Transcriptomic Analyses of the Adenoma-Carcinoma Sequence Identify Hallmarks Associated With the Onset of Colorectal Cancer

The concept of the adenoma-carcinoma sequence in colorectal cancer (CRC) is widely accepted. However, the relationship between the characteristics of the transcriptome and the adenoma-carcinoma sequence in CRC remains unclear. Here, the transcriptome profiles of 15 tissue samples from five CRC patients were generated by RNAseq. Six specific dynamic expression patterns of differentially expressed genes (DEGs) were generated by mFuzz. Weighted correlation network analysis showed that DEGs in cluster 4 were associated with carcinoma tissues, and those in cluster 6 were associated with non-normal tissues. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses identified metabolic dysregulation as a consistent finding throughout the transition process, whereas downregulation of the immune response occurred during normal to adenoma transition, and the upregulation of canonical pathways was associated with adenoma to carcinoma transition. Overall survival analysis of patients in cluster 6 identified TPD52L1 as a marker of poor prognosis, and cell proliferation, colony formation, wound healing, and Transwell invasion assays showed that high expression levels of TPD52L1 promoted malignant behaviors. In total, 70 proteins were identified as potential partners of hD53 by mass spectrometry. CRC formation was associated with three cancer hallmarks: dysregulation of metabolism, inactivation of the immune response, and activation of canonical cancer pathways. The TPD52L1 gene was identified as a potential marker to track tumor formation in CRC and as an indicator of poor patient prognosis.

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iNOS Expression by Tumor-Infiltrating Lymphocytes, PD-L1 and Prognosis in Non-Small-Cell Lung Cancer

Cancers ◽

10.3390/cancers12113276 ◽

2020 ◽

Vol 12 (11) ◽

pp. 3276

Author(s):

Alexandra Giatromanolaki ◽

Avgi Tsolou ◽

Eleftheria Daridou ◽

Maria Kouroupi ◽

Katerina Chlichlia ◽

...

Keyword(s):

Immune Response ◽

Overall Survival ◽

Small Cell Lung Carcinoma ◽

Expression Patterns ◽

Tumor Infiltrating Lymphocytes ◽

Small Cell ◽

Small Cell Lung ◽

Tissue Samples ◽

Cell Lung Carcinoma ◽

Infiltrating Lymphocytes

Background: Inducible Nitric Oxygen Synthase (iNOS) promotes the generation of NO in tissues. Its role in tumor progression and immune response is unclear. Methods: The immunohistochemical expression patterns of iNOS were studied in a series of 98 tissue samples of non-small-cell lung carcinoma (NSCLC), in parallel with the expression of hypoxia and anaerobic metabolism markers, PD-L1 and tumor-infiltrating lymphocytes (TILs). Results: iNOS is expressed by cancer cells in 19/98 (19.4%), while extensive expression by cancer-associated fibroblasts occurs in 8/98 (8.2%) cases. None of these patterns relate to stage or prognosis. Extensive infiltration of the tumor stroma by iNOS-expressing TILs (iNOS+TILs) occurs in 47/98 (48%) cases. This is related to low Hypoxia-Inducible Factor 1α (HIF1α), high PD-L1 expression and a better overall survival (p = 0.002). Expression of PD-L1, however, mitigates the beneficial effect of the presence of iNOS+TIL. Conclusions: Extensive expression of iNOS by TILs occurs in approximately 50% of NSCLCs, and this is significantly related to an improved overall survival. This brings forward the role of iNOS in anti-neoplastic lymphocyte biology, supporting iNOS+TILs as a putative marker of immune response. The value of this biomarker as a predictive and treatment-guiding tool for tumor immunotherapy demands further investigation.

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DNA methylation signatures predicting liver metastasis of colorectal cancer: A proof-of-concept pilot study.

Journal of Clinical Oncology ◽

10.1200/jco.2020.38.15_suppl.e16080 ◽

2020 ◽

Vol 38 (15_suppl) ◽

pp. e16080-e16080

Author(s):

Jianming Ying ◽

Weihua Li ◽

Kaihua Liu ◽

Cong Xiao ◽

Shuyu Wu ◽

...

Keyword(s):

Colorectal Cancer ◽

Liver Metastasis ◽

Early Detection ◽

Predictive Model ◽

Primary Tumor ◽

Metastatic Tumor ◽

Training Data ◽

Training Dataset ◽

Tissue Samples ◽

Normal Tissues

e16080 Background: Liver metastasis (LIM) is the leading cause of death in colorectal cancer (CRC) patients. Early detection of LIM may improve outcome in CRC patients. The aim of this study was to evaluate the feasibility of predicting LIM of CRC using methylation profiles. Methods: We performed Roche targeted (~5.5 million methylation sites) bisulfite sequencing of matched primary, metastatic and their adjacent normal tissue samples from 5 CRC patients with LIM, 5 patients with lung metastasis (LUM) and 8 patients without metastasis in the training cohort (n = 48 samples). Differential methylation regions (DMR) of LUM were identified and a predictive model was developed. The model was further validated in primary tumor sample from nine patients (6 with LIM). Results: By comparing primary tumor vs adjacent normal tissues and metastatic tumor vs adjacent normal tissues in CRC patients with LIM, we identified 28954 common DMRs which indicating the methylation characteristic of CRC with LIM. Similarly, 16187 DMRs were identified in patients with LUM. 9179 DMRs are shared in both LIM and LUM comparisons which should be the common characteristic of CRC tumor tissue regardless of the location of metastasis. 7008 DMRs are LUM specific and 19775 DMRs are LIM specific. In order to predict LIM in primary, early changes in LIM specific DMRs should be identified. Hence, we further selected 4134 DMRs by chossing significantly differentically methylated regions between LIM primary tissues and LUM primary tissues. To increase the ability of distinguishing LIM from other normal tissues and non-matastasis CRC tumors, 1215 DMRs were finally selected which also showed increasing or decreasing trend of methylation level through the progression of CRC. The final 1215 biomarkers were used to construct a random forest model using methlylation profile of 5 CRC patients with LIM as positive training data and 5 CRC patients with LUM as well as 8 patients without metastasis as negative training data. Through the feature recursive elimination method, one methylation site (chr8.72468901-72469000) was identified with ROC of 0.9 in the training dataset. The predictive model was validated in an independent dataset which is composed of 6 patients with LIM and 3 patients without metastasis, and achieved an AUC of 0.87. Conclusions: Our findings demonstrate the utility of methylation biomarkers for the molecular characterization of metastatic precursors, with implications for prediction and early detection of liver metastasis in CRC.

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The association between fecal enterotoxigenic B. fragilis with colorectal cancer

10.21203/rs.2.10895/v3 ◽

2019 ◽

Author(s):

Fakhri Haghi ◽

Elshan Goli ◽

Bahman Mirzaei ◽

Habib Zeighami

Keyword(s):

Colorectal Cancer ◽

Direct Detection ◽

Mucosal Immune Response ◽

Colorectal Disease ◽

Marker Genes ◽

Tissue Samples ◽

Potential Marker ◽

Paired Normal Tissue ◽

Stool Samples ◽

Pcr Targeting

Abstract Background Enterotoxigenic Bacteroides fragilis (ETBF) is an enterotoxin-producing bacterium that possibily has a role in the occurrence and progression of colorectal cancer (CRC) by modulating the mucosal immune response and inducing epithelial cell changes. The aim of this study was to investigate the frequency of ETBF in stool samples of CRC patients and healthy volunteers.Methods A total of 60 stool samples from confirmed CRC patients and 60 stool samples from healthy volunteers with no personal or familial history or diagnosis of colorectal disease were collected. Stool samples were screened for direct detection of B. fragilis using PCR targeting the marker genes of neu and bft. Enterotoxin isotypes bft-1, bft-2 and bft-3 were also detected in B. fragilis positive samples.Results The frequency of B. fragilis among CRC and control cases was 58.3% and 26.6%, respectively (P<0.05). The rate of bft gene in CRC cases was significantly higher than in controls (P<0.05). Also, the presence of bf t gene in CRC patients stage III was significantly higher than stages I and II (P< 0.05). Enterotoxin isotype bft-2 was detected with higher frequency among CRC patients than healthy control (P<0.05).Conclusion Our results show the association between fecal ETBF and CRC, and we suggest that detection of ETBF may be a potential marker for colorectal cancer diagnosis. However, additional investigations on tumor and paired normal tissue samples are required to substantiate this possible correlation.

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Organoids Are Limited in Modeling the Colon Adenoma–Carcinoma Sequence

Cells ◽

10.3390/cells10030488 ◽

2021 ◽

Vol 10 (3) ◽

pp. 488

Author(s):

Yoshihisa Tokumaru ◽

Masanori Oshi ◽

Ankit Patel ◽

Wanqing Tian ◽

Li Yan ◽

...

Keyword(s):

Colorectal Cancer ◽

Immune Response ◽

Immune Cells ◽

Enrichment Analysis ◽

Gene Set Enrichment Analysis ◽

Related Gene ◽

Gene Set Enrichment ◽

Colon Adenoma ◽

Tissue Samples ◽

Gene Sets

The colon adenoma–carcinoma sequence is a multistep genomic-altering process that occurs during colorectal cancer (CRC) carcinogenesis. Organoids are now commonly used to model both non-cancerous and cancerous tissue. This study aims to investigate how well organoids mimic tissues in the adenoma–carcinoma sequence by comparing their transcriptomes. A total of 234 tissue samples (48 adenomas and 186 CRC) and 60 organoid samples (15 adenomas and 45 CRC) were analyzed. We found that cell-proliferation-related gene sets were consistently enriched in both CRC tissues and organoids compared to adenoma tissues and organoids by gene set enrichment analysis (GSEA). None of the known pathways in the colon adenoma–carcinoma sequence were consistently enriched in CRC organoids. There was no enrichment of the tumor microenvironment-related gene sets in CRC organoids. CRC tissues enriched immune-response-related gene sets, whereas CRC organoids did not. The proportions of infiltrating immune cells were different between tissues and organoids, whereas there was no difference between cancer and adenoma organoids. The amounts of cancer stem cells and progenitor cells were not different between CRC and adenoma organoids, whereas a difference was noted between CRC and adenoma tissues. In conclusion, we demonstrated that organoids model only part of the adenoma–carcinoma sequence and should be used with caution after considering their limitations.

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The association between fecal enterotoxigenic B. fragilis with colorectal cancer

10.21203/rs.2.10895/v2 ◽

2019 ◽

Author(s):

Fakhri Haghi ◽

Elshan Goli ◽

Bahman Mirzaei ◽

Habib Zeighami

Keyword(s):

Colorectal Cancer ◽

Direct Detection ◽

Mucosal Immune Response ◽

Colorectal Disease ◽

Marker Genes ◽

Tissue Samples ◽

Potential Marker ◽

Paired Normal Tissue ◽

Stool Samples ◽

Pcr Targeting

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Effect of PHAP1 and SUMO2 on biological characteristics of Cervical squamous cell carcinoma

10.21203/rs.2.18625/v1 ◽

2019 ◽

Author(s):

Qian Liu ◽

Xiaohong Li ◽

Song Qin

Keyword(s):

Expression Patterns ◽

Cervical Squamous Cell Carcinoma ◽

Biological Characteristics ◽

Tumor Promoter ◽

Mrna Levels ◽

Rt Pcr ◽

Tissue Samples ◽

Normal Tissues ◽

The Relationship ◽

Hpv16 Infection

Abstract Background This study aimed to investigate the biological characteristics of PHAP1 and SUMO2 in CSCC and the relationship between the expression of the 2 genes and HPV16 infection. Method To detect the function of PHAP1 and SUMO2 in the occurrence and development of CSCC, we first compared their expression patterns in CSCC tissue samples, CIN and matched normal tissues through IHC, and RT-PCR. In addition, we carried on WB assay to test the expression of PHAP1 and SUMO2 in the SiHa, C33A and Ect1 cell lines. We analyzed the relationship between the expression of PHAP1 and SUMO2 and HPV16 infection. Result The results demonstrated that PHAP1 and SUMO2 expression at both the protein and mRNA levels was elevated in CSCC tissues compared with CIN and normal tissues. The expression of SUMO2 was significantly associated with lymph node metastasis (P=0.02), AJCC stage(p=0.024), but not other clinicopathological factors. The expression of PHAP1 and SUMO2 protein in SiHa, C33A cells was obviously higher than that in Ect1 cells. The expression of PHAP1 and SUMO2 was associated with a susceptibility to HPV16 infections. Conclusion Our results imply that PHAP1 and SUMO2 may be potential tumor promoter genes and may provide the biological basis for diagnosis, prognosis and treatment for CSCC.

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Expression Changes of the FOXE1 and Lncrna PTCSC2 Expression in Tumor Tissues Compared with Normal Tissues in Patients with Colorectal Cancer

Journal of Shahid Sadoughi University of Medical Sciences ◽

10.18502/ssu.v29i10.8213 ◽

2022 ◽

Author(s):

Marzieh Ghani Dehkordi ◽

Maryam Peymani

Keyword(s):

Colorectal Cancer ◽

Tumor Tissue ◽

Expression Patterns ◽

Study Groups ◽

Expression Level ◽

P Value ◽

Expression Levels ◽

Normal Tissues ◽

Tumor Tissues ◽

Significant Difference

Introduction: In recent studies, methylation of FOXE1 in colorectal cancer has been reported as a diagnostic biomarker. In this study for the first time, the expression of FOXE1 and PTCSC2 in colorectal cancer was investigated and their expression patterns in two healthy and tumor tissues of patients were compared. Methods: In this study, 40 tumor tissues with colorectal cancer and 40 adjacent normal samples were collected. Total RNA was extracted and cDNA synthesis followed. Then, the specific genes for lncRNA PTCSC2 and FOXE1 were amplified. The results were statistically analyzed by Graph Pad Prism software and a T-test was used to compare the expression levels of lncRNA PTCSC2 and FOXE1 in the patients and healthy group; p-value less than 0.05 was considered significant difference criteria. Results: In this study, the FOXE1 expression level was significantly decreased in tumor tissue (p-value = 0.005), whereas the lncRNA PTCSC2 expression level in tumor tissue was not significantly changed (p-value = 0.65). In addition, the expression levels of FOXE1 and lncRNA PTCSC2 did not show a significant relation with disease progression and age of the patients. ROC curve for changes in FOXE1 and lncRNA PTCSC2 expression showed that theFOXE1 gene could be a relatively appropriate independent variable (p-value = 0.03) to differentiate between the two study groups. Conclusion: According to the results of this study, changes in FOXE1 gene expression were significantly reduced in tumor samples and can be used as a biomarker in tumor diagnosis in colorectal cancer.

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Interaction Between Host MicroRNAs and the Gut Microbiota in Colorectal Cancer

10.1101/192401 ◽

2017 ◽

Author(s):

Ce Yuan ◽

Michael Burns ◽

Subbaya Subramanian ◽

Ran Blekhman

Keyword(s):

Colorectal Cancer ◽

Gut Microbiome ◽

Normal Tissue ◽

Microbial Community Composition ◽

Taxonomic Composition ◽

Integrated Analysis ◽

Tissue Samples ◽

Microbiome Composition ◽

Normal Tissues ◽

Mirnas Expression

AbstractBackgroundAlthough variation in gut microbiome composition has been linked with colorectal cancer (CRC), the factors that mediate the interactions between CRC tumors and the microbiome are poorly understood. MicroRNAs (miRNAs) are known to regulate CRC progression and patient survival outcomes. In addition, recent studies suggested that host miRNAs can also regulate bacterial growth and influence the composition of the gut microbiome. Here, we investigated the association between miRNAs expression in human CRC tumor and normal tissues and the microbiome composition associated with these same tissues.MethodWe sequenced the small RNAs from patient-matched tumor and normal tissue samples collected from 44 human CRC patients performed an integrated analysis with microbiome taxonomic composition data from these same samples. We then interrogated the functions of the bacteria correlated with miRNAs that were differentially expressed (DE) between tumor and matched normal tissues, as well as the functions of miRNAs correlated with bacterial taxa that have been previously associated with CRC, including Fusobacterium, Providencia, Bacteroides, Akkermansia, Roseburia, Porphyromonas, and Peptostreptococcus.ResultsWe identified 76 miRNAs as DE between CRC and normal tissue, including known oncogenic miRNAs miR-182, miR-503, and miR-17∼92. These DE miRNAs were correlated with the relative abundance of several bacterial taxa, including Firmicutes, Bacteroidetes, and Proteobacteria. Bacteria correlated with DE miRNAs were enriched with distinct predicted metabolic categories. Additionally, we found that miRNAs correlated with CRC-associated bacteria are predicted to regulate targets that are relevant for host-microbiome interactions, and highlight a possible role for miRNA-driven glycan production in the recruitment of pathogenic microbial taxa.ConclusionsOur work characterized a global relationship between microbial community composition and miRNA expression in human CRC tissues. Our results support a role for miRNAs in mediating a bi-directional host-microbiome interaction in CRC. In addition, we highlight sets of potentially interacting microbes and host miRNAs, suggesting several pathways that can be targeted via future therapies.

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The association between fecal enterotoxigenic B. fragilis with colorectal cancer

10.21203/rs.2.10895/v1 ◽

2019 ◽

Author(s):

Fakhri Haghi ◽

Elshan Goli ◽

Bahman Mirzaei ◽

Habib Zeighami

Keyword(s):

Colorectal Cancer ◽

Healthy Volunteers ◽

Direct Detection ◽

Mucosal Immune Response ◽

Colorectal Disease ◽

Marker Genes ◽

Tissue Samples ◽

Potential Marker ◽

Stool Samples ◽

Pcr Targeting

Abstract Background Enterotoxigenic Bacteroides fragilis (ETBF) is an enterotoxin-producing bacterium that possibily has a role in the occurrence and progression of colorectal cancer (CRC) by modulating the mucosal immune response and inducing epithelial cell changes. The aim of this study was to investigate the frequency of ETBF in stool samples of CRC patients and healthy volunteers. Methods A total of 60 stool samples from confirmed CRC patients and 60 stool samples from healthy volunteers with no personal or familial history or diagnosis of colorectal disease were collected. Stool samples were screened for direct detection of B. fragilis using PCR targeting the marker genes of neu and bft. Enterotoxin isotypes bft-1, bft-2 and bft-3 were also detected in B. fragilis positive samples. Results The frequency of B. fragilis among CRC and control cases was 58.3% and 26.6%, respectively (P<0.05). The rate of bft gene in CRC cases was significantly higher than in controls (P<0.05). Also, the presence of bft gene in CRC patients stage III was significantly higher than stages I and II (P< 0.05). Enterotoxin isotype bft-2 was detected with higher frequency among CRC patients than healthy control (P<0.05). Conclusion Our results show the association between fecal ETBF and CRC, and we suggest that detection of ETBF may be a potential marker for colorectal cancer diagnosis. However, additional investigations on tumor and paired normal tissue samples are required to substantiate this possible correlation.

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