM28-14 and lnc-YARS2-4) were identified. We then performed qRT-PCR validation of gastric cancer specimens and found that the expression of lnc-RFNG-1 and lnc-TRIM28-14 was significantly increased in gastric cancer tissues with peritoneal metastasis. Kaplan-Meier survival analysis showed shorter overall survival time (OS) for gastric cancer patients with high expression of lnc-TRIM28-14. Receiver operating characteristic curve (ROC) analysis showed that lnc-TRIM28-14 could improve the sensitivity and specificity of GCPM diagnosis. In addition, we identified three key mRNAs (CD93, COL3A1 and COL4A1) associated with gastric cancer peritoneal metastasis through WGCNA analysis and clinical specimen validation. Moreover, there was a positive correlation between lnc-TRIM28-14 and the expression of CD93 and COL4A1 in gastric cancer peritoneal metastasis, suggesting a regulatory relationship between them. Subsequent GO, KEGG and GSEA analysis suggested that ECM-receptor interaction and focal adhesion were the hub pathways of GCPM.ConclusionIn summary, lnc-RFNG-1, lnc-TRIM28-14, CD93, COL3A1 and COL4A1 could be novel tumor biomarkers and potential therapeutic targets for GCPM.

Abstract A011: Epigenetic vulnerabilities in patient-derived colorectal cancer organoids

Abstract Colorectal cancer (CRC) is a major cause of cancer-related deaths worldwide. Here, we established human patient-derived colorectal cancer organoid cultures (PDOs) to decipher the patient-specific DNA methylation profile and drug sensitivity towards 5-aza-2’-deoxycytidine, a DNA methyltransferase inhibitor. Organoid lines (n=15) were generated from adjacent normal mucosa and tumor tissue located in different anatomical sites of the colon and rectum. The derived PDOs were characterized on a histopathological level and reproduced the grade and differentiation capacity of their parental tumors. Additional genotypic profiling of PDOs showed a high degree of similarity to the original patient tumors. However, the stability of the DNA methylation landscape of human cancer organoids remains largely unknown. In genome-wide methylation analysis of long-term organoid cultures (up to 6 months in culture), we observed surprisingly stable methylation signatures that recapitulates the patient’s profile whilst demonstrating the vast intertumoral heterogeneity among patients. Strikingly, we identified a tumor-specific methylation signature that consisted of 39 CpG sites, which were unmethylated in normal epithelial cells but highly (91-96%) methylated in all tumor cells analyzed. This signature allows for the estimation of the percentage of tumor content in resected tissues and might represent potent biomarkers for early CRC diagnostics. Notably, it has been demonstrated that PDOs have the potential to predict clinical outcome and response to chemo- and radiation therapy in patients. Herein, drug screening with 5-aza-2’-deoxycytidine revealed heterogeneous responses and a clustering into drug sensitive, median and resistant organoid lines. ATAC- and RNA-seq analyses identified pathways rendering drug sensitivity and resistance. Our findings highlight the utility of PDOs as an advanced model system to study the role of the epigenome, especially DNA methylation, and its impact on tumor burden and vulnerability towards epigenetic modifiers. Citation Format: Loan Tran, Raheleh Sheibani Tezerji, Carlos Uziel Perez Malla, Anna Malzer, Ajna Logo, Katarina Misura, Theresia Mair, Thomas Dillinger, Madeleine Kuroll, Velina Atanasova, Julijan Kabiljo, Helga Schachner, Katharina Wöran, Judith Stift, Helmut Dolznig, Walter Pulverer, Michael Bergmann, Gerda Egger. Epigenetic vulnerabilities in patient-derived colorectal cancer organoids. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr A011.

Single-cell landscape and clinical outcomes of infiltrating B cells in colorectal cancer.

B cells constitute a major component of infiltrating immune cells in colorectal cancer (CRC). However, the characteristics of B cells and their clinical significance remain unclear. In this study, using single-cell RNA sequencing and multicolour immunofluorescence staining experiments, we identified five distinct subtypes of B cells with their marker genes, distribution patterns and functional properties in the CRC tumour microenvironment. Meanwhile, we found a higher proportion of IgG plasma cells in tumour sites than that in adjacent normal mucosal tissues. In addition, the CXCL13-producing CD8+ T cells in the tumour tissues could promote the formation of tertiary lymphoid structure (TLS) B cells, and the CCL28-CCR10 axis is pivotal for IgG plasma cell migration from the periphery of TLSs to the tumour stroma. Finally, we identified four distinct colon immune classes (CICs: A-D) and found that CD20+ B cells within TLSs were enriched in one immune-inflamed or hot tumour group (CIC D). This B cell-rich group, which was characterized by strong antigen presentation, IgG plasma cells accumulation, microsatellite instability-high (MSI-H) and high tumour mutation burden (TMB-H), as well as immunosuppressive property in particular, might become a potential predictive biomarker for future immunotherapy. Additionally, in an immunotherapy cohort, patients with the enrichment of B cells and TLSs were demonstrated to obtain significant therapeutic advantages. Together, our findings provide the detailed landscape of infiltrating B cells and their potential clinical significance in CRC.

Abstract 6306: Genomic analysis markers of stemness in oral cancer progression

Abstract Introduction: In clinical cancer treatment there is an continuing effort to identify limited gene sets from high dimensional data to predict risk, treatment response, etc. Oral carcinogenesis is a multistep process of mutations, disordered growth, and the development of invasion. In the oral cancer milieu, inflammation and stemness has been demonstrated to be cooperative during carcinogenesis. We hypothesized that differences in inflammation, stemness, and EMT might distinguish lesion and adjacent normal mucosa in our RNA Seq data on preneoplastic lesions. Once candidate genes are identified they might be applied to other oral mucosal specimens to identify risk for malignancy development. Materials and Methods: We collected lesion and adjacent normal mucosal tissues from 16 subjects with high risk leukoplakia and early oral cancer (T1N0 and T2N0). Sequencing libraries were generated using the Illumina Truseq Stranded mRNA library prep kit. Sequencing was performed on an Illumina Hiseq 3000 instrument with paired-end 75bp read and sequenced to an overall depth of 30 million reads per sample. Results: After developing a biospecimen collection procedure that functions in the senior author’s clinic flow, we were able to isolate sequenceable total RNA from 100% of the specimens we collected. We identified several hundred differentially expressed genes between lesion and adjacent normal. With regard to stemness, inflammation, and EMT we multiple candidate genes that could be incorporated into a limited gene set for further studies. Aldehyde dehydrogenase family members were of particular interest in the stemness candidate genes, for example. ALD 1A1 and ALD 3B1, were significantly upregulated in lesion versus normal (P&amp;lt; 0.02). Conclusions: We conclude there are differentially expressed inflammatory, EMT, and stemness in oral preneoplastic specimens. We have identified multiple candidate genes that could be assembled into a limited gene panel (12-24 genes) for further studies of oral cancer risk in mucosal lesions Citation Format: Gretchen Unger, Beverly G. Wuertz, Patrick Gaffney, Frank G. Ondrey. Genomic analysis markers of stemness in oral cancer progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6306.

Abstract 2800: Use of an optimized machine learning algorithm to develop DNA methylation markers for detecting colorectal cancer (CRC)

Abstract Introduction: Epigenetic changes including methylation occur early in tumorigenesis and are known to be highly pervasive across a tumor type. The DNA methylation pattern can vary between individuals with or without cancer and also in patients with cancer of different origins. In this study, we investigated the discovery of comprehensive markers and validation of the diagnostic and prognostic potential of colorectal cancer. Methods: Patients with various stage of colorectal cancer were eligible for the current study, mainly stage III. We generated genome-wide methylation data from 379 colorectal cancer (CRC) tissues and 330 available paired adjacent normal mucosa tissues from Korean patients by Illumina EPIC Human Methylation microarray targeting 860,000~ CpG sites. A machine learning algorithm was used to build an optimized prediction model and select the tumor specific markers based on through theses CpG sites. Then, the risk score was devised for prognosis using this marker set. Finally, in order to validate the rule of CpG sites, the genomic location and pathway enrichment analysis was performed by CHROMHMM and Metascape. Results: 379 colorectal cancer tissues and 330 paired adjacent normal mucosal tissues were included for analysis. Clinical stages of the included patients were, III in N (61.2%), II in N (19.5%), and IV in N (11.9%). A total of 305 methylation markers that showed statistically significant differences between normal and cancer tissues were selected. Our model could accurately identify CRC (areas under the curve for the training and validation cohorts: 0.968 and 0.984, respectively). Using our prediction model, the colorectal cancer patients were predicted as colorectal cancer accurately in the methylation data from TCGA (COREAD; colorectal cancer tissue DNA) and GEO dataset (plasma cfDNA from colorectal cancer patients). The risk score comprising the subset of 305 methylation markers was calculated, and poor prognosis was predicted in the high-risk score group (overall survival P &amp;lt;0.1, progression-free survival P &amp;lt; 0.01). Gene ontology (GO) enrichment analysis showed that the 305 CpG sites were enriched in transcription regulatory regions (160/305, 52.5%) and were associated with developmental process and carcinogenesis (GO: 0032502, P &amp;lt;0.001; C4721208, P &amp;lt;0.001). Conclusions: In summary, the performance of our prediction model with these 305 CpG sites was highly accurate for CRC diagnosis, and the optimized risk score could predict the prognosis of Korean CRC patients Citation Format: Jun-Kyu Kang, Su Yeon Kim, Yoojoo Lim, Hwang-Phill Kim, Tae-You Kim. Use of an optimized machine learning algorithm to develop DNA methylation markers for detecting colorectal cancer (CRC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2800.

The Invasion and Metastasis of Colon Adenocarcinoma (COAD) Induced by SALL4

Objective The development and progression of many cancers may be related to SALL4, the role and molecular mechanism of which are unclear in colon adenocarcinoma (COAD). Methods The SALL4 expression in adjacent normal mucosa tissues and carcinoma tissues of patients with COAD was detected through bioinformatic analysis based on TCGA database and immunohistochemistry. Single-cell analysis showed that the expression of SALL4 in normal tissue was noticeably low. GSEA analysis suggested that the SALL4 upregulated the GO and pathway of growth and cancer development and downregulated metabolization pathway. The relationship between lymph node metastasis, histological grading, clinical staging, and the expression of SALL4 in carcinoma tissues was analyzed. The upregulated or downregulated SALL4 expression of COAD cell lines was established. The influence of SALL4 on COAD cells invasion and proliferation was detected using plate cloning assay and Transwell. The expressions of EMT-related proteins E-cadherin, N-cadherin, vimentin, and Twist were detected by Western blot. The EMT phenotype was analyzed by immunofluorescence. Results The study confirmed that the expression of SALL4 was upregulated in COAD and positively correlated with the degree of tumor differentiation, tumor staging, and metastasis. The overexpression of SALL4 was related to a poor prognosis, promoted the invasion and proliferation of colorectal cancer cells, and accelerated the occurrence of EMT, which was characterized by upregulation of Twist, vimentin, and N-cadherin expressions and downregulation of E-cadherin. The immunofluorescence staining confirmed the EMT phenotype. On the contrary, knocking out SALL4 gene reversed EMT, weakened cell proliferation and invasion, inhibited upregulation of Twist, vimentin, and N-cadherin expressions and downregulation of E-cadherin. Conclusion To sum up, TNM grading, histological grading, and lymphatic metastasis were significantly correlated with SALL4 in tumor tissues. SALL4 played a vital role in tumor proliferation, invasion, and tumor EMT and may be a novel target for COAD.

Metagenomics analysis of cultured mucosal bacteria from colorectal cancer and adjacent normal mucosal tissues.

Introduction. Colorectal cancer (CRC) is one of the most common cancers worldwide. Multiple risk factors are involved in CRC development, including age, genetics, lifestyle, diet and environment. Of these, the role of the gut microbiota in cancer biology is increasingly recognized.Hypothesis/Gap Statement. Micro-organisms have been widely detected in stool samples, but few mucosal samples have been detected and sequenced in depth.Aim. Analysis of cultured mucosal bacteria from colorectal cancer and adjacent normal mucosal tissues with metagenomics sequencing.Methodology. Twenty-eight paired tumour and non-tumour tissues from 14 patients undergoing surgery for CRC were analysed. We removed the influence of eukaryotic cells via culture. The composition of mucosal microbiota in intestinal mucosa were detected and analysed with metagenomic sequencing.Results. Compared with non-cultured mucosal sample, 80 % bacteria species could be detected after culture. Moreover, after culture, additional 30 % bacteria could be detected, compared with non-cultured samples. Since after culture it was difficult to estimate the original abundance of microbiome, we focused on the identification of the CRC tissue-specific species. There were 298 bacterial species, which could only be cultured and detected in CRC tissues. Myroides odoratimimus and Cellulophaga baltica could be isolated from all the tumour samples of 14 CRC patients, suggesting that these species may be related to tumour occurrence and development. Further functional analysis indicated that bacteria from CRC tissues showed more active functions, including basic metabolism, signal transduction and survival activities.Conclusion. We used a new method based on culture to implement information on prokaryotic taxa, and related functions, which samples were from colorectal tissues. This method is suitable for removing eukaryotic contamination and detecting micro-organisms from other tissues.

Overexpression of IL-8 and Wnt2 is associated with prognosis of gastric cancer.

This study is to detect the expression of inflammatory factor or neutrophil-activating factor IL-8 and Wnt2 in gastric cancer (GC) and investigate the involvement of IL-8 and Wnt2 expressions in the clinicopathological indexes and prognosis. We detected the expression of IL-8 and Wnt2 in 100 GC tissues and 40 normal gastric mucosae using immunohistochemistry. The relationships between the IL-8 and Wnt2 expression and the clinicopathological characteristics were explored. The relationship between IL-8 expression, Wnt2 expression, and prognosis of GC was analyzed by survival curve and survival regression. The expression of IL-8 and Wnt2 in GC tissue was 64% and 75% respectively, which was significantly higher than that in adjacent normal gastric mucosa tissues, moreover, expressions of IL-8 and Wnt2 were positively correlated. The positive rate of IL-8 and Wnt2 expressions were correlated with lymph node metastasis and TNM staging （P < 0.01, and Wnt2 was also correlated with infiltration depth (P = 0.021), but there was no difference with age, sex, and differentiation (P > 0.05). The 3-year survival analysis showed that the survival rates of IL-8- and Wnt2-positive patients were 20% and 24%, respectively, which were significantly lower than those of negative patients. Cox regression analysis showed that IL-8 and Wnt2 may be independent factors affecting the prognosis of GC. Our data demonstrated that the overexpression of IL-8 and Wnt2 could be isolated prognostic factors in patients with GC and, possibly, may present new targets for the treatment of GC.

Long noncoding RNA SGO1-AS1 inactivates TGF\u03b2 signaling by facilitating TGFB1/2 mRNA decay and inhibits gastric carcinoma metastasis

BackgroundAlthough thousands of long noncoding RNAs (lncRNAs) have been annotated, only a few lncRNAs have been characterized functionally. In this study, we aimed to identify novel lncRNAs involved in the progression of gastric carcinoma (GC) and explore their regulatory mechanisms and clinical significance in GC.MethodsA lncRNA expression microarray was used to identify differential lncRNA expression profiles between paired GCs and adjacent normal mucosal tissues. Using the above method, the lncRNA SGO1-AS1 was selected for further study. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) and in situ hybridization (ISH) were performed to detect SGO1-AS1 expression in GC tissues. Gain-of-function and loss-of-function analyses were performed to investigate the functions of SGO1-AS1 and its upstream and downstream regulatory mechanisms in vitro and in vivo.ResultsSGO1-AS1 was downregulated in gastric carcinoma tissues compared to adjacent normal tissues, and its downregulation was positively correlated with advanced clinical stage, metastasis status and poor patient prognosis. The functional experiments revealed that SGO1-AS1 inhibited GC cell invasion and metastasis in vitro and in vivo. Mechanistically, SGO1-AS1 facilitated TGFB1/2 mRNA decay by competitively binding the PTBP1 protein, resulting in reduced TGFβ production and, thus, preventing the epithelial-to-mesenchymal transition (EMT) and metastasis. In addition, in turn, TGFβ inhibited SGO1-AS1 transcription by inducing ZEB1. Thus, SGO1-AS1 and TGFβ form a double-negative feedback loop via ZEB1 to regulate the EMT and metastasis.ConclusionsSGO1-AS1 functions as an endogenous inhibitor of the TGFβ pathway and suppresses gastric carcinoma metastasis, indicating a novel potential target for GC treatment.

Upregulation of prostaglandin E2 by inducible microsomal prostaglandin E synthase-1 in colon cancer.

PurposeProstaglandin E2 (PGE2) is known to promote carcinogenesis and cancer progression in colon cancer. Enzymes involved in the metabolism of PGE2 include cyclooxygenase (COX)-2, microsomal prostaglandin E synthase-1 (mPGES-1), and 15-prostaglandin dehydrogenase (15-PGDH). The current study aims to determine how PGE2 is expressed by examining patients with colorectal cancer and evaluating colon cancer cells to gain insight into changes in relevant enzymes upon induction of PGE2.MethodsThe concentration of PGE2 was measured in tumor tissues and adjacent normal mucosal tissues of 26 patients with colon cancer. The expression of COX-1, COX-2, mPGES-1, and 15-PGDH proteins was measured. The concentration of PGE2 in FET colon cancer cells was measured both in the initial status and after stimulation by tumor necrosis factor (TNF)-α. The expression levels of PGE2-related enzymes were measured as well.ResultsThere was no significant difference in the average concentration of PGE2, which was measured at 453.1 pg/mL in cancer tissues and 401.2 pg/mL in normal mucosa. Among PGE2-related enzymes, 15-PGDH was expressed at a lower level in tumor cells than in normal mucosa. In colon cancer cells, PGE2 was found to be upregulated upon stimulation by TNF-α, which led to strong induction of mPGES-1 without any change in the expression of COX-2 among the PGE2-related enzymes.ConclusionThese results demonstrated that PGE2 can be induced by stimuli such as TNF-α, and suggest that activation of mPGES-1 is more closely related than that of COX-2 in the induction of PGE2 on colon cancer.

Gastrokine 2 Regulates the Antitumor Effect of JAK2/STAT3 Pathway in Gastric Cancer.

GKN2 (gastrokine 2) mainly plays a regulatory role in gastric mucosal defense and cell protection mechanisms, and its role in gastric cancer has not been thoroughly elucidated. Immunohistochemistry was used to detect GKN2 and TFF1 expressions in 90 gastric cancer tissues, 48 neoplastic resection margins, and 22 normal gastric mucosa epithelia. It showed that the downregulation of GKN2 and TFF1 expressions in gastric cancer tissues was significantly different from that in adjacent normal gastric tissues and distal gastric mucosal tissues. Nevertheless, correlation analysis showed that GKN2 expression in gastric cancer tissues was independent of TFF1 expression. After overexpression of GKN2 was constructed in human gastric cancer cell line MKN28 with the Ad-GFP-GKN2 transfected, cell viability was measured by CCK-8 assay, and migration and invasion ability were analyzed by transwell migration assay and transwell invasion assay. It indicated that overexpression of GKN2 significantly reduced the viability of MKN28 and SGC7901 cells. Overexpression of GKN2 could also inhibit the migration and invasion ability in MKN28 and SGC7901 cells. In addition, upregulation of GKN2 can inactivate the JAK2/STAT3 pathway. Our data suggest that GKN2 and TFF1 play the antitumor role in gastric carcinoma, and TFF1 may not interact or cooperate with GKN2. GKN2 overexpression can inhibit the growth and metastasis by downregulating the JAK2/STAT3 pathway in gastric cancer cells.

Silence of circBANP increases radiosensitivity of colorectal cancer cells and inhibits growth of subcutaneous xenografts by up-regulating miR-338-3p expression

Objective: To investigate the effect of circBANP on radiosensitivity of colorectal cancer cells and subcutaneous transplanted tumor in nude mice and its potential molecular mechanism. Methods: The carcinoma and adjacent normal mucosal tissues of 20 patients with colorectal cancer who were surgically resected in Henan People's Hospital from January 2018 to January 2019 were selected. The radio-resistant colorectal cancer cell LoVo/R was established. Real-time quantitative polymerase chain reaction (RT-qPCR) was used to detect the expressions of circBANP and miR-338-3p. The radiation sensitivity was determined by cell clone formation experiment. Cell vitality was detected by using methyl thiazolyl tetrazolium (MTT). The expressions of autophagy-related protein microtubule-associated protein light chain 3 (LC3) and p62 were detected by western blot. The fluorescence intensity of LC3 in cells was detected by immunofluorescence assay. The downstream microRNAs (miRNAs) of circBANP were predicted by Circular RNA Interactome website and further verified by dual luciferase reporter gene assay. The transplanted tumor model of LoVo/R cells in nude mice was established, and the effect of circBANP on the growth of transplanted tumor after radiation was observed. Results: The expression levels of circBANP and miR-338-3p in colorectal cancer tissues were 3.21+ 0.29 and 0.47+ 0.04, respectively, which were significantly higher than 1.00+ 0.07 and 1.00+ 0.05 in adjacent tissues (P<0.05). The circBANP expression level of LoVo/R cells was 3.21±0.34, higher than 1.00±0.07 of LoVo cells (P<0.05), and the expression level of miR-338-3p of LoVo/R cells was 0.33±0.04, lower than 1.00±0.08 of LoVo cells (P<0.05). After 4 Gy irradiation, compared with the control group, the viability of LoVo/R cells in the circBANP silencing group [(34±4)% vs (62±6)%, P<0.05], the cell survival fraction (0.07±0.02 vs 0.27±0.04, P<0.05) were decreased, and the radiation sensitization ratio was 1.843, the expression of LC3Ⅱ/Ⅰin LoVo/R cells increased while p62 expression decreased, the cell autophagy was observed. Autophagy inhibitor chloroquine reversed the increased expression of LC3Ⅱ/Ⅰ and inhibited expression of p62 in LoVo/R cells induced by radiation, and promoted the suppression of cell viability and survival induced by radiation, the radiotherapy sensitization ratio was 1.780. Compared with control group after 4 Gy irradiation, the relative fluorescence intensity of LC3 in circBANP silencing LoVo/R cells decreased (0.11±0.01 vs 1.00±0.12, P<0.05), the expression of LC3-Ⅱ/Ⅰdecreased (1.25±0.13 vs 3.84±0.39, P<0.05) while p62 expression increased (2.76±0.29 vs 1.00±0.08, P<0.05). As predicted by Circular RNA Interactome website and confirmed by double luciferase reporter gene assay, miR-338-3p was the target gene of circBANP. The relative fluorescence intensity of LC3 in circBANP silencing + anti-miR-338-3p + 4 Gy group increased (7.32±0.72 vs 1.00±0.09, P<0.05), the expression level of LC3-Ⅱ/Ⅰ increased (4.13±0.43 vs 2.31±0.23, P<0.05) while p62 expression decreased (0.34±0.03 and 1.00±0.11, P<0.05), the radiotherapy sensitization ratio was 0.596. Nude mice subcutaneously transplanted tumor experiment showed that the tumor volume and weight of circBANP silencing group on 13, 16, 19, 22, 25, 28, and 31 days were lower than those of control group (P<0.05), while the tumor volume and weight of circBANP silencing + anti-miR-338-3p group on days of 13, 16, 19, 22, 25, 28 and 31 after inoculated were higher than those of circBANP+ anti-miR-NC group (P<0.05). Conclusions: CircBANP can regulate the radiosensitivity of colorectal cancer cells by regulating the expression of miR-338-3p, and affect the growth of transplanted tumor in nude mice. CircBANP may be a potential target for enhancing radiosensitivity of colorectal cancer cells.

Identification of RORγ as a favorable biomarker for colon cancer.

ObjectiveTo evaluate the expression of retinoid-related orphan receptor gamma (RORγ) and its potential role in the prognosis of colon cancer.MethodsThe Cancer Genome Atlas and GSE117606 were used to evaluate to RORγ levels in colon cancer, and real-time quantitative polymerase chain reaction was applied for validation. UALCAN and MEXPRESS were used to analyze the associations of RORγ expression with clinical parameters. The survival analysis was conducted in GEPIA.ResultsRORγ expression was significantly lower in colon tumors than in adjacent normal mucosa tissues. RORγ expression was significantly associated with tumor stage, lymph node metastasis, and liver metastasis. The area under the curve for diagnosis was 0.71. Decreased RORγ expression was positively correlated with the incidence of lymphatic invasion, microsatellite instability, the presence of residual tumor, venous invasion, and copy number variation. Overall survival was longer in patients with higher RORγ expression, especially those with microsatellite instability-high features. Methylation analysis revealed that hypermethylation of the RORγ promoter was associated with the colon cancer stage.ConclusionsRORγ downregulation could be a potential biomarker for colon cancer, especially for predicting prognosis. Decreased RORγ expression in colon tumor may be associated with promoter hypermethylation.