1
|
Liu F, Wu W, Cao W, Feng L, Yuan J, Ren Z, Dai N, Wang X, Li X, Yue S. EREG silencing inhibits tumorigenesis via inactivating ERK/p38 MAPK pathway in pancreatic ductal adenocarcinoma. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167336. [PMID: 38972433 DOI: 10.1016/j.bbadis.2024.167336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 06/20/2024] [Accepted: 07/01/2024] [Indexed: 07/09/2024]
Abstract
Epiregulin (EREG) is a member of the epidermal growth factor (EGF) family. An increasing body of evidence has demonstrated the pivotal role of EREG in the pathogenesis and progression of various malignancies. However, the clinical significance and biological role of EREG in pancreatic ductal adenocarcinoma (PDAC) have yet to be fully elucidated. We found that EREG is highly expressed in PDAC tissues compared with paracancerous tissues through public databases and clinical samples. High EREG expression predicted worse overall survival (OS) and recurrence-free survival (RFS) in patients with PDAC. Multivariate analysis revealed that EREG can serve as an independent prognostic indicator. In addition, EREG silencing inhibited PDAC cell proliferation, migration, progression, altered cell cycle, facilitated apoptosis in vitro and suppressed tumor growth in vivo. Conversely, EREG overexpression facilitated the proliferation, migration, and invasion in PaTu-8988 t cell. Through transcriptome sequencing and experimental verification, we found EREG mediates PDAC tumorigenesis through ERK/p38 MAPK signaling pathway. Moreover, we found EREG expression is closely related to PD-L1 expression in PDAC tissues and cells. Therefore, EREG is expected to be a prospective prognostic and therapeutic marker for PDAC.
Collapse
Affiliation(s)
- Fuyuan Liu
- Department of General Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Weikang Wu
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Weiwei Cao
- Department of clinical laboratory, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Liangyong Feng
- Department of General Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Juzheng Yuan
- Department of General Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Zhuohui Ren
- Department of General Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Niu Dai
- Department of General Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Xudan Wang
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China.
| | - Xiao Li
- Department of General Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China.
| | - Shuqiang Yue
- Department of General Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China.
| |
Collapse
|
2
|
Ai LJ, Li GD, Chen G, Sun ZQ, Zhang JN, Liu M. Molecular subtyping and the construction of a predictive model of colorectal cancer based on ion channel genes. Eur J Med Res 2024; 29:219. [PMID: 38576045 PMCID: PMC10993535 DOI: 10.1186/s40001-024-01819-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/29/2024] [Indexed: 04/06/2024] Open
Abstract
PURPOSE Colorectal cancer (CRC) is a highly heterogeneous malignancy with an unfavorable prognosis. The purpose of this study was to address the heterogeneity of CRC by categorizing it into ion channel subtypes, and to develop a predictive modeling based on ion channel genes to predict the survival and immunological states of patients with CRC. The model will provide guidance for personalized immunotherapy and drug treatment. METHODS A consistent clustering method was used to classify 619 CRC samples based on the expression of 279 ion channel genes. Such a method was allowed to investigate the relationship between molecular subtypes, prognosis, and immune infiltration. Furthermore, a predictive modeling was constructed for ion channels to evaluate the ion channel properties of individual tumors using the least absolute shrinkage and selection operator. The expression patterns of the characteristic genes were validated through molecular biology experiments. The effect of potassium channel tetramerization domain containing 9 (KCTD9) on CRC was verified by cellular functional experiments. RESULTS Four distinct ion channel subtypes were identified in CRC, each characterized by unique prognosis and immune infiltration patterns. Notably, Ion Cluster3 exhibited high levels of immune infiltration and a favorable prognosis, while Ion Cluster4 showed relatively lower levels of immune infiltration and a poorer prognosis. The ion channel score could predict overall survival, with lower scores correlated with longer survival. This score served as an independent prognostic factor and presented an excellent predictive efficacy in the nomogram. In addition, the score was closely related to immune infiltration, immunotherapy response, and chemotherapy sensitivity. Experimental evidence further confirmed that low expression of KCTD9 in tumor tissues was associated with an unfavorable prognosis in patients with CRC. The cellular functional experiments demonstrated that KCTD9 inhibited the proliferation, migration and invasion capabilities of LOVO cells. CONCLUSIONS Ion channel subtyping and scoring can effectively predict the prognosis and evaluate the immune microenvironment, immunotherapy response, and drug sensitivity in patients with CRC.
Collapse
Affiliation(s)
- Lian-Jie Ai
- Colorectal Tumor Surgery, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Guo-Dong Li
- General Surgery, The 4th Affiliated Hospital of Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Gang Chen
- General Surgery, The 4th Affiliated Hospital of Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Zi-Quan Sun
- Colorectal Tumor Surgery, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Jin-Ning Zhang
- Colorectal Tumor Surgery, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Ming Liu
- General Surgery, The 4th Affiliated Hospital of Harbin Medical University, Harbin, 150001, Heilongjiang, China.
| |
Collapse
|
3
|
Lukosevicius R, Alzbutas G, Varkalaite G, Salteniene V, Tilinde D, Juzenas S, Kulokiene U, Janciauskas D, Poskiene L, Adamonis K, Kiudelis G, Kupcinskas J, Skieceviciene J. 5'-Isoforms of miR-1246 Have Distinct Targets and Stronger Functional Impact Compared with Canonical miR-1246 in Colorectal Cancer Cells In Vitro. Int J Mol Sci 2024; 25:2808. [PMID: 38474054 DOI: 10.3390/ijms25052808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/05/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
Colorectal cancer (CRC) is a multifactorial disease involving genetic and epigenetic factors, such as miRNAs. Sequencing-based studies have revealed that miRNAs have many isoforms (isomiRs) with modifications at the 3'- and 5'-ends or in the middle, resulting in distinct targetomes and, consequently, functions. In the present study, we aimed to evaluate the putative targets and functional role of miR-1246 and its two 5'-isoforms (ISO-miR-1246_a and ISO-miR-1246_G) in vitro. Commercial Caco-2 cells of CRC origin were analyzed for the expression of WT-miR-1246 and its 5'-isoforms using small RNA sequencing data, and the overabundance of the two miR-1246 isoforms was determined in cells. The transcriptome analysis of Caco-2 cells transfected with WT-miR-1246, ISO-miR-1246_G, and ISO-miR-1246_a indicated the minor overlap of the targetomes between the studied miRNA isoforms. Consequently, an enrichment analysis showed the involvement of the potential targets of the miR-1246 isoforms in distinct signaling pathways. Cancer-related pathways were predominantly more enriched in dysregulated genes in ISO-miR-1246_G and ISO-miR-1246_a, whereas cell cycle pathways were more enriched in WT-miR-1246. The functional analysis of WT-miR-1246 and its two 5'-isoforms revealed that the inhibition of any of these molecules had a tumor-suppressive role (reduced cell viability and migration and promotion of early cell apoptosis) in CRC cells. However, the 5'-isoforms had a stronger effect on viability compared with WT-miR-1246. To conclude, this research shows that WT-miR-1246 and its two 5'-isoforms have different targetomes and are involved in distinct signaling pathways but collectively play an important role in CRC pathogenesis.
Collapse
Affiliation(s)
- Rokas Lukosevicius
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania
| | - Gediminas Alzbutas
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania
| | - Greta Varkalaite
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania
| | - Violeta Salteniene
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania
| | - Deimante Tilinde
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania
| | - Simonas Juzenas
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania
- Institute of Biotechnology, Life Science Centre, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Ugne Kulokiene
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania
| | - Dainius Janciauskas
- Department of Pathology, Medical Academy, Hospital of Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania
| | - Lina Poskiene
- Department of Pathology, Medical Academy, Hospital of Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania
| | - Kestutis Adamonis
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania
| | - Gediminas Kiudelis
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania
| | - Juozas Kupcinskas
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania
| | - Jurgita Skieceviciene
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania
| |
Collapse
|
4
|
Sun M, Xu B, Chen C, Zhu Y, Li X, Chen K. Tissue of origin prediction for cancer of unknown primary using a targeted methylation sequencing panel. Clin Epigenetics 2024; 16:25. [PMID: 38336771 PMCID: PMC10854167 DOI: 10.1186/s13148-024-01638-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
RATIONALE Cancer of unknown primary (CUP) is a group of rare malignancies with poor prognosis and unidentifiable tissue-of-origin. Distinct DNA methylation patterns in different tissues and cancer types enable the identification of the tissue of origin in CUP patients, which could help risk assessment and guide site-directed therapy. METHODS Using genome-wide DNA methylation profile datasets from The Cancer Genome Atlas (TCGA) and machine learning methods, we developed a 200-CpG methylation feature classifier for CUP tissue of origin prediction (MFCUP). MFCUP was further validated with public-available methylation array data of 2977 specimens and targeted methylation sequencing of 78 Formalin-fixed paraffin-embedded (FFPE) samples from a single center. RESULTS MFCUP achieved an accuracy of 97.2% in a validation cohort (n = 5923) representing 25 cancer types. When applied to an Infinium 450 K array dataset (n = 1052) and an Infinium EPIC (850 K) array dataset (n = 1925), MFCUP achieved an overall accuracy of 93.4% and 84.8%, respectively. Based on MFCUP, we established a targeted bisulfite sequencing panel and validated it with FFPE sections from 78 patients of 20 cancer types. This methylation sequencing panel correctly identified tissue of origin in 88.5% (69/78) of samples. We also found that the methylation levels of specific CpGs can distinguish one cancer type from others, indicating their potential as biomarkers for cancer diagnosis and screening. CONCLUSION Our methylation-based cancer classifier and targeted methylation sequencing panel can predict tissue of origin in diverse cancer types with high accuracy.
Collapse
Affiliation(s)
- Miaomiao Sun
- Department of Pathology, Henan Key Laboratory of Tumor Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Bo Xu
- Research and Development Division, Oriomics Biotech Inc, Hangzhou, China
| | - Chao Chen
- Department of Pathology, Henan Key Laboratory of Tumor Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Youjie Zhu
- Research and Development Division, Oriomics Biotech Inc, Hangzhou, China
| | - Xiaomo Li
- Research and Development Division, Oriomics Biotech Inc, Hangzhou, China.
| | - Kuisheng Chen
- Department of Pathology, Henan Key Laboratory of Tumor Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
| |
Collapse
|
5
|
Hosseini-Abgir A, Naghizadeh MM, Igder S, Miladpour B. Insilco prediction of the role of the FriZZled5 gene in colorectal cancer. Cancer Treat Res Commun 2023; 36:100751. [PMID: 37595345 DOI: 10.1016/j.ctarc.2023.100751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 07/27/2023] [Accepted: 08/14/2023] [Indexed: 08/20/2023]
Abstract
INTRODUCTION In this study, we aimed to elucidate the crosstalk between the Wnt/β-catenin signaling pathway and colorectal cancer (CRC) associated with inflammatory bowel disease (IBD) using a bioinformatics analysis of putative common biomarkers and a systems biology approach. MATERIALS AND METHODS The following criteria were used to search the GEO and ArrayExpress databases for terms related to CRC and IBD: 1. The dataset containing the transcriptomic data, and 2. Untreated samples by medications or drugs. A total of 42 datasets were selected for additional analysis. The GEO2R identified the differentially expressed genes. The genes involved in the Wnt signaling pathway were extracted from the KEGG database. Enrichment analysis and miRNA target prediction were conducted through the ToppGene online tool. RESULTS In CRC datasets, there were 1168 up- and 998 down-regulated probes, whereas, in IBD datasets, there were 256 up- and 200 down-regulated probes. There were 65 upregulated and 57 downregulated genes shared by CRC and IBD. According to KEGG, there were 166 genes in the Wnt pathway. FriZZled5 (FZD5) was a down-regulated gene in both CRC and IBD, as determined by the intersection of CRC- and IBD-related DEGs with the Wnt pathway. It was also demonstrated that miR-191, miR-885-5p, miR-378a-3p, and miR-396-3p affect the FriZZled5 gene expression. CONCLUSION It is possible that increased expression of miR-191 and miR-885-5p, or decreased expression of miR-378a -3p and miR396-3, in IBD and CRC results in decreased expression of the FZD5 gene. Based on the function of this gene, FZD5 may be a potential therapeutic target in IBD that progresses to CRC.
Collapse
Affiliation(s)
| | | | - Somayeh Igder
- Department of Clinical Biochemistry, Faculty of Medicine, Ahvaz Jundishapur University of Medical Science, Ahvaz, Iran
| | - Behnoosh Miladpour
- Department of Clinical Biochemistry, Fasa University of Medical Sciences, Fasa, Iran.
| |
Collapse
|
6
|
Zhang Z, Lu Y, Vosoughi S, Levy J, Christensen B, Salas L. HiTAIC: hierarchical tumor artificial intelligence classifier traces tissue of origin and tumor type in primary and metastasized tumors using DNA methylation. NAR Cancer 2023; 5:zcad017. [PMID: 37089814 PMCID: PMC10113876 DOI: 10.1093/narcan/zcad017] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/04/2023] [Accepted: 04/13/2023] [Indexed: 04/25/2023] Open
Abstract
Human cancers are heterogenous by their cell composition and origination site. Cancer metastasis generates the conundrum of the unknown origin of migrated tumor cells. Tracing tissue of origin and tumor type in primary and metastasized cancer is vital for clinical significance. DNA methylation alterations play a crucial role in carcinogenesis and mark cell fate differentiation, thus can be used to trace tumor tissue of origin. In this study, we employed a novel tumor-type-specific hierarchical model using genome-scale DNA methylation data to develop a multilayer perceptron model, HiTAIC, to trace tissue of origin and tumor type in 27 cancers from 23 tissue sites in data from 7735 tumors with high resolution, accuracy, and specificity. In tracing primary cancer origin, HiTAIC accuracy was 99% in the test set and 93% in the external validation data set. Metastatic cancers were identified with a 96% accuracy in the external data set. HiTAIC is a user-friendly web-based application through https://sites.dartmouth.edu/salaslabhitaic/. In conclusion, we developed HiTAIC, a DNA methylation-based algorithm, to trace tumor tissue of origin in primary and metastasized cancers. The high accuracy and resolution of tumor tracing using HiTAIC holds promise for clinical assistance in identifying cancer of unknown origin.
Collapse
Affiliation(s)
- Ze Zhang
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Quantitative Biomedical Sciences Program, Guarini School of Graduate and Advanced Studies, Dartmouth College, Hanover, NH, USA
| | - Yunrui Lu
- Quantitative Biomedical Sciences Program, Guarini School of Graduate and Advanced Studies, Dartmouth College, Hanover, NH, USA
| | - Soroush Vosoughi
- Department of Computer Science, Dartmouth College, Hanover, NH, USA
| | - Joshua J Levy
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Quantitative Biomedical Sciences Program, Guarini School of Graduate and Advanced Studies, Dartmouth College, Hanover, NH, USA
- Department of Pathology and Dermatology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Quantitative Biomedical Sciences Program, Guarini School of Graduate and Advanced Studies, Dartmouth College, Hanover, NH, USA
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Lucas A Salas
- To whom correspondence should be addressed. Tel: +1 603 646 5420;
| |
Collapse
|
7
|
Ghatak S, Satapathy SR, Sjölander A. DNA Methylation and Gene Expression of the Cysteinyl Leukotriene Receptors as a Prognostic and Metastatic Factor for Colorectal Cancer Patients. Int J Mol Sci 2023; 24:ijms24043409. [PMID: 36834820 PMCID: PMC9963074 DOI: 10.3390/ijms24043409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/19/2023] [Accepted: 01/31/2023] [Indexed: 02/11/2023] Open
Abstract
Colorectal cancer (CRC), one of the leading causes of cancer-related deaths in the western world, is the third most common cancer for both men and women. As a heterogeneous disease, colon cancer (CC) is caused by both genetic and epigenetic changes. The prognosis for CRC is affected by a variety of features, including late diagnosis, lymph node and distant metastasis. The cysteinyl leukotrienes (CysLT), as leukotriene D4 and C4 (LTD4 and LTC4), are synthesized from arachidonic acid via the 5-lipoxygenase pathway, and play an important role in several types of diseases such as inflammation and cancer. Their effects are mediated via the two main G-protein-coupled receptors, CysLT1R and CysLT2R. Multiple studies from our group observed a significant increase in CysLT1R expression in the poor prognosis group, whereas CysLT2R expression was higher in the good prognosis group of CRC patients. Here, we systematically explored and established the role of the CysLTRs, cysteinyl leukotriene receptor 1(CYSLTR1) and cysteinyl leukotriene receptor 2 (CYSLTR2) gene expression and methylation in the progression and metastasis of CRC using three unique in silico cohorts and one clinical CRC cohort. Primary tumor tissues showed significant CYSLTR1 upregulation compared with matched normal tissues, whereas it was the opposite for the CYSLTR2. Univariate Cox proportional-hazards (CoxPH) analysis yielded a high expression of CYSLTR1 and accurately predicted high-risk patients in terms of overall survival (OS; hazard ratio (HR) = 1.87, p = 0.03) and disease-free survival [DFS] Hazard ratio [HR] = 1.54, p = 0.05). Hypomethylation of the CYSLTR1 gene and hypermethylation of the CYSLTR2 gene were found in CRC patients. The M values of the CpG probes for CYSLTR1 are significantly lower in primary tumor and metastasis samples than in matched normal samples, but those for CYSLTR2 are significantly higher. The differentially upregulated genes between tumor and metastatic samples were uniformly expressed in the high-CYSLTR1 group. Two epithelial-mesenchymal transition (EMT) markers, E-cadherin (CDH1) and vimentin (VIM) were significantly downregulated and upregulated in the high-CYSLTR1 group, respectively, but the result was opposite to that of CYSLTR2 expression in CRC. CDH1 expression was high in patients with less methylated CYSLTR1 but low in those with more methylated CYSLTR2. The EMT-associated observations were also validated in CC SW620 cell-derived colonospheres, which showed decreased E-cadherin expression in the LTD4 stimulated cells, but not in the CysLT1R knockdown SW620 cells. The methylation profiles of the CpG probes for CysLTRs significantly predicted lymph node (area under the curve [AUC] = 0.76, p < 0.0001) and distant (AUC = 0.83, p < 0.0001) metastasis. Intriguingly, the CpG probes cg26848126 (HR = 1.51, p = 0.03) for CYSLTR1, and cg16299590 (HR = 2.14, p = 0.03) for CYSLTR2 significantly predicted poor prognosis in terms of OS, whereas the CpG probe cg16886259 for CYSLTR2 significantly predicts a poor prognosis group in terms of DFS (HR = 2.88, p = 0.03). The CYSLTR1 and CYSLTR2 gene expression and methylation results were successfully validated in a CC patient cohort. In this study, we have demonstrated that CysLTRs' methylation and gene expression profile are associated with the progression, prognosis, and metastasis of CRC, which might be used for the assessment of high-risk CRC patients after validating the result in a larger CRC cohort.
Collapse
|
8
|
Devall MA, Sun X, Eaton S, Cooper GS, Willis JE, Weisenberger DJ, Casey G, Li L. A Race-Specific, DNA Methylation Analysis of Aging in Normal Rectum: Implications for the Biology of Aging and Its Relationship to Rectal Cancer. Cancers (Basel) 2022; 15:cancers15010045. [PMID: 36612042 PMCID: PMC9817986 DOI: 10.3390/cancers15010045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/01/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Approximately 90% of colorectal cancer (CRC) develop over the age of 50, highlighting the important role of aging in CRC risk. African Americans (AAs) shoulder a greater CRC burden than European Americans (EA) and are more likely to develop CRC at a younger age. The effects of aging in AA and EA normal rectal tissue have yet to be defined. Here, we performed epigenome-wide DNA methylation analysis in the first, large-scale biracial cohort of normal rectum (n = 140 samples). We identified increased epigenetic age acceleration in EA than AA rectum (p = 3.91 × 10-4) using linear regression. We also identified differentially methylated regions (DMRs) associated with chronological aging in AA and EA, separately using DMRcate. Next, a consensus set of regions associated with cancer was identified through DMR analysis of two rectal cancer cohorts. The vast majority of AA DMRs were present in our analysis of aging in rectum of EA subjects, though rates of epigenetic drift were significantly greater in AA (p = 1.94 × 10-45). However, 3.66-fold more DMRs were associated with aging in rectum of EA subjects, many of which were also associated with rectal cancer. Our findings reveal a novel relationship between race, age, DNA methylation and rectal cancer risk that warrants further investigation.
Collapse
Affiliation(s)
- Matthew A. Devall
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Xiangqing Sun
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Stephen Eaton
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Gregory S. Cooper
- Department of Medicine, University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Joseph E. Willis
- Department of Pathology, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Daniel J. Weisenberger
- Department of Biochemistry and Molecular Medicine, University of Southern California, Los Angeles, CA 90007, USA
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
- University of Virginia Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
| | - Li Li
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
- University of Virginia Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
- Correspondence: ; Tel.: +1-434-982-3975
| |
Collapse
|
9
|
Roelands J, van der Ploeg M, Ijsselsteijn ME, Dang H, Boonstra JJ, Hardwick JCH, Hawinkels LJAC, Morreau H, de Miranda NFCC. Transcriptomic and immunophenotypic profiling reveals molecular and immunological hallmarks of colorectal cancer tumourigenesis. Gut 2022:gutjnl-2022-327608. [PMID: 36442992 DOI: 10.1136/gutjnl-2022-327608] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 11/12/2022] [Indexed: 11/29/2022]
Abstract
OBJECTIVE Biological insights into the stepwise development and progression of colorectal cancer (CRC) are imperative to develop tailored approaches for early detection and optimal clinical management of this disease. Here, we aimed to dissect the transcriptional and immunologic alterations that accompany malignant transformation in CRC and to identify clinically relevant biomarkers through spatial profiling of pT1 CRC samples. DESIGN We employed digital spatial profiling (GeoMx) on eight pT1 CRCs to study gene expression in the epithelial and stromal segments across regions of distinct histology, including normal mucosa, low-grade and high-grade dysplasia and cancer. Consecutive histology sections were profiled by imaging mass cytometry to reveal immune contextures. Finally, publicly available single-cell RNA-sequencing data was analysed to determine the cellular origin of relevant transcripts. RESULTS Comparison of gene expression between regions within pT1 CRC samples identified differentially expressed genes in the epithelium (n=1394 genes) and the stromal segments (n=1145 genes) across distinct histologies. Pathway analysis identified an early onset of inflammatory responses during malignant transformation, typified by upregulation of gene signatures such as innate immune sensing. We detected increased infiltration of myeloid cells and a shift in macrophage populations from pro-inflammatory HLA-DR+CD204- macrophages to HLA-DR-CD204+ immune-suppressive subsets from normal tissue through dysplasia to cancer, accompanied by the upregulation of the CD47/SIRPα 'don't eat me signal'. CONCLUSION Spatial profiling revealed the molecular and immunological landscape of CRC tumourigenesis at early disease stage. We identified biomarkers with strong association with disease progression as well as targetable immune processes that are exploitable in a clinical setting.
Collapse
Affiliation(s)
- Jessica Roelands
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Manon van der Ploeg
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Hao Dang
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jurjen J Boonstra
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - James C H Hardwick
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Lukas J A C Hawinkels
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | | |
Collapse
|
10
|
Targeting epiregulin in the treatment-damaged tumor microenvironment restrains therapeutic resistance. Oncogene 2022; 41:4941-4959. [PMID: 36202915 DOI: 10.1038/s41388-022-02476-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 09/13/2022] [Accepted: 09/16/2022] [Indexed: 01/10/2023]
Abstract
The tumor microenvironment (TME) represents a milieu enabling cancer cells to develop malignant properties, while concerted interactions between cancer and stromal cells frequently shape an "activated/reprogramed" niche to accelerate pathological progression. Here we report that a soluble factor epiregulin (EREG) is produced by senescent stromal cells, which non-cell-autonomously develop the senescence-associated secretory phenotype (SASP) upon DNA damage. Genotoxicity triggers EREG expression by engaging NF-κB and C/EBP, a process supported by elevated chromatin accessibility and increased histone acetylation. Stromal EREG reprograms the expression profile of recipient neoplastic cells in a paracrine manner, causing upregulation of MARCHF4, a membrane-bound E3 ubiquitin ligase involved in malignant progression, specifically drug resistance. A combinational strategy that empowers EREG-specific targeting in treatment-damaged TME significantly promotes cancer therapeutic efficacy in preclinical trials, achieving response indices superior to those of solely targeting cancer cells. In clinical oncology, EREG is expressed in tumor stroma and handily measurable in circulating blood of cancer patients post-chemotherapy. This study establishes EREG as both a targetable SASP factor and a new noninvasive biomarker of treatment-damaged TME, thus disclosing its substantial value in translational medicine.
Collapse
|
11
|
Zhan L, Sun C, Zhang Y, Zhang Y, Jia Y, Wang X, Li F, Li D, Wang S, Yu T, Zhang J, Li D. Four methylation-driven genes detected by linear discriminant analysis model from early-stage colorectal cancer and their methylation levels in cell-free DNA. Front Oncol 2022; 12:949244. [PMID: 36158666 PMCID: PMC9491101 DOI: 10.3389/fonc.2022.949244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/12/2022] [Indexed: 12/24/2022] Open
Abstract
The process of colorectal cancer (CRC) formation is considered a typical model of multistage carcinogenesis in which aberrant DNA methylation plays an important role. In this study, 752 methylation-driven genes (MDGs) were identified by the MethylMix package based on methylation and gene expression data of CRC in The Cancer Genome Atlas (TCGA). Iterative recursive feature elimination (iRFE) based on linear discriminant analysis (LDA) was used to determine the minimum MDGs (iRFE MDGs), which could distinguish between cancer and cancer-adjacent tissues. Further analysis indicated that the changes in methylation levels of the four iRFE MDGs, ADHFE1-Cluster1, CNRIP1-Cluster1, MAFB, and TNS4, occurred in adenoma tissues, while changes did not occur until stage IV in cell-free DNA. Furthermore, the methylation levels of iRFE MDGs were correlated with the genes involved in the reprogramming process of somatic cells to pluripotent stem cells, which is considered the common signature of cancer cells and embryonic stem cells. The above results indicated that the four iRFE MDGs may play roles in the early stage of colorectal carcinogenesis and highlighted the complicated relationship between tissue DNA and cell-free DNA (cfDNA).
Collapse
Affiliation(s)
- Lei Zhan
- Medical Oncology Department of Gastrointestinal Cancer, Liaoning Cancer Hospital and Institute, Cancer Hospital of China Medical University, Shenyang, China
| | - Changjian Sun
- Clinical Laboratory, Air Force Hospital of Northern Theater, PLA, Shenyang, China
| | - Yu Zhang
- Clinical Laboratory, Air Force Hospital of Northern Theater, PLA, Shenyang, China
| | - Yue Zhang
- Clinical Laboratory, Air Force Hospital of Northern Theater, PLA, Shenyang, China
| | - Yuzhe Jia
- Clinical Laboratory, Air Force Hospital of Northern Theater, PLA, Shenyang, China
| | - Xiaoyan Wang
- Clinical Laboratory, Air Force Hospital of Northern Theater, PLA, Shenyang, China
| | - Feifei Li
- Medical Oncology Department of Gastrointestinal Cancer, Liaoning Cancer Hospital and Institute, Cancer Hospital of China Medical University, Shenyang, China
| | - Donglin Li
- Orthopedics Department, Air Force Hospital of Northern Theater, PLA, Shenyang, China
| | - Shen Wang
- Department of Ultrasound and Special Diagnosis, Air Force Hospital of Northern Theater, PLA, Shenyang, China
| | - Tao Yu
- Nursing Department, Air Force Medical Center, PLA, Beijing, China
| | - Jingdong Zhang
- Medical Oncology Department of Gastrointestinal Cancer, Liaoning Cancer Hospital and Institute, Cancer Hospital of China Medical University, Shenyang, China
| | - Deyang Li
- Clinical Laboratory, Air Force Hospital of Northern Theater, PLA, Shenyang, China
- *Correspondence: Deyang Li,
| |
Collapse
|
12
|
Zhang L, Li D, Gao L, Fu J, Sun S, Huang H, Zhang D, Jia C, Zheng T, Cui B, Liu Y, Zhao Y. Promoter Methylation of QKI as a Potential Specific Biomarker for Early Detection of Colorectal Cancer. Front Genet 2022; 13:928150. [PMID: 36017498 PMCID: PMC9395658 DOI: 10.3389/fgene.2022.928150] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/24/2022] [Indexed: 11/16/2022] Open
Abstract
Early and specific detection of cancer provides an opportunity for appropriate treatment. Although studies have suggested that QKI is a tumor suppressor gene, no studies have evaluated the diagnostic utility of QKI methylation in colorectal cancer (CRC). Here, we evaluated the methylation status of QKI by integrating the methylation data of tissues and cell lines of multiple cancer types. The diagnostic performance of QKI was analyzed in the discovery dataset from the TCGA CRC 450K array (n = 440) and tested in the test sets (n = 845) from the GEO. The methylation level of QKI was further validated in our independent dataset (n = 388) using targeted bisulfite sequencing. All detected CpG sites in the QKI promoter showed CRC-specific hypermethylation in 31 types of tumor tissues. In the discovery dataset, six consecutive CpG sites achieved high diagnostic performances, with AUCs ranging from 0.821 to 0.930. In the test set, a region (chr6: 163,834,452–163,834,924) including four consecutive CpG sites had robust diagnostic ability in distinguishing CRC and adenoma from normal samples. In the validation dataset, similar robust results were observed in both early- and advanced-stage CRC patients. In addition, QKI exhibited hypermethylation in the cfDNA of patients with CRC (n = 14). Collectively, the QKI promoter is a CRC-specific methylation biomarker and holds great promise for improving the diagnosis using minimally invasive biopsy.
Collapse
Affiliation(s)
- Lei Zhang
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Dapeng Li
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Lijing Gao
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Jinming Fu
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Simin Sun
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Hao Huang
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Ding Zhang
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Chenyang Jia
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Ting Zheng
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
| | - Binbin Cui
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, China
- *Correspondence: Yashuang Zhao, ; Yanlong Liu, ; Binbin Cui,
| | - Yanlong Liu
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, China
- *Correspondence: Yashuang Zhao, ; Yanlong Liu, ; Binbin Cui,
| | - Yashuang Zhao
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin, China
- *Correspondence: Yashuang Zhao, ; Yanlong Liu, ; Binbin Cui,
| |
Collapse
|
13
|
Chen H, Ye C, Cai B, Zhang F, Wang X, Zhang J, Zhang Z, Guo Y, Yao Q. Berberine inhibits intestinal carcinogenesis by suppressing intestinal pro-inflammatory genes and oncogenic factors through modulating gut microbiota. BMC Cancer 2022; 22:566. [PMID: 35596224 PMCID: PMC9123795 DOI: 10.1186/s12885-022-09635-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 05/04/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The role of Berberine (BBR) in colorectal cancer (CRC) and gut microbiota has begun to appreciate. However, there was no direct evidence confirm that the gut microbiota regulated by BBR could inhibit CRC. This report investigated the effect of stool from BBR treated subjects and its effect on CRC. METHODS A mouse model for CRC was developed using azoxymethane (AOM) and dextran sulfate sodium (DSS). Intestinal tissue from affected mice were used to determine the efficacy of BBR against CRC. Stool samples were collected for the 16s rRNA gene sequencing and fecal microbiota transplantation (FMT). Finally, the mechanism of gut microbiota from BBR treated mice on CRC was explored using immunohistochemistry, RNA-Sequencing, quantitative RT-PCR, and western blot analyses. RESULTS BBR significantly reduced intestinal tumor development. The richness of gut microbiota were notably decreased by BBR. Specifically, the relative abundance of beneficial bacteria (Roseburia, Eubacterium, Ruminococcaceae, and Firmicutes_unclassified) was increased while the level of bacteria (Odoribacter, Muribaculum, Mucispirillum, and Parasutterella) was decreased by BBR treatment. FMT experiment determined that the mice fed with stool from BBR treated AOM/DSS mice demonstrated a relatively lower abundance of macroscopic polyps and a significantly lower expression of β-catenin, and PCNA in intestinal tissue than mice fed with stool from AOM/DSS mice. Mechanistically, intestinal tissue obtained from mice fed with stool from BBR treated AOM/DSS mice demonstrated a decreased expression of inflammatory cytokines including interleukin 1β (IL-1β), tumor necrosis factor-α (TNF-α), C-C motif chemokine 1 (Ccl1), Ccl6, and C-X-C motif ligand (Cxcl9). In addition, the NF-κB expression was greatly suppressed in mice fed with stool from BBR treated AOM/DSS mice. Real-time PCR arrays revealed a down-regulation of genes involved in cell proliferation, angiogenesis, invasiveness, and metastasis in mice fed with stool from BBR treated AOM/DSS mice. CONCLUSIONS Stool obtained from BBR treated AOM/DSS mice was able to increase colon length while simultaneously decreasing the density of macroscopic polyps, cell proliferation, inflammatory modulators and the expression of NF-κB. Therefore, it was concluded that suppression of pro-inflammatory genes and carcinogens factors by modulating gut microbiota was an important pathway for BBR to inhibit tumor growth in conventional mice.
Collapse
Affiliation(s)
- Haitao Chen
- Department of Integrated Chinese and Western Medicine, Institute of Basic Medicine and Cancer (IBMC), The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Chinese Academy of Sciences, 310022, Hangzhou, Zhejiang, China
| | - Chenxiao Ye
- Zhejiang Chinese Medical University, 310053, Hangzhou, Zhejiang, China
| | - Biyu Cai
- Zhejiang Chinese Medical University, 310053, Hangzhou, Zhejiang, China
| | - Fan Zhang
- Zhejiang Chinese Medical University, 310053, Hangzhou, Zhejiang, China
| | - Xuanying Wang
- Zhejiang Chinese Medical University, 310053, Hangzhou, Zhejiang, China
| | - Jin Zhang
- Zhejiang Chinese Medical University, 310053, Hangzhou, Zhejiang, China
| | - Zewei Zhang
- Department of Abdominal Surgical Oncology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), 310022, Hangzhou, Zhejiang, China
| | - Yong Guo
- Department of Oncology, The First Affiliated Hospital of Zhejiang Chinese Medical University, 310003, Hangzhou, Zhejiang, China.
| | - Qinghua Yao
- Department of Integrated Chinese and Western Medicine, Institute of Basic Medicine and Cancer (IBMC), The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Chinese Academy of Sciences, 310022, Hangzhou, Zhejiang, China. .,Key Laboratory of Traditional Chinese Medicine Oncology, Zhejiang Cancer Hospital, 310022, Hangzhou, China. .,Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, 310022, Hangzhou, Zhejiang, China.
| |
Collapse
|
14
|
Otsuki Y, Ouchi K, Takahashi S, Sasaki K, Sakamoto Y, Okita A, Ishioka C. Altered gene expression due to aberrant DNA methylation correlates with responsiveness to anti-EGFR antibody treatment. Cancer Sci 2022; 113:3221-3233. [PMID: 35403373 PMCID: PMC9459254 DOI: 10.1111/cas.15367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 03/26/2022] [Accepted: 04/03/2022] [Indexed: 11/29/2022] Open
Abstract
The cetuximab gene expression signature and DNA methylation status of colorectal cancer (CRC) are predictive of the therapeutic effects of anti‐epidermal growth factor receptor (EGFR) antibody therapy. As DNA methylation is a means of regulating gene expression, it may play an important role in the expression of cetuximab signature genes. This study aims to determine the effects of aberrant DNA methylation on the regulation of cetuximab signature gene expression. Comprehensive DNA methylation and gene expression data were retrieved from CRC patients in three tumor tissue (TT) cohorts and three normal colorectal mucosa/tumor tissue paired (NCM‐TT) cohorts. Of the 231 cetuximab signature genes, 57 exhibited an inverse correlation between the methylation of promoter CpG sites and gene expression level in multiple cohorts. About two‐thirds of the promoter CpG sites associated with the 57 genes exhibited this correlation. In all 57 gene promoter regions, the methylation levels in NCMs did not differ according to comparisons based on cetuximab signature or DNA methylation status classification of matched TTs. Thus, the altered expression of 57 genes was caused by aberrant DNA methylation during carcinogenesis. Analysis of the association between cetuximab signature or DNA methylation status and progression‐free survival (PFS) of anti‐EGFR antibody agents in the same cohort showed that DNA methylation status was most associated with PFS. In conclusion, we found that aberrant DNA methylation regulates specific gene expression in cetuximab signature during carcinogenesis, suggesting that it is one of the important determinants of sensitivity to anti‐EGFR antibody agents.
Collapse
Affiliation(s)
- Yasufumi Otsuki
- Department of Clinical Oncology, Institute of Development, Aging and Cancer, Tohoku University, Miyagi, Japan.,Department of Medical Oncology, Tohoku University Hospital, Miyagi, Japan
| | - Kota Ouchi
- Department of Clinical Oncology, Institute of Development, Aging and Cancer, Tohoku University, Miyagi, Japan.,Department of Medical Oncology, Tohoku University Hospital, Miyagi, Japan
| | - Shin Takahashi
- Department of Clinical Oncology, Institute of Development, Aging and Cancer, Tohoku University, Miyagi, Japan.,Department of Medical Oncology, Tohoku University Hospital, Miyagi, Japan
| | - Keiju Sasaki
- Department of Clinical Oncology, Institute of Development, Aging and Cancer, Tohoku University, Miyagi, Japan.,Department of Medical Oncology, Tohoku University Hospital, Miyagi, Japan
| | - Yasuhiro Sakamoto
- Department of Medical Oncology, Osaki Citizen Hospital, Miyagi, Japan
| | - Akira Okita
- Department of Medical Oncology, Osaki Citizen Hospital, Miyagi, Japan
| | - Chikashi Ishioka
- Department of Clinical Oncology, Institute of Development, Aging and Cancer, Tohoku University, Miyagi, Japan.,Department of Medical Oncology, Tohoku University Hospital, Miyagi, Japan.,Department of Clinical Oncology, Tohoku University Graduate School of Medicine, Miyagi, Japan
| |
Collapse
|
15
|
Colorectal Cancer Diagnosis: The Obstacles We Face in Determining a Non-Invasive Test and Current Advances in Biomarker Detection. Cancers (Basel) 2022; 14:cancers14081889. [PMID: 35454792 PMCID: PMC9029324 DOI: 10.3390/cancers14081889] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/04/2022] [Accepted: 04/06/2022] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Colorectal cancer (CRC) is one of the most common cancers in the western world. CRC originates from precursor adenomatous polyps, which may over time develop into cancer. Endoscopic evaluation remains the gold-standard investigation for the disease. In the absence of molecular tools for early detection, the removal of neoplastic adenomas via polypectomy remains an important measure to prevent dysplastic adenomas from evolving into invasive carcinoma. Colonoscopy is an intrusive procedure that provides an uncomfortable experience for patients. Kits for testing for the presence of blood hemoglobin in the stool are now widely used, and DNA methylation-based detection kits have been approved in the USA for testing the stool and plasma, but few other molecular biomarkers have found their way into medical practice. This review summarizes current trends in the detection and screening of CRC and provides a definitive review of emerging molecular biomarkers for CRC. Abstract Globally, colorectal cancer (CRC) is the third most common cancer, with 1.4 million new cases and over 700,000 deaths per annum. Despite being one of the most common cancers, few molecular approaches to detect CRC exist. Carcinoembryonic antigen (CEA) is a known serum biomarker that is used in CRC for monitoring disease recurrence or response to treatment. However, it can also be raised in multiple benign conditions, thus having no value in early detection or screening for CRC. Molecular biomarkers play an ever-increasing role in the diagnosis, prognosis, and outcome prediction of disease, however, only a limited number of biomarkers are available and none are suitable for early detection and screening of CRC. A PCR-based Epi proColon® blood plasma test for the detection of methylated SEPT9 has been approved by the USFDA for CRC screening in the USA, alongside a stool test for methylated DNA from CRC cells. However, these are reserved for patients who decline traditional screening methods. There remains an urgent need for the development of non-invasive molecular biomarkers that are highly specific and sensitive to CRC and that can be used routinely for early detection and screening. A molecular approach to the discovery of CRC biomarkers focuses on the analysis of the transcriptome of cancer cells to identify differentially expressed genes and proteins. A systematic search of the literature yielded over 100 differentially expressed CRC molecular markers, of which the vast majority are overexpressed in CRC. In terms of function, they largely belong to biological pathways involved in cell division, regulation of gene expression, or cell proliferation, to name a few. This review evaluates the current methods used for CRC screening, current availability of biomarkers, and new advances within the field of biomarker detection for screening and early diagnosis of CRC.
Collapse
|
16
|
Müller D, Győrffy B. DNA methylation-based diagnostic, prognostic, and predictive biomarkers in colorectal cancer. Biochim Biophys Acta Rev Cancer 2022; 1877:188722. [PMID: 35307512 DOI: 10.1016/j.bbcan.2022.188722] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/21/2022] [Accepted: 03/13/2022] [Indexed: 12/12/2022]
Abstract
DNA methylation is an epigenetic mechanism regulating gene expression. Changes in DNA methylation were suggested to be useful biomarkers for diagnosis, and for the determination of prognosis and treatment response. Here, we provide an overview of methylation-based biomarkers in colorectal cancer. First, we start with the two methylation-based diagnostic biomarkers already approved for colorectal cancer, SEPT9 and the combination of NDRG4 and BMP3. Then, we provide a list-based overview of new biomarker candidates depending on the sample source including plasma, stool, urine, and surgically removed tumor tissues. The most often identified markers like SDC2, VIM, APC, MGMT, SFRP1, SFRP2, and NDRG4 have distinct functions previously linked to tumor progression. Although numerous studies have identified tumor-specific methylation changes, most of these alterations were observed in a single study only. The lack of validation in independent samples means low reproducibility and is a major limitation. The genome-wide determination of methylation status (methylome) can provide data to solve these issues. In the third section of the review, methylome studies focusing on different aspects related to CRC, including precancerous lesions, CRC-specific changes, molecular subtypes, aging, and chemotherapy response are summarized. Notably, techniques simultaneously analyzing a large set of regions can also uncover epigenetic regulation of genes which have not yet been associated with tumorigenesis previously. A remaining constraint of studies published to date is the low patient number utilized in these preventing the identification of clinically valuable biomarker candidates. Either future large-scale studies or the integration of already available methylome-level data will be necessary to uncover biomarkers sufficiently robust for clinical application.
Collapse
Affiliation(s)
- Dalma Müller
- Dept. of Bioinformatics, Semmelweis University, Budapest, Hungary; Cancer Biomarker Research Group, RCNS, Budapest, Hungary
| | - Balázs Győrffy
- Dept. of Bioinformatics, Semmelweis University, Budapest, Hungary; Cancer Biomarker Research Group, RCNS, Budapest, Hungary.
| |
Collapse
|
17
|
Zhong X, Ni J, Jia Z, Yan H, Zhang Y, Liu Y. CBX3 is associated with metastasis and glutathione/glycosphingolipid metabolism in colon adenocarcinoma. J Gastrointest Oncol 2022; 13:246-255. [PMID: 35284119 PMCID: PMC8899731 DOI: 10.21037/jgo-22-97] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/18/2022] [Indexed: 09/08/2023] Open
Abstract
BACKGROUND Metastasis is the major cause of colon adenocarcinoma (COAD) mortality. Increasing studies demonstrated that the epigenetics and downstream expression change of pivotal genes may act as a major role in promoting COAD progression and metastasis. Therefore, identifying the dysregulation of key genes associating with COAD metastasis may provide a new strategy for the discovery of potential treatment targets. METHODS This study included a single-cell RNA sequencing profile consisting of 17,469 tumor cells derived from 23 samples, and 326 COADs available from The Cancer Genome Atlas (TCGA), etc. The study was performed using comparative analysis to characterize the role of CBX3 in COAD metastasis and progression. RESULTS This study revealed that the mRNA level of Chromebox homolog 3 (CBX3) in the metastatic COAD was significantly higher than that of the primary COAD and normal colon tissues (Wilcoxon's rank-sum test, P<0.05). Activation of CBX3 was involved in regulating an interaction network consisting of CCT6A, LSM5, and GGCT, etc., which may subsequently participate in glutathione metabolism. Besides, CBX3 also exhibited a negative correlation with glycosphingolipid metabolism, which may associate with the regulation of CBX3 on DNA methylation. Clinical data analysis demonstrated that patients with high CBX3 mRNA levels showed a nearly 2-fold shorter overall survival time than the control group (hazard ratio =1.59; likelihood ratio test, P=0.04). CONCLUSIONS Our study demonstrated that CBX3 overexpression is associated with COAD metastasis. CBX3 downstream regulation network involves in TCP1 complex, LSM family, and glutathione metabolism, which may provide a potential target for suppressing tumor metastasis.
Collapse
Affiliation(s)
- Xiaoling Zhong
- Department of Blood Transfusion, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Jun Ni
- Department of Clinical Laboratory, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Zhijun Jia
- Department of Nuclear Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Hong Yan
- Department of Clinical Laboratory, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ying Zhang
- Department of Obstetrics and Gynecology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Yunyun Liu
- Department of Pathology, The Fourth Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Department of Pathology, Nanjing Medical University, Nanjing, China
| |
Collapse
|
18
|
Smell Detection Agent Optimisation Framework and Systems Biology Approach to Detect Dys-Regulated Subnetwork in Cancer Data. Biomolecules 2021; 12:biom12010037. [PMID: 35053185 PMCID: PMC8774275 DOI: 10.3390/biom12010037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 11/23/2022] Open
Abstract
Network biology has become a key tool in unravelling the mechanisms of complex diseases. Detecting dys-regulated subnetworks from molecular networks is a task that needs efficient computational methods. In this work, we constructed an integrated network using gene interaction data as well as protein–protein interaction data of differentially expressed genes derived from the microarray gene expression data. We considered the level of differential expression as well as the topological weight of proteins in interaction network to quantify dys-regulation. Then, a nature-inspired Smell Detection Agent (SDA) optimisation algorithm is designed with multiple agents traversing through various paths in the network. Finally, the algorithm provides a maximum weighted module as the optimum dys-regulated subnetwork. The analysis is performed for samples of triple-negative breast cancer as well as colorectal cancer. Biological significance analysis of module genes is also done to validate the results. The breast cancer subnetwork is found to contain (i) valid biomarkers including PIK3CA, PTEN, BRCA1, AR and EGFR; (ii) validated drug targets TOP2A, CDK4, HDAC1, IL6, BRCA1, HSP90AA1 and AR; (iii) synergistic drug targets EGFR and BIRC5. Moreover, based on the weight values assigned to nodes in the subnetwork, PLK1, CTNNB1, IGF1, AURKA, PCNA, HSPA4 and GAPDH are proposed as drug targets for further studies. For colorectal cancer module, the analysis revealed the occurrence of approved drug targets TYMS, TOP1, BRAF and EGFR. Considering the higher weight values, HSP90AA1, CCNB1, AKT1 and CXCL8 are proposed as drug targets for experimentation. The derived subnetworks possess cancer-related pathways as well. The SDA-derived breast cancer subnetwork is compared with that of tools such as MCODE and Minimum Spanning Tree, and observed a higher enrichment (75%) of significant elements. Thus, the proposed nature-inspired algorithm is a novel approach to derive the optimum dys-regulated subnetwork from huge molecular network.
Collapse
|
19
|
Cheng WL, Feng PH, Lee KY, Chen KY, Sun WL, Van Hiep N, Luo CS, Wu SM. The Role of EREG/EGFR Pathway in Tumor Progression. Int J Mol Sci 2021; 22:ijms222312828. [PMID: 34884633 PMCID: PMC8657471 DOI: 10.3390/ijms222312828] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 12/12/2022] Open
Abstract
Aberrant activation of the epidermal growth factor receptor (EGFR/ERBB1) by erythroblastic leukemia viral oncogene homolog (ERBB) ligands contributes to various tumor malignancies, including lung cancer and colorectal cancer (CRC). Epiregulin (EREG) is one of the EGFR ligands and is low expressed in most normal tissues. Elevated EREG in various cancers mainly activates EGFR signaling pathways and promotes cancer progression. Notably, a higher EREG expression level in CRC with wild-type Kirsten rat sarcoma viral oncogene homolog (KRAS) is related to better efficacy of therapeutic treatment. By contrast, the resistance of anti-EGFR therapy in CRC was driven by low EREG expression, aberrant genetic mutation and signal pathway alterations. Additionally, EREG overexpression in non-small cell lung cancer (NSCLC) is anticipated to be a therapeutic target for EGFR-tyrosine kinase inhibitor (EGFR-TKI). However, recent findings indicate that EREG derived from macrophages promotes NSCLC cell resistance to EGFR-TKI treatment. The emerging events of EREG-mediated tumor promotion signals are generated by autocrine and paracrine loops that arise from tumor epithelial cells, fibroblasts, and macrophages in the tumor microenvironment (TME). The TME is a crucial element for the development of various cancer types and drug resistance. The regulation of EREG/EGFR pathways depends on distinct oncogenic driver mutations and cell contexts that allows specific pharmacological targeting alone or combinational treatment for tailored therapy. Novel strategies targeting EREG/EGFR, tumor-associated macrophages, and alternative activation oncoproteins are under development or undergoing clinical trials. In this review, we summarize the clinical outcomes of EREG expression and the interaction of this ligand in the TME. The EREG/EGFR pathway may be a potential target and may be combined with other driver mutation targets to combat specific cancers.
Collapse
Affiliation(s)
- Wan-Li Cheng
- Division of Cardiovascular Surgery, Department of Surgery, Wan Fang Hospital, Taipei Medical University, Taipei 11696, Taiwan;
- Division of Cardiovascular Surgery, Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Po-Hao Feng
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan; (P.-H.F.); (K.-Y.L.); (K.-Y.C.); (W.-L.S.); (N.V.H.); (C.-S.L.)
- Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Kang-Yun Lee
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan; (P.-H.F.); (K.-Y.L.); (K.-Y.C.); (W.-L.S.); (N.V.H.); (C.-S.L.)
- Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Kuan-Yuan Chen
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan; (P.-H.F.); (K.-Y.L.); (K.-Y.C.); (W.-L.S.); (N.V.H.); (C.-S.L.)
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Wei-Lun Sun
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan; (P.-H.F.); (K.-Y.L.); (K.-Y.C.); (W.-L.S.); (N.V.H.); (C.-S.L.)
- Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Nguyen Van Hiep
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan; (P.-H.F.); (K.-Y.L.); (K.-Y.C.); (W.-L.S.); (N.V.H.); (C.-S.L.)
- International PhD Program in Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Ching-Shan Luo
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan; (P.-H.F.); (K.-Y.L.); (K.-Y.C.); (W.-L.S.); (N.V.H.); (C.-S.L.)
| | - Sheng-Ming Wu
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan; (P.-H.F.); (K.-Y.L.); (K.-Y.C.); (W.-L.S.); (N.V.H.); (C.-S.L.)
- Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Correspondence:
| |
Collapse
|
20
|
Xiong Y, Xi S, Gara SK, Shan J, Gao J, Zhang M, Shukla V, Wang R, Hoang CD, Chen H, Schrump DS. Hookah Smoke Mediates Cancer-Associated Epigenomic and Transcriptomic Signatures in Human Respiratory Epithelial Cells. JTO Clin Res Rep 2021; 2:100181. [PMID: 34790904 PMCID: PMC8479631 DOI: 10.1016/j.jtocrr.2021.100181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/14/2021] [Accepted: 04/23/2021] [Indexed: 11/29/2022] Open
Abstract
Introduction Although communal smoking of hookah by means of water pipes is perceived to be a safe alternative to cigarette smoking, the effects of hookah smoke in respiratory epithelia have not been well characterized. This study evaluated epigenomic and transcriptomic effects of hookah smoke relative to cigarette smoke in human respiratory epithelial cells. Methods Primary normal human small airway epithelial cells from three donors and cdk4 and hTERT-immortalized small airway epithelial cells and human bronchial epithelial cells were cultured for 5 days in normal media with or without cigarette smoke condensates (CSCs) or water pipe condensates (WPCs). Cell count, immunoblot, RNA sequencing, quantitative real-time reverse-transcriptase polymerase chain reaction, methylation-specific polymerase chain reaction, and quantitative chromatin immunoprecipitation techniques were used to compare effects of hookah and cigarette smoke on cell proliferation, global histone marks, gene expression, and promoter-related chromatin structure. Results CSC and WPC decreased global H4K16ac and H4K20me3 histone marks and mediated distinct and overlapping cancer-associated transcriptome signatures and pathway modulations that were cell line dependent and stratified across lung cancer cells in a histology-specific manner. Epiregulin encoding a master regulator of EGFR signaling that is overexpressed in lung cancers was up-regulated, whereas FILIP1L and ABI3BP encoding mediators of senescence that are repressed in lung cancers were down-regulated by CSC and WPC. Induction of epiregulin and repression of FILIP1L and ABI3BP by these condensates coincided with unique epigenetic alterations within the respective promoters. Conclusions These findings support translational studies to ascertain if hookah-mediated epigenomic and transcriptomic alterations in cultured respiratory epithelia are detectable and clinically relevant in hookah smokers.
Collapse
Affiliation(s)
- Yin Xiong
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Sichuan Xi
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Sudheer Kumar Gara
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Jigui Shan
- The Biomedical Informatics and Data Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - James Gao
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Mary Zhang
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Vivek Shukla
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Ruihong Wang
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Chuong D Hoang
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Haobin Chen
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - David S Schrump
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| |
Collapse
|
21
|
Elsayed I, Li L, Sheahan K, Moran B, Bakheit S, Wang X. Adenoma to carcinoma: A portrait of molecular and immunological profiles of colorectal sporadic tumors. Int Immunopharmacol 2021; 100:108168. [PMID: 34562842 DOI: 10.1016/j.intimp.2021.108168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/08/2021] [Accepted: 09/15/2021] [Indexed: 12/24/2022]
Abstract
An in-depth investigation of the molecular and immunologic properties of colorectal adenoma is important for understanding the mechanisms of colorectal cancer (CRC) initiation and development through the adenoma pathway. We performed a meta-analysis of the gene expression data from seven CRC and colorectal sporadic conventional adenoma datasets. We compared the enrichment levels of immune signatures between adenoma, normal colon, and CRC, then applied immunohistochemistry to compare the CD3 + and CD8 + T cells infiltration using samples of adenoma, contiguous adenoma, and CRC. We identified differentially expressed genes (DEGs) between adenoma, normal colon, and CRC, then performed pathway, network, immune correlation, and survival analyses on the DEGs. Adenoma had lower enrichment levels of antitumor immune signatures (CD8 + T cells, NK cells, and MHC Class I) while higher levels of TGF-β and Th17 signatures. Immunohistochemistry revealed variations in CD3 + and CD8 + T cells infiltration between low-grade and high-grade adenomas and between adenoma, normal colon, and CRC. We identified two groups of genes, which we named (NACupGs and NACdownGs), with consistent expression elevation and reduction respectively across the normal, precancerous, and cancerous stages. 48% of the NACupGs had expression levels highly correlated with Treg and TGF-β immune signatures, of which 39% were inversely correlated with CRC survival. We conclude that anti-tumor immune response is reduced at the precancerous (adenoma) stage which is characterized by prominent TGF-β and Th17 activity. The alterations of molecular and immunological profiles in adenoma can provide new insights into the initiation and development of CRC.
Collapse
Affiliation(s)
- Inas Elsayed
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China; Department of Pharmacology, Faculty of Pharmacy, University of Gezira, Wad Madani 20, Sudan
| | - Lin Li
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
| | - Kieran Sheahan
- Centre for Colorectal Disease, St. Vincent's University Hospital, Elm Park Dublin 4, Ireland; School of Medicine and Medical Sciences, University College Dublin, Belfield Dublin 4, Ireland
| | - Bruce Moran
- Department of Pathology, St. Vincent's University Hospital, Elm Park Dublin 4, Ireland
| | - Salih Bakheit
- Hull Royal Infirmary, Hull University Hospital NHS Trust, Hull, East Yorkshire, UK
| | - Xiaosheng Wang
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China.
| |
Collapse
|
22
|
Neinavaie F, Ibrahim-Hashim A, Kramer AM, Brown JS, Richards CL. The Genomic Processes of Biological Invasions: From Invasive Species to Cancer Metastases and Back Again. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.681100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The concept of invasion is useful across a broad range of contexts, spanning from the fine scale landscape of cancer tumors up to the broader landscape of ecosystems. Invasion biology provides extraordinary opportunities for studying the mechanistic basis of contemporary evolution at the molecular level. Although the field of invasion genetics was established in ecology and evolution more than 50 years ago, there is still a limited understanding of how genomic level processes translate into invasive phenotypes across different taxa in response to complex environmental conditions. This is largely because the study of most invasive species is limited by information about complex genome level processes. We lack good reference genomes for most species. Rigorous studies to examine genomic processes are generally too costly. On the contrary, cancer studies are fortified with extensive resources for studying genome level dynamics and the interactions among genetic and non-genetic mechanisms. Extensive analysis of primary tumors and metastatic samples have revealed the importance of several genomic mechanisms including higher mutation rates, specific types of mutations, aneuploidy or whole genome doubling and non-genetic effects. Metastatic sites can be directly compared to primary tumor cell counterparts. At the same time, clonal dynamics shape the genomics and evolution of metastatic cancers. Clonal diversity varies by cancer type, and the tumors’ donor and recipient tissues. Still, the cancer research community has been unable to identify any common events that provide a universal predictor of “metastatic potential” which parallels findings in evolutionary ecology. Instead, invasion in cancer studies depends strongly on context, including order of events and clonal composition. The detailed studies of the behavior of a variety of human cancers promises to inform our understanding of genome level dynamics in the diversity of invasive species and provide novel insights for management.
Collapse
|
23
|
S100P contributes to promoter demethylation and transcriptional activation of SLC2A5 to promote metastasis in colorectal cancer. Br J Cancer 2021; 125:734-747. [PMID: 34188196 PMCID: PMC8405647 DOI: 10.1038/s41416-021-01306-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 01/20/2021] [Accepted: 02/02/2021] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND SLC2A5 is a high-affinity fructose transporter, which is frequently upregulated in multiple human malignant tumours. However, the function and molecular mechanism of SLC2A5 in colorectal cancer (CRC) remain unknown. METHODS We detected the expression levels of SLC2A5 in CRC tissues and CRC cell lines by western blotting, qRT-PCR and immunohistochemistry. CRC cell lines with stable overexpression or knockdown of SLC2A5 were constructed to evaluate the functional roles of SLC2A5 in vitro through conventional assays. An intrasplenic inoculation model was established in mice to investigate the effect of SLC2A5 in promoting metastasis in vivo. Methylation mass spectrometry sequencing, methylation specific PCR, bisulphite sequencing PCR, ChIP-qPCR and luciferase reporter assay were performed to investigate the molecular mechanism underlying transcriptional activation of SLC2A5. RESULTS We found that SLC2A5 was upregulated in colorectal tumour tissues. Functionally, a high level of SLC2A5 expression was associated with increased invasion and metastasis capacities of CRC cells both in vitro and in vivo. Mechanistically, we unveiled that S100P could integrate to a specific region of SLC2A5 promoter, thereby reducing its methylation levels and activating SLC2A5 transcription. CONCLUSIONS Our results reveal a novel mechanism that S100P mediates the promoter demethylation and transcription activation of SLC2A5, thereby promoting the metastasis of CRC.
Collapse
|
24
|
Leystra AA, Harvey KN, Kaunga E, Hensley H, Vanderveer LA, Devarajan K, Clapper ML. High Variability in Cellular Proliferation, Gene Expression, and Cytokine Production in the Nonneoplastic Colonic Epithelium of Young Apc+/Min-FCCC Mice. Front Oncol 2021; 11:705562. [PMID: 34513688 PMCID: PMC8429936 DOI: 10.3389/fonc.2021.705562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 08/09/2021] [Indexed: 12/31/2022] Open
Abstract
An urgent need exists to identify efficacious therapeutic preventive interventions for individuals who are at high risk of developing colorectal cancer. To maximize the benefits of preventive intervention, it is vital to identify the time interval during which the initiation of a preventive intervention will lead to an optimal outcome. The goal of the present study was to determine if oncogenic events can be detected in the nonneoplastic colonic mucosa of Apc+/Min-FCCC mice prior to formation of the first adenoma, thus defining an earlier point of intervention along the cancer continuum. Tissues taken at three potential points of intervention were characterized: prior to Apc mutation (wild type Apc+/+-FCCC mice); after initiation but prior to colon adenoma formation (tumor-free Apc+/Min-FCCC mice); and after formation of the first colon adenoma (tumor-bearing Apc+/Min-FCCC mice). Experimentation focused on molecular processes that are dysregulated in early colon lesions: 1) cellular proliferation (proliferative index and size of the proliferative zone); 2) cellular stemness (expression of Ascl2, Grem1, Lgr5 and Muc2); 3) EGFR signaling (expression of Ereg); and 4) inflammation (expression of Mmp9, Ptsg2, and Reg4, as well as secretion of 18 cytokines involved in immune activation and response). Interestingly, the nonneoplastic colonic mucosa of wild type, tumor-free Apc+/Min-FCCC , and tumor-bearing Apc+/Min-FCCC mice did not display significant differences in average epithelial cell proliferation (fold change 0.8-1.3, p≥0.11), mucosal gene expression (fold change 0.8-1.4, p≥0.22), or secretion of specific cytokines from colonic mucosa (fold change 0.2-1.5, p≥0.06). However, the level of cytokine secretion was highly variable, with many (22% of wild type, 31% of tumor-free Apc+/Min-FCCC , and 31% of tumor-bearing Apc+/Min-FCCC ) mice categorized as outliers (> 1.5 x interquartile ranges below the first quartile or above the third quartile) due to elevated expression of at least one cytokine. In summary, no differences were observed in proliferation, stemness, and EGFR signaling in the colonic mucosa of wild type vs Apc+/Min-FCCC mice, with low baseline cytokine expression, prior to the formation of the first colon adenoma. The results of this study provide valuable baseline data to inform the design of future cancer prevention studies.
Collapse
Affiliation(s)
- Alyssa A. Leystra
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Kristen N. Harvey
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Esther Kaunga
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Harvey Hensley
- Biological Imaging Facility, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Lisa A. Vanderveer
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Karthik Devarajan
- Biostatistics and Bioinformatics Facility, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Margie L. Clapper
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| |
Collapse
|
25
|
Hu C, Liu X, Zeng Y, Liu J, Wu F. DNA methyltransferase inhibitors combination therapy for the treatment of solid tumor: mechanism and clinical application. Clin Epigenetics 2021; 13:166. [PMID: 34452630 PMCID: PMC8394595 DOI: 10.1186/s13148-021-01154-x] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 08/16/2021] [Indexed: 12/15/2022] Open
Abstract
DNA methylation, an epigenetic modification, regulates gene transcription and maintains genome stability. DNA methyltransferase (DNMT) inhibitors can activate silenced genes at low doses and cause cytotoxicity at high doses. The ability of DNMT inhibitors to reverse epimutations is the basis of their use in novel strategies for cancer therapy. In this review, we examined the literature on DNA methyltransferase inhibitors. We summarized the mechanisms underlying combination therapy using DNMT inhibitors and clinical trials based on combining hypomethylation agents with other chemotherapeutic drugs. We also discussed the efficacy of such compounds as antitumor agents, the need to optimize treatment schedules and the regimens for maximal biologic effectiveness. Notably, the combination of DNMT inhibitors and chemotherapy and/or immune checkpoint inhibitors may provide helpful insights into the development of efficient therapeutic approaches.
Collapse
Affiliation(s)
- Chunhong Hu
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.,Hunan Cancer Mega-Data Intelligent Application and Engineering Research Centre, Changsha, 410011, Hunan, China
| | - Xiaohan Liu
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Yue Zeng
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Junqi Liu
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Fang Wu
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China. .,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China. .,Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China. .,Hunan Cancer Mega-Data Intelligent Application and Engineering Research Centre, Changsha, 410011, Hunan, China.
| |
Collapse
|
26
|
Wang YJ, Wang QW, Yu DH, Song CK, Guo ZX, Liu XP, Chen C, Yao J, Wang AF, Hu WD. Osteopontin improves sensitivity to tyrosine kinase inhibitor in lung adenocarcinoma in vitro by promoting epidermal growth factor receptor phosphorylation. J Cancer Res Clin Oncol 2021; 147:3245-3254. [PMID: 34255150 DOI: 10.1007/s00432-021-03731-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 07/06/2021] [Indexed: 11/29/2022]
Abstract
PURPOSE Tyrosine kinase inhibitors (TKIs) targeting epidermal growth factor receptor (EGFR) improve the prognosis of lung adenocarcinoma (LUAD). However, the factors affecting its clinical efficacy remain unclear. This study aimed to determine the correlation between Osteopontin (OPN) and EGFR, and explore the inhibitory effect of first-generation TKI gefitinib on LUAD cells. METHODS The correlation between OPN and EGFR was determined through bioinformatics technology, and the clinical information as well as samples of related patients were collected to verify the relationship between them. Using three different NSCLC cell lines A549, H1299 and PC9, we studied the effects of OPN expression and EGFR phosphorylation on the first-generation TKI's efficacy in vitro. RESULTS Our data revealed that OPN staining positively linked to a more advanced clinical stage. Compared with the control group, LUAD cells with elevated OPN levels are more sensitive to the growth inhibitory effect of TKI. Knocking down of OPN decreased the response of cells to gefitinib. Besides, OPN also upregulated the phosphorylation of EGFR, thereby affecting the effect of TKI. CONCLUSION OPN enhanced the sensitivity of LUAD cells to gefitinib by promoting EGFR phosphorylation. OPN may be a potential target for evaluating TKI efficacy and a potential target for molecular therapy.
Collapse
Affiliation(s)
- Yu-Jin Wang
- Department of Thoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Zhongnan Hospital, Wuhan University, No. 169, East Lake Road, Wuchang, Wuhan, 430071, Hubei, China
| | - Qing-Wen Wang
- Department of Thoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Zhongnan Hospital, Wuhan University, No. 169, East Lake Road, Wuchang, Wuhan, 430071, Hubei, China
| | - Dong-Hu Yu
- Department of Thoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Zhongnan Hospital, Wuhan University, No. 169, East Lake Road, Wuchang, Wuhan, 430071, Hubei, China
| | - Cong-Kuan Song
- Department of Thoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Zhongnan Hospital, Wuhan University, No. 169, East Lake Road, Wuchang, Wuhan, 430071, Hubei, China
| | - Zi-Xin Guo
- Department of Thoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.,Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Zhongnan Hospital, Wuhan University, No. 169, East Lake Road, Wuchang, Wuhan, 430071, Hubei, China
| | - Xiao-Ping Liu
- Department of Urology, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, China
| | - Chen Chen
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.,Human Genetics Resource Preservation Center of Hubei Province, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Jie Yao
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.,Human Genetics Resource Preservation Center of Hubei Province, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Ai-Fen Wang
- Department of Obstetrics and Gynecology, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, 77 S Changan Road, Zhangjiagang, Jiangsu, China
| | - Wei-Dong Hu
- Department of Thoracic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China. .,Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Zhongnan Hospital, Wuhan University, No. 169, East Lake Road, Wuchang, Wuhan, 430071, Hubei, China.
| |
Collapse
|
27
|
Choi HI, An GY, Baek M, Yoo E, Chai JC, Lee YS, Jung KH, Chai YG. BET inhibitor suppresses migration of human hepatocellular carcinoma by inhibiting SMARCA4. Sci Rep 2021; 11:11799. [PMID: 34083693 PMCID: PMC8175750 DOI: 10.1038/s41598-021-91284-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 05/24/2021] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most prevalent and poorly responsive cancers worldwide. Bromodomain and extraterminal (BET) inhibitors, such as JQ1 and OTX-015, inhibit BET protein binding to acetylated residues in histones. However, the physiological mechanisms and regulatory processes of BET inhibition in HCC remain unclear. To explore BET inhibitors’ potential role in the molecular mechanisms underlying their anticancer effects in HCC, we analyzed BET inhibitor-treated HCC cells’ gene expression profiles with RNA-seq and bioinformatics analysis. BET inhibitor treatment significantly downregulated genes related to bromodomain-containing proteins 4 (BRD4), such as ACSL5, SLC38A5, and ICAM2. Importantly, some cell migration-related genes, including AOC3, CCR6, SSTR5, and SCL7A11, were significantly downregulated. Additionally, bioinformatics analysis using Ingenuity Knowledge Base Ingenuity Pathway Analysis (IPA) revealed that SMARCA4 regulated migration response molecules. Furthermore, knockdown of SMARCA4 gene expression by siRNA treatment significantly reduced cell migration and the expression of migration-related genes. In summary, our results indicated that BET inhibitor treatment in HCC cell lines reduces cell migration through the downregulation of SMARCA4.
Collapse
Affiliation(s)
- Hae In Choi
- Department of Bionanotechnology, Hanyang University, Seoul, 04673, Republic of Korea
| | - Ga Yeong An
- Department of Bionanotechnology, Hanyang University, Seoul, 04673, Republic of Korea
| | - Mina Baek
- Institute of Natural Science and Technology, Hanyang University, Ansan, 15588, Republic of Korea.,Department of Molecular and Life Science, Hanyang University, Ansan, 15588, Republic of Korea
| | - Eunyoung Yoo
- Department of Bionanotechnology, Hanyang University, Seoul, 04673, Republic of Korea
| | - Jin Choul Chai
- College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea
| | - Young Seek Lee
- College of Veterinary Medicine, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Kyoung Hwa Jung
- Convergence Technology Campus of Korea Polytechnic II, Incheon, 21417, Republic of Korea. .,Department of Biopharmaceutical System, Gwangmyeong Convergence Technology Campus of Korea Polytechnic II, Gwangmyeong , 14222, Republic of Korea.
| | - Young Gyu Chai
- Department of Bionanotechnology, Hanyang University, Seoul, 04673, Republic of Korea. .,Department of Molecular and Life Science, Hanyang University, Ansan, 15588, Republic of Korea.
| |
Collapse
|
28
|
Chen KY, Tseng CH, Feng PH, Sun WL, Ho SC, Lin CW, Van Hiep N, Luo CS, Tseng YH, Chen TT, Liu WT, Lee KY, Wu SM. 3-Nitrobenzanthrone promotes malignant transformation in human lung epithelial cells through the epiregulin-signaling pathway. Cell Biol Toxicol 2021; 38:865-887. [PMID: 34036453 DOI: 10.1007/s10565-021-09612-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/27/2021] [Indexed: 02/06/2023]
Abstract
Exposure to environmental and occupational contaminants leads to lung cancer. 3-Nitrobenzanthrone (3-nitro-7H-benz[de]anthracen-7-one, 3-NBA) is a potential carcinogen in ambient air or diesel particulate matter. Studies have revealed that short-term exposure to 3-NBA induces cell death, reactive oxygen species activation, and DNA adduct formation and damage. However, details of the mechanism by which chronic exposure to 3-NBA influences lung carcinogenesis remain largely unknown. In this study, human lung epithelial BEAS-2B cells were continuously exposed to 0-10-μM 3-NBA for 6 months. NanoString analysis was conducted to evaluate gene expression in the cells, revealing that 3-NBA-mediated transformation results in a distinct gene expression signature including carbon cancer metabolism, metastasis, and angiogenesis. Alterations in tumor-promoting genes such as EREG (epiregulin), SOX9, E-cadherin, TWIST, and IL-6 were involved in epithelial cell aggressiveness. Kaplan-Meier plotter analyses indicated that increased EREG and IL-6 expressions in early-stage lung cancer cells are correlated with poor survival. In vivo xenografts on 3-NBA-transformed cells exhibited prominent tumor formation and metastasis. EREG knockout cells exposed to 3-NBA for a short period exhibited high apoptosis and low colony formation. By contrast, overexpression of EREG in 3-NBA-transformed cells markedly activated the PI3K/AKT and MEK/ERK signaling pathways, resulting in tumorigenicity. Furthermore, elevated IL-6 and EREG expressions synergistically led to STAT3 signaling activation, resulting in clonogenic cell survival and migration. Taken together, chronic exposure of human lung epithelial cells to 3-NBA leads to malignant transformation, in which the EREG signaling pathway plays a pivotal mediating role. • Short-term exposure of lung epithelial cells to 3-NBA can lead to ROS production and cell apoptosis. • Long-term chronic exposure to 3-NBA upregulates the levels of tumor-promoting genes such as EREG and IL-6. • Increased EREG expression in 3-NBA-transformed cells markedly contributes to tumorigenesis through PI3K/AKT and MEK/ERK activation and synergistically enhances the IL-6/STAT3 signaling pathway, which promotes tumorigenicity.
Collapse
Affiliation(s)
- Kuan-Yuan Chen
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Chien-Hua Tseng
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan.,Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Po-Hao Feng
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan.,Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Wei-Lun Sun
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan.,Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Shu-Chuan Ho
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan.,School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Cheng-Wei Lin
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Nguyen Van Hiep
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan.,International PhD Program in Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Ching-Shan Luo
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Yen-Han Tseng
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan.,Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Tzu-Tao Chen
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan.,Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Wen-Te Liu
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan.,Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Kang-Yun Lee
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan.,Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Sheng-Ming Wu
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan.,Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| |
Collapse
|
29
|
Della Chiara G, Gervasoni F, Fakiola M, Godano C, D'Oria C, Azzolin L, Bonnal RJP, Moreni G, Drufuca L, Rossetti G, Ranzani V, Bason R, De Simone M, Panariello F, Ferrari I, Fabbris T, Zanconato F, Forcato M, Romano O, Caroli J, Gruarin P, Sarnicola ML, Cordenonsi M, Bardelli A, Zucchini N, Ceretti AP, Mariani NM, Cassingena A, Sartore-Bianchi A, Testa G, Gianotti L, Opocher E, Pisati F, Tripodo C, Macino G, Siena S, Bicciato S, Piccolo S, Pagani M. Epigenomic landscape of human colorectal cancer unveils an aberrant core of pan-cancer enhancers orchestrated by YAP/TAZ. Nat Commun 2021; 12:2340. [PMID: 33879786 PMCID: PMC8058065 DOI: 10.1038/s41467-021-22544-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 03/18/2021] [Indexed: 02/07/2023] Open
Abstract
Cancer is characterized by pervasive epigenetic alterations with enhancer dysfunction orchestrating the aberrant cancer transcriptional programs and transcriptional dependencies. Here, we epigenetically characterize human colorectal cancer (CRC) using de novo chromatin state discovery on a library of different patient-derived organoids. By exploring this resource, we unveil a tumor-specific deregulated enhancerome that is cancer cell-intrinsic and independent of interpatient heterogeneity. We show that the transcriptional coactivators YAP/TAZ act as key regulators of the conserved CRC gained enhancers. The same YAP/TAZ-bound enhancers display active chromatin profiles across diverse human tumors, highlighting a pan-cancer epigenetic rewiring which at single-cell level distinguishes malignant from normal cell populations. YAP/TAZ inhibition in established tumor organoids causes extensive cell death unveiling their essential role in tumor maintenance. This work indicates a common layer of YAP/TAZ-fueled enhancer reprogramming that is key for the cancer cell state and can be exploited for the development of improved therapeutic avenues. The role of epigenetic deregulation in colorectal cancer (CRC) is not fully understood yet. Here the authors use patient-derived organoids, epigenomics and single-cell RNA-seq to reveal that YAP/TAZ are key regulators that bind to active enhancers in CRC and promote tumour survival.
Collapse
Affiliation(s)
- Giulia Della Chiara
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy.,Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy.,Human Organoid Models Integrative Center HOMIC, University of Milan, Milan, Italy.,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | - Federica Gervasoni
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy.,Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy.,Human Organoid Models Integrative Center HOMIC, University of Milan, Milan, Italy.,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | - Michaela Fakiola
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy.,Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Chiara Godano
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy.,Human Organoid Models Integrative Center HOMIC, University of Milan, Milan, Italy.,Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Claudia D'Oria
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy.,Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy.,Human Organoid Models Integrative Center HOMIC, University of Milan, Milan, Italy.,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | - Luca Azzolin
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Raoul Jean Pierre Bonnal
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy.,Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Giulia Moreni
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy.,Department of Medical Microbiology, Laboratory of Clinical Virology, Amsterdam University Medical Center, University of Amsterdam, AZ, Amsterdam, the Netherlands
| | - Lorenzo Drufuca
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy.,Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Grazisa Rossetti
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy.,Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Valeria Ranzani
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Ramona Bason
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy.,Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy.,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | - Marco De Simone
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy.,Technology Center for Genomics and Bioinformatics, Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA, USA
| | - Francesco Panariello
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy.,Telethon Institute of Genetics and Medicine TIGEM, Pozzuoli, Italy
| | - Ivan Ferrari
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | - Tanya Fabbris
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy
| | | | - Mattia Forcato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Oriana Romano
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Jimmy Caroli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Paola Gruarin
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Maria Lucia Sarnicola
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy
| | | | - Alberto Bardelli
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo (TO), Italy.,Department of Oncology, University of Torino, Candiolo (TO), Italy
| | | | | | | | - Andrea Cassingena
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Andrea Sartore-Bianchi
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Giuseppe Testa
- Human Organoid Models Integrative Center HOMIC, University of Milan, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.,Department of Experimental Oncology, European Institute of Oncology, IRCCS, Milan, Italy
| | - Luca Gianotti
- School of Medicine and Surgery, Milano-Bicocca University, and Department of Surgery, San Gerardo Hospital, Monza, Italy
| | - Enrico Opocher
- UO Chirurgia Epatobiliopancreatica e Digestiva Ospedale San Paolo, Milan, Italy.,Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | | | - Claudio Tripodo
- Tumor Immunology Unit, University of Palermo, Palermo, Italy.,Tumor and Microenvironment Histopathology Unit, IFOM, FIRC Institute of Molecular Oncology, Milan, Italy
| | - Giuseppe Macino
- Department of Cellular Biotechnologies and Hematology, La Sapienza University of Rome, Rome, Italy
| | - Salvatore Siena
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Silvio Bicciato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Stefano Piccolo
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy. .,Department of Molecular Medicine, University of Padua, Padua, Italy.
| | - Massimiliano Pagani
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy. .,Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy. .,Human Organoid Models Integrative Center HOMIC, University of Milan, Milan, Italy. .,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy.
| |
Collapse
|
30
|
Wang X, Chi P. Reactivation of oncogenes involved in G1/S transcription and apoptosis pathways by low dose decitabine promotes HT29 human colon cancer cell growth in vitro. Am J Transl Res 2020; 12:7938-7952. [PMID: 33437371 PMCID: PMC7791509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/01/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND To examine the effects of low-dose decitabine (DAC) on the proliferation of HT-29 cell lines, and to explore the central mechanism by which low-dose DAC affects HT-29 cell proliferation using a systematic biological approach. METHODS First, we examined the global effects of DAC on cell proliferation, the cell cycle, and apoptosis in HT29 colon cancer cells. Then, a series test of cluster (STC) analysis and weighted gene coexpression network analysis (WGCNA) were employed to identify critical pathways involved in the response to DAC treatment using 3 datasets from the GEO database. Finally, the expression changes and promoter methylation levels of hub genes were further confirmed by in vitro experiments. RESULTS Low-dose DAC (less than 1 µM) promoted the proliferation and colony formation ability of HT-29 cell lines. The results of the system-level analysis, including STC analysis, WGCNA, and Gene set variation analysis (GSVA), showed that DAC modulated 3 critical pathways: G1/S-specific transcription involved in E2F-mediated regulation of Cyclin E-associated events, apoptosis pathways, and EMT pathways. Subsequent in vitro experiments showed that low-dose DAC (0.1 µM) promoted G1/S-specific transcription and decreased apoptosis rates. Then, several regulatory hub oncogenes in these 3 pathways, CCNE1, E2F1, BCL2, PCNA, FOXC1, VIM, CXCL1, and VCAM1, were further confirmed to be activated by DAC at either the mRNA or protein level. We chose the oncogene BCL2 as an example and detected its methylation status and the effect of low-dose DAC on BCL2 expression. Data from TCGA and Oncomine databases demonstrated that BCL2 was decreased in colon cancer compared with normal mucosa. Further analysis showed that BCL2 had an increased degree of promoter methylation in 12 methylated sites in colon cancer compared with normal colon tissues. Bisulfite sequencing PCR showed that low-dose DAC decreased the methylation rate at the BCL2 promoter region. CONCLUSIONS We concluded that low-dose DAC treatment resulted in a cancer-promoting effect in HT29 cell lines. Mechanistically, high methylation levels at the promoter region of oncogenes with dominant effects in CRC, such as BCL2 in HT29, might play a role in suppressing CRC by inhibiting oncogene expression. Low-dose DAC treatment triggered BCL2 expression by decreasing its promoter methylation level, thereby resulting in cancer promotion.
Collapse
Affiliation(s)
- Xiaojie Wang
- Department of Colorectal Surgery, Union Hospital, Fujian Medical University People's Republic of China
| | - Pan Chi
- Department of Colorectal Surgery, Union Hospital, Fujian Medical University People's Republic of China
| |
Collapse
|
31
|
Wang Y, Zhang M, Hu X, Qin W, Wu H, Wei M. Colon cancer-specific diagnostic and prognostic biomarkers based on genome-wide abnormal DNA methylation. Aging (Albany NY) 2020; 12:22626-22655. [PMID: 33202377 PMCID: PMC7746390 DOI: 10.18632/aging.103874] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 07/25/2020] [Indexed: 12/11/2022]
Abstract
Abnormal DNA methylation is a major early contributor to colon cancer (COAD) development. We conducted a cohort-based systematic investigation of genome-wide DNA methylation using 299 COAD and 38 normal tissue samples from TCGA. Through conditional screening and machine learning with a training cohort, we identified one hypomethylated and nine hypermethylated differentially methylated CpG sites as potential diagnostic biomarkers, and used them to construct a COAD-specific diagnostic model. Unlike previous models, our model precisely distinguished COAD from nine other cancer types (e.g., breast cancer and liver cancer; error rate ≤ 0.05) and from normal tissues in the training cohort (AUC = 1). The diagnostic model was verified using a validation cohort from The Cancer Genome Atlas (AUC = 1) and five independent cohorts from the Gene Expression Omnibus (AUC ≥ 0.951). Using Cox regression analyses, we established a prognostic model based on six CpG sites in the training cohort, and verified the model in the validation cohort. The prognostic model sensitively predicted patients’ survival (p ≤ 0.00011, AUC ≥ 0.792) independently of important clinicopathological characteristics of COAD (e.g., gender and age). Thus, our DNA methylation analysis provided precise biomarkers and models for the early diagnosis and prognostic evaluation of COAD.
Collapse
Affiliation(s)
- Yilin Wang
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, Liaoning Province, P. R. China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang 110122, Liaoning Province, P. R. China
| | - Ming Zhang
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, Liaoning Province, P. R. China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang 110122, Liaoning Province, P. R. China
| | - Xiaoyun Hu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, Liaoning Province, P. R. China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang 110122, Liaoning Province, P. R. China
| | - Wenyan Qin
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, Liaoning Province, P. R. China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang 110122, Liaoning Province, P. R. China
| | - Huizhe Wu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, Liaoning Province, P. R. China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang 110122, Liaoning Province, P. R. China
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, Liaoning Province, P. R. China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang 110122, Liaoning Province, P. R. China
| |
Collapse
|
32
|
Li D, Zhang L, Fu J, Huang H, Sun S, Zhang D, Zhao L, Ucheojor Onwuka J, Zhao Y, Cui B. SCTR hypermethylation is a diagnostic biomarker in colorectal cancer. Cancer Sci 2020; 111:4558-4566. [PMID: 32970347 PMCID: PMC7734158 DOI: 10.1111/cas.14661] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/12/2020] [Accepted: 09/12/2020] [Indexed: 12/12/2022] Open
Abstract
Diagnostic markers for both colorectal cancer (CRC) and its precursor lesions are lacking. Although aberrant methylation of the secretin receptor (SCTR) gene was observed in CRC, the diagnostic performance has not been evaluated. Therefore, this study aimed to assess and verify the diagnostic value of SCTR methylation of CRC and its precursor lesions through integrating the largest methylation data. The diagnostic performance of SCTR methylation was analyzed in the discovery set from The Cancer Genome Atlas (TCGA) CRC methylation data (N = 440), and verified in a large-scale test set (N = 938) from the Gene Expression Omnibus (GEO). Targeted bisulfite sequencing analysis was developed and applied to detect the methylation status of SCTR in our independent validation set (N = 374). Our findings revealed that the SCTR gene was frequently hypermethylated at its CpG islands in CRC. In the TCGA discovery set, the diagnostic score was constructed using 4 CpG sites (cg01013590, cg20505223, cg07176264, and cg26009192) and achieved high diagnostic performance (area under the ROC curve [AUC] = 0.964). In the GEO test set, the diagnostic score had robust diagnostic ability to distinguish CRC (AUC = 0.948) and its precursor lesions (AUC = 0.954) from normal samples. Moreover, hypermethylation of the SCTR gene was also found in cell-free DNA samples collected from CRC patients, but not in those from healthy controls. In the validation set, consistent results were observed using the targeted bisulfite sequencing array. Our study highlights that hypermethylation at CpG islands of the SCTR gene is a potential diagnostic biomarker in CRCs and its precursor lesions.
Collapse
Affiliation(s)
- DaPeng Li
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, China
| | - Lei Zhang
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, China
| | - JinMing Fu
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, China
| | - Hao Huang
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, China
| | - SiMin Sun
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, China
| | - Ding Zhang
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, China
| | - LiYuan Zhao
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, China
| | - Justina Ucheojor Onwuka
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, China
| | - YaShuang Zhao
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, China
| | - BinBin Cui
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, China
| |
Collapse
|
33
|
miR-215 Targeting Novel Genes EREG, NIPAL1 and PTPRU Regulates the Resistance to E.coli F18 in Piglets. Genes (Basel) 2020; 11:genes11091053. [PMID: 32906628 PMCID: PMC7563519 DOI: 10.3390/genes11091053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/27/2020] [Accepted: 09/03/2020] [Indexed: 11/17/2022] Open
Abstract
Previous research has revealed that miR-215 might be an important miRNA regulating weaned piglets’ resistance to Escherichia coli (E. coli) F18. In this study, target genes of miR-215 were identified by RNA-seq, bioinformatics analysis and dual luciferase detection. The relationship between target genes and E. coli infection was explored by RNAi technology, combined with E. coli stimulation and enzyme linked immunosorbent assay (ELISA) detection. Molecular regulating mechanisms of target genes expression were analyzed by methylation detection of promoter regions and dual luciferase activity assay of single nucleotide polymorphisms (SNPs) in core promoter regions. The results showed that miR-215 could target EREG, NIPAL1 and PTPRU genes. Expression levels of three genes in porcine intestinal epithelial cells (IPEC-J2) in the RNAi group were significantly lower than those in the negative control pGMLV vector (pGMLV-NC) group after E. coli F18 stimulation, while cytokines levels of TNF-α and IL-1β in the RNAi group were significantly higher than in the pGMLV-NC group. Variant sites in the promoter region of three genes could affect their promoter activities. These results suggested that miR-215 could regulate weaned piglets’ resistance to E. coli F18 by targeting EREG, NIPAL1 and PTPRU genes. This study is the first to annotate new biological functions of EREG, NIPAL1 and PTPRU genes in pigs, and provides a new experimental basis and reference for the research of piglets disease-resistance breeding.
Collapse
|
34
|
Lin CY, Hsieh PL, Chou CL, Yang CC, Lee SW, Tian YF, Shiue YL, Li WS. High EREG Expression Is Predictive of Better Outcomes in Rectal Cancer Patients Receiving Neoadjuvant Concurrent Chemoradiotherapy. Oncology 2020; 98:549-557. [PMID: 32408308 DOI: 10.1159/000506991] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 03/02/2020] [Indexed: 11/19/2022]
Abstract
BACKGROUND/AIM A great proportion of patients with rectal cancer initially present with locally advanced disease and can potentially benefit from neoadjuvant concurrent chemoradiotherapy (CCRT) for downstaging before surgery. However, risk and clinical outcome stratification remain a great challenge. We aimed to find the potential biomarker to predict the effect of neoadjuvant CCRT on rectal cancer. METHODS We identified epiregulin (EREG) as the most significant predictive marker for neoadjuvant CCRT response from the published rectal cancer transcriptome data set GSE35452. We collected 172 biopsy specimens from rectal cancer patients who received neoadjuvant CCRT followed by radical proctectomy, performed EREG immunohistochemistry, and analyzed the H-scores. We further examined the correlations between the expression level of EREG and clinicopathological features, tumor regression grade, and survival, including disease-specific survival (DSS), locoregional recurrence-free survival (LRFS), and metastasis-free survival (MeFS). RESULTS High EREG expression was significantly related to early pretreatment (pre-Tx) and posttreatment (post-Tx) tumor status (T1, T2, p = 0.047 and p < 0.001), pre-Tx and post-Tx negative nodal status (N0, p < 0.001 and p = 0.004), less vascular and perineurial invasion (p = 0.015 and p = 0.023), and higher tumor regression grade (p < 0.001). In the survival analysis, high EREG expression was significantly associated with better DSS (p < 0.0001), LRFS (p = 0.0004), and MeFS (p < 0.0001). In the multivariate analysis, high EREG expression remained prognostically significant for better DSS (p = 0.003; hazard ratio: 5.599). CONCLUSION These data suggest that EREG is a potential predictive marker and therapeutic target in rectal cancer patients receiving neoadjuvant CCRT.
Collapse
Affiliation(s)
- Cheng-Yi Lin
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Chi Mei Medical Center, Tainan, Taiwan
| | - Pei-Ling Hsieh
- Department of Medical Imaging, Chi Mei Medical Center, Tainan, Taiwan
| | - Chia-Lin Chou
- Division of Colon and Rectal Surgery, Department of Surgery, Chi Mei Medical Center, Tainan, Taiwan.,Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Ching-Chieh Yang
- Department of Radiation Oncology, Chi Mei Medical Center, Tainan, Taiwan
| | - Sung-Wei Lee
- Department of Radiation Oncology, Chi Mei Medical Center, Liouying, Tainan, Taiwan
| | - Yu-Feng Tian
- Division of Colon and Rectal Surgery, Department of Surgery, Chi Mei Medical Center, Tainan, Taiwan
| | - Yow-Ling Shiue
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Wan-Shan Li
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan, .,Department of Pathology, Chi Mei Medical Center, Tainan, Taiwan,
| |
Collapse
|
35
|
Fan J, Li J, Guo S, Tao C, Zhang H, Wang W, Zhang Y, Zhang D, Ding S, Zeng C. Genome-wide DNA methylation profiles of low- and high-grade adenoma reveals potential biomarkers for early detection of colorectal carcinoma. Clin Epigenetics 2020; 12:56. [PMID: 32317010 PMCID: PMC7175491 DOI: 10.1186/s13148-020-00851-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/08/2020] [Indexed: 02/07/2023] Open
Abstract
Background Abnormal DNA methylation is a hallmark of human cancers and may be a promising biomarker for early diagnosis of human cancers. However, the majority of DNA methylation biomarkers that have been identified are based on the hypothesis that early differential methylation regions (DMRs) are maintained throughout carcinogenesis and could be detected at all stages of cancer. Methods In this study, we identified potential early biomarkers of colorectal cancer (CRC) development by genome-wide DNA methylation assay (Illumina infinium450, 450 K) of normal (N = 20) and pre-colorectal cancer samples including 18 low-grade adenoma (LGA) and 22 high-grade adenoma (HGA), integrated with GEO and ArrayExpress datasets (N = 833). Results We identified 209 and 8692 CpG sites that were significantly hyper-methylated in LGA and HGA, respectively. Pathway analysis identified nervous system-related methylation changes that are significantly associated with early adenoma development. Integration analysis revealed that DNA methylation in the promoter region of ADHFE1 has the most potential for being an early diagnostic biomarker for colorectal adenoma and cancer (sensitivity = 0.96, specificity = 0.95, area under the curve = 0.97). Conclusions Overall, we demonstrated that DNA methylation have been shown significant changes in the stage of LGA and HGA in the development of colon cancer. Genome-wide DNA methylation to LGA and HGA provided an important proxy to identify promising early diagnosis biomarkers for colorectal cancer.
Collapse
Affiliation(s)
- Jian Fan
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun Li
- Department of Gastroenterology, Peking University Third Hospital, Beijing, 100191, China
| | - Shicheng Guo
- Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53726, USA.,Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, 54449, USA
| | - Chengcheng Tao
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Haikun Zhang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenjing Wang
- Department of Gastroenterology, Peking University Third Hospital, Beijing, 100191, China
| | - Ying Zhang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dake Zhang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China. .,Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China.
| | - Shigang Ding
- Department of Gastroenterology, Peking University Third Hospital, Beijing, 100191, China.
| | - Changqing Zeng
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
| |
Collapse
|
36
|
Yamamoto Y, Saita T, Oka A, Kataoka H, Shin M. Localization and Accumulation Studies of Dacomitinib in Rat Intestines and Skin by Immunohistochemistry. Acta Histochem Cytochem 2019; 52:101-106. [PMID: 32001948 PMCID: PMC6983371 DOI: 10.1267/ahc.19031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 11/21/2019] [Indexed: 11/22/2022] Open
Abstract
Dacomitinib, a second-generation tyrosine kinase inhibitor, was irreversible inhibitor forming covalent bonds with the kinase domains of EGFR and other ErbB family receptors. Dacomitinib has been approved for the treatment of locally advanced or metastatic non-small cell lung cancer. In this study, we aimed to develop an immunohistochemistry to detect dacomitinib-ErbB family receptor conjugates. Immunostaining was performed in rat intestine and skin tissues after oral administration of dacomitinib. Following a single oral dose of dacomitinib, strong staining was observed after 24 hr in the ileum and colon, with only slight staining in the duodenum and jejunum. In the skin, strong staining was observed in the epidermis, hair follicles, and sebaceous glands. Moreover, significant amounts of dacomitinib remained for up to 72 hr post-administration in the ileum, colon, and skin. This report is the first to elucidate the localization and accumulation of dacomitinib in the rat intestine and skin and should be valuable during efforts to clarify the mechanism dacomitinib-induced diarrhea or skin toxicities.
Collapse
Affiliation(s)
- Yutaro Yamamoto
- Applied Life Science Department, Faculty of Biotechnology and Life Science, Sojo University
| | - Tetsuya Saita
- Applied Life Science Department, Faculty of Biotechnology and Life Science, Sojo University
| | - Asuki Oka
- Applied Life Science Department, Faculty of Biotechnology and Life Science, Sojo University
| | - Hiroto Kataoka
- Applied Life Science Department, Faculty of Biotechnology and Life Science, Sojo University
| | - Masashi Shin
- Applied Life Science Department, Faculty of Biotechnology and Life Science, Sojo University
| |
Collapse
|
37
|
Abstract
Tumor-specific DNA methylation can be used for cancer diagnostics and monitoring. We have recently reported a set of DNA methylation biomarkers that can distinguish plasma samples from lung cancer patients versus healthy controls with high sensitivity and specificity. Furthermore, the DNA methylation signal from the biomarker loci detected in plasma samples correlated with tumor size and decreased after surgical resection of lung tumors. In order to determine the timing of DNA methylation of these loci during carcinogenesis and thus the potential of the biomarkers to detect early stages of the disease we analyzed the DNA methylation of the biomarker loci in five precancerous conditions using available data from the GEO database. We found that the DNA methylation of the biomarker loci is gained early in carcinogenesis since most of the precancerous conditions already have biomarker loci hypermethylated. Moreover, these DNA methylation biomarkers are able to distinguish between precancerous lesions with malignant potential and those that stay benign where data is available. Taken together, the biomarkers have the potential to detect the earliest cancer stages; the only limitation to detection of cancer from plasma samples or other liquid biopsies is the timing when tumors start to shed enough DNA into body fluids.
Collapse
Affiliation(s)
- Lukas Vrba
- The University of Arizona Cancer Center, The University of Arizona, Tucson, Arizona, 85724, USA
| | - Bernard W Futscher
- The University of Arizona Cancer Center, The University of Arizona, Tucson, Arizona, 85724, USA.,Department of Pharmacology & Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona, 85724, USA
| |
Collapse
|
38
|
Choi H, Joe S, Nam H. Development of Tissue-Specific Age Predictors Using DNA Methylation Data. Genes (Basel) 2019; 10:genes10110888. [PMID: 31690030 PMCID: PMC6896025 DOI: 10.3390/genes10110888] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/01/2019] [Accepted: 11/01/2019] [Indexed: 12/17/2022] Open
Abstract
DNA methylation patterns have been shown to change throughout the normal aging process. Several studies have found epigenetic aging markers using age predictors, but these studies only focused on blood-specific or tissue-common methylation patterns. Here, we constructed nine tissue-specific age prediction models using methylation array data from normal samples. The constructed models predict the chronological age with good performance (mean absolute error of 5.11 years on average) and show better performance in the independent test than previous multi-tissue age predictors. We also compared tissue-common and tissue-specific aging markers and found that they had different characteristics. Firstly, the tissue-common group tended to contain more positive aging markers with methylation values that increased during the aging process, whereas the tissue-specific group tended to contain more negative aging markers. Secondly, many of the tissue-common markers were located in Cytosine-phosphate-Guanine (CpG) island regions, whereas the tissue-specific markers were located in CpG shore regions. Lastly, the tissue-common CpG markers tended to be located in more evolutionarily conserved regions. In conclusion, our prediction models identified CpG markers that capture both tissue-common and tissue-specific characteristics during the aging process.
Collapse
Affiliation(s)
- Heeyeon Choi
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science of Technology, Gwangju 61005, Korea.
| | - Soobok Joe
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science of Technology, Gwangju 61005, Korea.
| | - Hojung Nam
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science of Technology, Gwangju 61005, Korea.
| |
Collapse
|
39
|
Yamamoto Y, Saita T, Yamamoto Y, Sogawa R, Kimura S, Narisawa Y, Kimura S, Shin M. Immunohistochemical localization of afatinib in male rat intestines and skin after its oral administration. Acta Histochem 2019; 121:151439. [PMID: 31500866 DOI: 10.1016/j.acthis.2019.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/08/2019] [Accepted: 09/01/2019] [Indexed: 12/28/2022]
Abstract
Afatinib, a second-generation tyrosine kinase inhibitor, was designed to bind covalently to and irreversibly inhibit active ErbB family receptors. The major metabolites of afatinib in human plasma are adducts of afatinib covalently bound to plasma proteins via. the Michael addition reaction. These findings suggest that afatinib may form covalent bonds with proteins in tissue and be localized in tissue. However, there is no method for the specific detection of afatinib-protein conjugates localized in tissue. In this paper, we aimed to develop an immunohistochemical protocol to detect afatinib-protein conjugates. Immunostainings were performed with male rat intestinal tract and skin at 24 h after an oral administration of afatinib. In the intestinal tract, strong staining was observed in the ileum and colon, but only slight staining was observed in the duodenum and jejunum. In the skin, strong staining was observed in the epidermis, sebaceous glands and hair follicles. Immunohistochemistry for afatinib-protein conjugates could be a useful tool to detect the localization of such conjugates. This study is the first to elucidate the localization of afatinib-protein conjugates in the rat intestinal tract and skin and is expected to be of great use in efforts to clarify the mechanism underlying afatinib-induced diarrhoea or skin toxicities.
Collapse
|
40
|
Huang G, Cheng W, Xi F. Integrated genomic and methylation profile analysis to identify candidate tumor marker genes in patients with colorectal cancer. Oncol Lett 2019; 18:4503-4514. [PMID: 31611959 PMCID: PMC6781519 DOI: 10.3892/ol.2019.10799] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 07/11/2019] [Indexed: 12/15/2022] Open
Abstract
Aberrant genomic expression and methylation serve important roles in cancer development. Integrated analysis of genetic and methylation profiles may identify potential tumor marker genes for colorectal cancer (CRC) prediction. In the current study, DNA methylation and mRNA expression profiles associated with CRC were downloaded from The Cancer Genome Atlas database. Differentially expressed mRNAs and methylated genes between tumor samples and adjacent healthy tissues were identified. Candidate tumor marker genes and prognostic clinical factors were screened according to univariable and multivariable Cox regression analysis. A total of 218 DEGs with aberrant methylation levels were screened from tumor samples. A risk prediction model was constructed based on identified genes and clinical factors. Randomization tests were used to evaluate the performance of the prediction model, including area under the curve (AUC) calculation and cross-validation. Cox regression analysis revealed that eight genes and six prognostic clinical factors were significantly associated with survival outcomes. Functional and pathway enrichment analysis revealed that the eight genes were mainly involved in ‘cell adhesion’, ‘fatty acid metabolism’ and ‘cytokine receptor interaction’ pathways. After combining six clinical factors with eight genes, the accuracy of risk prediction model has been increased intensively. The P-values representing the association between risk grouping and prognosis decreased from 0.009 to 0.001 and the AUC increased from 0.992 to 0.999, indicating that the comprehensive risk prediction model exhibited a good performance for disease prognosis prediction. The current study integrated genomic and methylation profiles and identified eight tumor marker genes in CRC. These candidate genes may improve the prediction accuracy of CRC prognosis.
Collapse
Affiliation(s)
- Guojun Huang
- Department of Oncology, Pidu District People's Hospital, Chengdu, Sichuan 611730, P.R. China
| | - Wang Cheng
- Department of General Surgery, Pidu District People's Hospital, Chengdu, Sichuan 611730, P.R. China
| | - Fu Xi
- Department of Oncology, Pidu District People's Hospital, Chengdu, Sichuan 611730, P.R. China
| |
Collapse
|
41
|
Rodger EJ, Chatterjee A, Stockwell PA, Eccles MR. Characterisation of DNA methylation changes in EBF3 and TBC1D16 associated with tumour progression and metastasis in multiple cancer types. Clin Epigenetics 2019; 11:114. [PMID: 31383000 PMCID: PMC6683458 DOI: 10.1186/s13148-019-0710-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/22/2019] [Indexed: 12/21/2022] Open
Abstract
Background Characteristic DNA methylation differences have been identified between primary and metastatic melanomas at EBF3 and/or TBC1D16 gene loci. To further evaluate whether these epigenetic changes may act more generally as drivers of tumour onset and metastasis, we have investigated DNA methylation changes involving EBF3 and TBC1D16 in additional publicly available data of multiple different tumour types. Results Promoter hypermethylation and gene body hypomethylation of EBF3 were observed in a number of metastatic tumour types, when compared to normal or primary tumour tissues, as well as in tumour vs normal tissues and in a colorectal primary/metastasis pair, although not all tumour samples or primary/metastasis cancer pairs exhibited altered patterns of EBF3 methylation. In addition, hypomethylation of TBC1D16 was observed in multiple tumours, including a breast cancer primary/metastasis pair, and to a lesser degree in melanoma, although again not all tumours or cancer primary/metastasis pairs exhibited altered patterns of methylation. Conclusions These findings suggest characteristic DNA methylation changes in EBF3 and TBC1D16 are relatively common tumour-associated epigenetic events in multiple tumour types, which is consistent with a potential role as more general drivers of tumour progression.
Collapse
Affiliation(s)
- Euan J Rodger
- Department of Pathology, Dunedin School of Medicine, University of Otago, 56 Hanover Street, Dunedin, 9054, New Zealand. .,Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland, New Zealand.
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, 56 Hanover Street, Dunedin, 9054, New Zealand. .,Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland, New Zealand.
| | - Peter A Stockwell
- Department of Pathology, Dunedin School of Medicine, University of Otago, 56 Hanover Street, Dunedin, 9054, New Zealand
| | - Michael R Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, 56 Hanover Street, Dunedin, 9054, New Zealand. .,Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland, New Zealand.
| |
Collapse
|
42
|
Fornasiero EF, Rizzoli SO. Pathological changes are associated with shifts in the employment of synonymous codons at the transcriptome level. BMC Genomics 2019; 20:566. [PMID: 31288782 PMCID: PMC6617700 DOI: 10.1186/s12864-019-5921-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 06/20/2019] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The usage of different synonymous codons reflects the genome organization and has been connected to parameters such as mRNA abundance and protein folding. It is also been established that mutations targeting specific synonymous codons can trigger disease. RESULTS We performed a systematic meta-analysis of transcriptome results from 75 datasets representing 40 pathologies. We found that a subset of codons was preferentially employed in abundant transcripts, while other codons were preferentially found in low-abundance transcripts. By comparing control and pathological transcriptomes, we observed a shift in the employment of synonymous codons for every analyzed disease. For example, cancerous tissue employed preferentially A- or U-ending codons, shifting from G- or C-ending codons, which were preferred by control tissues. This analysis was able to discriminate patients and controls with high specificity and sensitivity. CONCLUSIONS Here we show that the employment of specific synonymous codons, quantified at the whole transcriptome level, changes profoundly in many diseases. We propose that the changes in codon employment offer a novel perspective for disease studies, and could be used to design new diagnostic tools.
Collapse
Affiliation(s)
- Eugenio F Fornasiero
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany.
- Center for Biostructural Imaging of Neurodegeneration (BIN), 37075, Göttingen, Germany.
| | - Silvio O Rizzoli
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany.
- Center for Biostructural Imaging of Neurodegeneration (BIN), 37075, Göttingen, Germany.
| |
Collapse
|
43
|
Zhang Y, Wu W, Qu H. Integrated Analysis of the Gene Expression Changes During Colorectal Cancer Progression by Bioinformatic Methods. J Comput Biol 2019; 26:1168-1176. [PMID: 31246501 DOI: 10.1089/cmb.2019.0056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We attempted to analyze the aberrant pathways and genes underlying the successive stages of colorectal cancer (CRC). The CRC related microarray data (GSE77953) were retrieved from Gene Expression Omnibus database, which included 17 colonic adenoma, 17 carcinoma, 11 CRC metastases, and 13 normal colonic epithelium samples. The differential expression patterns in colonic adenoma, carcinoma, and metastases were analyzed. Gene functional interaction (FI) and coexpressed network were constructed. Pathway enrichment analysis was performed to investigate the perturbed pathways, and disease-related genes were explored based on the Comparative Toxicogenomics Database. Total 438 genes were identified to be differentially expressed in colonic adenoma, 885 in carcinoma and 736 in metastases. The upregulated genes in adenoma were significantly related with ribosome, oxidative phosphorylation, and protein export related pathways. The downregulated genes in carcinoma and metastases were enriched in the same pathways, such as nitrogen metabolism, mineral absorption, and steroid hormone biosynthesis. FI network was constructed with 219 and 3914 edges, which were further divided to 12 modules. The genes in module 0 were closely related with ribosome, protein export, and RNA transport. Coexpressed genes were enriched in ribosome, protein export, and mineral absorption pathways. Total eight common upregulated genes were found to be the CRC-related genes such as RNF43 (ring finger protein 43), EIF3H (eukaryotic translation initiation factor 3 subunit H), and STRAP (serine/threonine kinase receptor associated protein). The common downregulated genes included ABCG2 (ATP binding cassette subfamily G member 2), GCG (glucagon), and SULT1A1 (sulfotransferase family 1A member 1). Oxidative phosphorylation, nitrogen metabolism, mineral absorption, and protein synthesis may significantly be perturbed in the progression of CRC. The overexpression of EIF3H may be the predictor for CRC formation.
Collapse
Affiliation(s)
- Yudong Zhang
- Department of General Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Wenxiang Wu
- Department of Obstetrics and Gynecology, Peking University First Hospital, Beijing, China
| | - Hao Qu
- Department of General Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| |
Collapse
|
44
|
Jurmeister P, Schöler A, Arnold A, Klauschen F, Lenze D, Hummel M, Schweizer L, Bläker H, Pfitzner BM, Mamlouk S, Sers C, Denkert C, Stichel D, Frost N, Horst D, von Laffert M, Capper D. DNA methylation profiling reliably distinguishes pulmonary enteric adenocarcinoma from metastatic colorectal cancer. Mod Pathol 2019; 32:855-865. [PMID: 30723296 DOI: 10.1038/s41379-019-0207-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 12/27/2018] [Accepted: 12/29/2018] [Indexed: 12/20/2022]
Abstract
Pulmonary enteric adenocarcinoma is a rare non-small cell lung cancer subtype. It is poorly characterized and cannot be distinguished from metastatic colorectal or upper gastrointestinal adenocarcinomas by means of routine pathological methods. As DNA methylation patterns are known to be highly tissue specific, we aimed to develop a methylation-based algorithm to differentiate these entities. To this end, genome-wide methylation profiles of 600 primary pulmonary, colorectal, and upper gastrointestinal adenocarcinomas obtained from The Cancer Genome Atlas and the Gene Expression Omnibus database were used as a reference cohort to train a machine learning algorithm. The resulting classifier correctly classified all samples from a validation cohort consisting of 680 primary pulmonary, colorectal and upper gastrointestinal adenocarcinomas, demonstrating the ability of the algorithm to reliably distinguish these three entities. We then analyzed methylation data of 15 pulmonary enteric adenocarcinomas as well as four pulmonary metastases and four primary colorectal adenocarcinomas with the algorithm. All 15 pulmonary enteric adenocarcinomas were reliably classified as primary pulmonary tumors and all four metastases as well as all four primary colorectal cancer samples were identified as colorectal adenocarcinomas. In a t-distributed stochastic neighbor embedding analysis, the pulmonary enteric adenocarcinoma samples did not form a separate methylation subclass but rather diffusely intermixed with other pulmonary cancers. Additional characterization of the pulmonary enteric adenocarcinoma series using fluorescence in situ hybridization, next-generation sequencing and copy number analysis revealed KRAS mutations in nine of 15 samples (60%) and a high number of structural chromosomal changes. Except for an unusually high rate of chromosome 20 gain (67%), the molecular data was mostly reminiscent of standard pulmonary adenocarcinomas. In conclusion, we provide sound evidence of the pulmonary origin of pulmonary enteric adenocarcinomas and in addition provide a publicly available machine learning-based algorithm to reliably distinguish these tumors from metastatic colorectal cancer.
Collapse
Affiliation(s)
- Philipp Jurmeister
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Institute of Pathology, Berlin, Germany. .,Charité Comprehensive Cancer Center (CCCC), Berlin, Germany.
| | - Anne Schöler
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
| | - Alexander Arnold
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | - Frederick Klauschen
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Institute of Pathology, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany.,German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dido Lenze
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | - Michael Hummel
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | - Leonille Schweizer
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany.,German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hendrik Bläker
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | - Berit Maria Pfitzner
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | - Soulafa Mamlouk
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Institute of Pathology, Berlin, Germany.,German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christine Sers
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Institute of Pathology, Berlin, Germany.,German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carsten Denkert
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Institute of Pathology, Berlin, Germany.,German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Damian Stichel
- Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nikolaj Frost
- Department of Infectious Diseases and Pneumonology, Charité University Hospital Berlin, Berlin, Germany
| | - David Horst
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Institute of Pathology, Berlin, Germany.,German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Maximilian von Laffert
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Institute of Pathology, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
| | - David Capper
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| |
Collapse
|
45
|
Cong Z, Li Q, Yang Y, Guo X, Cui L, You T. The SNP of rs6854845 suppresses transcription via the DNA looping structure alteration of super-enhancer in colon cells. Biochem Biophys Res Commun 2019; 514:734-741. [PMID: 31078271 DOI: 10.1016/j.bbrc.2019.04.190] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 04/28/2019] [Indexed: 12/01/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) identified by Genome-Wide Association Studies (GWASs) have been determined to closely connect with multiple diseases. Previous studies revealed one underlying mechanism that SNPs located within the regulatory elements could affect the encoding gene expression through long-range regulation. SNP rs6854845 was suggested to be a risk of colon cancer in human population. Nevertheless, the underlying molecular mechanism for colon carcinogenesis remains largely unknown. In present study, rs6854845 with G > T mutation in situ in FHC, HCT-116 and SW-480 cells were generated by Crispr/Cas9. The nearby chromatin organization was investigated by chromatin conformation capture (3C). And the expression of coding gene regulated by super-enhancer (SE) was detected by real-time PCR. We observed a significantly different pattern of the genome organization upon rs6854845 generation in colon epithelial cells but not in colon cancer cells. Moreover, we observed the shifted enrichment of H3K4me1 and H3K27ac at the SE (chr4:75.7M-76.0 M) where rs6854845 located. Furthermore, we observed that the transcription of the gene clusters regulated by SE were affected by rs6854845 in colon cells. Overall, our results demonstrated that SNP rs6854845 located in SE could destroy the long-range chromosomal interaction between SE and target gene clusters thereby affecting the transcription of these genes.
Collapse
Affiliation(s)
- Zhuangzhi Cong
- Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, 225 Changhai Road, Shanghai 200438, PR China
| | - Qinghua Li
- Department of Hepatobiliary Surgery, Shanghai East Hospital, Tongji University School of Medicine, 150 Ji-Mo Road, Shanghai, 200120, PR China
| | - Yongkang Yang
- Department of Hepatobiliary Surgery, Shanghai East Hospital, Tongji University School of Medicine, 150 Ji-Mo Road, Shanghai, 200120, PR China
| | - Xinlai Guo
- Department of Hepatobiliary Surgery, Shanghai East Hospital, Tongji University School of Medicine, 150 Ji-Mo Road, Shanghai, 200120, PR China
| | - Longjiu Cui
- Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, 225 Changhai Road, Shanghai 200438, PR China
| | - Tiangeng You
- Department of Biliary Surgery, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, 225 Changhai Road, Shanghai 200438, PR China.
| |
Collapse
|
46
|
The miR-186-3p/EREG axis orchestrates tamoxifen resistance and aerobic glycolysis in breast cancer cells. Oncogene 2019; 38:5551-5565. [PMID: 30967627 DOI: 10.1038/s41388-019-0817-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 01/10/2019] [Accepted: 03/26/2019] [Indexed: 02/07/2023]
Abstract
Tamoxifen resistance is one of the major challenges for its medical uses in estrogen receptor (ER)-positive breast cancer. Aerobic glycolysis, an anomalous characteristic of glucose metabolism in cancer cells, has been shown to associate with the resistance to chemotherapeutic agents. It remains, however, largely unclear whether and how tamoxifen resistance contributes to aerobic glycolysis in breast cancer. Here, we report that tamoxifen resistance is associated with enhanced glycolysis in ER-positive breast cancer cells. We demonstrate that EREG, an agonist of EGFR, has an important role in enhancing glycolysis via activating EGFR signaling and its downstream glycolytic genes in tamoxifen-resistant breast cancer cells. We further show that EREG is a direct target of miR-186-3p and that downregulation of miR-186-3p by tamoxifen results in EREG upregulation in tamoxifen-resistant breast cancer cells. Importantly, systemic delivery of cholesterol-modified agomiR-186-3p to mice bearing tamoxifen-resistant breast tumors effectively attenuates both tumor growth and [18F]-fluoro-deoxyglucose ([18F]-FDG) uptake. Together, our results reveal a novel molecular mechanism of resistance to hormone therapies in which the miR-186-3p/EREG axis orchestrates tamoxifen resistance and aerobic glycolysis in ER-positive breast cancer, suggesting targeting miR-186-3p as a promising strategy for therapeutic intervention in endocrine-resistant breast tumors.
Collapse
|
47
|
Barresi V, Cinnirella G, Valenti G, Spampinato G, Musso N, Castorina S, Condorelli DF. Gene expression profiles in genome instability-based classes of colorectal cancer. BMC Cancer 2018; 18:1265. [PMID: 30563495 PMCID: PMC6299572 DOI: 10.1186/s12885-018-5174-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 12/03/2018] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Broad copy number aberrations (BCNAs) represent a common form of genome instability in colorectal cancer (CRC). CRCs show large variations in their level of aneuploidy: microsatellite-instable (MSI) tumors are known to have a near-diploid karyotype while microsatellite-stable (MSS) tumors show high level of chromosomal instability. However, MSS tumors have great heterogeneity in the number of BCNAs, with a minor percentage of samples showing an almost normal karyotype. In the present work we subdivided MSS CRCs according to a "BCNA score" and characterized their transcriptome profiles, considered as a proxy to their phenotypic features. METHODS Microsatellite testing, genome-wide DNA copy number and whole-transcript expression analysis (HTA) were performed on 33 tumor samples and 25 normal colonic tissue samples from 32 CRC patients. 15.1% of the samples were MSI tumors (n = 5), whereas 84.9% were MSS tumors (n = 28). Gene expression data of 34 additional MSI tumors was retrieved from a public functional genomics data repository. RESULTS Using as a threshold the first quartile of the BCNA score distribution, MSS samples were classified as low-BCNA (LB, n = 7) or high-BCNA (HB, n = 21). LB tumors were enriched for mucinous CRCs and their gene-expression profile resembled that of MSI samples for what concerns a subset of genes involved in secretory processes, mucosal protection, and extracellular matrix remodeling. HB tumors were predominantly non-mucinous adenocarcinomas and showed overexpression of a subset of genes typical of surface colonocytes and EGF signaling. A large percentage of unclassified samples according to the consensus molecular subtypes (CMS) classifier was found in the LB group (43%), whereas 76% HB tumors belonged to CMS2. CONCLUSIONS A classification of colorectal tumors based on the number of BCNAs identifies two groups of MSS tumors which differ for histopathology and gene expression profile. Such information can be exploited for its translational relevance in different aspects of CRC clinical management.
Collapse
Affiliation(s)
- Vincenza Barresi
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Viale Santa Sofia 89-97, 95123 Catania, Italy
- Laboratory of Complex Systems, Scuola Superiore di Catania, University of Catania, Catania, Italy
| | - Giacomo Cinnirella
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Viale Santa Sofia 89-97, 95123 Catania, Italy
| | - Giovanna Valenti
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Viale Santa Sofia 89-97, 95123 Catania, Italy
| | - Giorgia Spampinato
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Viale Santa Sofia 89-97, 95123 Catania, Italy
| | - Nicolò Musso
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Viale Santa Sofia 89-97, 95123 Catania, Italy
| | - Sergio Castorina
- Department of Surgical Medical Sciences and Advanced Technologies “G. F. Ingrassia”, University of Catania, Catania, Italy
- Fondazione Mediterranea G.B. Morgagni, Catania, Italy
| | - Daniele F. Condorelli
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Viale Santa Sofia 89-97, 95123 Catania, Italy
- Laboratory of Complex Systems, Scuola Superiore di Catania, University of Catania, Catania, Italy
| |
Collapse
|
48
|
Dmitrijeva M, Ossowski S, Serrano L, Schaefer MH. Tissue-specific DNA methylation loss during ageing and carcinogenesis is linked to chromosome structure, replication timing and cell division rates. Nucleic Acids Res 2018; 46:7022-7039. [PMID: 29893918 PMCID: PMC6101545 DOI: 10.1093/nar/gky498] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/16/2018] [Accepted: 05/23/2018] [Indexed: 12/15/2022] Open
Abstract
DNA methylation is an epigenetic mechanism known to affect gene expression and aberrant DNA methylation patterns have been described in cancer. However, only a small fraction of differential methylation events target genes with a defined role in cancer, raising the question of how aberrant DNA methylation contributes to carcinogenesis. As recently a link has been suggested between methylation patterns arising in ageing and those arising in cancer, we asked which aberrations are unique to cancer and which are the product of normal ageing processes. We therefore compared the methylation patterns between ageing and cancer in multiple tissues. We observed that hypermethylation preferentially occurs in regulatory elements, while hypomethylation is associated with structural features of the chromatin. Specifically, we observed consistent hypomethylation of late-replicating, lamina-associated domains. The extent of hypomethylation was stronger in cancer, but in both ageing and cancer it was proportional to the replication timing of the region and the cell division rate of the tissue. Moreover, cancer patients who displayed more hypomethylation in late-replicating, lamina-associated domains had higher expression of cell division genes. These findings suggest that different cell division rates contribute to tissue- and cancer type-specific DNA methylation profiles.
Collapse
Affiliation(s)
- Marija Dmitrijeva
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Stephan Ossowski
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, Barcelona 08010, Spain
| | - Martin H Schaefer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| |
Collapse
|
49
|
Høye AM, Tolstrup SD, Horton ER, Nicolau M, Frost H, Woo JH, Mauldin JP, Frankel AE, Cox TR, Erler JT. Tumor endothelial marker 8 promotes cancer progression and metastasis. Oncotarget 2018; 9:30173-30188. [PMID: 30046396 PMCID: PMC6059023 DOI: 10.18632/oncotarget.25734] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 06/22/2018] [Indexed: 12/22/2022] Open
Abstract
Every year more than 8 million people suffer from cancer-related deaths worldwide [1]. Metastasis, the spread of cancer to distant sites, accounts for 90% of these deaths. A promising target for blocking tumor progression, without causing severe side effects [2], is Tumor Endothelial Marker 8 (TEM8), an integrin-like cell surface protein expressed predominantly in the tumor endothelium and in cancer cells [3, 4]. Here, we have investigated the role of TEM8 in cancer progression, angiogenesis and metastasis in invasive breast cancer, and validated the main findings and important results in colorectal cancer. We show that the loss of TEM8 in cancer cells results in inhibition of cancer progression, reduction in tumor angiogenesis and reduced metastatic burden in breast cancer mouse models. Furthermore, we show that TEM8 regulates cancer progression by affecting the expression levels of cell cycle-related genes. Taken together, our findings may have broad clinical and therapeutic potential for breast and colorectal primary tumor and metastasis treatment by targeting TEM8.
Collapse
Affiliation(s)
- Anette M Høye
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen (UCPH), Copenhagen, Denmark
| | - Sofie D Tolstrup
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen (UCPH), Copenhagen, Denmark
| | - Edward R Horton
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen (UCPH), Copenhagen, Denmark
| | - Monica Nicolau
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen (UCPH), Copenhagen, Denmark
| | - Helen Frost
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen (UCPH), Copenhagen, Denmark
| | - Jung H Woo
- Baylor Scott and White Health, Temple, TX, USA
| | | | - Arthur E Frankel
- University of South Alabama Mitchell Cancer Institute, Mobile, AL, USA
| | - Thomas R Cox
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen (UCPH), Copenhagen, Denmark.,The Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Cancer Division, St Vincent's Clinical School, Faculty of Medicine, UNSW, Sydney, Australia
| | - Janine T Erler
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen (UCPH), Copenhagen, Denmark
| |
Collapse
|
50
|
Wagle MC, Kirouac D, Klijn C, Liu B, Mahajan S, Junttila M, Moffat J, Merchant M, Huw L, Wongchenko M, Okrah K, Srinivasan S, Mounir Z, Sumiyoshi T, Haverty PM, Yauch RL, Yan Y, Kabbarah O, Hampton G, Amler L, Ramanujan S, Lackner MR, Huang SMA. A transcriptional MAPK Pathway Activity Score (MPAS) is a clinically relevant biomarker in multiple cancer types. NPJ Precis Oncol 2018; 2:7. [PMID: 29872725 PMCID: PMC5871852 DOI: 10.1038/s41698-018-0051-4] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 01/29/2018] [Accepted: 02/05/2018] [Indexed: 12/18/2022] Open
Abstract
KRAS- and BRAF-mutant tumors are often dependent on MAPK signaling for proliferation and survival and thus sensitive to MAPK pathway inhibitors. However, clinical studies have shown that MEK inhibitors are not uniformly effective in these cancers indicating that mutational status of these oncogenes does not accurately capture MAPK pathway activity. A number of transcripts are regulated by this pathway and are recurrently identified in genome-based MAPK transcriptional signatures. To test whether the transcriptional output of only 10 of these targets could quantify MAPK pathway activity with potential predictive or prognostic clinical utility, we created a MAPK Pathway Activity Score (MPAS) derived from aggregated gene expression. In vitro, MPAS predicted sensitivity to MAPK inhibitors in multiple cell lines, comparable to or better than larger genome-based statistical models. Bridging in vitro studies and clinical samples, median MPAS from a given tumor type correlated with cobimetinib (MEK inhibitor) sensitivity of cancer cell lines originating from the same tissue type. Retrospective analyses of clinical datasets showed that MPAS was associated with the sensitivity of melanomas to vemurafenib (HR: 0.596) and negatively prognostic of overall or progression-free survival in both adjuvant and metastatic CRC (HR: 1.5 and 1.4), adrenal cancer (HR: 1.7), and HER2+ breast cancer (HR: 1.6). MPAS thus demonstrates potential clinical utility that warrants further exploration.
Collapse
Affiliation(s)
- Marie-Claire Wagle
- 1Department of Oncology Biomarker Development, Genentech, 1 DNA Way, South San Francisco, CA 94080 USA
| | - Daniel Kirouac
- 2Department of Pre-Clinical and Translational PKPD, Genentech, 1 DNA Way, South San Francisco, CA 94080 USA
| | - Christiaan Klijn
- 3Department of Bioinformatics, Genentech, 1 DNA Way, South San Francisco, CA 94080 USA
| | - Bonnie Liu
- 1Department of Oncology Biomarker Development, Genentech, 1 DNA Way, South San Francisco, CA 94080 USA
| | - Shilpi Mahajan
- 1Department of Oncology Biomarker Development, Genentech, 1 DNA Way, South San Francisco, CA 94080 USA
| | - Melissa Junttila
- 4Department of Translational Oncology, Genentech, 1 DNA Way, South San Francisco, CA 94080 USA
| | - John Moffat
- 5Department of Biochemical and Cellular pharmacology, Genentech, 1 DNA Way, South San Francisco, CA 94080 USA
| | - Mark Merchant
- 4Department of Translational Oncology, Genentech, 1 DNA Way, South San Francisco, CA 94080 USA
| | - Ling Huw
- 1Department of Oncology Biomarker Development, Genentech, 1 DNA Way, South San Francisco, CA 94080 USA
| | - Matthew Wongchenko
- 1Department of Oncology Biomarker Development, Genentech, 1 DNA Way, South San Francisco, CA 94080 USA
| | - Kwame Okrah
- 6Department of Biostatistics, Genentech, 1 DNA Way, South San Francisco, CA 94080 USA
| | - Shrividhya Srinivasan
- 1Department of Oncology Biomarker Development, Genentech, 1 DNA Way, South San Francisco, CA 94080 USA
| | - Zineb Mounir
- 1Department of Oncology Biomarker Development, Genentech, 1 DNA Way, South San Francisco, CA 94080 USA
| | - Teiko Sumiyoshi
- 1Department of Oncology Biomarker Development, Genentech, 1 DNA Way, South San Francisco, CA 94080 USA
| | - Peter M Haverty
- 3Department of Bioinformatics, Genentech, 1 DNA Way, South San Francisco, CA 94080 USA
| | - Robert L Yauch
- 4Department of Translational Oncology, Genentech, 1 DNA Way, South San Francisco, CA 94080 USA
| | - Yibing Yan
- 1Department of Oncology Biomarker Development, Genentech, 1 DNA Way, South San Francisco, CA 94080 USA
| | - Omar Kabbarah
- 1Department of Oncology Biomarker Development, Genentech, 1 DNA Way, South San Francisco, CA 94080 USA
| | - Garret Hampton
- 1Department of Oncology Biomarker Development, Genentech, 1 DNA Way, South San Francisco, CA 94080 USA
| | - Lukas Amler
- 1Department of Oncology Biomarker Development, Genentech, 1 DNA Way, South San Francisco, CA 94080 USA
| | - Saroja Ramanujan
- 2Department of Pre-Clinical and Translational PKPD, Genentech, 1 DNA Way, South San Francisco, CA 94080 USA
| | - Mark R Lackner
- 1Department of Oncology Biomarker Development, Genentech, 1 DNA Way, South San Francisco, CA 94080 USA
| | - Shih-Min A Huang
- 1Department of Oncology Biomarker Development, Genentech, 1 DNA Way, South San Francisco, CA 94080 USA.,7Present Address: Bristol-Myers Squibb, 3551 Lawrenceville Princeton, Lawrence Township, NJ 08648 USA
| |
Collapse
|