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Claude E, Leclercq M, Thébault P, Droit A, Uricaru R. Optimizing hybrid ensemble feature selection strategies for transcriptomic biomarker discovery in complex diseases. NAR Genom Bioinform 2024; 6:lqae079. [PMID: 38993634 PMCID: PMC11237901 DOI: 10.1093/nargab/lqae079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 06/03/2024] [Accepted: 06/21/2024] [Indexed: 07/13/2024] Open
Abstract
Biomedical research takes advantage of omic data, such as transcriptomics, to unravel the complexity of diseases. A conventional strategy identifies transcriptomic biomarkers characterized by expression patterns associated with a phenotype by relying on feature selection approaches. Hybrid ensemble feature selection (HEFS) has become increasingly popular as it ensures robustness of the selected features by performing data and functional perturbations. However, it remains difficult to make the best suited choices at each step when designing such approaches. We conducted an extensive analysis of four possible HEFS scenarios for the identification of Stage IV colorectal, Stage I kidney and lung and Stage III endometrial cancer biomarkers from transcriptomic data. These scenarios investigate the use of two types of feature reduction by filters (differentially expressed genes and variance) conjointly with two types of resampling strategies (repeated holdout by distribution-balanced stratified and random stratified) for downstream feature selection through an aggregation of thousands of wrapped machine learning models. Based on our results, we emphasize the advantages of using HEFS approaches to identify complex disease biomarkers, given their ability to produce generalizable and stable results to both data and functional perturbations. Finally, we highlight critical issues that need to be considered in the design of such strategies.
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Affiliation(s)
- Elsa Claude
- Univ. Bordeaux, CNRS, Bordeaux INP, LaBRI, UMR 5800, F-33400 Talence, France
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Mickaël Leclercq
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Patricia Thébault
- Univ. Bordeaux, CNRS, Bordeaux INP, LaBRI, UMR 5800, F-33400 Talence, France
| | - Arnaud Droit
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Raluca Uricaru
- Univ. Bordeaux, CNRS, Bordeaux INP, LaBRI, UMR 5800, F-33400 Talence, France
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Iwabuchi E, Miki Y, Xu J, Kanai A, Ishida T, Sasano H, Suzuki T. Zinc transporter ZnT5 is associated with epithelial mesenchymal transition via SMAD1 in breast cancer. Int J Exp Pathol 2024. [PMID: 39138630 DOI: 10.1111/iep.12515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 07/16/2024] [Accepted: 07/27/2024] [Indexed: 08/15/2024] Open
Abstract
Zinc levels in breast cancer tissues have been reported to be higher than those in normal tissues. In addition, the expression levels of zinc transporters, including ZnT5 and ZnT6, are reportedly higher in breast cancer than in normal breast tissues. ZnT5 and ZnT6 also contribute to heterodimer formation and are involved in several biological functions. However, the functions of ZnT5 and ZnT6 heterodimers in breast cancer remain unknown. Therefore, we first investigated the immunolocalization of ZnT5 and ZnT6 in pathological breast cancer specimens and in MCF-7 and T-47D breast cancer cells. Next, we used small interfering RNA to assess cell viability and migration in ZnT5 knockdown MCF-7 and T-47D cells. Immunohistochemical analysis showed that the number of ZnT5-positive breast cancer cells was inversely correlated with the pathologic N factor status. ZnT5 knockdown had no effect on cell viability in the presence of 100 μM ZnCl2 in MCF-7 and T-47D cells. In a wound healing assay, 100 μM ZnCl2 treatment inhibited cell migration of MCF-7 and T-47D cells, whereas ZnT5 knockdown promoted cell migration, decreased E-cadherin expression and increased vimentin, slug and matrix metalloproteinase 9 expression. Antibody arrays showed that ZnT5 knockdown increased the expression of SMAD1, and that dorsomorphin treatment inhibited the promotion of migratory ability induced by ZnT5 knockdown. The results of this study revealed that both ZnT5 may be involved in less aggressive breast cancer subtypes, possibly through inhibition of cell migration.
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Affiliation(s)
- Erina Iwabuchi
- Department of Pathology and Histotechnology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yasuhiro Miki
- Department of Anatomic Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Junyao Xu
- The Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Zhejiang, Hangzhou, China
| | - Ayako Kanai
- Department of Breast Surgery, Hachinohe City Hospital, Aomori, Japan
| | - Takanori Ishida
- Department of Breast and Endocrine Surgical Oncology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hironobu Sasano
- Department of Anatomic Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takashi Suzuki
- Department of Pathology and Histotechnology, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Anatomic Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Pathology, Tohoku University Hospital, Sendai, Japan
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Lee YJ, Kim WR, Park EG, Lee DH, Kim JM, Shin HJ, Jeong HS, Roh HY, Kim HS. Exploring the Key Signaling Pathways and ncRNAs in Colorectal Cancer. Int J Mol Sci 2024; 25:4548. [PMID: 38674135 PMCID: PMC11050203 DOI: 10.3390/ijms25084548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/19/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
Colorectal cancer (CRC) is the third most prevalent cancer to be diagnosed, and it has a substantial mortality rate. Despite numerous studies being conducted on CRC, it remains a significant health concern. The disease-free survival rates notably decrease as CRC progresses, emphasizing the urgency for effective diagnostic and therapeutic approaches. CRC development is caused by environmental factors, which mostly lead to the disruption of signaling pathways. Among these pathways, the Wingless/Integrated (Wnt) signaling pathway, Phosphatidylinositol 3-kinase/protein kinase B/mammalian target of rapamycin (PI3K/AKT/mTOR) signaling pathway, Mitogen-Activated Protein Kinase (MAPK) signaling pathway, Transforming Growth Factor-β (TGF-β) signaling pathway, and p53 signaling pathway are considered to be important. These signaling pathways are also regulated by non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs). They have emerged as crucial regulators of gene expression in CRC by changing their expression levels. The altered expression patterns of these ncRNAs have been implicated in CRC progression and development, suggesting their potential as diagnostic and therapeutic targets. This review provides an overview of the five key signaling pathways and regulation of ncRNAs involved in CRC pathogenesis that are studied to identify promising avenues for diagnosis and treatment strategies.
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Affiliation(s)
- Yun Ju Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (Y.J.L.); (W.R.K.); (E.G.P.); (D.H.L.); (J.-m.K.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Woo Ryung Kim
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (Y.J.L.); (W.R.K.); (E.G.P.); (D.H.L.); (J.-m.K.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Eun Gyung Park
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (Y.J.L.); (W.R.K.); (E.G.P.); (D.H.L.); (J.-m.K.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Du Hyeong Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (Y.J.L.); (W.R.K.); (E.G.P.); (D.H.L.); (J.-m.K.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Jung-min Kim
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (Y.J.L.); (W.R.K.); (E.G.P.); (D.H.L.); (J.-m.K.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Hae Jin Shin
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (Y.J.L.); (W.R.K.); (E.G.P.); (D.H.L.); (J.-m.K.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Hyeon-su Jeong
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (Y.J.L.); (W.R.K.); (E.G.P.); (D.H.L.); (J.-m.K.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Hyun-Young Roh
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea
| | - Heui-Soo Kim
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea
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Mezher M, Abdallah S, Ashekyan O, Shoukari AA, Choubassy H, Kurdi A, Temraz S, Nasr R. Insights on the Biomarker Potential of Exosomal Non-Coding RNAs in Colorectal Cancer: An In Silico Characterization of Related Exosomal lncRNA/circRNA–miRNA–Target Axis. Cells 2023; 12:cells12071081. [PMID: 37048155 PMCID: PMC10093117 DOI: 10.3390/cells12071081] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/28/2023] [Accepted: 03/31/2023] [Indexed: 04/07/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common cancer types, ranking third after lung and breast cancers. As such, it demands special attention for better characterization, which may eventually result in the development of early detection strategies and preventive measures. Currently, components of bodily fluids, which may reflect various disease states, are being increasingly researched for their biomarker potential. One of these components is the circulating extracellular vesicles, namely, exosomes, which are demonstrated to carry various cargo. Of importance, the non-coding RNA cargo of circulating exosomes, especially long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and micro RNAs (miRNAs), may potentially serve as significant diagnostic and prognostic/predictive biomarkers. In this review, we present existing evidence on the diagnostic and prognostic/predictive biomarker value of exosomal non-coding RNAs in CRC. In addition, taking advantage of the miRNA sponging functionality of lncRNAs and circRNAs, we demonstrate an experimentally validated CRC exosomal non-coding RNA-regulated target gene axis benefiting from published miRNA sponging studies in CRC. Hence, we present a set of target genes and pathways downstream of the lncRNA/circRNA–miRNA–target axis along with associated significant Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, which may collectively serve to better characterize CRC and shed light on the significance of exosomal non-coding RNAs in CRC diagnosis and prognosis/prediction.
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Affiliation(s)
- Maria Mezher
- Department of Internal Medicine, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Samira Abdallah
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Ohanes Ashekyan
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Ayman Al Shoukari
- Department of Experimental Pathology, Immunology, and Microbiology, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Hayat Choubassy
- Faculty of Sciences, Lebanese University, Beirut P.O. Box 6573, Lebanon
| | - Abdallah Kurdi
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Sally Temraz
- Department of Internal Medicine, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Rihab Nasr
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
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Ding N, Luo H, Zhang T, Peng T, Yao Y, He Y. Correlation between SMADs and Colorectal Cancer Expression, Prognosis, and Immune Infiltrates. Int J Anal Chem 2023; 2023:8414040. [PMID: 36969909 PMCID: PMC10038740 DOI: 10.1155/2023/8414040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/20/2023] [Accepted: 02/03/2023] [Indexed: 03/26/2023] Open
Abstract
Background In recent years, the incidence and mortality of colorectal cancer (CRC) are increasing, and the 5-year survival rate of advanced metastatic CRC is poor. Small mothers against decapentaplegic (SMAD) superfamily are intracellular signal transduction proteins associated with the development and prognosis of a variety of tumors. At present, no study has systematically analysed the relationship between SMADs and CRC. Methods Here, R3.6.3 was used to analyse the expression of SMADs in pan-cancer and CRC. Protein expression of SMADs were analysed by Human Protein Atlas (HPA). Gene expression profiling interactive analysis (GEPIA) was used to evaluate the correlation between SMADs and tumor stage in CRC. The effect of R language and GEPIA on prognosis was analysed. Mutation rates of SMADs in CRC were determined by cBioPortal, and potentially related genes were predicted using GeneMANIA. R analysis was used to correlate immune cell infiltration in CRC. Results Both SMAD1 and SMAD2 were found to be weakly expressed in CRC and correlated with the immune invasion level. SMAD1 was correlated with patient prognosis, and SMAD2 was correlated with tumor stage. SMAD3, SMAD4, and SMAD7 were all expressed at low levels in CRC and associated with a variety of immune cells. SMAD3 and SMAD4 proteins were also expressed at low levels, and SMAD4 had the highest mutation rate. SMAD5 and SMAD6 were overexpressed in CRC, and SMAD6 was also associated with patient overall survival (OS) and CD8+ T cells, macrophages, and neutrophils. Conclusions Our results reveal innovative and strong evidence that SMADs can be used as biomarkers for the treatment and prognosis of CRC.
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Affiliation(s)
- Ning Ding
- 1Hunan University of Chinese Medicine, Changsha, Hunan 410208, China
| | - Hongbiao Luo
- 1Hunan University of Chinese Medicine, Changsha, Hunan 410208, China
- 2Department of Anorectal Surgery, Chenzhou NO. 1 People's Hospital, Chenzhou 423000, China
| | - Tao Zhang
- 1Hunan University of Chinese Medicine, Changsha, Hunan 410208, China
| | - Tianshu Peng
- 3Department of Anorectal Surgery, The Second Affiliated Hospital of Hunan University of Chinese Medicine, Changsha, Hunan 410005, China
| | - Yanru Yao
- 1Hunan University of Chinese Medicine, Changsha, Hunan 410208, China
| | - Yongheng He
- 4Department of Anorectal Surgery, The Affiliated Hospital of Hunan Academy of Traditional Chinese Medicine, Changsha, Hunan 410006, China
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Desai P, Awatiger MM, Mane DR. Evaluation of Immunoexpression of AJUBA Protein in Normal Oral Mucosa and Oral Squamous Cell Carcinoma. Appl Immunohistochem Mol Morphol 2023; 31:1-8. [PMID: 36222508 DOI: 10.1097/pai.0000000000001077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/18/2022] [Indexed: 12/13/2022]
Abstract
AJUBA is multifunctional scaffold protein which belongs to Zyxin family of proteins. It is known to have dual role in cancer as a tumor promoter and tumor suppressor. AJUBA has a key role in systemic malignancies like esophageal squamous cell carcinoma, colorectal cancer, cervical, breast, prostate cancer, etc. But there is very sparse literature available regarding its expression profile in oral squamous cell carcinoma (OSCC) and moreover its expression has not been observed in normal oral mucosa (NOM). Thus, the aim of this research is to explore the expression profile of AJUBA by immunohistochemical method in NOM and OSCC. Furthermore, we also evaluated the association of AJUBA expression with clinicopathologic parameters. A total of 84 samples of formalin fixed paraffin embedded tissue blocks comprising of 42 cases each of NOM and OSCC were subjected to detect immunoexpression of AJUBA. We found enhanced intense immune-expression of AJUBA in OSCC cases than compared with NOM and found to be statistically significant. The parameters specific to histologic tumor grade and inflammatory response in OSCC also found to have statistically significant with AJUBA expression. Our study is first of its kind to reveal AJUBA expression in basal and suprabasal layer of NOM suggestive of its definitive role in differentiation and stratification process. We also observed its intense expression in peripheral cell of tumor islands of OSCC cases, which can suggest its possible role in tumor growth and progression.
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Affiliation(s)
- Priyanka Desai
- Department of Oral Pathology and Microbiology, KLE VK Institute of Dental Sciences, KLE Academy of Higher Education and Research, Belagavi, Karnataka, India
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Tang Z, Jiang Y, Ding S, Jiang S, Tang R, Luo P. miR-370 impacts the biological behavior of lung cancer cells by targeting the SMAD1 signaling pathway. Am J Transl Res 2022; 14:8117-8128. [PMID: 36505312 PMCID: PMC9730076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/06/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND MicroRNAs (miRNAs) have been identified to play a role in the development and progression of lung cancer (LC). As of now, the expression and function of miR-370 in LC are still under investigation. Accordingly, this study explores the role and mechanism of miR-370 in LC. METHODS MiR-370 mimics or inhibitors were used to transfect A549 and NCI-H460 cells to overexpress or inhibit miR-370. The colony formation test and Cell Counting Kit-8 were conducted to detect the cell proliferation activity, and transwell test and wound healing test were conducted to evaluate the cell invasion and migration activities. In addition, the downstream target genes of miR-370 in LC were verified by dual luciferase reporter assay and western blot. RESULTS Compared to normal tissues and cell lineslines, the miR-370 expression in LC tissues and cells was decreased greatly. Compared to the negative control group, the up-regulation of miR-370 greatly intensified the apoptosis of NCI-H460 cells and weakened the migration, proliferation, and invasion of the cells. However, compared to the inhibitor-negative control group, the downregulation of miR-370 caused the opposite results. Additionally, SMAD family member 1 (SMAD1) was identified as a direct target of miR-370 in LC and could be inhibited by miR-370. Its overexpression restored the impact of miR-370 mimics on LC cells. CONCLUSION With low expression in LC tissues and cell lineslines, miR-370 is a tumor suppressor that weakens the growth, invasion as well as migration of LC cells by inhibiting SMAD1 expression. Our results may provide novel insights for the biological treatment of LC.
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Dommann N, Gavini J, Sánchez-Taltavull D, Baier FA, Birrer F, Loforese G, Candinas D, Stroka D. LIM protein Ajuba promotes liver cell proliferation through its involvement in DNA replication and DNA damage control. FEBS Lett 2022; 596:1746-1764. [PMID: 35535434 DOI: 10.1002/1873-3468.14371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/31/2022] [Accepted: 04/11/2022] [Indexed: 11/08/2022]
Abstract
The LIM-domain protein Ajuba is associated with cell proliferation, a fundamental process of tissue regeneration and cancer. We report that in the liver, Ajuba expression is increased during regeneration and in tumor cells and tissues. Knockout of Ajuba using CRISPR/Cas9 is embryonic lethal in mice. shRNA targeting of Ajuba reduces cell proliferation, delays cell entry into S-phase, reduces cell survival and tumor growth in vivo, and increases expression of the DNA damage marker γH2AX. Ajuba binding partners include proteins involved in DNA replication and damage, such as SKP2, MCM2, MCM7 and RPA70. Taken together, our data support that Ajuba promotes liver cell proliferation associated with development, regeneration, and tumor growth and is involved in DNA replication and damage repair.
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Affiliation(s)
- Noëlle Dommann
- Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Switzerland
| | - Jacopo Gavini
- Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Switzerland
| | - Daniel Sánchez-Taltavull
- Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Switzerland
| | - Felix Alexander Baier
- Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Switzerland
| | - Fabienne Birrer
- Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Switzerland
| | - Giulio Loforese
- Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Switzerland
| | - Daniel Candinas
- Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Switzerland
| | - Deborah Stroka
- Department of Visceral Surgery and Medicine, University of Bern, Inselspital, Bern University Hospital, Switzerland
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Zhou J, Wang M, Mao A, Zhao Y, Wang L, Xu Y, Jia H, Wang L. Long noncoding RNA MALAT1 sponging miR-26a-5p to modulate Smad1 contributes to colorectal cancer progression by regulating autophagy. Carcinogenesis 2021; 42:1370-1379. [PMID: 34313719 DOI: 10.1093/carcin/bgab069] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 07/16/2021] [Accepted: 07/26/2021] [Indexed: 01/05/2023] Open
Abstract
Accumulating evidences have suggested that bone morphogenetic protein (BMP) -Smad have a functional role in regulating autophagy in the development of human colorectal cancer (CRC). However, the regulatory mechanisms controlling this process remain unclear. Here, we showed that Smad1, the key effector of BMP2-Smad signaling, induces autophagy by upregulating autophagy-related gene 5 (ATG5) expression, and Smad1 binds to the proximal promoter to induce its expression. Moreover, BMP2 induces autophagy in CRC. Overexpression of Smad1 promotes tumorigenesis and migration of CRC cells, and knockdown of ATG5 is able to rescue the Smad1-induced promotion of CRC proliferation and migration partially. Mechanistically, metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) may act as a competing endogenous RNA by binding with miR-26a-5p competitively and thus modulating the de-repression of downstream target Smad1. Furthermore, clinical analysis results show that Smad1 is positively correlated with MALAT1 and negatively correlated with miR-26a-5p in CRC samples. In conclusion, our results demonstrated that Smad1 may serve as an oncogene in CRC through autophagy.
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Affiliation(s)
- Jiamin Zhou
- Department of Hepatic Surgery, Shanghai Cancer Center, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Miao Wang
- Department of Hepatic Surgery, Shanghai Cancer Center, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Anrong Mao
- Department of Hepatic Surgery, Shanghai Cancer Center, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yiming Zhao
- Department of Hepatic Surgery, Shanghai Cancer Center, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Longrong Wang
- Department of Hepatic Surgery, Shanghai Cancer Center, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ye Xu
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Colorectal Surgery, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Hao Jia
- Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lu Wang
- Department of Hepatic Surgery, Shanghai Cancer Center, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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Chen X, Liu W, Liu B. Ginsenoside Rh7 Suppresses Proliferation, Migration and Invasion of NSCLC Cells Through Targeting ILF3-AS1 Mediated miR-212/SMAD1 Axis. Front Oncol 2021; 11:656132. [PMID: 33996578 PMCID: PMC8116958 DOI: 10.3389/fonc.2021.656132] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/31/2021] [Indexed: 12/20/2022] Open
Abstract
It is reported that ginsenosides have a significant anti-tumor effect on a variety of tumors. However, the role and mechanism of Rh7 in non-small cell lung cancer (NSCLC) are unclear. In this study, we aimed to study the anti-tumor effect of Rh7 on the proliferation and progression of NSCLC. Bioinformatics analysis showed that ILF3-AS1 was regulated by ginsenoside Rh7 in NSCLC. Down-regulation of ILF3-AS1 could significantly inhibit the proliferation, metastasis and invasion of NSCLC. In addition, ILF3-AS1 negatively controlled miR-212, which in turn targeted SMAD1 expression, thereby regulating NSCLC cell viability and apoptosis. Our results indicate that ILF3-AS1 can be used as a diagnostic and therapeutic target for non-small cell lung cancer. It is discovered for the first time that ginsenoside Rh7 inhibits the expression of ILF3-AS1 and exerts antitumor effects.
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Affiliation(s)
| | - Wenguang Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
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Schleicher K, Schramek D. AJUBA: A regulator of epidermal homeostasis and cancer. Exp Dermatol 2021; 30:546-559. [PMID: 33372298 DOI: 10.1111/exd.14272] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 12/09/2020] [Accepted: 12/21/2020] [Indexed: 12/17/2022]
Abstract
The epidermis, outermost layer of the skin, is constantly renewing itself through proliferative and differentiation processes. These processes are vital to maintain proper epidermal integrity during skin development and homeostasis and for preventing skin diseases and cancers. The biological mechanisms that permit this balancing act are vast, where individual pathway regulators are known, but the exact regulatory control and cross-talk between simultaneously turning one biological pathway on and an opposing one off remain elusive. This review explores the diverse roles the scaffolding protein AJUBA plays during epidermal homeostasis and cancer. Initially identified for its role in promoting meiotic progression in oocytes through Grb2 and MAP kinase activity, AJUBA also maintains cytoskeletal tension permitting epidermal tissue development and responds to retinoic acid committing cells to initiate development of surface epidermal layer. AJUBA regulates proliferation of skin stem cells through Hippo and Wnt signalling and encourages mitotic commitment through Aurora-A, Aurora-B and CDK1. In addition, AJUBA also induces epidermal differentiation to maintain appropriate epidermal thickness and barrier function by activating Notch signalling and stabilizing catenins and actin during cellular remodelling. AJUBA also plays an imperative context-dependent tumor-promoting and tumor-suppressive role within epithelial cancers. AJUBA's abundant roles within the epidermis signify its importance as a molecular switchboard, vetting multiple signalling pathways to control epidermal biology.
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Affiliation(s)
- Krista Schleicher
- Molecular, Structural and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada.,Faculty of Medicine, Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Daniel Schramek
- Molecular, Structural and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada.,Faculty of Medicine, Molecular Genetics, University of Toronto, Toronto, ON, Canada
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12
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Mishra VS, Kumar N, Raza M, Sehrawat S. Amalgamation of PI3K and EZH2 blockade synergistically regulates invasion and angiogenesis: combination therapy for glioblastoma multiforme. Oncotarget 2020; 11:4754-4769. [PMID: 33473259 PMCID: PMC7771717 DOI: 10.18632/oncotarget.27842] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/24/2020] [Indexed: 12/12/2022] Open
Abstract
Glioblastoma multiforme is known as the primary malignant and most devastating form of tumor in central nervous system of adult population. Amongst all CNS cancers, Glioblastoma multiforme GBM is a rare grade IV astrocytoma and it has the worst prognosis initiated by metastasis to supra-tentorial region of the brain. Current options for the treatment include surgery, radiation therapy and chemotherapy. Substantial information of its pathology and molecular signaling exposed new avenues for generating innovative therapies. In our study, we have undertaken a novel combination approach for GBM treatment. PI3K signaling participates in cancer progression and plays a significant role in metastasis. Here, we are targeting PI3K signaling pathways in glioblastoma along with EZH2, a known transcriptional regulator. We found that targeting transcriptional regulator EZH2 and PI3K affect cellular migration and morphological changes. These changes in signatory activities of cancerous cells led to inhibit its progression in vitro. With further analysis we confirmed the angiogenic inhibition and reduction in stem-ness potential of GBM. Later, cytokine proteome array analysis revealed several participants of metastasis and tumor induced angiogenesis using combination regime. This study provides a significant reduction in GBM progression investigated using Glioblastoma Multiforme U-87 cells with effective combination of pharmacological inhibitors PI-103 and EPZ-6438. This strategy will be further used to combat GBM more innovatively along with the existing therapies.
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Affiliation(s)
- Vishnu S Mishra
- Precision NeuroOncology & NeuroVascular Disease Modeling Group, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, NCR 201314, India.,These authors contributed equally to this work
| | - Naveen Kumar
- Precision NeuroOncology & NeuroVascular Disease Modeling Group, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, NCR 201314, India.,These authors contributed equally to this work
| | - Masoom Raza
- Precision NeuroOncology & NeuroVascular Disease Modeling Group, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, NCR 201314, India
| | - Seema Sehrawat
- Precision NeuroOncology & NeuroVascular Disease Modeling Group, Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, NCR 201314, India
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13
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Liu C, Sheng M, Lin L, Li H, Guo S, Zhang J, Chen G, Chen H. NANOG regulates the proliferation of PCSCs via the TGF-β1/SMAD pathway. Open Med (Wars) 2020; 15:841-849. [PMID: 33336042 PMCID: PMC7712027 DOI: 10.1515/med-2020-0221] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 07/19/2020] [Accepted: 07/26/2020] [Indexed: 12/22/2022] Open
Abstract
Purpose In prostate cancer, castration resistance is a factor that frequently leads to death in individuals with this disease. Recent studies have suggested that prostate cancer stem cells (PCSCs) are pivotal regulators in the establishment of castration resistance. The nanog homeobox (NANOG) and the transforming growth factor (TGF)-β1/drosophila mothers against decapentaplegic protein (SMAD) signaling pathways are involved in several cancer stem cells but are not involved in PCSCs. The purpose of this study is to investigate the effect of NANOG on the proliferation of PCSCs regulated by the TGF-β1/SMAD signaling pathway. Methods In this study, we used flow cytometry to isolate CD44+/CD133+/NANOG+ PCSCs from DU145 prostate cancer cells. Then we used short hairpin RNA to silence NANOG and observed the biological behavior and the TGF-β1/SMAD signal of PCSCs. Results NANOG decreased PCSC proliferation, increased apoptosis, and blocked cell cycling at G0/G1. Furthermore, reduction in the TGF-β1, p15, and p-SMAD2 expression was observed. Conclusion These findings suggest that NANOG positively regulates the growth of PCSCs through the TGF-β1/SMAD signaling pathway.
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Affiliation(s)
- Changming Liu
- The Department of Urology, Mindong Hospital Affiliated to Fujian Medical University, Fuan, Fujian 355000, People's Republic of China
| | - Mingxiong Sheng
- The Department of Urology, Mindong Hospital Affiliated to Fujian Medical University, Fuan, Fujian 355000, People's Republic of China
| | - Liheng Lin
- The Department of Urology, Mindong Hospital Affiliated to Fujian Medical University, Fuan, Fujian 355000, People's Republic of China
| | - Huizhang Li
- The Department of Urology, Mindong Hospital Affiliated to Fujian Medical University, Fuan, Fujian 355000, People's Republic of China
| | - Shanming Guo
- The Department of Urology, Mindong Hospital Affiliated to Fujian Medical University, Fuan, Fujian 355000, People's Republic of China
| | - Jiabin Zhang
- The Department of Urology, Mindong Hospital Affiliated to Fujian Medical University, Fuan, Fujian 355000, People's Republic of China
| | - Guangbing Chen
- The Department of Urology, Mindong Hospital Affiliated to Fujian Medical University, Fuan, Fujian 355000, People's Republic of China
| | - Huihong Chen
- The Department of Urology, Mindong Hospital Affiliated to Fujian Medical University, Fuan, Fujian 355000, People's Republic of China
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14
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Dai ZT, Wang J, Zhao K, Xiang Y, Li JP, Zhang HM, Peng ZT, Liao XH. Integrated TCGA and GEO analysis showed that SMAD7 is an independent prognostic factor for lung adenocarcinoma. Medicine (Baltimore) 2020; 99:e22861. [PMID: 33126329 PMCID: PMC7598801 DOI: 10.1097/md.0000000000022861] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The lack of effective markers leads to missed optimal treatment times, resulting in poorer prognosis in most cancers. Drosophila mothers against decapentaplegic protein (SMAD) family members are important cytokines in the transforming growth factor-beta family. They jointly regulate the processes of cell growth, differentiation, and apoptosis. However, the expression of SMAD family genes in pan-cancers and their impact on prognosis have not been elucidated. Perl software and R software were used to perform expression analysis and survival curve analysis on the data collected by TCGA, GTEx, and GEO, and the potential regulatory pathways were determined through gene ontology enrichment and kyoto encyclopedia of genes and genomes enrichment analysis. It was found that SMAD7 and SMAD9 expression decreased in lung adenocarcinoma (LUAD), and their expression was positively correlated with survival time. Additionally, SMAD7 could be used as an independent prognostic factor for LUAD. In general, SMAD7 and SMAD9 can be used as prognostic markers of LUAD. Further, SMAD7 is expected to become a therapeutic target for LUAD.
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Affiliation(s)
- Zhou-Tong Dai
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan
| | - Jun Wang
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan
| | - Kai Zhao
- Huangshi Central Hospital, Huangshi
| | | | - Jia Peng Li
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan
| | - Hui-Min Zhang
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan
| | - Zi-Tan Peng
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan
- Hebei Kingsci Pharmaceutical Technology Co., Ltd, Shijiazhuang, Hebei, P.R. China
| | - Xing Hua Liao
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan
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15
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Karmokar PF, Shabnaz S, Aziz MA, Asaduzzaman M, Shahriar M, Bhuiyan MA, Mosaddek ASM, Islam MS. Variants of SMAD1 gene increase the risk of colorectal cancer in the Bangladeshi population. Tumour Biol 2020; 42:1010428320958955. [PMID: 32921281 DOI: 10.1177/1010428320958955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Colorectal cancer is the fourth most common type of malignancy worldwide that may develop due to the accumulation of several genetic variations. Different single nucleotide polymorphisms of SMAD1 gene are assumed to be linked with increased colorectal cancer risk. The current case-control study was conducted to verify the association of genetic polymorphisms of SMAD1 (rs11100883 and rs7661162) with colorectal cancer in the Bangladeshi population. This study was performed on 275 colorectal cancer patients and 300 healthy volunteers using polymerase chain reaction-restriction fragment length polymorphism method. The odds ratios were adjusted for age and sex with logistic regression analysis. In case of SMAD1 rs11100883 polymorphism, GA heterozygous genotype, GA + AA (dominant model), and minor allele "A" were significantly associated with colorectal cancer (adjusted odds ratio = 1.55, 95% confidence interval = 1.09-2.20, p = 0.014; adjusted odds ratio = 1.59, 95% confidence interval = 1.13-2.23, p = 0.008; and odds ratio = 1.35, 95% confidence interval = 1.06-1.73, p = 0.015, respectively) and the significance exists after the Bonferroni correction. Again, single nucleotide polymorphism rs7661162 showed significant association with an elevated colorectal cancer risk for AG heterozygous genotype, AG + GG (dominant model), AG versus AA + GG (overdominant model), and minor allele "G" (adjusted odds ratio = 1.78, 95% confidence interval = 1.24-2.56, p = 0.002; adjusted odds ratio = 1.68, 95% confidence interval = 1.18-2.39, p = 0.004; adjusted odds ratio = 1.76, 95% confidence interval = 1.23-2.53, p = 0.002; and odds ratio = 1.47, 95% confidence interval = 1.08-2.00, p = 0.014, respectively) and significance withstands after the Bonferroni correction. No significant age and gender differences between cases and controls were observed. In silico, gene expression analysis showed that the SMAD1 mRNA level was downregulated in the colon and rectal cancer tissues compared to healthy tissues. In conclusion, our findings indicate that SMAD1 rs11100883 and rs7661162 polymorphisms are responsible for increasing the susceptibility of colorectal cancer development in the Bangladeshi population.
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Affiliation(s)
| | - Samia Shabnaz
- Department of Pharmacy, University of Asia Pacific, Dhaka, Bangladesh
| | - Md Abdul Aziz
- Department of Pharmacy, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Md Asaduzzaman
- Department of Pharmacy, University of Asia Pacific, Dhaka, Bangladesh
| | - Mohammad Shahriar
- Department of Pharmacy, University of Asia Pacific, Dhaka, Bangladesh
| | | | | | - Mohammad Safiqul Islam
- Department of Pharmacy, Noakhali Science and Technology University, Noakhali, Bangladesh
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16
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Wang X, Chen Y, Liu W, Liu T, Sun D. Hsa_circ_0128846 promotes tumorigenesis of colorectal cancer by sponging hsa-miR-1184 and releasing AJUBA and inactivating Hippo/YAP signalling. J Cell Mol Med 2020; 24:9908-9924. [PMID: 32681581 PMCID: PMC7520282 DOI: 10.1111/jcmm.15590] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 06/13/2020] [Accepted: 06/17/2020] [Indexed: 12/24/2022] Open
Abstract
Hsa_circ_0128846 was found to be the most significantly up-regulated circRNA in our bioinformatics analysis. However, the role of hsa_circ_0128846 in colorectal cancer has not been explored. We thus aim to explore the influence and mechanism of hsa_circ_0128846 in colorectal cancer by sponging its downstream miRNA target miR-1184. We collected 40 colorectal cancer patients' tumour tissues to analyse the expression of hsa_circ_0128846, miR-1184 and AJUBA using qRT-PCR and Western blot where needed. Then, we constructed stably transfected SW480 and HCT116 cells to study the influence of hsa_circ_0128846, miR-1184 and AJUBA on colorectal cancer cell phenotypes. To obtain reliable results, a plethora of experiments including RNA immunoprecipitation assay, flow cytometry, EdU incorporation assay, wound healing migration assay, transwell invasion assay and live imaging of nude mice xenograft assay were performed. The binding relationship between hsa_circ_0128846, miR-1184 and AJUBA mRNA in colorectal cancer was validated by reported gene assay. In colorectal cancer tissues, circ_0128846 and AJUBA were both significantly up-regulated, while miR-1184 was significantly down-regulated compared with healthy tissues. Meanwhile, hsa_circ_0128846 can absorb miR-1184 to promote the progression of CRC in vivo and SW480 and HCT116 cell phenotypes in vitro. The knockdown of AJUBA, a downstream target of miR-1184, reversed the effect of miR-1184 in CRC cells via enhancing the phosphorylation of the Hippo/YAP signalling pathway proteins MST1, LATS1 and YAP. This study revealed that hsa_circ_0128846 contributed to the development of CRC by decreasing the expression of miR-1184, thereby increasing AJUBA expression and inactivating Hippo/YAP signalling.
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Affiliation(s)
- Xu Wang
- Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, China
| | - Yujia Chen
- Department of Gastrointestinal Surgery, The First Hospital of Jilin University, Changchun, China
| | - Wei Liu
- Department of Spinal Surgery, The First Hospital of Jilin University, Changchun, China
| | - Tao Liu
- Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, China
| | - Di Sun
- Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, China
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Dommann N, Sánchez-Taltavull D, Eggs L, Birrer F, Brodie T, Salm L, Baier FA, Medová M, Humbert M, Tschan MP, Beldi G, Candinas D, Stroka D. The LIM Protein Ajuba Augments Tumor Metastasis in Colon Cancer. Cancers (Basel) 2020; 12:cancers12071913. [PMID: 32679899 PMCID: PMC7409172 DOI: 10.3390/cancers12071913] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/12/2020] [Accepted: 07/13/2020] [Indexed: 12/13/2022] Open
Abstract
Colorectal cancer, along with its high potential for recurrence and metastasis, is a major health burden. Uncovering proteins and pathways required for tumor cell growth is necessary for the development of novel targeted therapies. Ajuba is a member of the LIM domain family of proteins whose expression is positively associated with numerous cancers. Our data shows that Ajuba is highly expressed in human colon cancer tissue and cell lines. Publicly available data from The Cancer Genome Atlas shows a negative correlation between survival and Ajuba expression in patients with colon cancer. To investigate its function, we transduced SW480 human colon cancer cells, with lentiviral constructs to knockdown or overexpress Ajuba protein. The transcriptome of the modified cell lines was analyzed by RNA sequencing. Among the pathways enriched in the differentially expressed genes, were cell proliferation, migration and differentiation. We confirmed our sequencing data with biological assays; cells depleted of Ajuba were less proliferative, more sensitive to irradiation, migrated less and were less efficient in colony formation. In addition, loss of Ajuba expression decreased the tumor burden in a murine model of colorectal metastasis to the liver. Taken together, our data supports that Ajuba promotes colon cancer growth, migration and metastasis and therefore is a potential candidate for targeted therapy.
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Affiliation(s)
- Noëlle Dommann
- Department of Biomedical Research, Visceral and Transplantation Surgery, University of Bern, Clinic of Visceral Surgery and Medicine, Bern University Hospital, 3008 Bern, Switzerland; (N.D.); (D.S.-T.); (L.E.); (F.B.); (T.B.); (L.S.); (F.A.B.); (G.B.); (D.C.)
| | - Daniel Sánchez-Taltavull
- Department of Biomedical Research, Visceral and Transplantation Surgery, University of Bern, Clinic of Visceral Surgery and Medicine, Bern University Hospital, 3008 Bern, Switzerland; (N.D.); (D.S.-T.); (L.E.); (F.B.); (T.B.); (L.S.); (F.A.B.); (G.B.); (D.C.)
| | - Linda Eggs
- Department of Biomedical Research, Visceral and Transplantation Surgery, University of Bern, Clinic of Visceral Surgery and Medicine, Bern University Hospital, 3008 Bern, Switzerland; (N.D.); (D.S.-T.); (L.E.); (F.B.); (T.B.); (L.S.); (F.A.B.); (G.B.); (D.C.)
| | - Fabienne Birrer
- Department of Biomedical Research, Visceral and Transplantation Surgery, University of Bern, Clinic of Visceral Surgery and Medicine, Bern University Hospital, 3008 Bern, Switzerland; (N.D.); (D.S.-T.); (L.E.); (F.B.); (T.B.); (L.S.); (F.A.B.); (G.B.); (D.C.)
| | - Tess Brodie
- Department of Biomedical Research, Visceral and Transplantation Surgery, University of Bern, Clinic of Visceral Surgery and Medicine, Bern University Hospital, 3008 Bern, Switzerland; (N.D.); (D.S.-T.); (L.E.); (F.B.); (T.B.); (L.S.); (F.A.B.); (G.B.); (D.C.)
| | - Lilian Salm
- Department of Biomedical Research, Visceral and Transplantation Surgery, University of Bern, Clinic of Visceral Surgery and Medicine, Bern University Hospital, 3008 Bern, Switzerland; (N.D.); (D.S.-T.); (L.E.); (F.B.); (T.B.); (L.S.); (F.A.B.); (G.B.); (D.C.)
| | - Felix Alexander Baier
- Department of Biomedical Research, Visceral and Transplantation Surgery, University of Bern, Clinic of Visceral Surgery and Medicine, Bern University Hospital, 3008 Bern, Switzerland; (N.D.); (D.S.-T.); (L.E.); (F.B.); (T.B.); (L.S.); (F.A.B.); (G.B.); (D.C.)
| | - Michaela Medová
- Department of Biomedical Research, Radiation Oncology, University of Bern, Bern University Hospital, 3008 Bern, Switzerland;
| | - Magali Humbert
- Institute of Pathology, University of Bern, 3008 Bern, Switzerland; (M.H.); (M.P.T.)
| | - Mario P. Tschan
- Institute of Pathology, University of Bern, 3008 Bern, Switzerland; (M.H.); (M.P.T.)
| | - Guido Beldi
- Department of Biomedical Research, Visceral and Transplantation Surgery, University of Bern, Clinic of Visceral Surgery and Medicine, Bern University Hospital, 3008 Bern, Switzerland; (N.D.); (D.S.-T.); (L.E.); (F.B.); (T.B.); (L.S.); (F.A.B.); (G.B.); (D.C.)
| | - Daniel Candinas
- Department of Biomedical Research, Visceral and Transplantation Surgery, University of Bern, Clinic of Visceral Surgery and Medicine, Bern University Hospital, 3008 Bern, Switzerland; (N.D.); (D.S.-T.); (L.E.); (F.B.); (T.B.); (L.S.); (F.A.B.); (G.B.); (D.C.)
| | - Deborah Stroka
- Department of Biomedical Research, Visceral and Transplantation Surgery, University of Bern, Clinic of Visceral Surgery and Medicine, Bern University Hospital, 3008 Bern, Switzerland; (N.D.); (D.S.-T.); (L.E.); (F.B.); (T.B.); (L.S.); (F.A.B.); (G.B.); (D.C.)
- Correspondence: ; Tel.: +41-31-632-27-48
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18
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Hristov BH, Chazelle B, Singh M. uKIN Combines New and Prior Information with Guided Network Propagation to Accurately Identify Disease Genes. Cell Syst 2020; 10:470-479.e3. [PMID: 32684276 PMCID: PMC7821437 DOI: 10.1016/j.cels.2020.05.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/24/2020] [Accepted: 05/19/2020] [Indexed: 12/23/2022]
Abstract
Protein interaction networks provide a powerful framework for identifying genes causal for complex genetic diseases. Here, we introduce a general framework, uKIN, that uses prior knowledge of disease-associated genes to guide, within known protein-protein interaction networks, random walks that are initiated from newly identified candidate genes. In large-scale testing across 24 cancer types, we demonstrate that our network propagation approach for integrating both prior and new information not only better identifies cancer driver genes than using either source of information alone but also readily outperforms other state-of-the-art network-based approaches. We also apply our approach to genome-wide association data to identify genes functionally relevant for several complex diseases. Overall, our work suggests that guided network propagation approaches that utilize both prior and new data are a powerful means to identify disease genes. uKIN is freely available for download at: https://github.com/Singh-Lab/uKIN.
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Affiliation(s)
- Borislav H Hristov
- Department of Computer Science, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Bernard Chazelle
- Department of Computer Science, Princeton University, Princeton, NJ 08544, USA
| | - Mona Singh
- Department of Computer Science, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
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19
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Ajuba: An emerging signal transducer in oncogenesis. Pharmacol Res 2019; 151:104546. [PMID: 31740385 DOI: 10.1016/j.phrs.2019.104546] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 11/05/2019] [Accepted: 11/13/2019] [Indexed: 12/12/2022]
Abstract
The LIM protein Ajuba contains an unstructured proline/glycine-rich preLIM region in the N terminus and conserved tandem LIM motifs in the C terminus. Additionally, Ajuba contains both nuclear export sequences (NES) and nuclear localization sequences (NLS), which enable Ajuba shuttle between the cytoplasm and the nucleus. Thus, Ajuba can act as a versatile scaffold participating in assembly of variety of protein complexes to execute multiple cellular functions including cell adhesion, motility, mitosis, survival, gene expression, microRNA processing and mechanical force sensing. Numerous studies have demonstrated that Ajuba plays important roles in oncogenesis and progression by regulating major signalling pathways such as Wnt, RAS/ERK, JAK/STAT and Hippo, and by acting as a co-regulator of key transcription factors such as Snail, Sp1 and nuclear hormone receptors. Clinically, Ajuba is highly expressed in various types of tumors and can be a marker for prognosis and diagnosis. In this review, we aim to summarize the up-to-date literatures on the signaling pathways mediated by Ajuba and its associated protein complexes in oncogenesis, and to discuss Ajuba as a potential target for new therapeutics to treat cancers.
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20
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Chen T, Pei J, Wang J, Luo R, Liu L, Wang L, Jia H. HBx-related long non-coding RNA 01152 promotes cell proliferation and survival by IL-23 in hepatocellular carcinoma. Biomed Pharmacother 2019; 115:108877. [PMID: 31054511 DOI: 10.1016/j.biopha.2019.108877] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 04/05/2019] [Accepted: 04/11/2019] [Indexed: 02/06/2023] Open
Abstract
Accumulating evidence suggests that long-noncoding RNA (lncRNA) plays important roles in hepatitis B virus (HBV) infections. However, the mechanism underlying how lncRNA regulate hepatocellular carcinoma process remains largely unknown. In this study we found that the expression of LINC01152 was significantly increased in HBV positive HCC tissues and cells and was induced by HBx in vitro. The overexpression of LINC01152 could increases HCC cell proliferation and promotes tumor formation in nude mice. Mechanistically, HBx could increase the transcription of LINC01152. Elevated LINC01152 binds to the promoter region of IL-23, promoting its transcriptional activity and upregulating the levels of Stat3 and p-Stat3. Our findings suggest that LINC01152 plays an important role in HBV-related hepatocellular carcinoma development and may serve as a therapeutic marker for hepatocellular carcinoma.
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Affiliation(s)
- Tianshi Chen
- Department of infectious diseases, Shanxi provincial people's hospital, Taiyuan 030012, China
| | - Jinxian Pei
- Department of infectious diseases, Shanxi provincial people's hospital, Taiyuan 030012, China
| | - Jinjiang Wang
- Department of infectious diseases, Shanxi provincial people's hospital, Taiyuan 030012, China
| | - Ruili Luo
- Department of infectious diseases, Shanxi provincial people's hospital, Taiyuan 030012, China
| | - Lina Liu
- Shanghai Basilica clinic, 88 Caoxi North Road, Shanghai 200030, China.
| | - Ling Wang
- Shanghai Basilica clinic, 88 Caoxi North Road, Shanghai 200030, China.
| | - Hao Jia
- Faculty of Basic Medicine, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China.
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21
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Wu W, Tan W, Ye S, Zhou Y, Quan J. Analysis of the promoter region of the human miR-32 gene in colorectal cancer. Oncol Lett 2019; 17:3743-3750. [PMID: 30881496 PMCID: PMC6403515 DOI: 10.3892/ol.2019.10042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 02/01/2019] [Indexed: 12/13/2022] Open
Abstract
The pathogenesis of colorectal cancer (CRC) is poorly understood. MicroRNA (miR)-32 upregulation in CRC tissues was previously reported, where it increased the proliferation, migration and invasion, and reduced apoptosis of CRC cells by inhibiting the expression of phosphatase and tensin homolog (PTEN). However, the mechanism underlying miR-32 upregulation remains unknown. miR-32 is an intronic miRNA located within intron 14 of the transmembrane protein 245 gene (TMEM245). The present study aimed to elucidate the biological pathways underlying miR-32 regulation in CRC. A truncated promoter containing the 5′-flanking region of TMEM245/miR-32 gene was constructed. The promoter region was analyzed by dual luciferase reporter assay in CRC cells. DNA pull-down assay and mass spectrometry (MS) were used to identify proteins binding to the core promoter. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and transcription factor (TF) analyses were used to identify the binding proteins. The −320 to −1 bp fragment of the 5′-flanking region exhibited the highest luciferase activity. The regions spanning −606 to −320 bp exhibited a significant decrease in luciferase activity, compared with the −320 to −1 bp fragment. DNA pull-down assay and MS revealed 403 potential miR-32 promoter binding proteins. GO and KEGG pathway analysis indicated that these proteins were involved in numerous physiological and biochemical processes, including ‘structural molecule activity’, ‘RNA binding’, ‘small molecule metabolic process’ and ‘biogenesis’. Furthermore, TF analysis revealed 10 potential interacting TFs, including SMAD family member 1 (SMAD1), signal transducer and activator of transcription 1 (STAT1) and forkhead box K1 (Foxk1). These results suggested that the core promoter region may be located within-320 to −1 bp of the 5′-flanking region of TMEM245/miR-32 gene, while the region from −606 to −320 bp may harbor repressive regulatory elements. The TFs SMAD1, STAT1 and Foxk1 may be involved in the transcriptional regulation of miR-32.
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Affiliation(s)
- Weiyun Wu
- Department of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, P.R. China
| | - Wenkai Tan
- Department of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, P.R. China
| | - Shicai Ye
- Department of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, P.R. China
| | - Yu Zhou
- Department of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, P.R. China
| | - Juanhua Quan
- Department of Gastroenterology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, P.R. China
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22
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Farooqi AA, de la Roche M, Djamgoz MBA, Siddik ZH. Overview of the oncogenic signaling pathways in colorectal cancer: Mechanistic insights. Semin Cancer Biol 2019; 58:65-79. [PMID: 30633978 DOI: 10.1016/j.semcancer.2019.01.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/29/2018] [Accepted: 01/07/2019] [Indexed: 02/07/2023]
Abstract
Colorectal cancer is a multifaceted disease which is therapeutically challenging. Based on insights gleaned from almost a quarter century of research, it is obvious that deregulation of spatio-temporally controlled signaling pathways play instrumental role in development and progression of colorectal cancer. High-throughput technologies have helped to develop a sharper and broader understanding of the wide ranging signal transduction cascades which also contribute to development of drug resistance, loss of apoptosis and, ultimately, of metastasis. In this review, we have set the spotlight on role of JAK/STAT, TGF/SMAD, Notch, WNT/β-Catenin, SHH/GLI and p53 pathways in the development and progression of colorectal cancer. We have also highlighted recent reports on TRAIL-mediated pathways and molecularly distinct voltage-gated sodium channels in colorectal cancer.
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Affiliation(s)
- Ammad Ahmad Farooqi
- Institute of Biomedical and Genetic Engineering (IBGE), Islamabad, Pakistan.
| | - Marc de la Roche
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom.
| | - Mustafa B A Djamgoz
- Imperial College London, Department of Life Sciences, Neuroscience Solutions to Cancer Research Group, South Kensington Campus, London, SW7 2AZ, United Kingdom; Cyprus International University, Biotechnology Research Centre, Haspolat, Mersin 10, North Cyprus, Turkey.
| | - Zahid H Siddik
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
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