Transcriptomic Profiling for the Autophagy Pathway in Colorectal Cancer

The role of autophagy in colorectal cancer (CRC) pathogenesis appears to be crucial. Autophagy acts both as a tumor suppressor, by removing redundant cellular material, and a tumor-promoting factor, by providing access to components necessary for growth, metabolism, and proliferation. To date, little is known about the expression of genes that play a basal role in the autophagy in CRC. In this study, we aimed to compare the expression levels of 46 genes involved in the autophagy pathway between tumor-adjacent and tumor tissue, employing large RNA sequencing (RNA-seq) and microarray datasets. Additionally, we verified our results using data on 38 CRC cell lines. Gene set enrichment analysis revealed a significant deregulation of autophagy-related gene sets in CRC. The unsupervised clustering of tumors using the mRNA levels of autophagy-related genes revealed the existence of two major clusters: microsatellite instability (MSI)-enriched and -depleted. In cluster 1 (MSI-depleted), ATG9B and LAMP1 genes were the most prominently expressed, whereas cluster 2 (MSI-enriched) was characterized by DRAM1 upregulation. CRC cell lines were also clustered according to MSI-enriched/-depleted subgroups. The moderate deregulation of autophagy-related genes in cancer tissue, as compared to adjacent tissue, suggests a prominent field cancerization or early disruption of autophagy. Genes differentiating these clusters are promising candidates for CRC targeting therapy worthy of further investigation.

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CMTM6 and PD-L1 coexpression is associated with an active immune microenvironment and a favorable prognosis in colorectal cancer

Journal for ImmunoTherapy of Cancer ◽

10.1136/jitc-2020-001638 ◽

2021 ◽

Vol 9 (2) ◽

pp. e001638

Author(s):

Qi-Hua Peng ◽

Chun-Hua Wang ◽

Hong-Min Chen ◽

Rong-Xin Zhang ◽

Zhi-Zhong Pan ◽

...

Keyword(s):

Colorectal Cancer ◽

T Cells ◽

Adjuvant Chemotherapy ◽

Prognostic Value ◽

Enrichment Analysis ◽

Gene Set Enrichment Analysis ◽

Comprehensive Treatment ◽

Mrna Levels ◽

Immune Microenvironment ◽

Favorable Prognosis

BackgroundCKLF-like MARVEL transmembrane domain-containing 6 (CMTM6), a programmed death-ligand 1 (PD-L1) regulator, is widely expressed in various tumors and regulates the immune microenvironment. However, its prognostic value remains controversial, and the roles of CMTM6 in colorectal cancer (CRC) are still unknown. In this study, we aimed to elaborate the expression patterns of CMTM6 and PD-L1 in CRC and investigate their relationship with the infiltration of T cells and the prognosis of patients with CRC.MethodsAnalysis of CMTM6 mRNA levels, gene ontology enrichment analysis and single-sample gene set enrichment analysis were performed in a The Cancer Genome Atlas colon cancer cohort. The expression of CMTM6 and PD-L1 and the infiltration of T cells in tumor tissues from our cohort containing 156 patients with CRC receiving adjuvant chemotherapy and 77 patients with CRC without chemotherapy were examined by immunohistochemistry assay.ResultsCMTM6 expression was upregulated in CRC compared with normal colon tissues, and CMTM6 levels were lower in advanced tumors than in early-stage tumors. High expression of CMTM6 correlated with lower pT stage and more CD4+/CD8+ tumor-infiltrating lymphocytes (TILs) and predicted a favorable prognosis in CRC. PD-L1 was expressed in CRC tissues at a low level, and PD-L1 positivity in tumor stroma (PD-L1(TS)), but not PD-L1 positivity in cancer cells (PD-L1(CC)), was associated with an increased density of CD4+ TILs and a favorable prognosis. The coexpression status of CMTM6 and PD-L1(TS) divided patients with CRC into three groups with low, moderate and high risks of progression and death, and patients with CMTM6High/PD-L1(TS)+ status had the longest survival. Moreover, the prognostic value of CMTM6/PD-L1 expression was more significant in patients with CRC treated with adjuvant chemotherapy than in those not treated with chemotherapy.ConclusionCMTM6 has a critical impact on the immune microenvironment and can be used as an independent prognostic factor for CRC. The coexpression status of CMTM6 and PD-L1 can be used as a new classification to stratify the risk of progression and death for patients with CRC, especially for patients receiving adjuvant chemotherapy. These findings may provide insights into improving responses to immunotherapy-included comprehensive treatment for CRC in the future.

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Robust Metabolic Transcriptional Components in 34,494 Patient-Derived Samples and Cell Lines

10.21203/rs.3.rs-659596/v1 ◽

2021 ◽

Author(s):

Vincent Christiaan Leeuwenburgh ◽

Carlos G. Urzúa-Traslaviña ◽

Arkajyoti Bhattacharya ◽

Marthe T.C. Walvoort ◽

Mathilde Jalving ◽

...

Keyword(s):

Cell Lines ◽

Expression Profiles ◽

Enrichment Analysis ◽

Gene Set Enrichment Analysis ◽

Metabolic Processes ◽

Gene Sets ◽

Transcriptional Changes ◽

Cancer Tissues ◽

Tumor Biopsies ◽

Transcriptional Landscape

Abstract Background: Patient-derived bulk expression profiles of cancers can provide insight into transcriptional changes that underlie reprogrammed metabolism in cancer. These profiles represent the average expression pattern of all heterogeneous tumor and non-tumor cells present in biopsies of tumor lesions. Hence, subtle transcriptional footprints of metabolic processes can be concealed by other biological processes and experimental artifacts. However, consensus Independent Component Analyses (c-ICA) can capture statistically independent transcriptional footprints, of both subtle and more pronounced metabolic processes. Methods: We performed c-ICA with 34,494 bulk expression profiles of patient-derived tumor biopsies, non-cancer tissues, and cell lines. Gene set enrichment analysis with 608 gene sets that describe metabolic processes was performed to identify transcriptional components enriched for metabolic processes (mTCs). The activity of these mTCs were determined in all samples to create a metabolic transcriptional landscape. Results: A set of 555 mTCs were identified of which many were robust across different datasets, platforms, and patient-derived tissues and cell lines. We demonstrate how the metabolic transcriptional landscape defined by the activity of these mTCs in samples can be used to explore associations between the metabolic transcriptome and drug sensitivities, patient outcomes, and the composition of the immune tumor microenvironment. Conclusions: To facilitate the use of our transcriptional metabolic landscape, we have provided access to all data via a web portal ( www.themetaboliclandscapeofcancer.com ). We believe this resource will contribute to the formulation of new hypotheses on how to metabolically engage the tumor or its (immune) microenvironment.

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Transcriptomic Analysis of the Differential Nephrotoxicity of Diverse Brominated Flame Retardants in Rat and Human Renal Cells

International Journal of Molecular Sciences ◽

10.3390/ijms221810044 ◽

2021 ◽

Vol 22 (18) ◽

pp. 10044

Author(s):

Lillie Marie A. Barnett ◽

Naomi E. Kramer ◽

Amanda N. Buerger ◽

Deirdre H. Love ◽

Joseph H. Bisesi ◽

...

Keyword(s):

Cell Lines ◽

Flame Retardants ◽

Molecular Mechanisms ◽

Annexin V ◽

Enrichment Analysis ◽

Brominated Flame Retardants ◽

Human Cells ◽

Gene Set Enrichment Analysis ◽

Coagulation Cascade ◽

Transcriptional Changes

Brominated flame retardants (BFRs) are environmentally persistent, are detected in humans, and some have been banned due to their potential toxicity. BFRs are developmental neurotoxicants and endocrine disruptors; however, few studies have explored their potential nephrotoxicity. We addressed this gap in the literature by determining the toxicity of three different BFRs (tetrabromobisphenol A (TBBPA), hexabromocyclododecane (HBCD), and tetrabromodiphenyl ether (BDE-47)) in rat (NRK 52E) and human (HK-2 and RPTEC) tubular epithelial cells. All compounds induced time- and concentration-dependent toxicity based on decreases in MTT staining and changes in cell and nuclear morphology. The toxicity of BFRs was chemical- and cell-dependent, and human cells were more susceptible to all three BFRs based on IC50s after 48 h exposure. BFRs also had chemical- and cell-dependent effects on apoptosis as measured by increases in annexin V and PI staining. The molecular mechanisms mediating this toxicity were investigated using RNA sequencing. Principal components analysis supported the hypothesis that BFRs induce different transcriptional changes in rat and human cells. Furthermore, BFRs only shared nine differentially expressed genes in rat cells and five in human cells. Gene set enrichment analysis demonstrated chemical- and cell-dependent effects; however, some commonalities were also observed. Namely, gene sets associated with extracellular matrix turnover, the coagulation cascade, and the SNS-related adrenal cortex response were enriched across all cell lines and BFR treatments. Taken together, these data support the hypothesis that BFRs induce differential toxicity in rat and human renal cell lines that is mediated by differential changes in gene expression.

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Potential Mechanism of Immune Evasion Associated with the Master Regulator ASCL2 in Microsatellite Stability in Colorectal Cancer

Journal of Immunology Research ◽

10.1155/2021/5964752 ◽

2021 ◽

Vol 2021 ◽

pp. 1-12

Author(s):

Qian Yang ◽

Guowei Huang ◽

Liyan Li ◽

Enmin Li ◽

Liyan Xu

Keyword(s):

Colorectal Cancer ◽

Immune Evasion ◽

Enrichment Analysis ◽

Gene Set Enrichment Analysis ◽

Novel Treatments ◽

T Cell Infiltration ◽

Immune Resistance ◽

Unbiased Gene ◽

Ifn Γ ◽

Microsatellite Stability

Colorectal cancer (CRC) has two major subtypes, microsatellite instability (MSI) and microsatellite stability (MSS) based on the genomic instability. In this study, using computational programs, we identified 9 master transcription factors (TFs) based on epigenomic profiling in MSS CRC samples. Notably, unbiased gene set enrichment analysis (GSEA) showed that several master TFs were strongly associated with immune-related functions in TCGA MSS CRC tissues, such as interferon gamma (IFN-γ) and interferon alpha (IFN-α) responses. Focusing to the top candidate, ASCL2, we found that CD8+ T cell infiltration was low in ASCL2 overexpressed MSS CRC samples. Compared with other gastrointestinal (GI) cancers (gastric cancer, MSI CRC, and esophageal cancer), ASCL2 is specifically upregulated in MSS CRC. Moreover, we identified 28 candidate genes in IFN-γ and IFN-α response pathways which were negatively correlated with ASCL2. Together, these results link transcriptional dysregulation with the immune evasion in MSS CRC, which may advance the understanding of immune resistance and contribute to developing novel treatments of MSS CRC.

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Identification of a Novel Epithelial-Mesenchymal Transition Gene Signature Regulated by KEAP1-NRF2 Pathway in Esophageal Carcinoma

10.21203/rs.3.rs-77379/v1 ◽

2020 ◽

Author(s):

Mohamed Elshaer ◽

Ahmed Hammad ◽

Xiu Jun Wang ◽

Xiuwen Tang

Keyword(s):

Cell Lines ◽

Epithelial Mesenchymal Transition ◽

Cancer Cell Line ◽

Enrichment Analysis ◽

Gene Signature ◽

Gene Set Enrichment Analysis ◽

The Cancer Genome Atlas ◽

Mesenchymal Transition ◽

Gene Set ◽

Over Expression

Abstract BackgroundKEAP1-NRF2 pathway alterations were identified in many cancers including, esophageal cancer (ESCA). Identifying biomarkers that are associated with mutations in this pathway will aid in defining this cancer subset; and hence in supporting precision and personalized medicine. MethodsIn this study, 182 tumor samples from the Cancer Genome Atlas (TCGA)-ESCA RNA-Seq V2 level 3 data were segregated into two groups KEAP1-NRF2-mutated (22) and wild-type (160).The two groups were subjected to differential gene expression analysis, and we performed Gene Set Enrichment Analysis (GSEA) to determine all significantly affected biological pathways. Then, the enriched gene set was integrated with the differentially expressed genes (DEGs) to identify a gene signature regulated by the KEAP1-NRF2 pathway in ESCA. Furthermore, we validated the gene signature using mRNA expression data of ESCA cell lines provided by the Cancer Cell Line Encyclopedia (CCLE). The identified signature was tested in 3 independent ESCA datasets to assess its prognostic value.ResultsWe identified 11 epithelial-mesenchymal transition (EMT) genes regulated by the KEAP1-NRF2 pathway in ESCA patients. Five of the 11 genes showed significant over-expression in KEAP1-NRF2-mutated ESCA cell lines. In addition, the over-expression of these five genes was significantly associated with poor survival in 3 independent ESCA datasets, including the TCGA-ESCA dataset.ConclusionAltogether, we identified a novel EMT 5-gene signature regulated by the KEAP1-NRF2 axis and this signature is strongly associated with metastasis and drug resistance in ESCA. These 5-genes are potential biomarkers and therapeutic targets for ESCA patients in whom the KEAP1-NRF2 pathway is altered.

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Deficiency of 15-LOX-1 Induces Radioresistance through Downregulation of MacroH2A2 in Colorectal Cancer

Cancers ◽

10.3390/cancers11111776 ◽

2019 ◽

Vol 11 (11) ◽

pp. 1776 ◽

Cited By ~ 1

Author(s):

Yoo Jin Na ◽

Bo Ram Kim ◽

Jung Lim Kim ◽

Sanghee Kang ◽

Yoon A. Jeong ◽

...

Keyword(s):

Colorectal Cancer ◽

Dna Damage ◽

Specific Treatment ◽

Enrichment Analysis ◽

Gene Set Enrichment Analysis ◽

Patient Specific ◽

Histone H2a ◽

Gene Set Enrichment ◽

Damage Response ◽

Radiation Induced

Despite the importance of radiation therapy, there are few radiation-related markers available for use in clinical practice. A larger catalog of such biomarkers is required to help clinicians decide when radiotherapy should be replaced with a patient-specific treatment. Arachidonate 15-lipoxygenase (15-LOX-1) enzyme is involved in polyunsaturated fatty acid metabolism. When colorectal cancer (CRC) cells were exposed to radiation, 15-LOX-1 was upregulated. To verify whether 15-LOX-1 protects against or induces DNA damage, we irradiated sh15-LOX-1 stable cells. We found that low 15-LOX-1 is correlated with radioresistance in CRC cells. These data suggest that the presence of 15-LOX-1 can be used as a marker for radiation-induced DNA damage. Consistent with this observation, gene-set-enrichment analysis based on microarray experiments showed that UV_RESPONSE was decreased in sh15-LOX-1 cells compared to shCon cells. Moreover, we discovered that the expression of the histone H2A variant macroH2A2 was sevenfold lower in sh15-LOX-1 cells. Overall, our findings present mechanistic evidence that macroH2A2 is transcriptionally regulated by 15-LOX-1 and suppresses the DNA damage response in irradiated cells by delaying H2AX activation.

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Mind Bomb 1 Promotes Pancreatic Cancer Proliferation by Activating β-Catenin Signaling

Journal of Nanoscience and Nanotechnology ◽

10.1166/jnn.2020.18755 ◽

2020 ◽

Vol 20 (12) ◽

pp. 7276-7282

Author(s):

Xiao Fu ◽

Neng Tang ◽

Weiqi Xie ◽

Liang Mao ◽

Yudong Qiu

Keyword(s):

Pancreatic Cancer ◽

Cancer Metastasis ◽

Mrna Level ◽

Enrichment Analysis ◽

Gene Expression Omnibus ◽

Gene Set Enrichment Analysis ◽

The Cancer Genome Atlas ◽

Pancreatic Tumors ◽

Mrna Levels ◽

Cancer Proliferation

Mind bomb 1 (MIB1), an E3 ligase, plays a vital role in chemo-resistance and cancer metastasis. According to The Cancer Genome Atlas (TCGA), MIB1 gene is preferentially amplified in pancreatic cancer. Copy number alterations in MIB1 gene are associated with worse survival. Gene Expression Omnibus (GEO) also showed that pancreatic cancer with high mRNA level of MIB1 tend to be more resistant to gemcitabine and higher mRNA levels of MIB1 are found in pancreatic tumors compared with adjacent normal tissues. MIB1 knockdown (KD) in Panc-1 and HPAF2 cell lines significantly inhibit proliferation and colony formation of pancreatic cancer. The gene set enrichment analysis (GSEA) has also showed that β-catenin is the downstream of MIB1. Western blot analysis showed that total and active β-catenin levels are decreased in MIB1 KD cells. β-catenin inhibitor also inhibits proliferation of Panc-1 and HPAF2 cells. We in this study implanted HPAF2 scramble and MIB1 KD cells orthotopically in athymic nude mice. Gemcitabine was used to treat the mice. Results revealed that after MIB1 KD HPAF2 cells were more sensitive to gemcitabine. In conclusion, we demonstrated that MIB1 promotes pancreatic cancer proliferation through activating β-catenin signaling. MIB1 may thus be a therapeutic target in pancreatic cancer therapy.

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Homeobox B9: A potential surrogate marker for bevacizumab in combination with chemotherapy in colorectal cancer.

Journal of Clinical Oncology ◽

10.1200/jco.2012.30.15_suppl.10531 ◽

2012 ◽

Vol 30 (15_suppl) ◽

pp. 10531-10531

Author(s):

Yoshinori Hoshino ◽

Tetsu Hayashida ◽

Akira Hirata ◽

Koji Okabayashi ◽

Hiroki Ochiai ◽

...

Keyword(s):

Colorectal Cancer ◽

Cell Lines ◽

Surrogate Marker ◽

Angiogenic Factors ◽

High Expression ◽

Mrna Levels ◽

Tgfβ Signaling ◽

Bevacizumab Treatment

10531 Background: Homeobox B9 (HOXB9) is known to be overexpressed in human breast cancer and profoundly related to tumorigenicity, lung metastasis and radio-resistance. (Hayashida, PNAS 2010, and Chiba, PNAS 2011). However, little is known about the relation between the expression of HOXB9 and angiogenesis in colorectal cancer (CRC). We aimed to clarify the impact of HOXB9 in CRC and evaluate the importance for bevacizumab treatment. Methods: The expression of HOXB9 in human CRC specimens was analyzed. Then, we introduced HOXB9 construct into human CRC cell lines and examined TGFβ signaling and angiogenic factors. Xenograft model was established by these cell lines either with or without the administration of bevacizumab (5mg/kg, weekly) intraperitoneally. Finally, we examined the mRNA levels of consecutive patients who were treated by chemotherapy with bevacizumab in our institute and calculated the Kaplan- Meier curve with log-rank test. Results: 47 of 69 surgical specimens (67%) showed positive expression of HOXB9 mRNA. The high HOXB9 mRNA levels significantly correlated with poor differentiation and liver metastasis. The HOXB9-overexpressed cell lines showed significantly higher expression of TGFβ signaling target genes and angiogenic factors. HOXB9 overexpression significantly increased tumor volume and burden with higher microvessel density in vivo, even though the cell proliferation decreased in vitro. Notably, HOXB9-overexpressed tumor was dramatically shrunk by administration of bevacizumab (tumor shrinkage rate; 93% vs. 42% in HT29, 83% vs. 27% in HCT116). Patients with high expression of HOXB9 in tumor showed significantly longer progression free and overall survival periods (n=39). Conclusions: Our results demonstrated that patients with high expression of HOXB9 in tumor had better prognosis with bevacizumab treatment but worse without. In vivo and in vitro experiments revealed that HOXB9 might orchestrate angiogenesis and establish positive feedback between cancer cells and microenvironment. Bevacizumab might inhibit the feedback to reduce tumor growth dramatically. Therefore, HOXB9 may work as a potential surrogate marker of bevacizumab treatment in CRC.

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Connecting gene expression subtypes of colorectal cancer (CRC) with cell lines and drug resistance.

Journal of Clinical Oncology ◽

10.1200/jco.2013.31.15_suppl.e14544 ◽

2013 ◽

Vol 31 (15_suppl) ◽

pp. e14544-e14544

Author(s):

Eva Budinska ◽

Jenny Wilding ◽

Vlad Calin Popovici ◽

Edoardo Missiaglia ◽

Arnaud Roth ◽

...

Keyword(s):

Gene Expression ◽

Cell Line ◽

Clinical Significance ◽

Cell Lines ◽

Drug Response ◽

Drug Sensitivity ◽

Expression Profiles ◽

Enrichment Analysis ◽

Gene Set Enrichment Analysis

e14544 Background: We identified CRC gene expression subtypes (ASCO 2012, #3511), which associate with established parameters of outcome as well as relevant biological motifs. We now substantiate their biological and potentially clinical significance by linking them with cell line data and drug sensitivity, primarily attempting to identify models for the poor prognosis subtypes Mesenchymal and CIMP-H like (characterized by EMT/stroma and immune-associated gene modules, respectively). Methods: We analyzed gene expression profiles of 35 publicly available cell lines with sensitivity data for 82 drug compounds, and our 94 cell lines with data on sensitivity for 7 compounds and colony morphology. As in vitro, stromal and immune-associated genes loose their relevance, we trained a new classifier based on genes expressed in both systems, which identifies the subtypes in both tissue and cell cultures. Cell line subtypes were validated by comparing their enrichment for molecular markers with that of our CRC subtypes. Drug sensitivity was assessed by linking original subtypes with 92 drug response signatures (MsigDB) via gene set enrichment analysis, and by screening drug sensitivity of cell line panels against our subtypes (Kruskal-Wallis test). Results: Of the cell lines 70% could be assigned to a subtype with a probability as high as 0.95. The cell line subtypes were significantly associated with their KRAS, BRAF and MSI status and corresponded to our CRC subtypes. Interestingly, the cell lines which in matrigel created a network of undifferentiated cells were assigned to the Mesenchymal subtype. Drug response studies revealed potential sensitivity of subtypes to multiple compounds, in addition to what could be predicted based on their mutational profile (e.g. sensitivity of the CIMP-H subtype to Dasatinib, p<0.01). Conclusions: Our data support the biological and potentially clinical significance of the CRC subtypes in their association with cell line models, including results of drug sensitivity analysis. Our subtypes might not only have prognostic value but might also be predictive for response to drugs. Subtyping cell lines further substantiates their significance as relevant model for functional studies.

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