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Chen CC, Tran W, Song K, Sugimoto T, Obusan MB, Wang L, Sheu KM, Cheng D, Ta L, Varuzhanyan G, Huang A, Xu R, Zeng Y, Borujerdpur A, Bayley NA, Noguchi M, Mao Z, Morrissey C, Corey E, Nelson PS, Zhao Y, Huang J, Park JW, Witte ON, Graeber TG. Temporal evolution reveals bifurcated lineages in aggressive neuroendocrine small cell prostate cancer trans-differentiation. Cancer Cell 2023; 41:2066-2082.e9. [PMID: 37995683 PMCID: PMC10878415 DOI: 10.1016/j.ccell.2023.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 08/25/2023] [Accepted: 10/30/2023] [Indexed: 11/25/2023]
Abstract
Trans-differentiation from an adenocarcinoma to a small cell neuroendocrine state is associated with therapy resistance in multiple cancer types. To gain insight into the underlying molecular events of the trans-differentiation, we perform a multi-omics time course analysis of a pan-small cell neuroendocrine cancer model (termed PARCB), a forward genetic transformation using human prostate basal cells and identify a shared developmental, arc-like, and entropy-high trajectory among all transformation model replicates. Further mapping with single cell resolution reveals two distinct lineages defined by mutually exclusive expression of ASCL1 or ASCL2. Temporal regulation by groups of transcription factors across developmental stages reveals that cellular reprogramming precedes the induction of neuronal programs. TFAP4 and ASCL1/2 feedback are identified as potential regulators of ASCL1 and ASCL2 expression. Our study provides temporal transcriptional patterns and uncovers pan-tissue parallels between prostate and lung cancers, as well as connections to normal neuroendocrine cell states.
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Affiliation(s)
- Chia-Chun Chen
- Department of Molecular and Medical Pharmacology, University of California Los Angeles (UCLA), Los Angeles, CA, USA
| | - Wendy Tran
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA
| | - Kai Song
- Department of Bioengineering, UCLA, Los Angeles, CA, USA
| | - Tyler Sugimoto
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA
| | - Matthew B Obusan
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA
| | - Liang Wang
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA
| | - Katherine M Sheu
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA
| | - Donghui Cheng
- Eli and Edythe Broad Stem Cell Research Center, UCLA, Los Angeles, CA, USA
| | - Lisa Ta
- Department of Molecular and Medical Pharmacology, University of California Los Angeles (UCLA), Los Angeles, CA, USA
| | - Grigor Varuzhanyan
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA
| | - Arthur Huang
- Department of Molecular and Medical Pharmacology, University of California Los Angeles (UCLA), Los Angeles, CA, USA
| | - Runzhe Xu
- Department of Biological Chemistry, UCLA, Los Angeles, CA, USA
| | - Yuanhong Zeng
- Department of Molecular and Medical Pharmacology, University of California Los Angeles (UCLA), Los Angeles, CA, USA
| | - Amirreza Borujerdpur
- Department of Molecular and Medical Pharmacology, University of California Los Angeles (UCLA), Los Angeles, CA, USA
| | - Nicholas A Bayley
- Department of Molecular and Medical Pharmacology, University of California Los Angeles (UCLA), Los Angeles, CA, USA
| | - Miyako Noguchi
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA
| | - Zhiyuan Mao
- Department of Molecular and Medical Pharmacology, University of California Los Angeles (UCLA), Los Angeles, CA, USA
| | - Colm Morrissey
- Department of Urology, University of Washington School of Medicine, Seattle, WA, USA
| | - Eva Corey
- Department of Urology, University of Washington School of Medicine, Seattle, WA, USA
| | - Peter S Nelson
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA; Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Yue Zhao
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA; Department of Pathology, College of Basic Medical Sciences and the First Hospital, China Medical University, Shenyang, China
| | - Jiaoti Huang
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Jung Wook Park
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Owen N Witte
- Department of Molecular and Medical Pharmacology, University of California Los Angeles (UCLA), Los Angeles, CA, USA; Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA; Eli and Edythe Broad Stem Cell Research Center, UCLA, Los Angeles, CA, USA; Molecular Biology Institute, UCLA, Los Angeles, CA, USA; Parker Institute for Cancer Immunotherapy, UCLA, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA.
| | - Thomas G Graeber
- Department of Molecular and Medical Pharmacology, University of California Los Angeles (UCLA), Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA; Crump Institute for Molecular Imaging, UCLA, Los Angeles, CA, USA; California NanoSystems Institute, UCLA, Los Angeles, CA, USA; Metabolomics Center, UCLA, Los Angeles, CA, USA.
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Zhang D, Ni QQ, Liang QY, He LL, Qiu BW, Zhang LJ, Mou TY, Le CC, Huang Y, Li TT, Wang SY, Ding YQ, Jiao HL, Ye YP. ASCL2 induces an immune excluded microenvironment by activating cancer-associated fibroblasts in microsatellite stable colorectal cancer. Oncogene 2023; 42:2841-2853. [PMID: 37591954 PMCID: PMC10504082 DOI: 10.1038/s41388-023-02806-3] [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: 11/17/2022] [Revised: 07/28/2023] [Accepted: 08/03/2023] [Indexed: 08/19/2023]
Abstract
Proficient mismatch repair or microsatellite stable (pMMR/MSS) colorectal cancers (CRCs) are vastly outnumbered by deficient mismatch repair or microsatellite instability-high (dMMR/MSI-H) tumors and lack a response to immune checkpoint inhibitors (ICIs). In this study, we reported two distinct expression patterns of ASCL2 in pMMR/MSS and dMMR/MSI-H CRCs. ASCL2 is overexpressed in pMMR/MSS CRCs and maintains a stemness phenotype, accompanied by a lower density of tumor-infiltrating lymphocytes (TILs) than those in dMMR/MSI CRCs. In addition, coadministration of anti-PD-L1 antibodies facilitated T cell infiltration and provoked strong antitumor immunity and tumor regression in the MC38/shASCL2 mouse CRC model. Furthermore, overexpression of ASCL2 was associated with increased TGFB levels, which stimulate local Cancer-associated fibroblasts (CAFs) activation, inducing an immune-excluded microenvironment. Consistently, mice with deletion of Ascl2 specifically in the intestine (Villin-Cre+, Ascl2 flox/flox, named Ascl2 CKO) revealed fewer activated CAFs and higher proportions of infiltrating CD8+ T cells; We further intercrossed Ascl2 CKO with ApcMin/+ model suggesting that Ascl2-deficient expression in intestinal represented an immune infiltrating environment associated with a good prognosis. Together, our findings indicated ASCL2 induces an immune excluded microenvironment by activating CAFs through transcriptionally activating TGFB, and targeting ASCL2 combined with ICIs could present a therapeutic opportunity for MSS CRCs.
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Affiliation(s)
- Dan Zhang
- Department of Pathology, School of Basic Medical Sciences and Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Qi-Qi Ni
- Department of Pathology, School of Basic Medical Sciences and Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Qiao-Yan Liang
- Department of Pathology, School of Basic Medical Sciences and Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Li-Ling He
- Department of Pathology, School of Basic Medical Sciences and Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Bo-Wen Qiu
- Department of Pathology, School of Basic Medical Sciences and Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Ling-Jie Zhang
- Department of Pathology, School of Basic Medical Sciences and Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Ting-Yu Mou
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Chen-Chen Le
- Department of Pathology, School of Basic Medical Sciences and Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Yuan Huang
- Department of Pathology, School of Basic Medical Sciences and Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Ting-Ting Li
- Department of Pathology, School of Basic Medical Sciences and Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Shu-Yang Wang
- Department of Pathology, School of Basic Medical Sciences and Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Yan-Qing Ding
- Department of Pathology, School of Basic Medical Sciences and Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China.
| | - Hong-Li Jiao
- Department of Pathology, School of Basic Medical Sciences and Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China.
| | - Ya-Ping Ye
- Department of Pathology, School of Basic Medical Sciences and Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China.
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Han S, Jin X, Hu T, Chi F. ARHGAP25 suppresses the development of breast cancer by an ARHGAP25/Wnt/ASCL2 feedback loop. Carcinogenesis 2023; 44:369-382. [PMID: 37326327 DOI: 10.1093/carcin/bgad042] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/18/2023] [Accepted: 06/14/2023] [Indexed: 06/17/2023] Open
Abstract
Downregulation of ARHGAP25 was found in the tumor samples from breast cancer patients and five breast cancer cell lines. However, its precise role and molecular mechanisms in breast cancer remain completely unknown. Herein, we found that knockdown of ARHGAP25 in breast cancer cells promoted proliferation, migration and invasion of breast cancer cells. Mechanistically, ARHGAP25 silence facilitated the activation of the Wnt/β-catenin pathway and the upregulation of its downstream molecules (including c-Myc, Cyclin D1, PCNA, MMP2, MMP9, Snail and ASCL2) by directly regulating Rac1/PAK1 in breast cancer cells. In vivo xenograft experiments indicated ARHGAP25 silence promoted tumor growth and activated the Wnt/β-catenin pathway. In contrast, overexpression of ARHGAP25 in vitro and in vivo impeded all of the above cancer properties. Intriguingly, ASCL2, a downstream target of the Wnt/β-catenin pathway, transcriptionally repressed the expression of ARHGAP25 and therefore constituted a negative feedback loop. Moreover, bioinformatics analysis indicated that ARHGAP25 was significantly correlated with tumor immune cell infiltration and the survival of patients with different immune cell subgroups in breast cancer. Collectively, our work revealed that ARHGAP25 suppressed tumor progression of breast cancer. It provides a novel insight for the treatment of breast cancer.
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Affiliation(s)
- Sijia Han
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Xueying Jin
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Tianyu Hu
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Feng Chi
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
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AT7867 Inhibits the Growth of Colorectal Cancer Stem-Like Cells and Stemness by Regulating the Stem Cell Maintenance Factor Ascl2 and Akt Signaling. Stem Cells Int 2023; 2023:4199052. [PMID: 36824410 PMCID: PMC9943616 DOI: 10.1155/2023/4199052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 01/18/2023] [Accepted: 01/25/2023] [Indexed: 02/16/2023] Open
Abstract
Cancer stem cells (CSCs) are the core factors leading to recurrence, insensitivity to radiotherapy and chemotherapy, and immunotherapy resistance in patients with colorectal cancer. AT7867, a potent oral AKT inhibitor, was found to have antitumor activity in colorectal cancer; however, the effect on colorectal cancer stem cells is still unclear. This study was conducted to clarify the molecular mechanism underlying the CSC growth inhibitory effects of AT7867. We cultured colorectal cancer cells (CRCs) in a serum-free medium and enriched colorectal cancer stem cells. Subsequently, the effects of AT7867 on CSCs were analyzed by CCK-8, colony formation, flow cytometry, and immunofluorescence assays. The results indicated that AT7867 induces G2/M phase arrest and cell apoptosis in cancer stem cells. Subsequently, we identified Ascl2 as the main gene affecting the stemness of colorectal cancer in AT7867 by RNA sequencing. The current study showed that Ascl2 is involved in the metastasis, invasion, and proliferation of CRCs. The next experiments demonstrated that overexpression of Ascl2 did affect the therapeutic effect of AT7867 on CRC stemness. Furthermore, compared with other Akt inhibitors, AT7867 could promote the differentiation of colorectal cancer stem cells. Thus, AT7867 might be a potential antitumor drug candidate to treat CRC by targeting CSCs.
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Takamizawa Y, Shida D, Horie T, Tsukamoto S, Esaki M, Shimada K, Kondo T, Kanemitsu Y. Prognostic Role for Primary Tumor Location in Patients With Colorectal Liver Metastases: A Comparison of Right-Sided Colon, Left-Sided Colon, and Rectum. Dis Colon Rectum 2023; 66:233-242. [PMID: 35714342 DOI: 10.1097/dcr.0000000000002228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
BACKGROUND Although right-sided colon cancer is increasingly recognized as having a worse prognosis than left-sided colorectal cancer for colorectal liver metastases, little is known about the differences between the left-sided colon and rectum. OBJECTIVE This study evaluated the prognostic value of primary tumor location in patients with colorectal liver metastases by examining the left-sided colon and rectum separately. DESIGN This was a retrospective study from 2003 to 2017. SETTINGS The study was conducted in a National Cancer Center Hospital. PATIENTS The study cohort included 489 patients with colorectal liver metastases from right-sided colon cancer ( n = 119, 24%), left-sided colon cancer ( n = 251, 51%), or rectal cancer ( n = 119, 24%) who underwent hepatic resection. MAIN OUTCOME MEASURES Primary outcomes were relapse-free survival and overall survival. RESULTS Five-year relapse-free survival rates for patients with right-sided colon cancer, left-sided colon cancer, and rectal cancer were 28.6%, 34.1%, and 26.4%, and 5-year overall survival rates were 53.9%, 70.3%, and 60.8%. Multivariable analysis revealed significant differences in relapse-free survival and overall survival between left-sided colon cancer and rectal cancer (relapse-free survival: HR = 1.37, p = 0.03; overall survival: HR = 1.49, p = 0.03) and between left-sided colon cancer and right-sided colon cancer (relapse-free survival: HR = 1.39, p = 0.02; overall survival: HR = 1.60, p = 0.01), but not between right-sided colon cancer and rectal cancer. In patients with recurrence ( n = 325), left-sided colon cancer had the lowest multiple-site recurrence rate and the highest surgical resection rate for recurrence (left-sided colon cancer, 20%/46%; right-sided colon cancer, 32%/30%; rectal cancer, 26%/39%). LIMITATIONS This study was retrospective in design. CONCLUSIONS Rectal cancer was associated with worse relapse-free survival and overall survival compared with left-sided colon cancer in patients with colorectal liver metastases who underwent hepatic resection. Our findings suggest that the left-sided colon and rectum should be considered distinct entities in colorectal liver metastases. See Video Abstract at http://links.lww.com/DCR/B882 . PAPEL PRONSTICO DE LA UBICACIN DEL TUMOR PRIMARIO EN PACIENTES CON METSTASIS HEPTICAS COLORRECTALES UNA COMPARACIN ENTRE COLON DERECHO, COLON IZQUIERDO Y RECTO ANTECEDENTES:Aunque se reconoce cada vez más que el cáncer de colon del lado derecho tiene un peor pronóstico que el cáncer colorrectal del lado izquierdo para las metástasis hepáticas colorrectales, se sabe poco acerca de las diferencias entre el recto y el colon del lado izquierdo.OBJETIVO:Este estudio evaluó el valor pronóstico de la ubicación del tumor primario en pacientes con metástasis hepáticas colorrectales examinando el recto y el colon del lado izquierdo por separado.DISEÑO:Este fue un estudio retrospectivo de 2003 a 2017.ENTORNO CLÍNICO:El estudio se llevó a cabo en un Hospital del Centro Nacional de Cáncer.PACIENTES:La cohorte del estudio incluyó a 489 pacientes con metástasis hepáticas colorrectales de cáncer de colon del lado derecho (n = 119, 24%), cáncer de colon del lado izquierdo (n = 251, 51%) o cáncer de recto (n = 119, 24%). %) que fueron sometidos a resección hepática.PRINCIPALES MEDIDAS DE VALORACIÓN:Los resultados primarios fueron la supervivencia sin recaídas y la supervivencia general.RESULTADOS:Las tasas de supervivencia sin recaída a cinco años para los pacientes con cáncer de colon derecho, cáncer de colon izquierdo y cáncer de recto fueron del 28,6%, 34,1%, y 26,4%, respectivamente, y las tasas de supervivencia general a los 5 años fueron del 53,9%, 70,3%, y 60,8%, respectivamente. El análisis multivariable reveló diferencias significativas en la supervivencia sin recaída y la supervivencia general entre el cáncer de colon izquierdo y el cáncer de recto (supervivencia sin recaída: HR = 1,37, p = 0,03; supervivencia general: HR = 1,49, p = 0,03) y entre el cáncer de colon izquierdo y el cáncer de colon del lado derecho (supervivencia libre de recaídas: HR = 1,39, p = 0,02; supervivencia global: HR = 1,60, p = 0,01), pero no entre el cáncer de colon del lado derecho y el cáncer de recto. En pacientes con recurrencia (n = 325), el cáncer de colon izquierdo tuvo la tasa de recurrencia en sitios múltiples más baja y la tasa de resección quirúrgica más alta por recurrencia (cáncer de colon izquierdo, 20%/46%; cáncer de colon derecho, 32%/30%; cáncer de recto, 26%/39%).LIMITACIONES:Este estudio fue de diseño retrospectivo.CONCLUSIONES:El cáncer de recto se asoció con una peor supervivencia sin recaída y una supervivencia general peor en comparación con el cáncer de colon izquierdo en pacientes con metástasis hepáticas colorrectales que se sometieron a resección hepática. Nuestros hallazgos sugieren que el colon y el recto del lado izquierdo deben considerarse entidades distintas en las metástasis hepáticas colorrectales. Consulte Video Resumen en http://links.lww.com/DCR/B882 . (Tradducción-Dr. Ingrid Melo ).
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Affiliation(s)
- Yasuyuki Takamizawa
- Department of Colorectal Surgery, National Cancer Center Hospital, Chuo-ku, Tokyo, Japan
- Department of Comprehensive Oncology, Nagasaki University Graduate School of Biomedical Sciences, Chuo-ku, Tokyo, Japan
| | - Dai Shida
- Department of Colorectal Surgery, National Cancer Center Hospital, Chuo-ku, Tokyo, Japan
- Division of Frontier Surgery, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Tomoko Horie
- Department of Colorectal Surgery, National Cancer Center Hospital, Chuo-ku, Tokyo, Japan
| | - Shunsuke Tsukamoto
- Department of Colorectal Surgery, National Cancer Center Hospital, Chuo-ku, Tokyo, Japan
| | - Minoru Esaki
- Department of Hepatobiliary and Pancreatic Surgery, National Cancer Center Hospital, Chuo-ku, Tokyo, Japan
| | - Kazuaki Shimada
- Department of Hepatobiliary and Pancreatic Surgery, National Cancer Center Hospital, Chuo-ku, Tokyo, Japan
| | - Tadashi Kondo
- Department of Comprehensive Oncology, Nagasaki University Graduate School of Biomedical Sciences, Chuo-ku, Tokyo, Japan
- Division of Rare Cancer Research, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
| | - Yukihide Kanemitsu
- Department of Colorectal Surgery, National Cancer Center Hospital, Chuo-ku, Tokyo, Japan
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Zheng Z, Zhan S, Zhou Y, Huang G, Chen P, Li B. Pediatric Crohn's disease diagnosis aid via genomic analysis and machine learning. Front Pediatr 2023; 11:991247. [PMID: 37033178 PMCID: PMC10076664 DOI: 10.3389/fped.2023.991247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 03/10/2023] [Indexed: 04/11/2023] Open
Abstract
Introduction Determination of pediatric Crohn's disease (CD) remains a major diagnostic challenge. However, the rapidly emerging field of artificial intelligence has demonstrated promise in developing diagnostic models for intractable diseases. Methods We propose an artificial neural network model of 8 gene markers identified by 4 classification algorithms based on Gene Expression Omnibus database for diagnostic of pediatric CD. Results The model achieved over 85% accuracy and area under ROC curve value in both training set and testing set for diagnosing pediatric CD. Additionally, immune infiltration analysis was performed to address why these markers can be integrated to develop a diagnostic model. Conclusion This study supports further clinical facilitation of precise disease diagnosis by integrating genomics and machine learning algorithms in open-access database.
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Affiliation(s)
- Zhiwei Zheng
- Department of Pediatrics, Zhongshan Hospital of Traditional Chinese Medicine Affiliated to Guangzhou University of Traditional Chinese Medicine, Zhongshan, China
- Correspondence: Zhiwei Zheng
| | - Sha Zhan
- School of Chinese Medicine, Jinan University, Guangzhou, China
| | - Yongmao Zhou
- Department of Pediatrics, Zhongshan Hospital of Traditional Chinese Medicine Affiliated to Guangzhou University of Traditional Chinese Medicine, Zhongshan, China
| | - Ganghua Huang
- Department of Pediatrics, The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Guangzhou, China
| | - Pan Chen
- Department of Pediatrics, Zhongshan Hospital of Traditional Chinese Medicine Affiliated to Guangzhou University of Traditional Chinese Medicine, Zhongshan, China
| | - Baofei Li
- Department of Pediatrics, Zhongshan Hospital of Traditional Chinese Medicine Affiliated to Guangzhou University of Traditional Chinese Medicine, Zhongshan, China
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Liu C, Liu D, Wang F, Xie J, Liu Y, Wang H, Rong J, Xie J, Wang J, Zeng R, Zhou F, Peng J, Xie Y. Identification of a glycolysis- and lactate-related gene signature for predicting prognosis, immune microenvironment, and drug candidates in colon adenocarcinoma. Front Cell Dev Biol 2022; 10:971992. [PMID: 36081904 PMCID: PMC9445192 DOI: 10.3389/fcell.2022.971992] [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: 06/17/2022] [Accepted: 07/28/2022] [Indexed: 11/26/2022] Open
Abstract
Background: Colon adenocarcinoma (COAD), a malignant gastrointestinal tumor, has the characteristics of high mortality and poor prognosis. Even in the presence of oxygen, the Warburg effect, a major metabolic hallmark of almost all cancer cells, is characterized by increased glycolysis and lactate fermentation, which supports biosynthesis and provides energy to sustain tumor cell growth and proliferation. However, a thorough investigation into glycolysis- and lactate-related genes and their association with COAD prognosis, immune cell infiltration, and drug candidates is currently lacking. Methods: COAD patient data and glycolysis- and lactate-related genes were retrieved from The Cancer Genome Atlas (TCGA) and Gene Set Enrichment Analysis (GSEA) databases, respectively. After univariate Cox regression analysis, a nonnegative matrix factorization (NMF) algorithm was used to identify glycolysis- and lactate-related molecular subtypes. Least absolute shrinkage and selection operator (LASSO) Cox regression identified twelve glycolysis- and lactate-related genes (ADTRP, ALDOB, APOBEC1, ASCL2, CEACAM7, CLCA1, CTXN1, FLNA, NAT2, OLFM4, PTPRU, and SNCG) related to prognosis. The median risk score was employed to separate patients into high- and low-risk groups. The prognostic efficacy of the glycolysis- and lactate-related gene signature was assessed using Kaplan–Meier (KM) survival and receiver operating characteristic (ROC) curve analyses. The nomogram, calibration curves, decision curve analysis (DCA), and clinical impact curve (CIC) were employed to improve the clinical applicability of the prognostic signature. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed on differentially expressed genes (DEGs) from the high- and low-risk groups. Using CIBERSORT, ESTIMATE, and single-sample GSEA (ssGSEA) algorithms, the quantities and types of tumor-infiltrating immune cells were assessed. The tumor mutational burden (TMB) and cytolytic (CYT) activity scores were calculated between the high- and low-risk groups. Potential small-molecule agents were identified using the Connectivity Map (cMap) database and validated by molecular docking. To verify key core gene expression levels, quantitative real-time polymerase chain reaction (qRT–PCR) assays were conducted. Results: We identified four distinct molecular subtypes of COAD. Cluster 2 had the best prognosis, and clusters 1 and 3 had poor prognoses. High-risk COAD patients exhibited considerably poorer overall survival (OS) than low-risk COAD patients. The nomogram precisely predicted patient OS, with acceptable discrimination and excellent calibration. GO and KEGG pathway enrichment analyses of DEGs revealed enrichment mainly in the “glycosaminoglycan binding,” “extracellular matrix,” “pancreatic secretion,” and “focal adhesion” pathways. Patients in the low-risk group exhibited a larger infiltration of memory CD4+ T cells and dendritic cells and a better prognosis than those in the high-risk group. The chemotherapeutic agent sensitivity of patients categorized by risk score varied significantly. We predicted six potential small-molecule agents binding to the core target of the glycolysis- and lactate-related gene signature. ALDOB and APOBEC1 mRNA expression was increased in COAD tissues, whereas CLCA1 and OLFM4 mRNA expression was increased in normal tissues. Conclusion: In summary, we identified molecular subtypes of COAD and developed a glycolysis- and lactate-related gene signature with significant prognostic value, which benefits COAD patients by informing more precise and effective treatment decisions.
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Affiliation(s)
- Cong Liu
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, Jiangxi, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Gastroenterology, Nanchang, China
| | - Dingwei Liu
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, Jiangxi, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Gastroenterology, Nanchang, China
| | - Fangfei Wang
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, Jiangxi, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Gastroenterology, Nanchang, China
| | - Jun Xie
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, Jiangxi, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Gastroenterology, Nanchang, China
| | - Yang Liu
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, Jiangxi, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Gastroenterology, Nanchang, China
| | - Huan Wang
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, Jiangxi, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Gastroenterology, Nanchang, China
| | - Jianfang Rong
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, Jiangxi, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Gastroenterology, Nanchang, China
| | - Jinliang Xie
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, Jiangxi, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Gastroenterology, Nanchang, China
| | - Jinyun Wang
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, Jiangxi, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Gastroenterology, Nanchang, China
| | - Rong Zeng
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, Jiangxi, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Gastroenterology, Nanchang, China
| | - Feng Zhou
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, Jiangxi, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Gastroenterology, Nanchang, China
| | - Jianxiang Peng
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, Jiangxi, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Gastroenterology, Nanchang, China
| | - Yong Xie
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Gastroenterology Institute of Jiangxi Province, Nanchang, Jiangxi, China
- Key Laboratory of Digestive Diseases of Jiangxi Province, Nanchang, Jiangxi, China
- Jiangxi Clinical Research Center for Gastroenterology, Nanchang, China
- *Correspondence: Yong Xie,
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8
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Zeng C, Qi G, Shen Y, Li W, Zhu Q, Yang C, Deng J, Lu W, Liu Q, Jin J. DPEP1 promotes drug resistance in colon cancer cells by forming a positive feedback loop with ASCL2. Cancer Med 2022; 12:412-424. [PMID: 35670012 PMCID: PMC9844606 DOI: 10.1002/cam4.4926] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/12/2022] [Accepted: 05/24/2022] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Drug resistance is an important factor affecting the efficacy of chemotherapy in patients with colon cancer. However, clinical markers for diagnosing drug resistance of tumor cells are not only a few in number, but also low in specificity, and the mechanism of action of tumor cell drug resistance remains unclear. METHODS Dipeptidase 1 (DPEP1) expression was analyzed using the cancer genome atlas (TCGA) and genotype-Tissue Expression pan-cancer data. Survival analysis was performed using the survival package in R software to assess the prognostic value of DPEP1 expression in colon cancer. Correlation and Venn analyses were adopted to identify key genes. Immunohistochemistry, western blot, qRT-PCR, Co-immunoprecipitation, and dual-luciferase reporter experiments were carried out to explore the underlying associations between DPEP1 and Achaete scute-like 2 (ASCL2). MTT assays were used to evaluate the role of DPEP1 and ASCL2 in colon cancer drug resistance. RESULTS DPEP1 was highly expressed in colon cancer tissues. DPEP1 expression correlated negatively with disease-specific survival but not with overall survival. Bioinformatics analysis and experiments showed that the expressions of DPEP1 and ASCL2 in colon cancer tissues were markedly positively correlated. Mechanistic research indicated that DPEP1 enhanced the stability of protein ASCL2 by inhibiting its ubiquitination-mediated degradation. In turn, ASCL2 functioned as a transcription factor to activate the transcriptional activity of the DPEP1 gene and boost its expression. Furthermore, DPEP1 also could enhance the expression of colon cancer stem cell markers (LGR5, CD133, and CD44), which strengthened the tolerance of colon cancer cells to chemotherapy drugs. CONCLUSIONS Our findings reveal that the DPEP1 enhances the stemness of tumor cells by forming a positive feedback loop with ASCL2 to improve resistance to chemotherapy drugs.
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Affiliation(s)
- Cheng Zeng
- Department of OncologyWujin Hospital Affiliated with Jiangsu UniversityChangzhouJiangsu ProvinceChina
| | - Guoping Qi
- Department of OncologyWujin Hospital Affiliated with Jiangsu UniversityChangzhouJiangsu ProvinceChina
| | - Ying Shen
- Department of OncologyWujin Hospital Affiliated with Jiangsu UniversityChangzhouJiangsu ProvinceChina,Department of OncologyWujin Clinical College of Xuzhou Medical UniversityChangzhouJiangsu ProvinceChina
| | - Wenjing Li
- Department of OncologyWujin Hospital Affiliated with Jiangsu UniversityChangzhouJiangsu ProvinceChina,Department of OncologyWujin Clinical College of Xuzhou Medical UniversityChangzhouJiangsu ProvinceChina
| | - Qi Zhu
- Department of OncologyWujin Hospital Affiliated with Jiangsu UniversityChangzhouJiangsu ProvinceChina,Department of OncologyWujin Clinical College of Xuzhou Medical UniversityChangzhouJiangsu ProvinceChina
| | - Chunxia Yang
- Department of OncologyWujin Hospital Affiliated with Jiangsu UniversityChangzhouJiangsu ProvinceChina,Department of OncologyWujin Clinical College of Xuzhou Medical UniversityChangzhouJiangsu ProvinceChina
| | - Jianzhong Deng
- Department of OncologyWujin Hospital Affiliated with Jiangsu UniversityChangzhouJiangsu ProvinceChina,Department of OncologyWujin Clinical College of Xuzhou Medical UniversityChangzhouJiangsu ProvinceChina
| | - Wenbin Lu
- Department of OncologyWujin Hospital Affiliated with Jiangsu UniversityChangzhouJiangsu ProvinceChina,Department of OncologyWujin Clinical College of Xuzhou Medical UniversityChangzhouJiangsu ProvinceChina
| | - Qian Liu
- Department of OncologyWujin Hospital Affiliated with Jiangsu UniversityChangzhouJiangsu ProvinceChina,Department of OncologyWujin Clinical College of Xuzhou Medical UniversityChangzhouJiangsu ProvinceChina
| | - Jianhua Jin
- Department of OncologyWujin Hospital Affiliated with Jiangsu UniversityChangzhouJiangsu ProvinceChina,Department of OncologyWujin Clinical College of Xuzhou Medical UniversityChangzhouJiangsu ProvinceChina
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9
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Hozhabri H, Ghasemi Dehkohneh RS, Razavi SM, Razavi SM, Salarian F, Rasouli A, Azami J, Ghasemi Shiran M, Kardan Z, Farrokhzad N, Mikaeili Namini A, Salari A. Comparative analysis of protein-protein interaction networks in metastatic breast cancer. PLoS One 2022; 17:e0260584. [PMID: 35045088 PMCID: PMC8769308 DOI: 10.1371/journal.pone.0260584] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 11/12/2021] [Indexed: 12/27/2022] Open
Abstract
Metastatic lesions leading causes of the majority of deaths in patients with the breast cancer. The present study aimed to provide a comprehensive analysis of the differentially expressed genes (DEGs) in the brain (MDA-MB-231 BrM2) and lung (MDA-MB-231 LM2) metastatic cell lines obtained from breast cancer patients compared with those who have primary breast cancer. We identified 981 and 662 DEGs for brain and lung metastasis, respectively. Protein-protein interaction (PPI) analysis revealed seven shared (PLCB1, FPR1, FPR2, CX3CL1, GABBR2, GPR37, and CXCR4) hub genes between brain and lung metastasis in breast cancer. Moreover, GNG2 and CXCL8, C3, and PTPN6 in the brain and SAA1 and CCR5 in lung metastasis were found as unique hub genes. Besides, five co-regulation of clusters via seven important co-expression genes (COL1A2, LUM, SPARC, THBS2, IL1B, CXCL8, THY1) were identified in the brain PPI network. Clusters screening followed by biological process (BP) function and pathway enrichment analysis for both metastatic cell lines showed that complement receptor signalling, acetylcholine receptor signalling, and gastric acid secretion pathways were common between these metastases, whereas other pathways were site-specific. According to our findings, there are a set of genes and functional pathways that mark and mediate breast cancer metastasis to the brain and lungs, which may enable us understand the molecular basis of breast cancer development in a deeper levele to the brain and lungs, which may help us gain a more complete understanding of the molecular underpinnings of breast cancer development.
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Affiliation(s)
- Hossein Hozhabri
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
- Salari Institute of Cognitive and Behavioral Disorders (SICBD), Karaj, Alborz, Iran
- Systems Biology Research Lab, Bioinformatics Group, Systems Biology of the Next Generation Company (SBNGC), Qom, Iran
| | - Roxana Sadat Ghasemi Dehkohneh
- Salari Institute of Cognitive and Behavioral Disorders (SICBD), Karaj, Alborz, Iran
- Systems Biology Research Lab, Bioinformatics Group, Systems Biology of the Next Generation Company (SBNGC), Qom, Iran
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Seyed Morteza Razavi
- Salari Institute of Cognitive and Behavioral Disorders (SICBD), Karaj, Alborz, Iran
- Systems Biology Research Lab, Bioinformatics Group, Systems Biology of the Next Generation Company (SBNGC), Qom, Iran
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
- * E-mail: (AS); (SMR)
| | - S. Mostafa Razavi
- Department of Chemical, Biomolecular and Corrosion Engineering, The University of Akron, Akron, Ohio, United States of America
| | - Fatemeh Salarian
- Systems Biology Research Lab, Bioinformatics Group, Systems Biology of the Next Generation Company (SBNGC), Qom, Iran
- Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Azade Rasouli
- Systems Biology Research Lab, Bioinformatics Group, Systems Biology of the Next Generation Company (SBNGC), Qom, Iran
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Jalil Azami
- Systems Biology Research Lab, Bioinformatics Group, Systems Biology of the Next Generation Company (SBNGC), Qom, Iran
- Faculty of Veterinary Medicine, Urmia University, Urmia, Iran
| | - Melika Ghasemi Shiran
- Salari Institute of Cognitive and Behavioral Disorders (SICBD), Karaj, Alborz, Iran
- Systems Biology Research Lab, Bioinformatics Group, Systems Biology of the Next Generation Company (SBNGC), Qom, Iran
- Department of Biology, Faculty of Sciences, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Zahra Kardan
- Systems Biology Research Lab, Bioinformatics Group, Systems Biology of the Next Generation Company (SBNGC), Qom, Iran
- Department of Cellular Molecular Biology, Faculty of Life Science and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Negar Farrokhzad
- Systems Biology Research Lab, Bioinformatics Group, Systems Biology of the Next Generation Company (SBNGC), Qom, Iran
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran
| | - Arsham Mikaeili Namini
- Systems Biology Research Lab, Bioinformatics Group, Systems Biology of the Next Generation Company (SBNGC), Qom, Iran
- Department of Animal Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Ali Salari
- Salari Institute of Cognitive and Behavioral Disorders (SICBD), Karaj, Alborz, Iran
- Systems Biology Research Lab, Bioinformatics Group, Systems Biology of the Next Generation Company (SBNGC), Qom, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- * E-mail: (AS); (SMR)
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10
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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.
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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
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11
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Zhang T, Yuan K, Wang Y, Xu M, Cai S, Chen C, Ma J. Identification of Candidate Biomarkers and Prognostic Analysis in Colorectal Cancer Liver Metastases. Front Oncol 2021; 11:652354. [PMID: 34422629 PMCID: PMC8371911 DOI: 10.3389/fonc.2021.652354] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 07/19/2021] [Indexed: 02/02/2023] Open
Abstract
Background Colorectal cancer (CRC), one of the most common malignant tumors worldwide, has a high mortality rate, especially for patients with CRC liver metastasis (CLM). However, CLM pathogenesis remains unclear. Methods We integrated multiple cohort datasets and databases to clarify and verify potential key candidate biomarkers and signal transduction pathways in CLM. GEO2R, DAVID 6.8, ImageGP, STRING, UALCAN, ONCOMINE, THE HUMAN PROTEIN ATLAS, GEPIA 2.0, cBioPortal, TIMER 2.0, DRUGSURV, CRN, GSEA 4.0.3, FUNRICH 3.1.3 and R 4.0.3 were utilized in this study. Results Sixty-three pairs of matched colorectal primary cancer and liver metastatic gene expression profiles were screened from three gene expression profiles (GSE6988, GSE14297 and GSE81558). Thirty-one up-regulated genes and four down-regulated genes were identified from these three gene expression profiles and verified by another gene expression profiles (GSE 49355) and TCGA database. Two pathways (IGFBP-IGF signaling pathway and complement-coagulation cascade), eighteen key differentially expressed genes (DEGs), six hub genes (SPARCL1, CDH2, CP, HP, TF and SERPINA5) and two biomarkers (CDH2 and SPARCL1) with significantly prognostic values were screened by multi-omics data analysis and verified by Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) cohort. Conclusions In this study, we identified a robust set of potential candidate biomarkers in CLM, which would provide potential value for early diagnosis and prognosis, and would promote molecular targeting therapy for CRC and CLM.
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Affiliation(s)
- Tianhao Zhang
- Division of Gastrointestinal Surgery Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Kaitao Yuan
- Division of Gastrointestinal Surgery Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yingzhao Wang
- Division of Gastrointestinal Surgery Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Mingze Xu
- Division of Gastrointestinal Surgery Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shirong Cai
- Division of Gastrointestinal Surgery Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Chuangqi Chen
- Division of Gastrointestinal Surgery Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jinping Ma
- Division of Gastrointestinal Surgery Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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12
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Shen HY, Wei FZ, Liu Q. Differential analysis revealing APOC1 to be a diagnostic and prognostic marker for liver metastases of colorectal cancer. World J Clin Cases 2021; 9:3880-3894. [PMID: 34141744 PMCID: PMC8180235 DOI: 10.12998/wjcc.v9.i16.3880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/10/2021] [Accepted: 03/23/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most malignant gastrointestinal cancers worldwide. The liver is the most important metastatic target organ, and liver metastasis is the leading cause of death in patients with CRC. Owing to the lack of sensitive biomarkers and unclear molecular mechanism, the occurrence of liver metastases cannot be predicted and the clinical outcomes are bad for liver metastases. Therefore, it is very important to identify the diagnostic or prognostic markers for liver metastases of CRC.
AIM To investigate the highly differentially expressed genes (HDEGs) and prognostic marker for liver metastases of CRC.
METHODS Data from three NCBI Gene Expression Omnibus (GEO) datasets were used to show HDEGs between liver metastases of CRC and tumour or normal samples. These significantly HDEGs of the three GEO datasets take the interactions. And these genes were screened through an online tool to explore the prognostic value. Then, TIMER and R package were utilized to investigate the immunity functions of the HDEGs and gene set enrichment analysis was used to explore their potential functions.
RESULTS Based on the selection criteria, three CRC datasets for exploration (GSE14297, GSE41258, and GSE49355) were chosen. Venn diagrams were used to show HDEGs common to the six groups and 47 HDEGs were obtained. The HDEGs were shown by using STRING and Cytoscape software. Based on the TCGA database, APOC1 showed significantly different expression between N2 and N0, and N2 and N1. And there was also a significant difference in expression between T2 and T4, and between T2 and T3. In 20 paired CRC and normal tissues, quantitative real-time polymerase chain reaction illustrated that the APOC1 mRNA was strongly upregulated in CRC tissues (P = 0.014). PrognoScan and GEPIA2 revealed the prognostic value of APOC1 for overall survival and disease-free survival in CRC (P < 0.05). TIMER showed that APOC1 has a close relationship with immune infiltration (P < 0.05).
CONCLUSION APOC1 is a biomarker that is associated with both the diagnosis and prognosis of liver metastases of CRC.
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Affiliation(s)
- Hai-Yu Shen
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Fang-Ze Wei
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Qian Liu
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
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13
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Hepatic stellate cells suppress NK cell-sustained breast cancer dormancy. Nature 2021; 594:566-571. [PMID: 34079127 DOI: 10.1038/s41586-021-03614-z] [Citation(s) in RCA: 130] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 05/04/2021] [Indexed: 12/15/2022]
Abstract
The persistence of undetectable disseminated tumour cells (DTCs) after primary tumour resection poses a major challenge to effective cancer treatment1-3. These enduring dormant DTCs are seeds of future metastases, and the mechanisms that switch them from dormancy to outgrowth require definition. Because cancer dormancy provides a unique therapeutic window for preventing metastatic disease, a comprehensive understanding of the distribution, composition and dynamics of reservoirs of dormant DTCs is imperative. Here we show that different tissue-specific microenvironments restrain or allow the progression of breast cancer in the liver-a frequent site of metastasis4 that is often associated with a poor prognosis5. Using mouse models, we show that there is a selective increase in natural killer (NK) cells in the dormant milieu. Adjuvant interleukin-15-based immunotherapy ensures an abundant pool of NK cells that sustains dormancy through interferon-γ signalling, thereby preventing hepatic metastases and prolonging survival. Exit from dormancy follows a marked contraction of the NK cell compartment and the concurrent accumulation of activated hepatic stellate cells (aHSCs). Our proteomics studies on liver co-cultures implicate the aHSC-secreted chemokine CXCL12 in the induction of NK cell quiescence through its cognate receptor CXCR4. CXCL12 expression and aHSC abundance are closely correlated in patients with liver metastases. Our data identify the interplay between NK cells and aHSCs as a master switch of cancer dormancy, and suggest that therapies aimed at normalizing the NK cell pool might succeed in preventing metastatic outgrowth.
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14
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Zhang XL, Hu LP, Yang Q, Qin WT, Wang X, Xu CJ, Tian GA, Yang XM, Yao LL, Zhu L, Nie HZ, Li Q, Xu Q, Zhang ZG, Zhang YL, Li J, Wang YH, Jiang SH. CTHRC1 promotes liver metastasis by reshaping infiltrated macrophages through physical interactions with TGF-β receptors in colorectal cancer. Oncogene 2021; 40:3959-3973. [PMID: 33986509 DOI: 10.1038/s41388-021-01827-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 04/13/2021] [Accepted: 04/27/2021] [Indexed: 02/03/2023]
Abstract
Metastasis is a major cause of cancer-related deaths. Tumor-intrinsic properties can determine whether tumor metastasis occurs or not. Here, by comparing the gene expression patterns in primary colorectal cancer (CRC) patients with or without metastasis, we found that Collagen Triple Helix Repeat Containing 1 (CTHRC1) in primary CRC served as a metastasis-associated gene. Animal experiments verified that CTHRC1 secreted by CRC cells promoted hepatic metastasis, which was closely correlated with macrophage infiltration. Depletion of macrophages by liposomal clodronate largely abolished the promoting effect of CTHRC1 on CRC liver metastasis. Furthermore, we demonstrated that CTHRC1 modulated macrophage polarization to M2 phenotypes through TGF-β signaling. A mechanistic study revealed that CTHRC1 bound directly to TGF-β receptor II and TGF-β receptor III, stabilized the TGF-β receptor complex, and activated TGF-β signaling. The combination treatment of CTHRC1 monoclonal antibody and anti-PD-1 blocking antibody effectively suppressed CRC hepatic metastasis. Taken together, our data demonstrated that CTHRC1 is an intrinsic marker of CRC metastasis and further revealed that CTHRC1 promoted CRC liver metastasis by reshaping infiltrated macrophages through TGF-β signaling, suggesting that CTHRC1 could be a potential biomarker for the early prediction of and a therapeutic target of CRC hepatic metastasis.
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Affiliation(s)
- Xue-Li Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Li-Peng Hu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qin Yang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wei-Ting Qin
- Department of Radiation Oncology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xu Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chun-Jie Xu
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Guang-Ang Tian
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao-Mei Yang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lin-Li Yao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Zhu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hui-Zhen Nie
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qing Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qing Xu
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhi-Gang Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yan-Li Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Jun Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Ya-Hui Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Shu-Heng Jiang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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15
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Zeng D, Wang M, Wu J, Lin S, Ye Z, Zhou R, Wang G, Wu J, Sun H, Bin J, Liao Y, Li N, Shi M, Liao W. Immunosuppressive Microenvironment Revealed by Immune Cell Landscape in Pre-metastatic Liver of Colorectal Cancer. Front Oncol 2021; 11:620688. [PMID: 33833986 PMCID: PMC8021849 DOI: 10.3389/fonc.2021.620688] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/22/2021] [Indexed: 12/12/2022] Open
Abstract
Background: Colorectal cancer, the fourth leading cause of cancer mortality, is prone to metastasis, especially to the liver. The pre-metastatic microenvironment comprising various resident stromal cells and immune cells is essential for metastasis. However, how the dynamic evolution of immune components facilitates pre-metastatic niche formation remains unclear. Methods: Utilizing RNA-seq data from our orthotopic colorectal cancer mouse model, we applied single sample gene set enrichment analysis and Cell type Identification By Estimating Relative Subsets Of RNA Transcripts to investigate the tumor microenvironment landscape of pre-metastatic liver, and define the exact role of myeloid-derived suppressor cells (MDSCs) acting in the regulation of infiltrating immune cells and gene pathways activation. Flow cytometry analysis was conducted to quantify the MDSCs levels in human and mice samples. Results: In the current work, based on the high-throughput transcriptome data, we depicted the immune cell infiltration pattern of pre-metastatic liver and highlighted MDSCs as the dominant altered cell type. Notably, flow cytometry analysis showed that high frequencies of MDSCs, was detected in the pre-metastatic liver of orthotopic colorectal cancer tumor-bearing mice, and in the peripheral blood of patients with stage I-III colorectal cancer. MDSCs accumulation in the liver drove immunosuppressive factors secretion and immune checkpoint score upregulation, consequently shaping the pre-metastatic niche with sustained immune suppression. Metabolic reprogramming such as upregulated glycolysis/gluconeogenesis and HIF-1 signaling pathways in the primary tumor was also demonstrated to correlate with MDSCs infiltration in the pre-metastatic liver. Some chemokines were identified as a potential mechanism for MDSCs recruitment. Conclusion: Collectively, our study elucidates the alterations of MDSCs during pre-metastatic niche transformation, and illuminates the latent biological mechanism by which primary tumors impact MDSC aggregation in the targeted liver.
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Affiliation(s)
- Dongqiang Zeng
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Miaohong Wang
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jiani Wu
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Siheng Lin
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zilan Ye
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Rui Zhou
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Gaofeng Wang
- Department of Dermatology, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Jianhua Wu
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Huiying Sun
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jianping Bin
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yulin Liao
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Nailin Li
- Department of Medicine-Solna, Clinical Pharmacology Group, Karolinska Institutet, Stockholm, Sweden
| | - Min Shi
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Wangjun Liao
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
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16
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Sphyris N, Hodder MC, Sansom OJ. Subversion of Niche-Signalling Pathways in Colorectal Cancer: What Makes and Breaks the Intestinal Stem Cell. Cancers (Basel) 2021; 13:1000. [PMID: 33673710 PMCID: PMC7957493 DOI: 10.3390/cancers13051000] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 12/12/2022] Open
Abstract
The intestinal epithelium fulfils pleiotropic functions in nutrient uptake, waste elimination, and immune surveillance while also forming a barrier against luminal toxins and gut-resident microbiota. Incessantly barraged by extraneous stresses, the intestine must continuously replenish its epithelial lining and regenerate the full gamut of specialized cell types that underpin its functions. Homeostatic remodelling is orchestrated by the intestinal stem cell (ISC) niche: a convergence of epithelial- and stromal-derived cues, which maintains ISCs in a multipotent state. Following demise of homeostatic ISCs post injury, plasticity is pervasive among multiple populations of reserve stem-like cells, lineage-committed progenitors, and/or fully differentiated cell types, all of which can contribute to regeneration and repair. Failure to restore the epithelial barrier risks seepage of toxic luminal contents, resulting in inflammation and likely predisposing to tumour formation. Here, we explore how homeostatic niche-signalling pathways are subverted in tumorigenesis, enabling ISCs to gain autonomy from niche restraints ("ISC emancipation") and transform into cancer stem cells capable of driving tumour initiation, progression, and therapy resistance. We further consider the implications of the pervasive plasticity of the intestinal epithelium for the trajectory of colorectal cancer, the emergence of distinct molecular subtypes, the propensity to metastasize, and the development of effective therapeutic strategies.
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Affiliation(s)
- Nathalie Sphyris
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK; (N.S.); (M.C.H.)
| | - Michael C. Hodder
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK; (N.S.); (M.C.H.)
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK
| | - Owen J. Sansom
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK; (N.S.); (M.C.H.)
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK
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17
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Angius A, Scanu AM, Arru C, Muroni MR, Rallo V, Deiana G, Ninniri MC, Carru C, Porcu A, Pira G, Uva P, Cossu-Rocca P, De Miglio MR. Portrait of Cancer Stem Cells on Colorectal Cancer: Molecular Biomarkers, Signaling Pathways and miRNAome. Int J Mol Sci 2021; 22:1603. [PMID: 33562604 PMCID: PMC7915330 DOI: 10.3390/ijms22041603] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/02/2021] [Accepted: 02/02/2021] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is a leading cause of cancer death worldwide, and about 20% is metastatic at diagnosis and untreatable. Increasing evidence suggests that the heterogeneous nature of CRC is related to colorectal cancer stem cells (CCSCs), a small cells population with stemness behaviors and responsible for tumor progression, recurrence, and therapy resistance. Growing knowledge of stem cells (SCs) biology has rapidly improved uncovering the molecular mechanisms and possible crosstalk/feedback loops between signaling pathways that directly influence intestinal homeostasis and tumorigenesis. The generation of CCSCs is probably connected to genetic changes in members of signaling pathways, which control self-renewal and pluripotency in SCs and then establish function and phenotype of CCSCs. Particularly, various deregulated CCSC-related miRNAs have been reported to modulate stemness features, controlling CCSCs functions such as regulation of cell cycle genes expression, epithelial-mesenchymal transition, metastasization, and drug-resistance mechanisms. Primarily, CCSC-related miRNAs work by regulating mainly signal pathways known to be involved in CCSCs biology. This review intends to summarize the epigenetic findings linked to miRNAome in the maintenance and regulation of CCSCs, including their relationships with different signaling pathways, which should help to identify specific diagnostic, prognostic, and predictive biomarkers for CRC, but also develop innovative CCSCs-targeted therapies.
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Affiliation(s)
- Andrea Angius
- Institute of Genetic and Biomedical Research (IRGB), CNR, Cittadella Universitaria di Cagliari, 09042 Monserrato, Italy;
| | - Antonio Mario Scanu
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via P. Manzella, 4, 07100 Sassari, Italy; (A.M.S.); (M.R.M.); (G.D.); (M.C.N.); (A.P.); (P.C.-R.)
| | - Caterina Arru
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (C.A.); (C.C.); (G.P.)
| | - Maria Rosaria Muroni
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via P. Manzella, 4, 07100 Sassari, Italy; (A.M.S.); (M.R.M.); (G.D.); (M.C.N.); (A.P.); (P.C.-R.)
| | - Vincenzo Rallo
- Institute of Genetic and Biomedical Research (IRGB), CNR, Cittadella Universitaria di Cagliari, 09042 Monserrato, Italy;
| | - Giulia Deiana
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via P. Manzella, 4, 07100 Sassari, Italy; (A.M.S.); (M.R.M.); (G.D.); (M.C.N.); (A.P.); (P.C.-R.)
| | - Maria Chiara Ninniri
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via P. Manzella, 4, 07100 Sassari, Italy; (A.M.S.); (M.R.M.); (G.D.); (M.C.N.); (A.P.); (P.C.-R.)
| | - Ciriaco Carru
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (C.A.); (C.C.); (G.P.)
| | - Alberto Porcu
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via P. Manzella, 4, 07100 Sassari, Italy; (A.M.S.); (M.R.M.); (G.D.); (M.C.N.); (A.P.); (P.C.-R.)
| | - Giovanna Pira
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (C.A.); (C.C.); (G.P.)
| | - Paolo Uva
- IRCCS G. Gaslini, 16147 Genoa, Italy;
| | - Paolo Cossu-Rocca
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via P. Manzella, 4, 07100 Sassari, Italy; (A.M.S.); (M.R.M.); (G.D.); (M.C.N.); (A.P.); (P.C.-R.)
- Department of Diagnostic Services, “Giovanni Paolo II” Hospital, ASSL Olbia-ATS Sardegna, 07026 Olbia, Italy
| | - Maria Rosaria De Miglio
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via P. Manzella, 4, 07100 Sassari, Italy; (A.M.S.); (M.R.M.); (G.D.); (M.C.N.); (A.P.); (P.C.-R.)
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18
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Amin V, Ağaç D, Barnes SD, Çobanoğlu MC. Accurate differential analysis of transcription factor activity from gene expression. Bioinformatics 2020; 35:5018-5029. [PMID: 31099391 DOI: 10.1093/bioinformatics/btz398] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 04/02/2019] [Accepted: 05/08/2019] [Indexed: 12/17/2022] Open
Abstract
MOTIVATION Activity of transcriptional regulators is crucial in elucidating the mechanism of phenotypes. However regulatory activity hypotheses are difficult to experimentally test. Therefore, we need accurate and reliable computational methods for regulator activity inference. There is extensive work in this area, however, current methods have difficulty with one or more of the following: resolving activity of TFs with overlapping regulons, reflecting known regulatory relationships, or flexible modeling of TF activity over the regulon. RESULTS We present Effector and Perturbation Estimation Engine (EPEE), a method for differential analysis of transcription factor (TF) activity from gene expression data. EPEE addresses each of these principal challenges in the field. Firstly, EPEE collectively models all TF activity in a single multivariate model, thereby accounting for the intrinsic coupling among TFs that share targets, which is highly frequent. Secondly, EPEE incorporates context-specific TF-gene regulatory networks and therefore adapts the analysis to each biological context. Finally, EPEE can flexibly reflect different regulatory activity of a single TF among its potential targets. This allows the flexibility to implicitly recover other regulatory influences such as co-activators or repressors. We comparatively validated EPEE in 15 datasets from three well-studied contexts, namely immunology, cancer, and hematopoiesis. We show that addressing the aforementioned challenges enable EPEE to outperform alternative methods and reliably produce accurate results. AVAILABILITY AND IMPLEMENTATION https://github.com/Cobanoglu-Lab/EPEE. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Viren Amin
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Didem Ağaç
- Department of Immunology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Spencer D Barnes
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Murat Can Çobanoğlu
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
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19
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Yamaguchi N, Weinberg EM, Nguyen A, Liberti MV, Goodarzi H, Janjigian YY, Paty PB, Saltz LB, Kingham TP, Loo JM, de Stanchina E, Tavazoie SF. PCK1 and DHODH drive colorectal cancer liver metastatic colonization and hypoxic growth by promoting nucleotide synthesis. eLife 2019; 8:e52135. [PMID: 31841108 PMCID: PMC7299340 DOI: 10.7554/elife.52135] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 12/15/2019] [Indexed: 01/09/2023] Open
Abstract
Colorectal cancer (CRC) is a major cause of human death. Mortality is primarily due to metastatic organ colonization, with the liver being the main organ affected. We modeled metastatic CRC (mCRC) liver colonization using patient-derived primary and metastatic tumor xenografts (PDX). Such PDX modeling predicted patient survival outcomes. In vivo selection of multiple PDXs for enhanced metastatic colonization capacity upregulated the gluconeogenic enzyme PCK1, which enhanced liver metastatic growth by driving pyrimidine nucleotide biosynthesis under hypoxia. Consistently, highly metastatic tumors upregulated multiple pyrimidine biosynthesis intermediary metabolites. Therapeutic inhibition of the pyrimidine biosynthetic enzyme DHODH with leflunomide substantially impaired CRC liver metastatic colonization and hypoxic growth. Our findings provide a potential mechanistic basis for the epidemiologic association of anti-gluconeogenic drugs with improved CRC metastasis outcomes, reveal the exploitation of a gluconeogenesis enzyme for pyrimidine biosynthesis under hypoxia, and implicate DHODH and PCK1 as metabolic therapeutic targets in CRC metastatic progression.
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Affiliation(s)
- Norihiro Yamaguchi
- Laboratory of Systems Cancer BiologyThe Rockefeller UniversityNew YorkUnited States
| | - Ethan M Weinberg
- Laboratory of Systems Cancer BiologyThe Rockefeller UniversityNew YorkUnited States
| | - Alexander Nguyen
- Laboratory of Systems Cancer BiologyThe Rockefeller UniversityNew YorkUnited States
| | - Maria V Liberti
- Laboratory of Systems Cancer BiologyThe Rockefeller UniversityNew YorkUnited States
| | - Hani Goodarzi
- Laboratory of Systems Cancer BiologyThe Rockefeller UniversityNew YorkUnited States
| | - Yelena Y Janjigian
- Gastrointestinal Oncology ServiceMemorial Sloan-Kettering Cancer CenterNew YorkUnited States
| | - Philip B Paty
- Colorectal ServiceMemorial Sloan-Kettering Cancer CenterNew YorkUnited States
| | - Leonard B Saltz
- Gastrointestinal Oncology ServiceMemorial Sloan-Kettering Cancer CenterNew YorkUnited States
| | - T Peter Kingham
- Hepatopancreatobiliary ServiceMemorial Sloan-Kettering Cancer CenterNew YorkUnited States
| | - Jia Min Loo
- Laboratory of Systems Cancer BiologyThe Rockefeller UniversityNew YorkUnited States
| | - Elisa de Stanchina
- Antitumor Assessment Core FacilityMemorial Sloan-Kettering Cancer CenterNew YorkUnited States
| | - Sohail F Tavazoie
- Laboratory of Systems Cancer BiologyThe Rockefeller UniversityNew YorkUnited States
- Department of MedicineMemorial Sloan-Kettering Cancer CenterNew YorkUnited States
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20
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Liu Z, Wang X, Jiang K, Ji X, Zhang YA, Chen Z. TNFα-induced Up-regulation of Ascl2 Affects the Differentiation and Proliferation of Neural Stem Cells. Aging Dis 2019; 10:1207-1220. [PMID: 31788333 PMCID: PMC6844591 DOI: 10.14336/ad.2018.1028] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 10/28/2018] [Indexed: 01/11/2023] Open
Abstract
The molecular mediators underlying the effects of inflammation on neural stem cells (NSCs) are not fully characterized. In this study, we identified Ascl2 as a downstream basic helix-loop-helix (bHLH) transcription factor in NSCs following exposure to TNFα. Under normal conditions, Ascl2 expression is inhibited at post-transcriptional levels by miR-26a, which targets the 3’ untranslated region (UTR) of Ascl2. Upon exposure to TNFα, miR-26a expression is reduced, which leads to up-regulation of Ascl2. Overexpression of Ascl2 promotes neuronal differentiation, reduces proliferation, and increases the level of cleaved CASPASE 3 in NSCs, as observed in the in vitro and in ovo experiments. Ascl2 may serve in NSCs as a standby factor that readily responds to TNFα, which is often induced in inflammatory situations. In a chronic inflammatory condition with consistent up-regulation of TNFα, overexpression of Ascl2 may inhibit neurogenesis as a net result.
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Affiliation(s)
- Zhongfeng Liu
- 1Cell Therapy Center, Beijing Institute of Geriatrics, Xuanwu Hospital, Capital Medical University, and Key Laboratory of Neurodegeneration, Ministry of Education, Beijing, China.,2Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China.,3Center of Parkinson's Disease, Beijing Institute for Brain Disorders, Beijing, China
| | - Xuan Wang
- 1Cell Therapy Center, Beijing Institute of Geriatrics, Xuanwu Hospital, Capital Medical University, and Key Laboratory of Neurodegeneration, Ministry of Education, Beijing, China.,2Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China.,3Center of Parkinson's Disease, Beijing Institute for Brain Disorders, Beijing, China
| | - Kewen Jiang
- 4Department of Neurology, the Children's Hospital School of Medicine, Zhejiang University, Hangzhou, China
| | - Xunming Ji
- 5Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Y Alex Zhang
- 1Cell Therapy Center, Beijing Institute of Geriatrics, Xuanwu Hospital, Capital Medical University, and Key Laboratory of Neurodegeneration, Ministry of Education, Beijing, China
| | - Zhiguo Chen
- 1Cell Therapy Center, Beijing Institute of Geriatrics, Xuanwu Hospital, Capital Medical University, and Key Laboratory of Neurodegeneration, Ministry of Education, Beijing, China.,2Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China.,3Center of Parkinson's Disease, Beijing Institute for Brain Disorders, Beijing, China
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21
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Kasprzak A, Adamek A. Insulin-Like Growth Factor 2 (IGF2) Signaling in Colorectal Cancer-From Basic Research to Potential Clinical Applications. Int J Mol Sci 2019; 20:ijms20194915. [PMID: 31623387 PMCID: PMC6801528 DOI: 10.3390/ijms20194915] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 09/27/2019] [Accepted: 09/30/2019] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common cancers in men and women worldwide as well as is the leading cause of death in the western world. Almost a third of the patients has or will develop liver metastases. While genetic as well as epigenetic mechanisms are important in CRC pathogenesis, the basis of the most cases of cancer is unknown. High spatial and inter-patient variability of the molecular alterations qualifies this cancer in the group of highly heterogeneous tumors, which makes it harder to elucidate the mechanisms underlying CRC progression. Determination of highly sensitive and specific early diagnosis markers and understanding the cellular and molecular mechanism(s) of cancer progression are still a challenge of the current era in oncology of solid tumors. One of the accepted risk factors for CRC development is overexpression of insulin-like growth factor 2 (IGF2), a 7.5-kDa peptide produced by liver and many other tissues. IGF2 is the first gene discovered to be parentally imprinted. Loss of imprinting (LOI) or aberrant imprinting of IGF2 could lead to IGF2 overexpression, increased cell proliferation, and CRC development. IGF2 as a mitogen is associated with increased risk of developing colorectal neoplasia. Higher serum IGF2 concentration as well as its tissue overexpression in CRC compared to control are associated with metastasis. IGF2 protein was one of the three candidates for a selective marker of CRC progression and staging. Recent research indicates dysregulation of different micro- and long non-coding RNAs (miRNAs and lncRNAs, respectively) embedded within the IGF2 gene in CRC carcinogenesis, with some of them indicated as potential diagnostic and prognostic CRC biomarkers. This review systematises the knowledge on the role of genetic and epigenetic instabilities of IGF2 gene, free (active form of IGF2) and IGF-binding protein (IGFBP) bound (inactive form), paracrine/autocrine secretion of IGF2, as well as mechanisms of inducing dysplasia in vitro and tumorigenicity in vivo. We have tried to answer which molecular changes of the IGF2 gene and its regulatory mechanisms have the most significance in initiation, progression (including liver metastasis), prognosis, and potential anti-IGF2 therapy in CRC patients.
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Affiliation(s)
- Aldona Kasprzak
- Department of Histology and Embryology, University of Medical Sciences, Swiecicki Street 6, 60-781 Poznan, Poland.
| | - Agnieszka Adamek
- Department of Infectious Diseases, Hepatology and Acquired Immunodeficiencies, University of Medical Sciences, Szwajcarska Street 3, 61-285 Poznan, Poland.
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22
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Yokota K, Tanaka Y, Harada H, Kaida T, Nakamoto S, Soeno T, Fujiyama Y, Yokota M, Kojo K, Miura H, Yamanashi T, Sato T, Nakamura T, Watanabe M, Yamashita K. WiNTRLINC1/ASCL2/c-Myc Axis Characteristics of Colon Cancer with Differentiated Histology at Young Onset and Essential for Cell Viability. Ann Surg Oncol 2019; 26:4826-4834. [DOI: 10.1245/s10434-019-07780-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Indexed: 12/20/2022]
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23
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Allgayer H, Leupold JH, Patil N. Defining the "Metastasome": Perspectives from the genome and molecular landscape in colorectal cancer for metastasis evolution and clinical consequences. Semin Cancer Biol 2019; 60:1-13. [PMID: 31362074 DOI: 10.1016/j.semcancer.2019.07.018] [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: 05/28/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 02/07/2023]
Abstract
Metastasis still poses the highest challenge for personalized therapy in cancer, partly due to a still incomplete understanding of its molecular evolution. We recently presented the most comprehensive whole-genome study of colorectal metastasis vs. matched primary tumors and suggested novel components of disease progression and metastasis evolution, some of them potentially relevant for targeted therapy. In this review, we try to put these findings into perspective with latest discoveries of colleagues and recent literature, and propose a systematic international team effort to collectively define the "metastasome", a term we introduce to summarize all genomic, epigenomic, transcriptomic, further -omic, molecular and functional characteristics rendering metastases different from primary tumors. Based on recent discoveries, we propose a revised metastasis model for colorectal cancer which is based on a common ancestor clone, early dissemination but flexible early or late stage clonal separation paralleling stromal interactions. Furthermore, we discuss hypotheses on site-specific metastasis, colorectal cancer progression, metastasis-targeted diagnosis and therapy, and metastasis prevention based on latest metastasome data.
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Affiliation(s)
- Heike Allgayer
- Department of Experimental Surgery - Cancer Metastasis, Medical Faculty Mannheim, Theodor Kutzer Ufer 1-3, 68135, Mannheim, Ruprecht Karls University of Heidelberg, Germany; Centre for Biomedicine and Medical Technology Mannheim (CBTM), Medical Faculty Mannheim, Ludolf-Krehl-Str. 6, 68135, Mannheim, Ruprecht Karls University of Heidelberg, Germany.
| | - Jörg H Leupold
- Department of Experimental Surgery - Cancer Metastasis, Medical Faculty Mannheim, Theodor Kutzer Ufer 1-3, 68135, Mannheim, Ruprecht Karls University of Heidelberg, Germany; Centre for Biomedicine and Medical Technology Mannheim (CBTM), Medical Faculty Mannheim, Ludolf-Krehl-Str. 6, 68135, Mannheim, Ruprecht Karls University of Heidelberg, Germany
| | - Nitin Patil
- Department of Experimental Surgery - Cancer Metastasis, Medical Faculty Mannheim, Theodor Kutzer Ufer 1-3, 68135, Mannheim, Ruprecht Karls University of Heidelberg, Germany; Centre for Biomedicine and Medical Technology Mannheim (CBTM), Medical Faculty Mannheim, Ludolf-Krehl-Str. 6, 68135, Mannheim, Ruprecht Karls University of Heidelberg, Germany
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24
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Tanaka T, Kojima K, Yokota K, Tanaka Y, Ooizumi Y, Ishii S, Nishizawa N, Yokoi K, Ushiku H, Kikuchi M, Kojo K, Minatani N, Katoh H, Sato T, Nakamura T, Sawanobori M, Watanabe M, Yamashita K. Comprehensive Genetic Search to Clarify the Molecular Mechanism of Drug Resistance Identifies ASCL2-LEF1/TSPAN8 Axis in Colorectal Cancer. Ann Surg Oncol 2019; 26:1401-1411. [PMID: 30706227 DOI: 10.1245/s10434-019-07172-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND Treatment-resistance genes limiting anticancer therapy have not been well clarified in colorectal cancer (CRC). We explored gene expression profiles to identify biomarkers for predicting treatment resistance to an anticancer drug in CRC. METHODS Six CRC cell lines were treated with phenylbutyrate (PB). The gene expression profiles were then compared using microarrays (harboring 54,675 genes), and genes associated with PB resistance were identified. Candidate genes were functionally examined in cell lines and clinically validated for treatment resistance in clinical samples. RESULTS Both DLD1 and HCT15 cells were PB resistant, while HCT116 cells were identified as PB sensitive. On microarray analysis, among the PB resistance-related genes, the expression of the genes ASCL2, LEF1, and TSPAN8 was clearly associated with PB resistance. PB-sensitive cells transfected with one of these three genes exhibited significant (P < 0.001) augmentation of PB resistance; ASCL2 induced expression of both LEF1 and TSPAN8, while neither LEF1 nor TSPAN8 induced ASCL2. RNA interference via ASCL2 knockdown made PB-resistant cells sensitive to PB and inhibited both genes. ASCL2 knockdown also played a critical role in sensitivity to treatment by 5-fluorouracil and radiotherapy in addition to PB. Finally, ASCL2 expression was significantly correlated with histological grade of rectal cancer with preoperative chemoradiation therapy. CONCLUSIONS ASCL2 was identified as a causative gene involved in therapeutic resistance against anticancer treatments in CRC.
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Affiliation(s)
- Toshimichi Tanaka
- Department of Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Keita Kojima
- Department of Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Kazuko Yokota
- Department of Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Yoko Tanaka
- Department of Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Yosuke Ooizumi
- Department of Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Satoru Ishii
- Department of Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Nobuyuki Nishizawa
- Department of Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Keigo Yokoi
- Department of Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Hideki Ushiku
- Department of Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Mariko Kikuchi
- Department of Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Ken Kojo
- Department of Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Naoko Minatani
- Department of Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Hiroshi Katoh
- Department of Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Takeo Sato
- Department of Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Takatoshi Nakamura
- Department of Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | | | - Masahiko Watanabe
- Department of Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Keishi Yamashita
- Epigenetic Treatment Research Group, Chiyoda-ku, Tokyo, Japan. .,Division of Advanced Surgical Oncology, Department of Research and Development Center for New Medical Frontiers, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan.
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Rioux CR, Clapper ML, Cooper HS, Michaud J, St Amant N, Koohsari H, Workman L, Kaunga E, Hensley H, Pilorget A, Gerard C. Self-antigen MASH2 combined with the AS15 immunostimulant induces tumor protection in colorectal cancer mouse models. PLoS One 2019; 14:e0210261. [PMID: 30682058 PMCID: PMC6347180 DOI: 10.1371/journal.pone.0210261] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 12/19/2018] [Indexed: 12/15/2022] Open
Abstract
Human achaete scute homolog 2 (HASH2) and its murine ortholog MASH2 are potential targets for colorectal cancer immunotherapy. We assessed immunogenicity and antitumor potential of recombinant MASH2 protein combined with AS15 immunostimulant (recMASH2+AS15) in CB6F1 and Apc+/Min-FCCC mice. CB6F1 mice received 4 injections of recMASH2+AS15 or AS15 alone before challenge with TC1-MASH2 tumor cells (Tumor Challenge). Apc+/Min-FCCC mice received 9 injections of recMASH2+AS15 or vehicle (phosphate buffer saline [PBS] or AS15 alone), before (two independent Prophylactic Studies) or after (Immunotherapy) colon adenomas were detectable by colonoscopy. CB6F1 mice immunized with recMASH2+AS15 had a significantly smaller mean tumor size and improved survival rate compared to controls (104 mm2 vs. 197 mm2 [p = 0.009] and 67% vs. 7% [p = 0.001], respectively). In Prophylactic Study 1, the mean number of colon adenomas was significantly lower in Apc+/Min-FCCC mice receiving recMASH2+AS15 compared to PBS (1.8 [95% confidence interval 1.0–3.3] vs. 5.2 [3.7–7.4], p = 0.003). Fewer microadenomas were observed in recMASH2+AS15 groups compared to PBS in both Prophylactic Studies (Study 1: mean 0.4 [0.2–1.0] vs. 1.5 [0.9–2.4], p = 0.009; Study 2: 0.4 [0.2–0.6] vs. 1.1 [0.8–1.5], p = 0.001). In the Immunotherapy Study, fewer colon adenomas tended to be observed in recMASH2+AS15-treated mice (4.1 [2.9–6.0]) compared to controls (AS15 4.7 [3.3–6.6]; PBS 4.9 [3.5–6.9]; no significant difference). recMASH2+AS15 induced MASH2-specific antibody and CD4+ responses in both mouse models. recMASH2+AS15 partially protected mice against MASH2-expressing tumors and reduced spontaneous colorectal adenomas in Apc+/Min-FCCC mice, indicating that MASH2/HASH2 antigens are targets for colorectal cancer immunotherapy.
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Affiliation(s)
| | - Margie L. Clapper
- Fox Chase Cancer Center, Philadelphia, PA, United States of America
- * E-mail:
| | - Harry S. Cooper
- Fox Chase Cancer Center, Philadelphia, PA, United States of America
| | | | | | | | - Laura Workman
- Fox Chase Cancer Center, Philadelphia, PA, United States of America
| | - Esther Kaunga
- Fox Chase Cancer Center, Philadelphia, PA, United States of America
| | - Harvey Hensley
- Fox Chase Cancer Center, Philadelphia, PA, United States of America
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Torén W, Ansari D, Andersson R. Immunohistochemical investigation of prognostic biomarkers in resected colorectal liver metastases: a systematic review and meta-analysis. Cancer Cell Int 2018; 18:217. [PMID: 30602942 PMCID: PMC6307223 DOI: 10.1186/s12935-018-0715-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 12/18/2018] [Indexed: 02/07/2023] Open
Abstract
Background Many studies have investigated the prognostic role of biomarkers in colorectal liver metastases (CRLM). However, no biomarker has been established in routine clinical practice. The aim of this study was to scrutinize the current literature for biomarkers evaluated by immunohistochemistry as prognostic markers in patients with resected CRLM. Methods A systematic review was performed according to the PRISMA guidelines. Articles were identified in the PubMed database with selected search terms and by cross-references search. The REMARK quality criteria were applied. Markers were included if they reported the prognostic impact of immunohistochemical markers in a multivariable setting in relation to overall survival (OS). A meta-analysis was conducted when more than one original article provided survival data of a marker. Results In total, 26 biomarkers were identified as independent significant markers for OS in resected CRLM. These biomarkers were found to be involved in multiple oncogenic signalling pathways that control cell growth, apoptosis, angiogenesis and evasion of immune detection. Among these biomarker candidates were Ki-67, EGFR, p53, hTERT, CD34, TSP-1, KISS1, Aurora kinase A and CDX2. CD34 and TSP-1 were reported as significantly associated with survival by more than one study and where therefore pooled in a meta-analysis. Conclusion A number of independent prognostic biomarkers for resected CRLM were identified. However, most markers were evaluated in a retrospective setting with small patient cohorts, without external validation. Large, prospective, multicentre studies with standardised methods are needed before biomarkers can translated into the clinic.
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Affiliation(s)
- William Torén
- Department of Surgery, Clinical Sciences Lund, Lund University and Skåne University Hospital, SE-221 85 Lund, Sweden
| | - Daniel Ansari
- Department of Surgery, Clinical Sciences Lund, Lund University and Skåne University Hospital, SE-221 85 Lund, Sweden
| | - Roland Andersson
- Department of Surgery, Clinical Sciences Lund, Lund University and Skåne University Hospital, SE-221 85 Lund, Sweden
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27
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Ye J, Liu S, Shang Y, Chen H, Wang R. R-spondin1/Wnt-enhanced Ascl2 autoregulation controls the self-renewal of colorectal cancer progenitor cells. Cell Cycle 2018; 17:1014-1025. [PMID: 29886802 DOI: 10.1080/15384101.2018.1469874] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The Wnt signaling pathway controls stem cell identity in the intestinal epithelium and cancer stem cells (CSCs). The transcription factor Ascl2 (Wnt target gene) is fate decider of intestinal cryptic stem cells and colon cancer stem cells. It is unclear how Wnt signaling is translated into Ascl2 expression and keeping the self-renewal of CRC progenitor cells. We showed that the exogenous Ascl2 in colorectal cancer (CRC) cells activated the endogenous Ascl2 expression via a direct autoactivatory loop, including Ascl2 binding to its own promoter and further transcriptional activation. Higher Ascl2 expression in human CRC cancerous tissues led to greater enrichment in Ascl2 immunoprecipitated DNA within the Ascl2 promoter in the CRC cancerous sample than the peri-cancerous mucosa. Ascl2 binding to its own promoter and inducing further transcriptional activation of the Ascl2 gene was predominant in the CD133+CD44+ CRC population. R-spondin1/Wnt activated Ascl2 expression dose-dependently in the CD133+CD44+ CRC population, but not in the CD133-CD44- CRC population, which was caused by differences in Ascl2 autoregulation under R-spondin1/Wnt activation. R-spondin1/Wnt treatment in the CD133+CD44+ or CRC CD133-CD44- populations exerted a different pattern of stemness maintenance, which was defined by alterations of the mRNA levels of stemness-associated genes, the protein expression levels (Bmi1, C-myc, Oct-4 and Nanog) and tumorsphere formation. The results indicated that Ascl2 autoregulation formed a transcriptional switch that was enhanced by Wnt signaling in the CD133+CD44+ CRC population, thus conferring their self-renewal.
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Affiliation(s)
- Jun Ye
- a Institute of Gastroenterology of PLA, Southwest Hospital , Third Military Medical University , Chongqing , China
| | - Shanxi Liu
- a Institute of Gastroenterology of PLA, Southwest Hospital , Third Military Medical University , Chongqing , China
| | - Yangyang Shang
- a Institute of Gastroenterology of PLA, Southwest Hospital , Third Military Medical University , Chongqing , China
| | - Haoyuan Chen
- a Institute of Gastroenterology of PLA, Southwest Hospital , Third Military Medical University , Chongqing , China
| | - Rongquan Wang
- a Institute of Gastroenterology of PLA, Southwest Hospital , Third Military Medical University , Chongqing , China
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28
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Bu P, Chen KY, Xiang K, Johnson C, Crown SB, Rakhilin N, Ai Y, Wang L, Xi R, Astapova I, Han Y, Li J, Barth BB, Lu M, Gao Z, Mines R, Zhang L, Herman M, Hsu D, Zhang GF, Shen X. Aldolase B-Mediated Fructose Metabolism Drives Metabolic Reprogramming of Colon Cancer Liver Metastasis. Cell Metab 2018; 27:1249-1262.e4. [PMID: 29706565 PMCID: PMC5990465 DOI: 10.1016/j.cmet.2018.04.003] [Citation(s) in RCA: 155] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 01/18/2018] [Accepted: 04/02/2018] [Indexed: 02/07/2023]
Abstract
Cancer metastasis accounts for the majority of cancer-related deaths and remains a clinical challenge. Metastatic cancer cells generally resemble cells of the primary cancer, but they may be influenced by the milieu of the organs they colonize. Here, we show that colorectal cancer cells undergo metabolic reprogramming after they metastasize and colonize the liver, a key metabolic organ. In particular, via GATA6, metastatic cells in the liver upregulate the enzyme aldolase B (ALDOB), which enhances fructose metabolism and provides fuel for major pathways of central carbon metabolism during tumor cell proliferation. Targeting ALDOB or reducing dietary fructose significantly reduces liver metastatic growth but has little effect on the primary tumor. Our findings suggest that metastatic cells can take advantage of reprogrammed metabolism in their new microenvironment, especially in a metabolically active organ such as the liver. Manipulation of involved pathways may affect the course of metastatic growth.
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Affiliation(s)
- Pengcheng Bu
- Key Laboratory of RNA Biology, Key Laboratory of Protein and Peptide Pharmaceutical, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA.
| | - Kai-Yuan Chen
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Kun Xiang
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Christelle Johnson
- Department of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA; School of Electrical and Computer Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Scott B Crown
- Molecular Physiology Institute, Duke University, Durham, NC 27701, USA
| | - Nikolai Rakhilin
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; School of Electrical and Computer Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Yiwei Ai
- Department of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Lihua Wang
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Rui Xi
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Inna Astapova
- Molecular Physiology Institute, Duke University, Durham, NC 27701, USA; Department of Medicine, Duke University, Durham, NC 27701, USA
| | - Yan Han
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Jiahe Li
- Department of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Bradley B Barth
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Min Lu
- Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - Ziyang Gao
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Robert Mines
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Liwen Zhang
- Key Laboratory of RNA Biology, Key Laboratory of Protein and Peptide Pharmaceutical, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mark Herman
- Molecular Physiology Institute, Duke University, Durham, NC 27701, USA; Department of Medicine, Duke University, Durham, NC 27701, USA
| | - David Hsu
- Department of Medicine, Duke University, Durham, NC 27701, USA; Division of Medical Oncology, Duke Cancer Institute, Duke University, Durham, NC 27710, USA
| | - Guo-Fang Zhang
- Molecular Physiology Institute, Duke University, Durham, NC 27701, USA; Department of Medicine, Duke University, Durham, NC 27701, USA
| | - Xiling Shen
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA.
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Abstract
High-throughput biological technologies are routinely used to generate gene expression profiling or cytogenetics data. To achieve high performance, methods available in the literature become more specialized and often require high computational resources. Here, we propose a new versatile method based on the data-ordering rank values. We use linear algebra, the Perron-Frobenius theorem and also extend a method presented earlier for searching differentially expressed genes for the detection of recurrent copy number aberration. A result derived from the proposed method is a one-sample Student's t-test based on rank values. The proposed method is to our knowledge the only that applies to gene expression profiling and to cytogenetics data sets. This new method is fast, deterministic, and requires a low computational load. Probabilities are associated with genes to allow a statistically significant subset selection in the data set. Stability scores are also introduced as quality parameters. The performance and comparative analyses were carried out using real data sets. The proposed method can be accessed through an R package available from the CRAN (Comprehensive R Archive Network) website: https://cran.r-project.org/web/packages/fcros .
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Affiliation(s)
- Doulaye Dembélé
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U 1258, Université de Strasbourg, Illkirch-Graffenstaden, France
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30
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The intestinal stem cell regulating gene ASCL2 is required for L1-mediated colon cancer progression. Cancer Lett 2018; 424:9-18. [PMID: 29551399 DOI: 10.1016/j.canlet.2018.03.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/07/2018] [Accepted: 03/14/2018] [Indexed: 12/27/2022]
Abstract
Aberrant Wnt/β-catenin signaling is a common event during human colorectal cancer (CRC) development. Previously, we characterized members of the L1 family of cell adhesion receptors as targets of β-catenin-LEF1/TCF transactivation that are expressed at the invasive CRC tissue edge. Overexpression of L1 in CRC cells confers enhanced motility, tumorigenesis and liver metastasis. We identified several downstream targets of L1-mediated signaling that are considered key intestinal stem cell signature genes. Here, we investigated the involvement of ASCL2, a Wnt target gene and key determinant of intestinal stem cell state, in L1-mediated CRC progression. In L1 overexpressing CRC cells we found an increase in ASCL2, a decrease in E-cadherin and accumulation of nuclear β-catenin, β-catenin-LEF1/TCF transactivation and target gene expression. The increase in ASCL2 by L1 overexpression enhanced ASCL2 target gene expression, conferred increased motility, tumorigenesis and metastasis, similar to L1 overexpression. Suppression of ASCL2 in cells expressing L1 blocked these tumorigenic properties. In human CRC tissue, ASCL2 was detected in the nuclei of cells at invasive areas of the tumor that also expressed L1. The results suggest that increased ASCL2 expression is a critical step in L1-mediated CRC progression.
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31
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Zhi J, Sun J, Wang Z, Ding W. Support vector machine classifier for prediction of the metastasis of colorectal cancer. Int J Mol Med 2018; 41:1419-1426. [PMID: 29328363 PMCID: PMC5819940 DOI: 10.3892/ijmm.2018.3359] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 12/13/2017] [Indexed: 12/17/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common cancers and a major cause of mortality. The present study aimed to identify potential biomarkers for CRC metastasis and uncover the mechanisms underlying the etiology of the disease. The five datasets GSE68468, GSE62321, GSE22834, GSE14297 and GSE6988 were utilized in the study, all of which contained metastatic and non-metastatic CRC samples. Among them, three datasets were integrated via meta-analysis to identify the differentially expressed genes (DEGs) between the two types of samples. A protein-protein interaction (PPI) network was constructed for these DEGs. Candidate genes were then selected by the support vector machine (SVM) classifier based on the betweenness centrality (BC) algorithm. A CRC dataset from The Cancer Genome Atlas database was used to evaluate the accuracy of the SVM classifier. Pathway enrichment analysis was carried out for the SVM-classified gene signatures. In total, 358 DEGs were identified by meta‑analysis. The top ten nodes in the PPI network with the highest BC values were selected, including cAMP responsive element binding protein 1 (CREB1), cullin 7 (CUL7) and signal sequence receptor 3 (SSR3). The optimal SVM classification model was established, which was able to precisely distinguish between the metastatic and non-metastatic samples. Based on this SVM classifier, 40 signature genes were identified, which were mainly enriched in protein processing in endoplasmic reticulum (e.g., SSR3), AMPK signaling pathway (e.g., CREB1) and ubiquitin mediated proteolysis (e.g., FBXO2, CUL7 and UBE2D3) pathways. In conclusion, the SVM-classified genes, including CREB1, CUL7 and SSR3, precisely distinguished the metastatic CRC samples from the non-metastatic ones. These genes have the potential to be used as biomarkers for the prognosis of metastatic CRC.
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Affiliation(s)
- Jiajun Zhi
- Department of Colorectal Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, P.R. China
| | - Jiwei Sun
- Department of Colorectal Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, P.R. China
| | - Zhongchuan Wang
- Department of Colorectal Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, P.R. China
| | - Wenjun Ding
- Department of Colorectal Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, P.R. China
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32
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Circulating tumor cells exhibit stem cell characteristics in an orthotopic mouse model of colorectal cancer. Oncotarget 2017; 7:27232-42. [PMID: 27029058 PMCID: PMC5053645 DOI: 10.18632/oncotarget.8373] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 03/14/2016] [Indexed: 12/22/2022] Open
Abstract
The prognosis of colorectal cancer (CRC) is closely linked to the occurrence of distant metastases, which putatively develop from circulating tumor cells (CTCs) shed into circulation by the tumor. As far more CTCs are shed than eventually metastases develop, only a small subfraction of CTCs harbor full tumorigenic potential. The aim of this study was to further characterize CRC-derived CTCs to eventually identify the clinically relevant subfraction of CTCs.We established an orthotopic mouse model of CRC which reliably develops metastases and CTCs. We were able to culture the resulting CTCs in vitro, and demonstrated their tumor-forming capacity when re-injected into mice. The CTCs were then subjected to qPCR expression profiling, revealing downregulation of epithelial and proliferation markers. Genes associated with cell-cell adhesion (claudin-7, CD166) were significantly downregulated, indicating a more metastatic phenotype of CTCs compared to bulk tumor cells derived from hepatic metastases. The stem cell markers DLG7 and BMI1 were significantly upregulated in CTC, indicating a stem cell-like phenotype and increased capacity of tumor formation and self-renewal. In concert with their in vitro and in vivo tumorigenicity, these findings indicate stem cell properties of mouse-derived CTCs.In conclusion, we developed an orthotopic mouse model of CRC recapitulating the process of CRC dissemination. CTCs derived from this model exhibit stem-cell like characteristics and are able to form colonies in vitro and tumors in vivo. Our results provide new insight into the biology of CRC-derived CTCs and may provide new therapeutic targets in the metastatic cascade of CRC.
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33
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Wei X, Ye J, Shang Y, Chen H, Liu S, Liu L, Wang R. Ascl2 activation by YAP1/KLF5 ensures the self-renewability of colon cancer progenitor cells. Oncotarget 2017; 8:109301-109318. [PMID: 29312609 PMCID: PMC5752522 DOI: 10.18632/oncotarget.22673] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 11/08/2017] [Indexed: 01/09/2023] Open
Abstract
Achaete scute-like 2 (Ascl2) is the Wnt signaling target, its regulation by other signaling is undefined. Now we demonstrated that CD133+/CD44+ cell population from HT-29 or Caco-2 cells exhibited cancer stem cell (CSC) properties with highly expressed Ascl2, which is related to the Hippo signaling pathway. YAP1 interference in CD133+/CD44+ HT-29 or Caco-2 cells reduced their proliferation, colony-forming ability and tumorsphere formation in vitro and inhibited the ‘stemness’-associated genes and Ascl2 expression. Enforcing YAP1 expression in HT-29 or Caco-2 cells triggered the opposite changes. Ascl2 interference reversed the phenotype of YAP1-enforced expressed HT-29 or Caco-2 cells. Krüppel-like factor 5 (KLF5) protein, not KLF5 mRNA levels, were increased due to YAP1 overexpression which is reported to prevent KLF5 degradation. Co-immunoprecipitation (Co-IP) assays demonstrated that YAP1 bound with KLF5 in HT-29 and Caco-2 cells. Luciferase and chromatin immunoprecipitation (ChIP) assays indicated that both YAP1 and KLF5 bound to the first two loci with GC-boxes in Ascl2 promoter and induced Ascl2 transcription. The decreased Ascl2 transcription by YAP1 interference required an intact KLF5 binding site (GC-box) within Ascl2 promoter, KLF5 knockdown reduced YAP1 binding and Ascl2 luciferase reporter activity upon YAP1 overexpression. Positive correlation among YAP1 and Ascl2 mRNA levels was observed in colorectal cancer (CRC) samples. Thus, our study demonstrated that Ascl2, a fate decider of CRC progenitor cells can be activated by the Hippo signaling pathway in CRC progenitor cells, and ensured their self-renewability.
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Affiliation(s)
- Xiaolong Wei
- Institute of Gastroenterology of PLA, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Jun Ye
- Institute of Gastroenterology of PLA, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Yangyang Shang
- Institute of Gastroenterology of PLA, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Haoyuan Chen
- Institute of Gastroenterology of PLA, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Shanxi Liu
- Institute of Gastroenterology of PLA, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Li Liu
- Institute of Gastroenterology of PLA, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Rongquan Wang
- Institute of Gastroenterology of PLA, Southwest Hospital, Third Military Medical University, Chongqing, China
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34
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Liu G, Dong C, Wang X, Hou G, Zheng Y, Xu H, Zhan X, Liu L. Regulatory activity based risk model identifies survival of stage II and III colorectal carcinoma. Oncotarget 2017; 8:98360-98370. [PMID: 29228695 PMCID: PMC5716735 DOI: 10.18632/oncotarget.21312] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 08/26/2017] [Indexed: 02/07/2023] Open
Abstract
Clinical and pathological indicators are inadequate for prognosis of stage II and III colorectal carcinoma (CRC). In this study, we utilized the activity of regulatory factors, univariate Cox regression and random forest for variable selection and developed a multivariate Cox model to predict the overall survival of Stage II/III colorectal carcinoma in GSE39582 datasets (469 samples). Patients in low-risk group showed a significant longer overall survival and recurrence-free survival time than those in high-risk group. This finding was further validated in five other independent datasets (GSE14333, GSE17536, GSE17537, GSE33113, and GSE37892). Besides, associations between clinicopathological information and risk score were analyzed. A nomogram including risk score was plotted to facilitate the utilization of risk score. The risk score model is also demonstrated to be effective on predicting both overall and recurrence-free survival of chemotherapy received patients. After performing Gene Set Enrichment Analysis (GSEA) between high and low risk groups, we found that several cell-cell interaction KEGG pathways were identified. Funnel plot results showed that there was no publication bias in these datasets. In summary, by utilizing the regulatory activity in stage II and III colorectal carcinoma, the risk score successfully predicts the survival of 1021 stage II/III CRC patients in six independent datasets.
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Affiliation(s)
- Gang Liu
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Chuanpeng Dong
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xing Wang
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Guojun Hou
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Yu Zheng
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Huilin Xu
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xiaohui Zhan
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lei Liu
- Shanghai Public Health Clinical Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
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Hartung F, Wang Y, Aronow B, Weber GF. A core program of gene expression characterizes cancer metastases. Oncotarget 2017; 8:102161-102175. [PMID: 29254233 PMCID: PMC5731943 DOI: 10.18632/oncotarget.22240] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 08/31/2017] [Indexed: 11/25/2022] Open
Abstract
While aberrant expression or splicing of metastasis genes conveys to cancers the ability to break through tissue barriers and disseminate, the genetic basis for organ preference in metastasis formation has remained incompletely understood. Utilizing the gene expression profiles from 653 GEO datasets, we investigate whether the signatures by diverse cancers in various metastatic sites display common features. We corroborate the meta-analysis in a murine model. Metastases are generally characterized by a core program of gene expression that induces the oxidative metabolism, activates vascularization/tissue remodeling, silences extracellular matrix interactions, and alters ion homeostasis. This program distinguishes metastases from their originating primary tumors as well as from their target host tissues. Site-selectivity is accomplished through specific components that adjust to the target micro-environment. The same functional groups of gene expression programs are activated in the metastases of B16-F10 cells to various target organs. It remains to be investigated whether these genetic signatures precede implantation and thus determine organ preference or are shaped by the target site and are thus a consequence of implantation. Conceivably, chemotherapy of disseminated cancer might be more efficacious if selected to match the genetic makeup of the metastases rather than the organ of origin by the primary tumor.
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Affiliation(s)
- Franz Hartung
- University of Cincinnati Academic Health Center, Cincinnati, OH, USA
| | - Yunguan Wang
- Computational Medicine Center, Cincinnati Children's Hospital, Cincinnati, OH, USA
| | - Bruce Aronow
- Computational Medicine Center, Cincinnati Children's Hospital, Cincinnati, OH, USA
| | - Georg F Weber
- University of Cincinnati Academic Health Center, Cincinnati, OH, USA
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36
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Østrup O, Dagenborg VJ, Rødland EA, Skarpeteig V, Silwal-Pandit L, Grzyb K, Berstad AE, Fretland ÅA, Mælandsmo GM, Børresen-Dale AL, Ree AH, Edwin B, Nygaard V, Flatmark K. Molecular signatures reflecting microenvironmental metabolism and chemotherapy-induced immunogenic cell death in colorectal liver metastases. Oncotarget 2017; 8:76290-76304. [PMID: 29100312 PMCID: PMC5652706 DOI: 10.18632/oncotarget.19350] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/26/2017] [Indexed: 01/05/2023] Open
Abstract
Background Metastatic colorectal cancer (CRC) is associated with highly variable clinical outcome and response to therapy. The recently identified consensus molecular subtypes (CMS1-4) have prognostic and therapeutic implications in primary CRC, but whether these subtypes are valid for metastatic disease is unclear. We performed multi-level analyses of resectable CRC liver metastases (CLM) to identify molecular characteristics of metastatic disease and evaluate the clinical relevance. Methods In this ancillary study to the Oslo-CoMet trial, CLM and tumor-adjacent liver tissue from 46 patients were analyzed by profiling mutations (targeted sequencing), genome-wide copy number alteration (CNAs), and gene expression. Results Somatic mutations and CNAs detected in CLM were similar to reported primary CRC profiles, while CNA profiles of eight metastatic pairs suggested intra-patient divergence. A CMS classifier tool applied to gene expression data, revealed the cohort to be highly enriched for CMS2. Hierarchical clustering of genes with highly variable expression identified two subgroups separated by high or low expression of 55 genes with immune-related and metabolic functions. Importantly, induction of genes and pathways associated with immunogenic cell death (ICD) was identified in metastases exposed to neoadjuvant chemotherapy (NACT). Conclusions The uniform classification of CLM by CMS subtyping may indicate that novel class discovery approaches need to be explored to uncover clinically useful stratification of CLM. Detected gene expression signatures support the role of metabolism and chemotherapy in shaping the immune microenvironment of CLM. Furthermore, the results point to rational exploration of immune modulating strategies in CLM, particularly by exploiting NACT-induced ICD.
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Affiliation(s)
- Olga Østrup
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Vegar Johansen Dagenborg
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Einar Andreas Rødland
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Veronica Skarpeteig
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Laxmi Silwal-Pandit
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Krzysztof Grzyb
- Department of Pathology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Audun Elnæs Berstad
- Department of Radiology, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Åsmund Avdem Fretland
- Department of Hepato-Pancreato-Biliary Surgery, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- The Intervention Centre, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Gunhild Mari Mælandsmo
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- Department of Pharmacy, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Anne-Lise Børresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Anne Hansen Ree
- Department of Oncology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Bjørn Edwin
- Department of Hepato-Pancreato-Biliary Surgery, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- The Intervention Centre, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Vigdis Nygaard
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Kjersti Flatmark
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- Department of Gastroenterological Surgery, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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Shang Y, Chen H, Ye J, Wei X, Liu S, Wang R. HIF-1α/Ascl2/miR-200b regulatory feedback circuit modulated the epithelial-mesenchymal transition (EMT) in colorectal cancer cells. Exp Cell Res 2017; 360:243-256. [PMID: 28899657 DOI: 10.1016/j.yexcr.2017.09.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 09/06/2017] [Accepted: 09/08/2017] [Indexed: 12/17/2022]
Abstract
We have reported that Achaete scute-like 2 (Ascl2) transcriptionally repressed miR-200 family members and affected the epithelial-mesenchymal transition (EMT)-mesenchymal-epithelial transition (MET) plasticity in colorectal cancer (CRC) cells. However, little is known about the regulation of the Ascl2/miR-200 axis. Here, we found that hypoxia inducible factor-1α (HIF-1α) mRNA levels were positively correlated with Ascl2 mRNA levels and inversely correlated with miR-200b in CRC samples. Mechanistically, we showed that Ascl2 was a downstream target of HIF-1α and had a critical role in the EMT phenotype induced by hypoxia or HIF-1α over-expression. Hypoxia or HIF-1α over-expression activated Ascl2 expression in CRC cells in a direct transcriptional mechanism via binding with the hypoxia-response element (HRE) at the proximal Ascl2 promoter. HIF-1α-induced Ascl2 expression repressed miR-200b expression to induce EMT occurrence. Furthermore, we found HIF-1α was a direct target of miR-200b. MiR-200b bound with the 3'-UTR of HIF-1α in CRC cells. HIF-1α/Ascl2/miR-200b regulatory feedback circuit modulated the EMT-MET plasticity of CRC cells. Our results confirmed a novel HIF-1α/Ascl2/miR-200b regulatory feedback circuit in modulating EMT-MET plasticity of CRC cells, which could serve as a possible therapeutic target.
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Affiliation(s)
- Yangyang Shang
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing 400038, PR China
| | - Haoyuan Chen
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing 400038, PR China
| | - Jun Ye
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing 400038, PR China
| | - Xiaolong Wei
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing 400038, PR China
| | - Shanxi Liu
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing 400038, PR China
| | - Rongquan Wang
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing 400038, PR China.
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Yang Q, Bavi P, Wang JY, Roehrl MH. Immuno-proteomic discovery of tumor tissue autoantigens identifies olfactomedin 4, CD11b, and integrin alpha-2 as markers of colorectal cancer with liver metastases. J Proteomics 2017; 168:53-65. [DOI: 10.1016/j.jprot.2017.06.021] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 06/03/2017] [Accepted: 06/26/2017] [Indexed: 11/29/2022]
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Fowler KL, Wieck MM, Hilton AE, Hou X, Schlieve CR, Grikscheit TC. Marked stem/progenitor cell expansion occurs early after murine ileostomy: a new model. J Surg Res 2017; 220:182-196. [PMID: 29180181 DOI: 10.1016/j.jss.2017.06.079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 06/09/2017] [Accepted: 06/28/2017] [Indexed: 01/16/2023]
Abstract
BACKGROUND Improving treatment for short bowel syndrome requires a better understanding of how intestinal adaptation is affected by factors like mechanoluminal stimulation. We hypothesized that in mice, luminal diversion via an ileostomy would drive adaptive changes similar to those seen in human intestine after diversion while offering the opportunity to study the immediate events after resection that precede intestinal adaptation. MATERIALS AND METHODS With Institutional Animal Care and Use Committee approval, a distal ileostomy with a long distal Hartman's was created in 9- to 14-week-old C57/B6 mice (n = 8). Control mice only had a midline laparotomy without stoma formation (n = 5). A rim of tissue from the proximal stoma was resected as a historical control for the proximal segment. Postoperatively, mice received a high-protein liquid diet and water ad libitum. On day 3, tissue from both the proximal and distal limbs were collected for histologic and RNA analysis. Morphometric measures, immunofluorescent antigen detection, and RNA expression were compared with Student paired t-tests with a P value < 0.05 considered significant. RESULTS At 3 d, survival for mice with an ileostomy was 87% and average weight loss was 12.5% of initial weight compared to 6.05% for control mice. Compared to the distal limb, the proximal limb in mice with an ileostomy demonstrated significantly taller villi with deeper and wider crypts. The proximal limb also had decreased expression of intestinal stem cell markers lgr5, bmi1, sox9, and ascl2. Fewer goblet and enteroendocrine cells per hemivillus were also noted in the proximal limb. In control mice, none of these measures were significant between proximal and distal ileum except for villus height. CONCLUSIONS This new murine ileostomy model allows study of intestinal adaptation without intestinal anastomosis, which can be technically challenging and morbid.
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Affiliation(s)
- Kathryn L Fowler
- Developmental Biology and Regenerative Medicine Program, The Saban Research Institute at Children's Hospital Los Angeles, Los Angeles, California
| | - Minna M Wieck
- Developmental Biology and Regenerative Medicine Program, The Saban Research Institute at Children's Hospital Los Angeles, Los Angeles, California; Division of Pediatric Surgery, Department of Surgery, Children's Hospital Los Angeles, Los Angeles, California
| | - Ashley E Hilton
- Keck Medical School, University of Southern California, Los Angeles, California
| | - Xiaogang Hou
- Developmental Biology and Regenerative Medicine Program, The Saban Research Institute at Children's Hospital Los Angeles, Los Angeles, California
| | - Christopher R Schlieve
- Developmental Biology and Regenerative Medicine Program, The Saban Research Institute at Children's Hospital Los Angeles, Los Angeles, California; Division of Pediatric Surgery, Department of Surgery, Children's Hospital Los Angeles, Los Angeles, California
| | - Tracy C Grikscheit
- Developmental Biology and Regenerative Medicine Program, The Saban Research Institute at Children's Hospital Los Angeles, Los Angeles, California; Division of Pediatric Surgery, Department of Surgery, Children's Hospital Los Angeles, Los Angeles, California; Keck Medical School, University of Southern California, Los Angeles, California.
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Roles of Wnt Target Genes in the Journey of Cancer Stem Cells. Int J Mol Sci 2017; 18:ijms18081604. [PMID: 28757546 PMCID: PMC5577996 DOI: 10.3390/ijms18081604] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 07/19/2017] [Accepted: 07/20/2017] [Indexed: 12/12/2022] Open
Abstract
The importance of Wnt/β-catenin signaling in cancer stem cells (CSCs) has been acknowledged; however, the mechanism through which it regulates the biological function of CSCs and promotes cancer progression remains elusive. Hence, to understand the intricate mechanism by which Wnt controls stemness, the specific downstream target genes of Wnt were established by analyzing the genetic signatures of multiple types of metastatic cancers based on gene set enrichment. By focusing on the molecular function of Wnt target genes, the biological roles of Wnt were interpreted in terms of CSC dynamics from initiation to metastasis. Wnt signaling participates in cancer initiation by generating CSCs from normal stem cells or non-CSCs and augmenting persistent growth at the primary region, which is resistant to anti-cancer therapy. Moreover, it assists CSCs in invading nearby tissues and in entering the blood stream, during which the negative feedback of the Wnt signaling pathway maintains CSCs in a dormant state that is suitable for survival. When CSCs arrive at distant organs, another burst of Wnt signaling induces CSCs to succeed in re-initiation and colonization. This comprehensive understanding of Wnt target genes provides a plausible explanation for how Wnt allows CSCs variation during cancer progression.
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Kanda Y, Osaki M, Onuma K, Sonoda A, Kobayashi M, Hamada J, Nicolson GL, Ochiya T, Okada F. Amigo2-upregulation in Tumour Cells Facilitates Their Attachment to Liver Endothelial Cells Resulting in Liver Metastases. Sci Rep 2017; 7:43567. [PMID: 28272394 PMCID: PMC5341090 DOI: 10.1038/srep43567] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 01/25/2017] [Indexed: 02/06/2023] Open
Abstract
Since liver metastasis is the main cause of death in cancer patients, we attempted to identify the driver gene involved. QRsP-11 fibrosarcoma cells were injected into the spleens of syngeneic mice to isolate tumour sub-populations that colonize the liver. Cells from liver metastatic nodules were established and subsequently injected intrasplenically for selection. After 12 cycles, the cell subline LV12 was obtained. Intravenous injection of LV12 cells produced more liver metastases than QRsP-11 cells, whereas the incidence of lung metastases was similar to that of QRsP-11 cells. LV12 cells adhered to liver-derived but not to lung-derived endothelial cells. DNA chip analysis showed that amphoterin-induced gene and open reading frame 2 (Amigo2) was overexpressed in LV12 cells. siRNA-mediated knockdown of Amigo2 expression in LV12 cells attenuated liver endothelial cell adhesion. Ex vivo imaging showed that suppression of Amigo2 in luciferase-expressing LV12 cells reduced attachment/metastasis to liver to the same level as that observed with QRsP-11 cells. Forced expression of Amigo2 in QRsP-11 cells increased liver endothelial cell adhesion and liver metastasis. Additionally, Amigo2 expression in human cancers was higher in liver metastatic lesions than in primary lesions. Thus, Amigo2 regulated tumour cell adhesion to liver endothelial cells and formation of liver metastases.
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Affiliation(s)
- Yusuke Kanda
- Division of Pathological Biochemistry, Tottori University Faculty of Medicine, Yonago, Japan
| | - Mitsuhiko Osaki
- Division of Pathological Biochemistry, Tottori University Faculty of Medicine, Yonago, Japan.,Chromosome Engineering Research Center, Tottori University, Yonago, Japan
| | - Kunishige Onuma
- Division of Pathological Biochemistry, Tottori University Faculty of Medicine, Yonago, Japan
| | - Ayana Sonoda
- Division of Pathological Biochemistry, Tottori University Faculty of Medicine, Yonago, Japan
| | - Masanobu Kobayashi
- Health Sciences University of Hokkaido, School of Nursing and Social Services, Ishikari-Tobetsu, Japan
| | - Junichi Hamada
- Health Sciences University of Hokkaido, School of Nursing and Social Services, Ishikari-Tobetsu, Japan
| | - Garth L Nicolson
- Department of Molecular Pathology, The Institute for Molecular Medicine, South Laguna Beach, CA, USA
| | - Takahiro Ochiya
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, Japan
| | - Futoshi Okada
- Division of Pathological Biochemistry, Tottori University Faculty of Medicine, Yonago, Japan.,Chromosome Engineering Research Center, Tottori University, Yonago, Japan
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42
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Blaj C, Schmidt EM, Lamprecht S, Hermeking H, Jung A, Kirchner T, Horst D. Oncogenic Effects of High MAPK Activity in Colorectal Cancer Mark Progenitor Cells and Persist Irrespective of RAS Mutations. Cancer Res 2017; 77:1763-1774. [PMID: 28202525 DOI: 10.1158/0008-5472.can-16-2821] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 12/16/2016] [Accepted: 01/10/2017] [Indexed: 12/28/2022]
Abstract
About 40% of colorectal cancers have mutations in KRAS accompanied by downstream activation of MAPK signaling, which promotes tumor invasion and progression. Here, we report that MAPK signaling shows strong intratumoral heterogeneity and unexpectedly remains regulated in colorectal cancer irrespective of KRAS mutation status. Using primary colorectal cancer tissues, xenograft models, and MAPK reporter constructs, we showed that tumor cells with high MAPK activity resided specifically at the leading tumor edge, ceased to proliferate, underwent epithelial-mesenchymal transition (EMT), and expressed markers related to colon cancer stem cells. In KRAS-mutant colon cancer, regulation of MAPK signaling was preserved through remaining wild-type RAS isoforms. Moreover, using a lineage tracing strategy, we provide evidence that high MAPK activity marked a progenitor cell compartment of growth-fueling colon cancer cells in vivo Our results imply that differential MAPK signaling balances EMT, cancer stem cell potential, and tumor growth in colorectal cancer. Cancer Res; 77(7); 1763-74. ©2017 AACR.
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Affiliation(s)
- Cristina Blaj
- Pathologisches Institut, Ludwig-Maximilians-Universität München, München, Germany
| | - Eva Marina Schmidt
- Pathologisches Institut, Ludwig-Maximilians-Universität München, München, Germany
| | - Sebastian Lamprecht
- Pathologisches Institut, Ludwig-Maximilians-Universität München, München, Germany
| | - Heiko Hermeking
- Pathologisches Institut, Ludwig-Maximilians-Universität München, München, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas Jung
- Pathologisches Institut, Ludwig-Maximilians-Universität München, München, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Kirchner
- Pathologisches Institut, Ludwig-Maximilians-Universität München, München, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Horst
- Pathologisches Institut, Ludwig-Maximilians-Universität München, München, Germany. .,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
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Dienstmann R, Vermeulen L, Guinney J, Kopetz S, Tejpar S, Tabernero J. Consensus molecular subtypes and the evolution of precision medicine in colorectal cancer. Nat Rev Cancer 2017; 17:79-92. [PMID: 28050011 DOI: 10.1038/nrc.2016.126] [Citation(s) in RCA: 529] [Impact Index Per Article: 75.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Critical driver genomic events in colorectal cancer have been shown to affect the response to targeted agents that were initially developed under the 'one gene, one drug' paradigm of precision medicine. Our current knowledge of the complexity of the cancer genome, clonal evolution patterns under treatment pressure and pharmacodynamic effects of target inhibition support the transition from a one gene, one drug approach to a 'multi-gene, multi-drug' model when making therapeutic decisions. Better characterization of the transcriptomic subtypes of colorectal cancer, encompassing tumour, stromal and immune components, has revealed convergent pathway dependencies that mandate a 'multi-molecular' perspective for the development of therapies to treat this disease.
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Affiliation(s)
- Rodrigo Dienstmann
- Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona 08035, Spain
- Sage Bionetworks, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, WA 98109, Seattle, USA
| | - Louis Vermeulen
- Laboratory for Experimental Oncology and Radiobiology (LEXOR), Center for Experimental Molecular Medicine (CEMM), Academic Medical Center (AMC), University of Amsterdam, 1012 WX Amsterdam, The Netherlands
| | - Justin Guinney
- Sage Bionetworks, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, WA 98109, Seattle, USA
| | - Scott Kopetz
- The University of Texas, M.D. Anderson Cancer Center, 1515 Holcombe Blvd, Houston, Texas 77030, USA
| | - Sabine Tejpar
- Digestive Oncology Unit, University Hospital Gasthuisberg, Herestraat 49, 3000 Leuven, Belgium
| | - Josep Tabernero
- Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona 08035, Spain
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Rokavec M, Horst D, Hermeking H. Cellular Model of Colon Cancer Progression Reveals Signatures of mRNAs, miRNA, lncRNAs, and Epigenetic Modifications Associated with Metastasis. Cancer Res 2017; 77:1854-1867. [DOI: 10.1158/0008-5472.can-16-3236] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 01/11/2017] [Indexed: 11/16/2022]
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A prognostic classifier for patients with colorectal cancer liver metastasis, based on AURKA, PTGS2 and MMP9. Oncotarget 2016; 7:2123-34. [PMID: 26497206 PMCID: PMC4811521 DOI: 10.18632/oncotarget.6188] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 10/04/2015] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Prognosis of patients with colorectal cancer liver metastasis (CRCLM) is estimated based on clinicopathological models. Stratifying patients based on tumor biology may have additional value. METHODS Tissue micro-arrays (TMAs), containing resected CRCLM and corresponding primary tumors from a multi-institutional cohort of 507 patients, were immunohistochemically stained for 18 candidate biomarkers. Cross-validated hazard rate ratios (HRRs) for overall survival (OS) and the proportion of HRRs with opposite effect (P(HRR < 1) or P(HRR > 1)) were calculated. A classifier was constructed by classification and regression tree (CART) analysis and its prognostic value determined by permutation analysis. Correlations between protein expression in primary tumor-CRCLM pairs were calculated. RESULTS Based on their putative prognostic value, EGFR (P(HRR < 1) = .02), AURKA (P(HRR < 1) = .02), VEGFA (P(HRR < 1) = .02), PTGS2 (P(HRR < 1) = .01), SLC2A1 (P(HRR > 1) < 01), HIF1α (P(HRR > 1) = .06), KCNQ1 (P(HRR > 1) = .09), CEA (P (HRR > 1) = .05) and MMP9 (P(HRR < 1) = .07) were included in the CART analysis (n = 201). The resulting classifier was based on AURKA, PTGS2 and MMP9 expression and was associated with OS (HRR 2.79, p < .001), also after multivariate analysis (HRR 3.57, p < .001). The prognostic value of the biomarker-based classifier was superior to the clinicopathological model (p = .001). Prognostic value was highest for colon cancer patients (HRR 5.71, p < .001) and patients not treated with systemic therapy (HRR 3.48, p < .01). Classification based on protein expression in primary tumors could be based on AURKA expression only (HRR 2.59, p = .04). CONCLUSION A classifier was generated for patients with CRCLM with improved prognostic value compared to the standard clinicopathological prognostic parameters, which may aid selection of patients who may benefit from adjuvant systemic therapy.
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46
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Zhao H, Shi ZZ, Jiang R, Zhao DB, Zhou HT, Liang JW, Bi XY, Zhao JJ, Li ZY, Zhou JG, Huang Z, Zhang YF, Wang J, Xu X, Cai Y, Wang MR, Zhang Y. Metastasis associated genomic aberrations in stage II rectal cancer. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0453-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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47
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Carrasco-Garcia E, Lopez L, Aldaz P, Arevalo S, Aldaregia J, Egaña L, Bujanda L, Cheung M, Sampron N, Garcia I, Matheu A. SOX9-regulated cell plasticity in colorectal metastasis is attenuated by rapamycin. Sci Rep 2016; 6:32350. [PMID: 27571710 PMCID: PMC5004104 DOI: 10.1038/srep32350] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 08/08/2016] [Indexed: 12/31/2022] Open
Abstract
The cancer stem cell (CSC) hypothesis proposes a hierarchical organization of tumors, in which stem-like cells sustain tumors and drive metastasis. The molecular mechanisms underlying the acquisition of CSCs and metastatic traits are not well understood. SOX9 is a transcription factor linked to stem cell maintenance and commonly overexpressed in solid cancers including colorectal cancer. In this study, we show that SOX9 levels are higher in metastatic (SW620) than in primary colorectal cancer cells (SW480) derived from the same patient. This elevated expression correlated with enhanced self-renewal activity. By gain and loss-of-function studies in SW480 and SW620 cells respectively, we reveal that SOX9 levels modulate tumorsphere formation and self-renewal ability in vitro and tumor initiation in vivo. Moreover, SOX9 regulates migration and invasion and triggers the transition between epithelial and mesenchymal states. These activities are partially dependent on SOX9 post-transcriptional modifications. Importantly, treatment with rapamycin inhibits self-renewal and tumor growth in a SOX9-dependent manner. These results identify a functional role for SOX9 in regulating colorectal cancer cell plasticity and metastasis, and provide a strong rationale for a rapamycin-based therapeutic strategy.
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Affiliation(s)
| | - Lidia Lopez
- Cellular Oncology group, Biodonostia Institute, San Sebastian, Spain
| | - Paula Aldaz
- Cellular Oncology group, Biodonostia Institute, San Sebastian, Spain
| | - Sara Arevalo
- Cellular Oncology group, Biodonostia Institute, San Sebastian, Spain
| | - Juncal Aldaregia
- Cellular Oncology group, Biodonostia Institute, San Sebastian, Spain
| | - Larraitz Egaña
- Cellular Oncology group, Biodonostia Institute, San Sebastian, Spain
| | - Luis Bujanda
- Department of Gastroenterology, Hospital Donostia and Instituto Biodonostia, University of the Basque Country, Centro de Investigacion Biomedica en Red en Enfermedades Hepaticas y Digestivas (CIBERehd), San Sebastian, Spain
| | - Martin Cheung
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Nicolas Sampron
- Cellular Oncology group, Biodonostia Institute, San Sebastian, Spain
| | - Idoia Garcia
- Cellular Oncology group, Biodonostia Institute, San Sebastian, Spain.,IKERBASQUE, Basque Foundation, Bilbao, Spain
| | - Ander Matheu
- Cellular Oncology group, Biodonostia Institute, San Sebastian, Spain.,IKERBASQUE, Basque Foundation, Bilbao, Spain
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Shang Y, Pan Q, Chen L, Ye J, Zhong X, Li X, Meng L, Guo J, Tian Y, He Y, Chen W, Peng Z, Wang R. Achaete scute-like 2 suppresses CDX2 expression and inhibits intestinal neoplastic epithelial cell differentiation. Oncotarget 2016; 6:30993-1006. [PMID: 26307678 PMCID: PMC4741583 DOI: 10.18632/oncotarget.5206] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 08/13/2015] [Indexed: 12/30/2022] Open
Abstract
The role of Achaete scute-like 2 (Ascl2) in colorectal cancer (CRC) cell differentiation is unknown. LS174T, HT-29 and Caco-2 cells have high Ascl2 expression, while Lovo and SW480 cells have low Ascl2 expression. LS174T and HT-29 cells with Ascl2 knockdown were transfected with caudal type homeobox 2 (CDX2) promoter constructs and used for luciferase assays and chromatin immunoprecipitation (ChIP) assays. Ascl2 knockdown promoted differentiation of CRC cells into a goblet cell phenotype, as determined by increased expression of MUC2, TFF3, and CDX2. Ascl2 knockdown activated CDX2 expression through a transcriptional mechanism via direct binding of Ascl2 to the proximal E-box of the CDX2 promoter. Ascl2 over-expression in Lovo and SW480 cells inhibited a goblet cell phenotype, as determined by reduced CDX2 and MUC2 expression. Inverse correlations between Ascl2 and CDX2, and Ascl2 and MUC2 mRNA levels, as well as Ascl2 and CDX2 protein levels were observed in CRC cancerous samples. This study demonstrates CDX2 repression by Ascl2 and highlights a role for Ascl2 in CRC cell differentiation. These findings suggest that the Ascl2/CDX2 axis may serve as a potential therapeutic target in colorectal cancer.
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Affiliation(s)
- Yangyang Shang
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, P. R. China
| | - Qiong Pan
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, P. R. China
| | - Lei Chen
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, P. R. China
| | - Jun Ye
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, P. R. China
| | - Xiaoli Zhong
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, P. R. China
| | - Xiaohuan Li
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, P. R. China
| | - Linkuan Meng
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, P. R. China
| | - Jin Guo
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, P. R. China
| | - Yin Tian
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, P. R. China
| | - Yonghong He
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, P. R. China
| | - Wensheng Chen
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, P. R. China
| | - Zhihong Peng
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, P. R. China
| | - Rongquan Wang
- Department of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, P. R. China
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IGF2 knockdown in two colorectal cancer cell lines decreases survival, adhesion and modulates survival-associated genes. Tumour Biol 2016; 37:12485-12495. [PMID: 27337954 DOI: 10.1007/s13277-016-5115-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 06/09/2016] [Indexed: 12/22/2022] Open
Abstract
Increased expression of insulin-like growth factor 2 (IGF2) is found in tumors of colorectal cancer (CRC) patients exhibiting a gained region on chromosome 11q15 and is implicated in poor patient survival. This study analyzes in vitro phenotypic- and gene expression changes associated with IGF2 shRNA-mediated knockdown. Initially, doxycycline inducible IGF2 knockdown cell lines were generated in the CRC cell lines SW480 and LS174T. The cells were analyzed for changes in proliferation, cell cycle, apoptosis, adhesion, and invasion. Expression profiling analysis was performed, and, for a subset of the identified genes, expression was validated by qRT-PCR and Western blot. IGF2 knockdown inhibited cell proliferation in both cell lines induced G1 cell cycle blockade and decreased adhesion to several extracellular matrix proteins. Knockdown of IGF2 did not alter invasiveness in SW480 cells, while a slight increase in apoptosis was seen only in the LS174T cell line. Knockdown of IGF2 in SW480 deregulated 58 genes, several of which were associated with proliferation and cell-cell/cell-ECM contacts. A subset of these genes, including CDK2, YAP1, and BIRC5 (Survivin), are members of a common network. This study supports the concept of direct autocrine/paracrine tumor cell activation through IGF2 and a shows role of IGF2 in CRC proliferation, adhesion and, to a limited extent, apoptosis.
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50
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A Positive Regulatory Loop between a Wnt-Regulated Non-coding RNA and ASCL2 Controls Intestinal Stem Cell Fate. Cell Rep 2016; 15:2588-96. [DOI: 10.1016/j.celrep.2016.05.038] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 04/04/2016] [Accepted: 05/06/2016] [Indexed: 12/21/2022] Open
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