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Lai J, Zhou Z, Hu K, Yu H, Su X, Niu X, Li H, Mao S. N6-methyladenosine methylation analysis of long noncoding RNAs and mRNAs in 5-FU-resistant colon cancer cells. Epigenetics 2024; 19:2298058. [PMID: 38145548 PMCID: PMC10761136 DOI: 10.1080/15592294.2023.2298058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 12/13/2023] [Indexed: 12/27/2023] Open
Abstract
N6 methyladenosine (m6A), methylation at the sixth N atom of adenosine, is the most common and abundant modification in mammalian mRNAs and non-coding RNAs. Increasing evidence shows that the alteration of m6A modification level could regulate tumour proliferation, metastasis, self-renewal, and immune infiltration by regulating the related expression of tumour genes. However, the role of m6A modification in colorectal cancer (CRC) drug resistance is unclear. Here, MeRIP-seq and RNA-seq techniques were utilized to obtain mRNA, lncRNA expression, and their methylation profiles in 5-Fluorouracil (5-FU)-resistant colon cancer HCT-15 cells and control cells. In addition, we performed detailed bioinformatics analysis as well as in vitro experiments of lncRNA to explore the function of lncRNA with differential m6A in CRC progression and drug resistance. In this study, we obtained the m6A methylomic landscape of CRC cells and resistance group cells by MeRIP-seq and RNA-seq. We identified 3698 differential m6A peaks, of which 2224 were hypermethylated, and 1474 were hypomethylated. Among the lncRNAs, 60 were hypermethylated, and 38 were hypomethylated. GO and KEGG analysis annotations showed significant enrichment of endocytosis and MAPK signalling pathways. Moreover, knockdown of lncRNA ADIRF-AS1 and AL139035.1 promoted CRC proliferation and invasive metastasis in vitro. lncRNA- mRNA network showed that ADIRF-AS1 and AL139035.1 May play a key role in regulating drug resistance formation. We provide the first m6A methylation profile in 5-FU resistance CRC cells and analyse the functions of differential m6A-modified mRNAs and lncRNAs. Our results indicated that differential m6A RNAs were significantly associated with MAPK signalling and endocytosis after induction of 5-FU resistance. Knockdown of LncRNA ADIRF-AS1 and AL139035.1 promotes CRC progression and might be critical in regulating drug resistance formation.
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Affiliation(s)
- Jie Lai
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Department of General Surgery, Pingxiang People’s Hospital, Pingxiang, Jiangxi, China
| | - Zhiyong Zhou
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Kan Hu
- Department of General Surgery, Pingxiang People’s Hospital, Pingxiang, Jiangxi, China
| | - HongLong Yu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Xingyao Su
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Xiaoqiang Niu
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Huizi Li
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Shengxun Mao
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
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Feng X, He S, Chen Y, Zhang L. Deubiquitinase BRCC3 promotes the migration, invasion and EMT progression of colon adenocarcinoma by stabilizing MET expression. Genes Genomics 2024; 46:637-646. [PMID: 38470543 DOI: 10.1007/s13258-024-01508-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/24/2024] [Indexed: 03/14/2024]
Abstract
BACKGROUND Breast cancer type 1 susceptibility protein/breast cancer type 2 susceptibility protein-containing complex subunit 3 (BRCC3), a deubiquitinase (DUBs), is overexpressed in various cancers. However, the underlying biological roles of BRCC3 in adenocarcinoma colon (COAD) have yet to be decrypted. OBJECTIVE In this work, we explored the potential biological function of BRCC3 in the natural process of COAD cells. METHODS The expression levels of BRCC3 in COAD tissues and cell lines were investigated via quantitative real time polymerase chain reaction and western blotting analyses. Meanwhile, short hairpin RNAs targeting BRCC3 (sh-BRCC3) or mesenchymal-epithelial transition factor (MET) (sh-MET) were used to investigate the biological function, including proliferation, apoptosis, migration, invasion, and epithelial-mesenchymal transition (EMT) progression in COAD cells. Furthermore, the expression levels of EMT-related biomarkers were detected with western blotting analysis. Furthermore, we also performed Co-IP assay to identify the correlation between BRCC3 and MET. RESULTS BRCC3 expression was increased in COAD tissues and cell lines. ShRNA-mediated downmodulation of BRCC3 in COAD cell lines induced EMT progression. BRCC3 knockdown resulted in decreased migration as well as invasion and increased apoptosis of SW480 and Lovo cells. Besides, MET was regulated by BRCC3 and involved in the migration, invasion, and EMT in SW480 and Lovo cells. Finally, we uncovered that the overexpressed MET reversed the effects of BRCC3 knockdown in COAD cell development. CONCLUSIONS BRCC3 acted as a critical factor in the development of COAD by deubiquitinating and stabilizing MET, which might provide an emerging biomarker for the therapeutic and diagnosis strategy of COAD.
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Affiliation(s)
- Xiu Feng
- Department of Oncology, Nantong First People's Hospital and Affiliated Hospital 2 of Nantong University, No.666 Shengli Road, Chongchuan District, Nantong, 226000, Jiangsu, China
| | - Shengnan He
- Department of Oncology, Nantong First People's Hospital and Affiliated Hospital 2 of Nantong University, No.666 Shengli Road, Chongchuan District, Nantong, 226000, Jiangsu, China
| | - Ying Chen
- Department of Oncology, Nantong First People's Hospital and Affiliated Hospital 2 of Nantong University, No.666 Shengli Road, Chongchuan District, Nantong, 226000, Jiangsu, China.
| | - Liang Zhang
- Department of Oncology, Nantong First People's Hospital and Affiliated Hospital 2 of Nantong University, No.666 Shengli Road, Chongchuan District, Nantong, 226000, Jiangsu, China.
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Golrokh FJ, Tolami HF, Ghanbarirad M, Mahmoudi A, Tabassi NR, Alkinani TA, Taramsari SM, Aghajani S, Taati H, Akbari F, Noveiri MJS, Hedayati M, Ghasemipour T, Salehzadeh A. Apoptosis induction in colon cancer cells (SW480) by BiFe 2O 4@Ag nanocomposite synthesized from Chlorella vulgaris extract and evaluation the expression of CASP8, BAX and BCL2 genes. J Trace Elem Med Biol 2024; 83:127369. [PMID: 38176316 DOI: 10.1016/j.jtemb.2023.127369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/25/2023] [Accepted: 12/13/2023] [Indexed: 01/06/2024]
Abstract
BACKGROUND The use of nanomaterials in cancer diagnosis and treatment has received considerable interest. Preparation of nanoscale complex molecules could be considered to improve the efficacy and minimize toxicity of the product. This work aimed to biosynthesize BiFe2O4@Ag nanocomposite using the Chlorella vulgaris extract and its cytotoxic effect on colon cancer cell line. METHODS The physicochemical properties of the bioengineered BiFe2O4 @Ag were investigated by Transmission Electron Microscopy (TEM), Field Emission Scanning Electron Microscopy (FE-SEM), Zeta potential, Dynamic Light Scattering (DLS), Fourier Transform Infrared Spectroscopy (FT-IR), Energy Dispersive X-ray Spectroscopy (EDX), Vibrating-sample Magnetometer (VSM) and X-ray Diffraction Analysis (XRD). The cytotoxic potential of BiFe2O4 @Ag was evaluated by MTT assay against SW480 colon cancer cell line. The expression levels of apoptotic genes including BAX, BCL2 and CASP8 were determined by Real-time PCR. The rate of apoptosis and necrosis of the cancer cells as well as the cell cycle analysis were evaluated by flow cytometry. RESULTS Physicochemical assays indicated the nanoscale synthesis (10-70 nm) and functionalization of BiFe2O4 nanoparticles by Ag atoms. The VSM analysis revealed the magnetism of BiFe2O4 @Ag nanocomposite. According to the MTT assay, colon cancer cells (SW480) were considerably more sensitive to BiFe2O4 @Ag nanocomposite than normal cells. Apoptotic cell percentage increased from 1.93% to 73.66%, after exposure to the nanocomposite. Cell cycle analysis confirmed an increase in the number of the cells in subG1 and G0/G1 phases among nanocomposite treated cells. Moreover, treating the colon cancer cells with BiFe2O4 @Ag caused an increase in the expression of CASP8, BAX, and BCL2 genes by 3.1, 2.6, and 1.2 folds, respectively. Moreover, activity of Caspase-3 protein increased by 2.4 folds and apoptotic morphological changes appeared which confirms that exposure to the nanocomposite induces extrinsic pathway of apoptosis in colon cancer cells. CONCLUSION The considerable anticancer potential of the synthesized BiFe2O4 @Ag nanocomposite seems to be related to the induction of oxidative stress which leads to inhibit cell cycle progression and cell proliferation. This study reveals that the BiFe2O4 @Ag is a potent compound to be used in biomedical fields.
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Affiliation(s)
| | - Hedyeh Fazel Tolami
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran
| | - Maryam Ghanbarirad
- Department of Biology, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Aida Mahmoudi
- Department of Biology, Damghan Branch, Islamic Azad University, Damghan, Iran
| | | | | | | | - Shahrzad Aghajani
- Department of Biology, Rasht Branch, Islamic Azad University, Rasht, Iran
| | - Hadi Taati
- Department of Biology, Rasht Branch, Islamic Azad University, Rasht, Iran
| | - Fatemeh Akbari
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | | | | | | | - Ali Salehzadeh
- Department of Biology, Rasht Branch, Islamic Azad University, Rasht, Iran.
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Karaca C, Demir Karaman E, Leblebici A, Kurter H, Ellidokuz H, Koc A, Ellidokuz EB, Isik Z, Basbinar Y. New treatment alternatives for primary and metastatic colorectal cancer by an integrated transcriptome and network analyses. Sci Rep 2024; 14:8762. [PMID: 38627442 PMCID: PMC11021540 DOI: 10.1038/s41598-024-59101-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
Metastatic colorectal cancer (CRC) is still in need of effective treatments. This study applies a holistic approach to propose new targets for treatment of primary and liver metastatic CRC and investigates their therapeutic potential in-vitro. An integrative analysis of primary and metastatic CRC samples was implemented for alternative target and treatment proposals. Integrated microarray samples were grouped based on a co-expression network analysis. Significant gene modules correlated with primary CRC and metastatic phenotypes were identified. Network clustering and pathway enrichments were applied to gene modules to prioritize potential targets, which were shortlisted by independent validation. Finally, drug-target interaction search led to three agents for primary and liver metastatic CRC phenotypes. Hesperadin and BAY-1217389 suppress colony formation over a 14-day period, with Hesperadin showing additional efficacy in reducing cell viability within 48 h. As both candidates target the G2/M phase proteins NEK2 or TTK, we confirmed their anti-proliferative properties by Ki-67 staining. Hesperadinin particular arrested the cell cycle at the G2/M phase. IL-29A treatment reduced migration and invasion capacities of TGF-β induced metastatic cell lines. In addition, this anti-metastatic treatment attenuated TGF-β dependent mesenchymal transition. Network analysis suggests IL-29A induces the JAK/STAT pathway in a preventive manner.
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Affiliation(s)
- Caner Karaca
- Department of Translational Oncology, Institute of Health Sciences, Dokuz Eylul University, Izmir, Turkey
| | - Ezgi Demir Karaman
- Department of Computer Engineering, Faculty of Engineering, Dokuz Eylul University, Izmir, Turkey
| | - Asim Leblebici
- Department of Translational Oncology, Institute of Health Sciences, Dokuz Eylul University, Izmir, Turkey
| | - Hasan Kurter
- Department of Translational Oncology, Institute of Health Sciences, Dokuz Eylul University, Izmir, Turkey
| | - Hulya Ellidokuz
- Department of Preventive Oncology, Institute of Oncology, Dokuz Eylul University, Izmir, Turkey
| | - Altug Koc
- Department of Translational Oncology, Institute of Health Sciences, Dokuz Eylul University, Izmir, Turkey
| | - Ender Berat Ellidokuz
- Department of Gastroenterology, Faculty of Medicine, Dokuz Eylul University, Izmir, Turkey
| | - Zerrin Isik
- Department of Computer Engineering, Faculty of Engineering, Dokuz Eylul University, Izmir, Turkey.
| | - Yasemin Basbinar
- Department of Translational Oncology, Institute of Oncology, Dokuz Eylul University, Izmir, Turkey.
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Malviya G, Lannagan TR, Johnson E, Mackintosh A, Bielik R, Peters A, Soloviev D, Brown G, Jackstadt R, Nixon C, Gilroy K, Campbell A, Sansom OJ, Lewis DY. Noninvasive Stratification of Colon Cancer by Multiplex PET Imaging. Clin Cancer Res 2024; 30:1518-1529. [PMID: 38493804 PMCID: PMC11016897 DOI: 10.1158/1078-0432.ccr-23-1063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/30/2023] [Accepted: 02/14/2024] [Indexed: 03/19/2024]
Abstract
PURPOSE The current approach for molecular subtyping of colon cancer relies on gene expression profiling, which is invasive and has limited ability to reveal dynamics and spatial heterogeneity. Molecular imaging techniques, such as PET, present a noninvasive alternative for visualizing biological information from tumors. However, the factors influencing PET imaging phenotype, the suitable PET radiotracers for differentiating tumor subtypes, and the relationship between PET phenotypes and tumor genotype or gene expression-based subtyping remain unknown. EXPERIMENTAL DESIGN In this study, we conducted 126 PET scans using four different metabolic PET tracers, [18F]fluorodeoxy-D-glucose ([18F]FDG), O-(2-[18F]fluoroethyl)-l-tyrosine ([18F]FET), 3'-deoxy-3'-[18F]fluorothymidine ([18F]FLT), and [11C]acetate ([11C]ACE), using a spectrum of five preclinical colon cancer models with varying genetics (BMT, AKPN, AK, AKPT, KPN), at three sites (subcutaneous, orthograft, autochthonous) and at two tumor stages (primary vs. metastatic). RESULTS The results demonstrate that imaging signatures are influenced by genotype, tumor environment, and stage. PET imaging signatures exhibited significant heterogeneity, with each cancer model displaying distinct radiotracer profiles. Oncogenic Kras and Apc loss showed the most distinctive imaging features, with [18F]FLT and [18F]FET being particularly effective, respectively. The tissue environment notably impacted [18F]FDG uptake, and in a metastatic model, [18F]FET demonstrated higher uptake. CONCLUSIONS By examining factors contributing to PET-imaging phenotype, this study establishes the feasibility of noninvasive molecular stratification using multiplex radiotracer PET. It lays the foundation for further exploration of PET-based subtyping in human cancer, thereby facilitating noninvasive molecular diagnosis.
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Affiliation(s)
- Gaurav Malviya
- Cancer Research UK Scotland Institute, Garscube Estate, Glasgow, United Kingdom
- School of Cancer Sciences, University of Glasgow; Glasgow, United Kingdom
| | | | - Emma Johnson
- Cancer Research UK Scotland Institute, Garscube Estate, Glasgow, United Kingdom
| | - Agata Mackintosh
- Cancer Research UK Scotland Institute, Garscube Estate, Glasgow, United Kingdom
| | - Robert Bielik
- Cancer Research UK Scotland Institute, Garscube Estate, Glasgow, United Kingdom
| | - Adam Peters
- Cancer Research UK Scotland Institute, Garscube Estate, Glasgow, United Kingdom
| | - Dmitry Soloviev
- Cancer Research UK Scotland Institute, Garscube Estate, Glasgow, United Kingdom
| | - Gavin Brown
- Cancer Research UK Scotland Institute, Garscube Estate, Glasgow, United Kingdom
| | - Rene Jackstadt
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
- Cancer Progression and Metastasis Group, German Cancer Research Center (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany. German Cancer Consortium (DKTK), Germany
| | - Colin Nixon
- Cancer Research UK Scotland Institute, Garscube Estate, Glasgow, United Kingdom
| | - Kathryn Gilroy
- Cancer Research UK Scotland Institute, Garscube Estate, Glasgow, United Kingdom
| | - Andrew Campbell
- Cancer Research UK Scotland Institute, Garscube Estate, Glasgow, United Kingdom
| | - Owen J. Sansom
- Cancer Research UK Scotland Institute, Garscube Estate, Glasgow, United Kingdom
- School of Cancer Sciences, University of Glasgow; Glasgow, United Kingdom
| | - David Y. Lewis
- Cancer Research UK Scotland Institute, Garscube Estate, Glasgow, United Kingdom
- School of Cancer Sciences, University of Glasgow; Glasgow, United Kingdom
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Fonseca P, Cui W, Struyf N, Tong L, Chaurasiya A, Casagrande F, Zhao H, Fernando D, Chen X, Tobin NP, Seashore-Ludlow B, Lundqvist A, Hartman J, Göndör A, Östling P, Holmgren L. A phenotypic screening approach to target p60AmotL2-expressing invasive cancer cells. J Exp Clin Cancer Res 2024; 43:107. [PMID: 38594748 PMCID: PMC11003180 DOI: 10.1186/s13046-024-03031-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/26/2024] [Indexed: 04/11/2024] Open
Abstract
BACKGROUND Tumor cells have the ability to invade and form small clusters that protrude into adjacent tissues, a phenomenon that is frequently observed at the periphery of a tumor as it expands into healthy tissues. The presence of these clusters is linked to poor prognosis and has proven challenging to treat using conventional therapies. We previously reported that p60AmotL2 expression is localized to invasive colon and breast cancer cells. In vitro, p60AmotL2 promotes epithelial cell invasion by negatively impacting E-cadherin/AmotL2-related mechanotransduction. METHODS Using epithelial cells transfected with inducible p60AmotL2, we employed a phenotypic drug screening approach to find compounds that specifically target invasive cells. The phenotypic screen was performed by treating cells for 72 h with a library of compounds with known antitumor activities in a dose-dependent manner. After assessing cell viability using CellTiter-Glo, drug sensitivity scores for each compound were calculated. Candidate hit compounds with a higher drug sensitivity score for p60AmotL2-expressing cells were then validated on lung and colon cell models, both in 2D and in 3D, and on colon cancer patient-derived organoids. Nascent RNA sequencing was performed after BET inhibition to analyse BET-dependent pathways in p60AmotL2-expressing cells. RESULTS We identified 60 compounds that selectively targeted p60AmotL2-expressing cells. Intriguingly, these compounds were classified into two major categories: Epidermal Growth Factor Receptor (EGFR) inhibitors and Bromodomain and Extra-Terminal motif (BET) inhibitors. The latter consistently demonstrated antitumor activity in human cancer cell models, as well as in organoids derived from colon cancer patients. BET inhibition led to a shift towards the upregulation of pro-apoptotic pathways specifically in p60AmotL2-expressing cells. CONCLUSIONS BET inhibitors specifically target p60AmotL2-expressing invasive cancer cells, likely by exploiting differences in chromatin accessibility, leading to cell death. Additionally, our findings support the use of this phenotypic strategy to discover novel compounds that can exploit vulnerabilities and specifically target invasive cancer cells.
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Affiliation(s)
- Pedro Fonseca
- Department of Oncology and Pathology, Karolinska Institutet, U2, Bioclinicum J6:20, Solnavägen 30, 171 64, Solna, Stockholm, Sweden
| | - Weiyingqi Cui
- Department of Oncology and Pathology, Karolinska Institutet, U2, Bioclinicum J6:20, Solnavägen 30, 171 64, Solna, Stockholm, Sweden
| | - Nona Struyf
- Department of Oncology and Pathology, Karolinska Institutet, U2, Bioclinicum J6:20, Solnavägen 30, 171 64, Solna, Stockholm, Sweden
- Science for Life Laboratory, Tomtebodavägen 23a, 171 65, Stockholm, Sweden
| | - Le Tong
- Department of Oncology and Pathology, Karolinska Institutet, U2, Bioclinicum J6:20, Solnavägen 30, 171 64, Solna, Stockholm, Sweden
| | - Ayushi Chaurasiya
- Department of Oncology and Pathology, Karolinska Institutet, U2, Bioclinicum J6:20, Solnavägen 30, 171 64, Solna, Stockholm, Sweden
| | - Felipe Casagrande
- Department of Oncology and Pathology, Karolinska Institutet, U2, Bioclinicum J6:20, Solnavägen 30, 171 64, Solna, Stockholm, Sweden
| | - Honglei Zhao
- Department of Oncology and Pathology, Karolinska Institutet, U2, Bioclinicum J6:20, Solnavägen 30, 171 64, Solna, Stockholm, Sweden
| | - Dinura Fernando
- Department of Oncology and Pathology, Karolinska Institutet, U2, Bioclinicum J6:20, Solnavägen 30, 171 64, Solna, Stockholm, Sweden
| | - Xinsong Chen
- Department of Oncology and Pathology, Karolinska Institutet, U2, Bioclinicum J6:20, Solnavägen 30, 171 64, Solna, Stockholm, Sweden
| | - Nicholas P Tobin
- Department of Oncology and Pathology, Karolinska Institutet, U2, Bioclinicum J6:20, Solnavägen 30, 171 64, Solna, Stockholm, Sweden
- Breast Center, Karolinska Comprehensive Cancer Center, Karolinska University Hospital, Stockholm, Sweden
| | - Brinton Seashore-Ludlow
- Department of Oncology and Pathology, Karolinska Institutet, U2, Bioclinicum J6:20, Solnavägen 30, 171 64, Solna, Stockholm, Sweden
- Science for Life Laboratory, Tomtebodavägen 23a, 171 65, Stockholm, Sweden
| | - Andreas Lundqvist
- Department of Oncology and Pathology, Karolinska Institutet, U2, Bioclinicum J6:20, Solnavägen 30, 171 64, Solna, Stockholm, Sweden
| | - Johan Hartman
- Department of Oncology and Pathology, Karolinska Institutet, U2, Bioclinicum J6:20, Solnavägen 30, 171 64, Solna, Stockholm, Sweden
| | - Anita Göndör
- Department of Oncology and Pathology, Karolinska Institutet, U2, Bioclinicum J6:20, Solnavägen 30, 171 64, Solna, Stockholm, Sweden
- Department of Clinical Molecular Biology, University of Oslo, Akershus Universitetssykehus, 1478, Lørenskog, Oslo, Norway
| | - Päivi Östling
- Department of Oncology and Pathology, Karolinska Institutet, U2, Bioclinicum J6:20, Solnavägen 30, 171 64, Solna, Stockholm, Sweden
- Science for Life Laboratory, Tomtebodavägen 23a, 171 65, Stockholm, Sweden
| | - Lars Holmgren
- Department of Oncology and Pathology, Karolinska Institutet, U2, Bioclinicum J6:20, Solnavägen 30, 171 64, Solna, Stockholm, Sweden.
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7
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Mouillet-Richard S, Gougelet A, Passet B, Brochard C, Le Corre D, Pitasi CL, Joubel C, Sroussi M, Gallois C, Lavergne J, Castille J, Vilotte M, Daniel-Carlier N, Pilati C, de Reyniès A, Djouadi F, Colnot S, André T, Taieb J, Vilotte JL, Romagnolo B, Laurent-Puig P. Wnt, glucocorticoid and cellular prion protein cooperate to drive a mesenchymal phenotype with poor prognosis in colon cancer. J Transl Med 2024; 22:337. [PMID: 38589873 PMCID: PMC11003154 DOI: 10.1186/s12967-024-05164-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 04/04/2024] [Indexed: 04/10/2024] Open
Abstract
BACKGROUND The mesenchymal subtype of colorectal cancer (CRC), associated with poor prognosis, is characterized by abundant expression of the cellular prion protein PrPC, which represents a candidate therapeutic target. How PrPC is induced in CRC remains elusive. This study aims to elucidate the signaling pathways governing PrPC expression and to shed light on the gene regulatory networks linked to PrPC. METHODS We performed in silico analyses on diverse datasets of in vitro, ex vivo and in vivo models of mouse CRC and patient cohorts. We mined ChIPseq studies and performed promoter analysis. CRC cell lines were manipulated through genetic and pharmacological approaches. We created mice combining conditional inactivation of Apc in intestinal epithelial cells and overexpression of the human prion protein gene PRNP. Bio-informatic analyses were carried out in two randomized control trials totalizing over 3000 CRC patients. RESULTS In silico analyses combined with cell-based assays identified the Wnt-β-catenin and glucocorticoid pathways as upstream regulators of PRNP expression, with subtle differences between mouse and human. We uncover multiple feedback loops between PrPC and these two pathways, which translate into an aggravation of CRC pathogenesis in mouse. In stage III CRC patients, the signature defined by PRNP-CTNNB1-NR3C1, encoding PrPC, β-catenin and the glucocorticoid receptor respectively, is overrepresented in the poor-prognosis, mesenchymal subtype and associates with reduced time to recurrence. CONCLUSIONS An unleashed PrPC-dependent vicious circle is pathognomonic of poor prognosis, mesenchymal CRC. Patients from this aggressive subtype of CRC may benefit from therapies targeting the PRNP-CTNNB1-NR3C1 axis.
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Affiliation(s)
- Sophie Mouillet-Richard
- Centre de Recherche Des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, 75006, Paris, France.
- Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France.
| | - Angélique Gougelet
- Centre de Recherche Des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, 75006, Paris, France
| | - Bruno Passet
- University of Paris-Saclay, INRAE, AgroParisTech, UMR1313 GABI, 78350, Jouy-en-Josas, France
| | - Camille Brochard
- Centre de Recherche Des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, 75006, Paris, France
- Institut du Cancer Paris CARPEM, APHP, Department of Pathology, APHP.Centre-Université Paris Cité, Hôpital Européen G. Pompidou, Paris, France
| | - Delphine Le Corre
- Centre de Recherche Des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, 75006, Paris, France
- Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France
| | - Caterina Luana Pitasi
- Université Paris Cité, Institut Cochin, Inserm, CNRS, F-75014, Paris, France
- Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France
| | - Camille Joubel
- Centre de Recherche Des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, 75006, Paris, France
- Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France
| | - Marine Sroussi
- Centre de Recherche Des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, 75006, Paris, France
- Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France
| | - Claire Gallois
- Centre de Recherche Des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, 75006, Paris, France
- Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France
- Institut du Cancer Paris CARPEM, APHP, Hepatogastroenterology and GI Oncology Department, APHP.Centre-Université Paris Cité, Hôpital Européen G. Pompidou, Paris, France
| | - Julien Lavergne
- Centre de Recherche Des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, 75006, Paris, France
- Histology, Imaging and Cytometry Center (CHIC), Paris, France
| | - Johan Castille
- University of Paris-Saclay, INRAE, AgroParisTech, UMR1313 GABI, 78350, Jouy-en-Josas, France
| | - Marthe Vilotte
- University of Paris-Saclay, INRAE, AgroParisTech, UMR1313 GABI, 78350, Jouy-en-Josas, France
| | - Nathalie Daniel-Carlier
- University of Paris-Saclay, INRAE, AgroParisTech, UMR1313 GABI, 78350, Jouy-en-Josas, France
| | - Camilla Pilati
- Centre de Recherche Des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, 75006, Paris, France
- Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France
| | - Aurélien de Reyniès
- Centre de Recherche Des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, 75006, Paris, France
- Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France
| | - Fatima Djouadi
- Centre de Recherche Des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, 75006, Paris, France
- Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France
| | - Sabine Colnot
- Centre de Recherche Des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, 75006, Paris, France
- Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France
| | - Thierry André
- Saint-Antoine Hospital, INSERM, Unité Mixte de Recherche Scientifique 938, Sorbonne Université, Paris, France
| | - Julien Taieb
- Centre de Recherche Des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, 75006, Paris, France
- Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France
- Institut du Cancer Paris CARPEM, APHP, Hepatogastroenterology and GI Oncology Department, APHP.Centre-Université Paris Cité, Hôpital Européen G. Pompidou, Paris, France
| | - Jean-Luc Vilotte
- University of Paris-Saclay, INRAE, AgroParisTech, UMR1313 GABI, 78350, Jouy-en-Josas, France
| | - Béatrice Romagnolo
- Université Paris Cité, Institut Cochin, Inserm, CNRS, F-75014, Paris, France
- Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France
| | - Pierre Laurent-Puig
- Centre de Recherche Des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité, 75006, Paris, France.
- Equipe Labellisée Ligue Nationale Contre Le Cancer, Paris, France.
- Institut du Cancer Paris CARPEM, APHP, Department of Biology, APHP.Centre-Université Paris Cité, Hôpital Européen G. Pompidou, Paris, France.
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8
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Kurian CJ, Markabawi D. CRE24-033: Complete Remission of Microsatellite Instability-High (MSI-H) Oligometastatic Poorly Differentiated Colon Adenocarcinoma After a Single Dose of Immunotherapy. J Natl Compr Canc Netw 2024; 22:CRE24-033. [PMID: 38579798 DOI: 10.6004/jnccn.2023.7316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024]
Affiliation(s)
| | - Danny Markabawi
- 1MD Anderson Cancer Center at Cooper University Healthcare, Camden, NJ
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9
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Gao L, Tian Y, Chen E. The Construction of a Multi-Gene Risk Model for Colon Cancer Prognosis and Drug Treatments Prediction. Int J Mol Sci 2024; 25:3954. [PMID: 38612764 PMCID: PMC11011764 DOI: 10.3390/ijms25073954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
In clinical practice, colon cancer is a prevalent malignant tumor of the digestive system, characterized by a complex and progressive process involving multiple genes and molecular pathways. Historically, research efforts have primarily focused on investigating individual genes; however, our current study aims to explore the collective impact of multiple genes on colon cancer and to identify potential therapeutic targets associated with these genes. For this research, we acquired the gene expression profiles and RNA sequencing data of colon cancer from TCGA. Subsequently, we conducted differential gene expression analysis using R, followed by GO and KEGG pathway enrichment analyses. To construct a protein-protein interaction (PPI) network, we selected survival-related genes using the log-rank test and single-factor Cox regression analysis. Additionally, we performed LASSO regression analysis, immune infiltration analysis, mutation analysis, and cMAP analysis, as well as an investigation into ferroptosis. Our differential expression and survival analyses identified 47 hub genes, and subsequent LASSO regression analysis refined the focus to 23 key genes. These genes are closely linked to cancer metastasis, proliferation, apoptosis, cell cycle regulation, signal transduction, cancer microenvironment, immunotherapy, and neurodevelopment. Overall, the hub genes discovered in our study are pivotal in colon cancer and are anticipated to serve as important biological markers for the diagnosis and treatment of the disease.
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Affiliation(s)
- Liyang Gao
- Institute of Preventive Genomic Medicine, School of Life Sciences, Northwest University, Xi’an 710069, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi’an 710069, China
| | - Ye Tian
- Institute of Preventive Genomic Medicine, School of Life Sciences, Northwest University, Xi’an 710069, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi’an 710069, China
| | - Erfei Chen
- Institute of Preventive Genomic Medicine, School of Life Sciences, Northwest University, Xi’an 710069, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi’an 710069, China
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10
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Peng Y, Zhang Z, Yang G, Dai Z, Cai X, Liu Z, Yun Q, Xu L. N6-methyladenosine reader protein IGF2BP1 suppresses CD8 + T cells-mediated tumor cytotoxicity and apoptosis in colon cancer. Apoptosis 2024; 29:331-343. [PMID: 37848671 DOI: 10.1007/s10495-023-01893-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2023] [Indexed: 10/19/2023]
Abstract
Tumor immune escape is an important manner for colon cancer to escape effective killing by immune system. Currently, the immune checkpoint PD-1/PD-L1-targeted immunotherapy has emerged as a promising therapeutic strategy in colon cancer. Here, present work aims to investigate the biological function of N6-methyladenosine (m6A) reader insulin-like growth factor 2 mRNA binding protein 1 (IGF2BP1) in regulating colon cancer's immune escape and CD8 + T cells-mediated tumor cytotoxicity and apoptosis. Results illustrated that IGF2BP1 was closely correlated to the colon cancer patients' poor clinical outcome. Functionally, upregulation of IGF2BP1 suppressed the CD8+ T-cells mediated antitumor immunity through reducing their tumor cytotoxicity. Mechanistically, MeRIP-Seq revealed that programmed death ligand 1 (PD-L1) mRNA had a remarkable m6A modified site on 3'-UTR genomic. Moreover, PD-L1 acted as the target of IGF2BP1, which enhanced the stability of PD-L1 mRNA. Overall, these results indicated that IGF2BP1 targeted PD-L1 to accelerate the immune escape in colon cancer by reducing CD8 + T cells-mediated tumor cytotoxicity in m6A-dependent manner. The findings demonstrate the potential of m6A-targeted immune checkpoint blockade in colon cancer, providing a novel insight for colon cancer immune escape and antitumor immunity in further precise treatment.
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Affiliation(s)
- Yao Peng
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen, 518055, China
- Shenzhen University Clinical Medical Academy, Shenzhen, 518055, China
- Shenzhen University International Cancer Center, Shenzhen, 518055, China
| | - Zhili Zhang
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen, 518055, China
- Shenzhen University Clinical Medical Academy, Shenzhen, 518055, China
- Shenzhen University International Cancer Center, Shenzhen, 518055, China
| | - Gongli Yang
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen, 518055, China
| | - Zhongming Dai
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen, 518055, China
| | - Xunchao Cai
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen, 518055, China
- Shenzhen University Clinical Medical Academy, Shenzhen, 518055, China
| | - Zhenyu Liu
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen, 518055, China
| | - Qian Yun
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen, 518055, China
| | - Long Xu
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen, 518055, China.
- Shenzhen University Clinical Medical Academy, Shenzhen, 518055, China.
- Shenzhen University International Cancer Center, Shenzhen, 518055, China.
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11
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Gagliano T, Kerschbamer E, Baccarani U, Minisini M, Di Giorgio E, Dalla E, Weichenberger CX, Cherchi V, Terrosu G, Brancolini C. Changes in chromatin accessibility and transcriptional landscape induced by HDAC inhibitors in TP53 mutated patient-derived colon cancer organoids. Biomed Pharmacother 2024; 173:116374. [PMID: 38447451 DOI: 10.1016/j.biopha.2024.116374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/08/2024] Open
Abstract
Here we present the generation and characterization of patient-derived organoids (PDOs) from colorectal cancer patients. PDOs derived from two patients with TP53 mutations were tested with two different HDAC inhibitors (SAHA and NKL54). Cell death induction, transcriptome, and chromatin accessibility changes were analyzed. HDACIs promote the upregulation of low expressed genes and the downregulation of highly expressed genes. A similar differential effect is observed at the level of chromatin accessibility. Only SAHA is a potent inducer of cell death, which is characterized by the upregulation of BH3-only genes BIK and BMF. Up-regulation of BIK is associated with increased accessibility in an intronic region that has enhancer properties. SAHA, but not NKL54, also causes downregulation of BCL2L1 and decreases chromatin accessibility in three distinct regions of the BCL2L1 locus. Both inhibitors upregulate the expression of innate immunity genes and members of the MHC family. In summary, our exploratory study indicates a mechanism of action for SAHA and demonstrate the low efficacy of NKL54 as a single agent for apoptosis induction, using two PDOs. These observations need to be validated in a larger cohort of PDOs.
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Affiliation(s)
- Teresa Gagliano
- Department of Medicine, Università degli Studi di Udine, Institute for Biomedicine, P.le Kolbe 4, Udine 33100, Italy
| | - Emanuela Kerschbamer
- Department of Medicine, Università degli Studi di Udine, Institute for Biomedicine, P.le Kolbe 4, Udine 33100, Italy
| | - Umberto Baccarani
- Department of Medicine, Università degli Studi di Udine, Institute for Biomedicine, P.le Kolbe 4, Udine 33100, Italy
| | - Martina Minisini
- Department of Medicine, Università degli Studi di Udine, Institute for Biomedicine, P.le Kolbe 4, Udine 33100, Italy
| | - Eros Di Giorgio
- Department of Medicine, Università degli Studi di Udine, Institute for Biomedicine, P.le Kolbe 4, Udine 33100, Italy
| | - Emiliano Dalla
- Department of Medicine, Università degli Studi di Udine, Institute for Biomedicine, P.le Kolbe 4, Udine 33100, Italy
| | | | - Vittorio Cherchi
- General Surgery Clinic and Liver Transplant Center, University-Hospital of Udine, Udine, Italy
| | - Giovanni Terrosu
- Department of Medicine, Università degli Studi di Udine, Institute for Biomedicine, P.le Kolbe 4, Udine 33100, Italy
| | - Claudio Brancolini
- Department of Medicine, Università degli Studi di Udine, Institute for Biomedicine, P.le Kolbe 4, Udine 33100, Italy.
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12
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Fatima I, Ahmad R, Barman S, Gowrikumar S, Pravoverov K, Primeaux M, Fisher KW, Singh AB, Dhawan P. Albendazole inhibits colon cancer progression and therapy resistance by targeting ubiquitin ligase RNF20. Br J Cancer 2024; 130:1046-1058. [PMID: 38278978 PMCID: PMC10951408 DOI: 10.1038/s41416-023-02570-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 12/08/2023] [Accepted: 12/21/2023] [Indexed: 01/28/2024] Open
Abstract
BACKGROUND The repurposing of FDA-approved drugs for anti-cancer therapies is appealing due to their established safety profiles and pharmacokinetic properties and can be quickly moved into clinical trials. Cancer progression and resistance to conventional chemotherapy remain the key hurdles in improving the clinical management of colon cancer patients and associated mortality. METHODS High-throughput screening (HTS) was performed using an annotated library of 1,600 FDA-approved drugs to identify drugs with strong anti-CRC properties. The candidate drug exhibiting most promising inhibitory effects in in-vitro studies was tested for its efficacy using in-vivo models of CRC progression and chemoresistance and patient derived organoids (PTDOs). RESULTS Albendazole, an anti-helminth drug, demonstrated the strongest inhibitory effects on the tumorigenic potentials of CRC cells, xenograft tumor growth and organoids from mice. Also, albendazole sensitized the chemoresistant CRC cells to 5-fluorouracil (5-FU) and oxaliplatin suggesting potential to treat chemoresistant CRC. Mechanistically, Albendazole treatment modulated the expression of RNF20, to promote apoptosis in CRC cells by delaying the G2/M phase and suppressing anti-apoptotic-Bcl2 family transcription. CONCLUSIONS Albendazole, an FDA approved drug, carries strong therapeutic potential to treat colon cancers which are aggressive and potentially resistant to conventional chemotherapeutic agents. Our findings also lay the groundwork for further clinical testing.
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Affiliation(s)
- Iram Fatima
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Rizwan Ahmad
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Susmita Barman
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Saiprasad Gowrikumar
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Kristina Pravoverov
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Mark Primeaux
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Kurt W Fisher
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Amar B Singh
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
- Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
- VA Nebraska-Western Iowa Health Care System, Omaha, NE, USA
| | - Punita Dhawan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA.
- Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA.
- VA Nebraska-Western Iowa Health Care System, Omaha, NE, USA.
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13
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Liu Y, Zhao J, Huang B, Liang Y, Jiang G, Zhou X, Chen Y, He T, Zheng M, Huang Z. Identification and validation of an immunotherapeutic signature for colon cancer based on the regulatory patterns of ferroptosis and their association with the tumor microenvironment. Biochim Biophys Acta Mol Cell Res 2024; 1871:119698. [PMID: 38387508 DOI: 10.1016/j.bbamcr.2024.119698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 02/04/2024] [Accepted: 02/15/2024] [Indexed: 02/24/2024]
Abstract
The integrated landscape of ferroptosis regulatory patterns and their association with colon microenvironment have been demonstrated in recent studies. However, the ferroptosis-related immunotherapeutic signature for colon cancer (CC) remains unclear. We comprehensively evaluated 1623 CC samples, identified patterns of ferroptosis modification based on ferroptosis-associated genes, and systematically correlated these patterns with tumor microenvironment (TME) cell infiltration characteristics. In addition, the ferroptosis-regulated gene score (FRG-score) was constructed to quantify the pattern of ferroptosis alterations in individual tumors. Three distinct patterns of ferroptosis modification were identified, including antioxidant defense, iron toxicity, and lipid peroxidation. The characteristics of TME cell infiltration under these three patterns were highly consistent with the three immune phenotypes of tumors, including immune-inflamed, immune-excluded and immune-desert phenotypes. We also demonstrated that evaluation of ferroptosis regulatory patterns within individual tumors can predict tumor inflammatory status, tumor subtype, TME stromal activity, genetic variation, and clinical outcome. Immunotherapy cohorts confirmed that patients with low FRG-scores showed remarkable therapeutic and clinical benefits. Furthermore, the hub gene apolipoprotein L6 (APOL6), a drug-sensitive target associated with cancer cell ferroptosis, was identified through our proposed novel key gene screening process and validated in CC cell lines and scRNA-seq.
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Affiliation(s)
- Yong Liu
- Key Laboratory of Computer-Aided Drug Design of Dongguan City, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523710, Guangdong, PR China; Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan 523808, Guangdong, PR China
| | - Junzhang Zhao
- Department of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, Guangdong, PR China
| | - Baoxiang Huang
- Key Laboratory of Computer-Aided Drug Design of Dongguan City, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523710, Guangdong, PR China; Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan 523808, Guangdong, PR China
| | - Youcheng Liang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, PR China
| | - Guanming Jiang
- Dongguan Institute of Clinical Oncology Research in Dongguan People's Hospital, Dongguan 523018, Guangdong, PR China
| | - Xinglin Zhou
- Key Laboratory of Computer-Aided Drug Design of Dongguan City, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523710, Guangdong, PR China; Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan 523808, Guangdong, PR China
| | - Yilin Chen
- Key Laboratory of Computer-Aided Drug Design of Dongguan City, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523710, Guangdong, PR China; Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan 523808, Guangdong, PR China
| | - Tao He
- School of Basic Medicine, Guangdong Medical University, Dongguan 523018, Guangdong, PR China
| | - Mingbin Zheng
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan 523808, Guangdong, PR China; National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, Southern University of Science and Technology, Shenzhen 518112, Guangdong, PR China.
| | - Zunnan Huang
- Key Laboratory of Computer-Aided Drug Design of Dongguan City, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523710, Guangdong, PR China; Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Guangdong Medical University, Dongguan 523808, Guangdong, PR China.
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14
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Sears CL, Queen J. Whittling down the bacterial subspecies that might drive colon cancer. Nature 2024; 628:275-276. [PMID: 38509290 DOI: 10.1038/d41586-024-00662-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
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15
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Wang S, Wang L, Qiu M, Lin Z, Qi W, Lv J, Wang Y, Lu Y, Li X, Chen W, Qiu W. Constructing and validating a risk model based on neutrophil-related genes for evaluating prognosis and guiding immunotherapy in colon cancer. J Gene Med 2024; 26:e3684. [PMID: 38618694 DOI: 10.1002/jgm.3684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/25/2024] [Accepted: 03/03/2024] [Indexed: 04/16/2024] Open
Abstract
BACKGROUND Colon cancer is one of the most common digestive tract malignancies. Although immunotherapy has brought new hope to colon cancer patients, there is still a large proportion of patients who do not benefit from immunotherapy. Studies have shown that neutrophils can interact with immune cells and immune factors to affect the prognosis of patients. METHODS We first determined the infiltration level of neutrophils in tumors using the CIBERSORT algorithm and identified key genes in the final risk model by Spearman correlation analysis and subsequent Cox analysis. The risk score of each patient was obtained by multiplying the Cox regression coefficient and the gene expression level, and patients were divided into two groups based on the median of risk score. Differences in overall survival (OS) and progression-free survival (PFS) were assessed by Kaplan-Meier survival analysis, and model accuracy was validated in independent dataset. Differences in immune infiltration and immunotherapy were evaluated by immunoassay. Finally, immunohistochemistry and western blotting were performed to verify the expression of the three genes in the colon normal and tumor tissues. RESULTS We established and validated a risk scoring model based on neutrophil-related genes in two independent datasets, The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database, with SLC11A1 and SLC2A3 as risk factors and MMP3 as a protective factor. A new nomogram was constructed and validated by combining clinical characteristics and the risk score model to better predict patients OS and PFS. Immune analysis showed that patients in the high-risk group had immune cell infiltration level, immune checkpoint level and tumor mutational burden, and were more likely to benefit from immunotherapy. CONCLUSIONS The low-risk group showed better OS and PFS than the high-risk group in the neutrophil-related gene-based risk model. Patients in the high-risk group presented higher immune infiltration levels and tumor mutational burden and thus may be more responsive to immunotherapy.
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Affiliation(s)
- Shasha Wang
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, China
- Department of Oncology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Lili Wang
- Department of Oncology, Rizhao Central Hospital, Rizhao, China
| | - Mingxiu Qiu
- Department Second of Respiratory and Critical Care, Qingdao Municipal Hospital, Qingdao, China
| | - Zhongkun Lin
- Department of Oncology, Shandong Provincial Third Hospital, Shandong University, Jinan, China
| | - Weiwei Qi
- Department of Oncology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Jing Lv
- Department of Oncology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yan Wang
- Department of Oncology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yangyang Lu
- Department of Oncology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiaoxuan Li
- Department of Oncology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Wenzhi Chen
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, China
| | - Wensheng Qiu
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, China
- Department of Oncology, Affiliated Hospital of Qingdao University, Qingdao, China
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16
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Susanto AC, Hartajanie L, Wu CC. α‑Phellandrene enhances the apoptosis of HT‑29 cells induced by 5‑fluorouracil by modulating the mitochondria‑dependent pathway. Oncol Rep 2024; 51:61. [PMID: 38456489 PMCID: PMC10940876 DOI: 10.3892/or.2024.8720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/09/2024] [Indexed: 03/09/2024] Open
Abstract
α‑Phellandrene (α‑PA), a natural constituent of herbs, inhibits cancer cell viability and proliferation. 5‑Fluorouracil (5‑FU) is a frequently utilized chemotherapeutic medicine for the treatment of colon cancer, which works by triggering cancer cell apoptosis. The present study examined how the combination of α‑PA and 5‑FU affects the suppression of human colon cancer cells by promoting apoptosis. The impact of this treatment on cell viability, apoptosis, and the expression levels of Bcl‑2 family members, caspase family members and mitochondria‑related molecules in HT‑29 cells was assessed by the MTT assay, immunocytochemistry, western blotting and quantitative PCR. The combination of 5‑FU and α‑PA had a synergistic inhibitory effect on cell viability, as determined by assessing the combination index value. Bax protein expression levels were higher in the 50, 100 or 250 µM α‑PA combined with 5‑FU groups compared with those in the 5‑FU alone group (P<0.05). By contrast, Bcl‑2 protein expression levels and mitochondrial membrane potential (MMP, ΔΨm) were lower in the 100 or 250 µM α‑PA combined with 5‑FU groups than those in the 5‑FU alone group (P<0.05). In addition, hexokinase‑2 (HK‑2) protein expression levels were lower in the 50, 100 or 250 µM α‑PA combined with 5‑FU groups than those in the 5‑FU alone group (P<0.05). Compared with 5‑FU alone, after HT‑29 cells were treated with 50, 100 or 250 µM α‑PA combined with 5‑FU, the mRNA expression levels of extrinsic‑induced apoptotic molecules, including caspase‑8 and Bid, were higher (P<0.05). Treatment with 50, 100 or 250 µM α‑PA combined with 5‑FU also increased the mRNA expression levels of cytochrome c, caspase‑9 and caspase‑3, regulating intrinsic apoptosis (P<0.05). These results showed that α‑PA and 5‑FU had a synergistic effect on reducing the viability of human colon cancer HT‑29 cells by inducing extrinsic and intrinsic apoptosis pathways. The mechanism by which apoptosis is induced may involve the intrinsic apoptosis pathway that activates the mitochondria‑dependent pathway, including regulating the expression levels of Bcl‑2 family members, including Bax, Bcl‑2 and Bid, regulating MMP and HK‑2 expression levels, and increasing the expression of caspase cascade molecules, including caspase‑9 and caspase‑3. In addition, it may involve the extrinsic apoptosis pathway that activates caspase‑8 and caspase‑3 leading to apoptosis.
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Affiliation(s)
- Anita Caroline Susanto
- Department of Food and Nutrition, Providence University, Taichung 43301, Taiwan, R.O.C
- Faculty of Food Technology, Soegijapranata Catholic University, Semarang 50234, Indonesia
| | - Laksmi Hartajanie
- Faculty of Food Technology, Soegijapranata Catholic University, Semarang 50234, Indonesia
| | - Chih-Chung Wu
- Department of Food and Nutrition, Providence University, Taichung 43301, Taiwan, R.O.C
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17
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Fan Q, Wu GB, Chen M, Zheng L, Li HJ, Xiang LZ, Luo M. Analysis of disulfidptosis- and cuproptosis-related LncRNAs in modulating the immune microenvironment and chemosensitivity in colon adenocarcinoma. IET Syst Biol 2024; 18:55-75. [PMID: 38458989 PMCID: PMC10996446 DOI: 10.1049/syb2.12089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 01/09/2024] [Accepted: 01/28/2024] [Indexed: 03/10/2024] Open
Abstract
The main objective was to establish a prognostic model utilising long non-coding RNAs associated with disulfidptosis and cuproptosis. The data for RNA-Sequence and clinicopathological information of Colon adenocarcinoma (COAD) were acquired from The Cancer Genome Atlas. A prognostic model was constructed using Cox regression and the Least Absolute Shrinkage and Selection Operator method. The model's predictive ability was assessed through principal component analysis, Kaplan-Meier analysis, nomogram etc. The ability of identifying the rates of overall survival, infiltration of immune cells, and chemosensitivity was also explored. In vitro experiments were conducted for the validation of differential expression and function of lncRNAs. A disulfidptosis and cuproptosis-related lncRNA prognostic model was constructed. The prognostic model exhibits excellent independent predictive capability for patient outcomes. Based on the authors' model, the high-risk group exhibited higher tumour mutation burdened worse survival. Besides, differences in immune cell infiltration and responsiveness to chemotherapeutic medications exist among patients with different risk scores. Furthermore, aberrant expressions in certain lncRNAs have been validated in HCT116 cells. In particular, FENDRR and SNHG7 could affect the proliferation and migration of colorectal cancer cells. Our study developed a novel prognostic signature, providing valuable insights into prognosis, immune infiltration, and chemosensitivity in COAD patients.
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Affiliation(s)
- Qiang Fan
- Department of General Surgery, Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guang-Bo Wu
- Department of General Surgery, Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Min Chen
- Department of General Surgery, Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lei Zheng
- Department of General Surgery, Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hong-Jie Li
- Department of General Surgery, Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lv-Zhu Xiang
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Meng Luo
- Department of General Surgery, Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
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18
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Zhang H, Liu R, Jing Z, Li C, Fan W, Li H, Li H, Ren J, Cui S, Zhao W, Yu L, Bai Y, Liu S, Fang C, Yang W, Wei Y, Li L, Peng S. LRRC8A as a central mediator promotes colon cancer metastasis by regulating PIP5K1B/PIP2 pathway. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167066. [PMID: 38350542 DOI: 10.1016/j.bbadis.2024.167066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/15/2024]
Abstract
Colorectal cancer (CRC) has been the third most common malignancy and the second cause of cancer-related mortality. As the core of volume-sensitive chloride currents, leucine-rich repeat-containing 8A (LRRC8A) contributes to tumor progression but is not consistent, especially for whom the roles in colon carcinoma metastasis were not fully elucidated. Herein, LRRC8A proteins were found highly expressed in hematogenous metastasis from human colorectal cancer samples. The oxaliplatin-resistant HCT116 cells highly expressed LRRC8A, which was related to impaired proliferation and enhanced migration. The over-expressed LRRC8A slowed proliferation and increased migration ex vivo and in vivo. The elevated LRRC8A upregulated the focal adhesion, MAPK, AMPK, and chemokine signaling pathways via phosphorylation and dephosphorylation. Inhibition of LRRC8A impeded the TNF-α signaling cascade and TNF-α-induced migration. LRRC8A binding to PIP5K1B regulated the PIP2 formation, providing a platform for LRRC8A to mediate cell signaling transduction. Importantly, LRRC8A self-regulated its transcription via NF-κB1 and NF-κB2 pathways and the upregulation of NIK/NF-κB2/LRRC8A transcriptional axis was unfavorable for colon cancer patients. Collectively, our findings reveal that LRRC8A is a central mediator in mediating multiple signaling pathways to promote metastasis and targeting LRRC8A proteins could become a potential clinical biomarker-driven treatment strategy for colon cancer patients.
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Affiliation(s)
- Haifeng Zhang
- Department of Pathology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China.
| | - Rong Liu
- Department of Pathology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China
| | - Zhenghui Jing
- Department of Pathology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China
| | - Chunying Li
- School of Nursing, Li Shui University, Lishui, Zhejiang 323020, China
| | - Wentao Fan
- Guangzhou Huayin Medical Laboratory Center. Ltd, Guangzhou, Guangdong 510663, China
| | - Houli Li
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Hongbing Li
- Department of Internal Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Jie Ren
- Department of Internal Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Shiyu Cui
- Department of Pathology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China
| | - Wenbao Zhao
- Department of Pathology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China
| | - Lei Yu
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, China
| | - Yuhui Bai
- Key Laboratory of Sports Technique, Tactics and Physical Function of General Administration of Sport of China, Scientific Research Center, Guangzhou Sport University, Guangzhou, Guangdong 510500, China
| | - Shujing Liu
- Key Laboratory of Sports Technique, Tactics and Physical Function of General Administration of Sport of China, Scientific Research Center, Guangzhou Sport University, Guangzhou, Guangdong 510500, China
| | - Chunlu Fang
- Key Laboratory of Sports Technique, Tactics and Physical Function of General Administration of Sport of China, Scientific Research Center, Guangzhou Sport University, Guangzhou, Guangdong 510500, China
| | - Wenqi Yang
- Key Laboratory of Sports Technique, Tactics and Physical Function of General Administration of Sport of China, Scientific Research Center, Guangzhou Sport University, Guangzhou, Guangdong 510500, China
| | - Yuan Wei
- Key Laboratory of Sports Technique, Tactics and Physical Function of General Administration of Sport of China, Scientific Research Center, Guangzhou Sport University, Guangzhou, Guangdong 510500, China
| | - Liangming Li
- Key Laboratory of Sports Technique, Tactics and Physical Function of General Administration of Sport of China, Scientific Research Center, Guangzhou Sport University, Guangzhou, Guangdong 510500, China; School of Sport and Health Sciences, Guangzhou Sport University, Guangzhou, Guangdong 510500, China
| | - Shuang Peng
- Key Laboratory of Sports Technique, Tactics and Physical Function of General Administration of Sport of China, Scientific Research Center, Guangzhou Sport University, Guangzhou, Guangdong 510500, China; School of Sport and Health Sciences, Guangzhou Sport University, Guangzhou, Guangdong 510500, China.
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19
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Li Y, Wang S, Li G, Gao C, Cui Z, Cong M, Hu J, Zhang M, Jin X, Sun H, Kong D. The RNA-binding protein RBMS3 inhibits the progression of colon cancer by regulating the stability of LIMS1 mRNA. Cancer Med 2024; 13:e7129. [PMID: 38618967 PMCID: PMC11017296 DOI: 10.1002/cam4.7129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 03/02/2024] [Accepted: 03/11/2024] [Indexed: 04/16/2024] Open
Abstract
BACKGROUND The RNA-binding motif single-stranded interacting protein 3 (RBMS3) is a constituent of the RNA-binding motif (RBM) protein family, which assumes a pivotal role in governing cellular biogenesis processes such as the cell cycle and apoptosis. Despite an abundance of studies elucidating RBMS3's divergent roles in the genesis and advancement of various tumors, its involvement in colon cancer remains enigmatic. METHODS The present investigation employed data analysis from TCGA and GTEx to unveil that RBMS3 expression demonstrated a diminished presence in colon cancer tissues when juxtaposed with normal colon tissues. The effect of RBMS3 and LIM zinc finger domain 1 (LIMS1) on colon cancer was substantiated via animal models and cellular experiments. The connection between RBMS3 and LIM zinc finger domain 1 (LIMS1) was verified by molecular biology methods. RESULTS The study conclusively ascertained that augmenting RBMS3 expression quells the proliferation, migration, and invasion of colon cancer cells. Furthermore, the inquiry unveiled a plausible mechanism through which RBMS3 impacts the expression of LIMS1 by modulating its mRNA stability. The investigation ascertained that RBMS3 inhibits the progression of colon cancer by regulating LIMS1. The inhibitory function of LIMS1 and RBMS3 is closely intertwined in colon cancer, with knocking down LIMS1 being able to rescue the inhibitory effect of RBMS3 overexpression on the functionality of colon cancer cell CONCLUSIONS: The discernments delineate RBMS3 as a novel suppressor of cancer via LIMS1, thereby bestowing fresh therapeutic possibilities and illuminating the intricacies of colon cancer.
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Affiliation(s)
- Yafei Li
- Department of PathologyHarbin Medical UniversityHarbinChina
| | - Shuoshuo Wang
- Department of PathologyHarbin Medical UniversityHarbinChina
| | - Guoli Li
- Department of Anus and Intestine SurgeryChifeng Municipal HospitalChifengChina
| | - Chunyang Gao
- Department of AnatomyHarbin Medical UniversityHarbinChina
| | - Zihan Cui
- Department of PathologyHarbin Medical UniversityHarbinChina
| | - Mingqi Cong
- Department of PathologyHarbin Medical UniversityHarbinChina
| | - Jie Hu
- Central Operating DepartmentThe First Affiliated Hospital of Harbin Medical UniversityHarbinChina
| | - Minghui Zhang
- Department of OncologyChifeng Municipal HospitalChifengChina
| | - Xiaoming Jin
- Department of PathologyHarbin Medical UniversityHarbinChina
| | - Haiying Sun
- Gastrointestinal Rehabilitation CenterBeijing Rehabilitation Hospital of Capital Medical UniversityBeijingChina
- Gastroenterology DepartmentFirst Hospital of DandongDandongChina
| | - Dan Kong
- Department of GynaecologyTumor Hospital of Harbin Medical UniversityHarbinChina
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20
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Rao C, Tong J, Yang Y. Mechanistic insights into FEN1-mediated drug sensitivity and risk signature in colon cancer: An integrative bioinformatics study. Medicine (Baltimore) 2024; 103:e37517. [PMID: 38552056 PMCID: PMC10977573 DOI: 10.1097/md.0000000000037517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 02/15/2024] [Indexed: 04/02/2024] Open
Abstract
The overexpression of Flap endonuclease 1 (FEN1) has been implicated in drug resistance and prognosis across various cancer types. However, the precise role of FEN1 in colon cancer remains to be fully elucidated. In this study, we employed comprehensive datasets from The Cancer Genome Atlas, Gene Expression Omnibus, and Human Protein Atlas to examine FEN1 expression and assess its correlation with clinical pathology and prognosis in colon cancer. We utilized the pRRophetic algorithm to evaluate drug sensitivity and performed differential expression analysis to identify genes associated with FEN1-mediated drug sensitivity. Gene set enrichment analysis was conducted to further investigate these genes. Additionally, single-cell sequencing analysis was employed to explore the relationship between FEN1 expression and functional states. Cox regression analysis was implemented to construct a prognostic model, and a nomogram for prognosis was developed. Our analysis of The Cancer Genome Atlas and Gene Expression Omnibus datasets revealed a significant upregulation of FEN1 in colon cancer. However, while FEN1 expression showed no notable correlation with prognosis, it displayed associations with metastasis. Single-cell sequencing analysis further confirmed a positive correlation between FEN1 expression and colon cancer metastasis. Furthermore, we detected marked discrepancies in drug responsiveness between the High_FEN1 and Low_FEN1 groups, identifying 342 differentially expressed genes. Enrichment analysis showed significant suppression in processes related to DNA replication, spliceosome, and cell cycle pathways in the Low_FEN1 group, while the calcium signaling pathway, cAMP signaling pathway, and other pathways were activated. Of the 197 genes differentially expressed and strongly linked to FEN1 expression, 39 were significantly implicated in colon cancer prognosis. Finally, we constructed a risk signature consisting of 5 genes, which, when combined with drug treatment and pathological staging, significantly improved the prediction of colon cancer prognosis. This study offers novel insights into the interplay among FEN1 expression levels, colon cancer metastatic potential, and sensitivity to therapeutic agents. Furthermore, we successfully developed a multi-gene prognostic risk signature derived from FEN1.
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Affiliation(s)
- Chunhui Rao
- Department of Proctology, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Jingfei Tong
- Department of Proctology, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Yan Yang
- Department of Otolaryngology, Banshan Community Health Service Center, Gongshu District, Hangzhou, Zhejiang, China
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21
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Chomiak AA, Tiedemann RL, Liu Y, Kong X, Cui Y, Wiseman AK, Thurlow KE, Cornett EM, Topper MJ, Baylin SB, Rothbart SB. Select EZH2 inhibitors enhance viral mimicry effects of DNMT inhibition through a mechanism involving NFAT:AP-1 signaling. Sci Adv 2024; 10:eadk4423. [PMID: 38536911 PMCID: PMC10971413 DOI: 10.1126/sciadv.adk4423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 02/21/2024] [Indexed: 04/05/2024]
Abstract
DNA methyltransferase inhibitor (DNMTi) efficacy in solid tumors is limited. Colon cancer cells exposed to DNMTi accumulate lysine-27 trimethylation on histone H3 (H3K27me3). We propose this Enhancer of Zeste Homolog 2 (EZH2)-dependent repressive modification limits DNMTi efficacy. Here, we show that low-dose DNMTi treatment sensitizes colon cancer cells to select EZH2 inhibitors (EZH2is). Integrative epigenomic analysis reveals that DNMTi-induced H3K27me3 accumulates at genomic regions poised with EZH2. Notably, combined EZH2i and DNMTi alters the epigenomic landscape to transcriptionally up-regulate the calcium-induced nuclear factor of activated T cells (NFAT):activating protein 1 (AP-1) signaling pathway. Blocking this pathway limits transcriptional activating effects of these drugs, including transposable element and innate immune response gene expression involved in viral defense. Analysis of primary human colon cancer specimens reveals positive correlations between DNMTi-, innate immune response-, and calcium signaling-associated transcription profiles. Collectively, we show that compensatory EZH2 activity limits DNMTi efficacy in colon cancer and link NFAT:AP-1 signaling to epigenetic therapy-induced viral mimicry.
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Affiliation(s)
- Alison A. Chomiak
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | | | - Yanqing Liu
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Xiangqian Kong
- Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Ying Cui
- Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Ashley K. Wiseman
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Kate E. Thurlow
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Evan M. Cornett
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indiana University, Indianapolis, IN 46202, USA
| | - Michael J. Topper
- Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Stephen B. Baylin
- Department of Oncology, the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Scott B. Rothbart
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
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22
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He L, Li H, Wang Y, Li W, Gao L, Xu B, Hu J, He P, Pu W, Sun G, Wang Z, Han Q, Liu B, Chen H. Complete remission in a pretreated, microsatellite-stable, KRAS-mutated colon cancer patient after treatment with sintilimab and bevacizumab and platinum-based chemotherapy: a case report and literature review. Front Immunol 2024; 15:1354613. [PMID: 38617840 PMCID: PMC11010642 DOI: 10.3389/fimmu.2024.1354613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/01/2024] [Indexed: 04/16/2024] Open
Abstract
Metastatic colon cancer remains an incurable disease, and it is difficult for existing treatments to achieve the desired clinical outcome, especially for colon cancer patients who have received first-line treatment. Although immune checkpoint inhibitors (ICIs) have demonstrated durable clinical efficacy in a variety of solid tumors, their response requires an inflammatory tumor microenvironment. However, microsatellite-stable (MSS) colon cancer, which accounts for the majority of colorectal cancers, is a cold tumor that does not respond well to ICIs. Combination regimens open the door to the utility of ICIs in cold tumors. Although combination therapies have shown their advantage even for MSS colon cancer, it remains unclear whether combination therapies show their advantage in patients with pretreated metastatic colon cancer. We report a patient who has achieved complete remission and good tolerance with sintilimab plus bevacizumab and platinum-based chemotherapy after postoperative recurrence. The patient had KRAS mutation and MSS-type colon cancer, and his PD-1+CD8+ and CD3-CD19-CD14+CD16-HLA-DR were both positive. He has achieved a progression-free survival of 43 months and is still being followed up at our center. The above results suggest that this therapeutic regimen is a promising treatment modality for the management of pretreated, MSS-type and KRAS-mutated metastatic colorectal cancer although its application to the general public still needs to be validated in clinical trials.
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Affiliation(s)
- Lijuan He
- Lanzhou University Second Hospital, Lanzhou, China
- Department of Surgical Oncology, Lanzhou University Second Hospital, Lanzhou, China
| | - Haiyuan Li
- Lanzhou University Second Hospital, Lanzhou, China
- Department of Surgical Oncology, Lanzhou University Second Hospital, Lanzhou, China
| | - Yunpeng Wang
- Lanzhou University Second Hospital, Lanzhou, China
- Department of Surgical Oncology, Lanzhou University Second Hospital, Lanzhou, China
| | - Weidong Li
- Lanzhou University Second Hospital, Lanzhou, China
- Department of Pathology, Lanzhou University Second Hospital, Lanzhou, China
| | - Lei Gao
- Lanzhou University Second Hospital, Lanzhou, China
- Department of Surgical Oncology, Lanzhou University Second Hospital, Lanzhou, China
| | - Bo Xu
- Lanzhou University Second Hospital, Lanzhou, China
- Department of Surgical Oncology, Lanzhou University Second Hospital, Lanzhou, China
| | - Jike Hu
- Lanzhou University Second Hospital, Lanzhou, China
- Department of Surgical Oncology, Lanzhou University Second Hospital, Lanzhou, China
| | - Puyi He
- Lanzhou University Second Hospital, Lanzhou, China
- Department of Surgical Oncology, Lanzhou University Second Hospital, Lanzhou, China
| | - Weigao Pu
- Lanzhou University Second Hospital, Lanzhou, China
- Department of Surgical Oncology, Lanzhou University Second Hospital, Lanzhou, China
| | - Guodong Sun
- Lanzhou University Second Hospital, Lanzhou, China
- Department of Surgical Oncology, Lanzhou University Second Hospital, Lanzhou, China
| | - Zhuanfang Wang
- Lanzhou University Second Hospital, Lanzhou, China
- Department of Surgical Oncology, Lanzhou University Second Hospital, Lanzhou, China
| | - Qinying Han
- Lanzhou University Second Hospital, Lanzhou, China
- Department of Surgical Oncology, Lanzhou University Second Hospital, Lanzhou, China
| | - Ben Liu
- Lanzhou University Second Hospital, Lanzhou, China
- Department of Surgical Oncology, Lanzhou University Second Hospital, Lanzhou, China
| | - Hao Chen
- Lanzhou University Second Hospital, Lanzhou, China
- Department of Surgical Oncology, Lanzhou University Second Hospital, Lanzhou, China
- Gansu Provincial Key Laboratory Of Environmental Oncology, Lanzhou, China
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23
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Tian Z, Han C, Xu L, Teng Z, Song W. MGCNSS: miRNA-disease association prediction with multi-layer graph convolution and distance-based negative sample selection strategy. Brief Bioinform 2024; 25:bbae168. [PMID: 38622356 PMCID: PMC11018511 DOI: 10.1093/bib/bbae168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/14/2024] [Accepted: 03/31/2024] [Indexed: 04/17/2024] Open
Abstract
Identifying disease-associated microRNAs (miRNAs) could help understand the deep mechanism of diseases, which promotes the development of new medicine. Recently, network-based approaches have been widely proposed for inferring the potential associations between miRNAs and diseases. However, these approaches ignore the importance of different relations in meta-paths when learning the embeddings of miRNAs and diseases. Besides, they pay little attention to screening out reliable negative samples which is crucial for improving the prediction accuracy. In this study, we propose a novel approach named MGCNSS with the multi-layer graph convolution and high-quality negative sample selection strategy. Specifically, MGCNSS first constructs a comprehensive heterogeneous network by integrating miRNA and disease similarity networks coupled with their known association relationships. Then, we employ the multi-layer graph convolution to automatically capture the meta-path relations with different lengths in the heterogeneous network and learn the discriminative representations of miRNAs and diseases. After that, MGCNSS establishes a highly reliable negative sample set from the unlabeled sample set with the negative distance-based sample selection strategy. Finally, we train MGCNSS under an unsupervised learning manner and predict the potential associations between miRNAs and diseases. The experimental results fully demonstrate that MGCNSS outperforms all baseline methods on both balanced and imbalanced datasets. More importantly, we conduct case studies on colon neoplasms and esophageal neoplasms, further confirming the ability of MGCNSS to detect potential candidate miRNAs. The source code is publicly available on GitHub https://github.com/15136943622/MGCNSS/tree/master.
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Affiliation(s)
- Zhen Tian
- School of Computer and Artificial Intelligence, Zhengzhou University, Zhengzhou 450000, China
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324000, China
| | - Chenguang Han
- School of Computer and Artificial Intelligence, Zhengzhou University, Zhengzhou 450000, China
| | - Lewen Xu
- School of Computer and Artificial Intelligence, Zhengzhou University, Zhengzhou 450000, China
| | - Zhixia Teng
- College of Computer and Control Engineering, Northeast Forestry University, Harbin 150040, China
| | - Wei Song
- School of Computer and Artificial Intelligence, Zhengzhou University, Zhengzhou 450000, China
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24
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Wang Y, Gao JZ, Sakaguchi T, Maretzky T, Gurung P, Narayanan NS, Short S, Xiong Y, Kang Z. LRRK2 G2019S Promotes Colon Cancer Potentially via LRRK2-GSDMD Axis-Mediated Gut Inflammation. Cells 2024; 13:565. [PMID: 38607004 PMCID: PMC11011703 DOI: 10.3390/cells13070565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/20/2024] [Accepted: 03/22/2024] [Indexed: 04/13/2024] Open
Abstract
Leucine-rich repeat kinase 2 (LRRK2) is a serine-threonine protein kinase belonging to the ROCO protein family. Within the kinase domain of LRRK2, a point mutation known as LRRK2 G2019S has emerged as the most prevalent variant associated with Parkinson's disease. Recent clinical studies have indicated that G2019S carriers have an elevated risk of cancers, including colon cancer. Despite this observation, the underlying mechanisms linking LRRK2 G2019S to colon cancer remain elusive. In this study, employing a colitis-associated cancer (CAC) model and LRRK2 G2019S knock-in (KI) mouse model, we demonstrate that LRRK2 G2019S promotes the pathogenesis of colon cancer, characterized by increased tumor number and size in KI mice. Furthermore, LRRK2 G2019S enhances intestinal epithelial cell proliferation and inflammation within the tumor microenvironment. Mechanistically, KI mice exhibit heightened susceptibility to DSS-induced colitis, with inhibition of LRRK2 kinase activity ameliorating colitis severity and CAC progression. Our investigation also reveals that LRRK2 G2019S promotes inflammasome activation and exacerbates gut epithelium necrosis in the colitis model. Notably, GSDMD inhibitors attenuate colitis in LRRK2 G2019S KI mice. Taken together, our findings offer experimental evidence indicating that the gain-of-kinase activity in LRRK2 promotes colorectal tumorigenesis, suggesting LRRK2 as a potential therapeutic target in colon cancer patients exhibiting hyper LRRK2 kinase activity.
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Affiliation(s)
- Yuhang Wang
- Department of Pathology, University of Iowa, Iowa City, IA 52242, USA
| | - Joyce Z. Gao
- Department of Pathology, University of Iowa, Iowa City, IA 52242, USA
| | - Taylor Sakaguchi
- Department of Pathology, University of Iowa, Iowa City, IA 52242, USA
| | - Thorsten Maretzky
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Prajwal Gurung
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Nandakumar S. Narayanan
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA 52242, USA
- Department of Neurology, University of Iowa, Iowa City, IA 52242, USA
| | - Sarah Short
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Yiqin Xiong
- Department of Pathology, University of Iowa, Iowa City, IA 52242, USA
| | - Zizhen Kang
- Department of Pathology, University of Iowa, Iowa City, IA 52242, USA
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25
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Hermosilla VE, Gyenis L, Rabalski AJ, Armijo ME, Sepúlveda P, Duprat F, Benítez-Riquelme D, Fuentes-Villalobos F, Quiroz A, Hepp MI, Farkas C, Mastel M, González-Chavarría I, Jackstadt R, Litchfield DW, Castro AF, Pincheira R. Casein kinase 2 phosphorylates and induces the SALL2 tumor suppressor degradation in colon cancer cells. Cell Death Dis 2024; 15:223. [PMID: 38493149 PMCID: PMC10944491 DOI: 10.1038/s41419-024-06591-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 02/29/2024] [Accepted: 03/05/2024] [Indexed: 03/18/2024]
Abstract
Spalt-like proteins are Zinc finger transcription factors from Caenorhabditis elegans to vertebrates, with critical roles in development. In vertebrates, four paralogues have been identified (SALL1-4), and SALL2 is the family's most dissimilar member. SALL2 is required during brain and eye development. It is downregulated in cancer and acts as a tumor suppressor, promoting cell cycle arrest and cell death. Despite its critical functions, information about SALL2 regulation is scarce. Public data indicate that SALL2 is ubiquitinated and phosphorylated in several residues along the protein, but the mechanisms, biological consequences, and enzymes responsible for these modifications remain unknown. Bioinformatic analyses identified several putative phosphorylation sites for Casein Kinase II (CK2) located within a highly conserved C-terminal PEST degradation motif of SALL2. CK2 is a serine/threonine kinase that promotes cell proliferation and survival and is often hyperactivated in cancer. We demonstrated that CK2 phosphorylates SALL2 residues S763, T778, S802, and S806 and promotes SALL2 degradation by the proteasome. Accordingly, pharmacological inhibition of CK2 with Silmitasertib (CX-4945) restored endogenous SALL2 protein levels in SALL2-deficient breast MDA-MB-231, lung H1299, and colon SW480 cancer cells. Silmitasertib induced a methuosis-like phenotype and cell death in SW480 cells. However, the phenotype was significantly attenuated in CRISPr/Cas9-mediated SALL2 knockout SW480 cells. Similarly, Sall2-deficient tumor organoids were more resistant to Silmitasertib-induced cell death, confirming that SALL2 sensitizes cancer cells to CK2 inhibition. We identified a novel CK2-dependent mechanism for SALL2 regulation and provided new insights into the interplay between these two proteins and their role in cell survival and proliferation.
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Affiliation(s)
- V E Hermosilla
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Transducción de Señales y Cáncer, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Dept of Orofacial Sciences and Dept of Anatomy, University of California-San Francisco, San Francisco, CA, USA
| | - L Gyenis
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, Canada
| | - A J Rabalski
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, Canada
- Odyssey Therapeutics, Boston, MA, USA
| | - M E Armijo
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Transducción de Señales y Cáncer, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - P Sepúlveda
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Transducción de Señales y Cáncer, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - F Duprat
- Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - D Benítez-Riquelme
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Transducción de Señales y Cáncer, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - F Fuentes-Villalobos
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Transducción de Señales y Cáncer, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Inmunovirología. Departamento de Microbiologia. Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - A Quiroz
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Transducción de Señales y Cáncer, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - M I Hepp
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Transducción de Señales y Cáncer, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Investigación en Ciencias Biomédicas, Departamento de Ciencias Básicas y Morfología, Facultad de Medicina, Universidad Católica de la Santísima Concepción, Concepción, Chile
| | - C Farkas
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Transducción de Señales y Cáncer, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Laboratorio de Investigación en Ciencias Biomédicas, Departamento de Ciencias Básicas y Morfología, Facultad de Medicina, Universidad Católica de la Santísima Concepción, Concepción, Chile
| | - M Mastel
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg. Cancer Progression and Metastasis Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - I González-Chavarría
- Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - R Jackstadt
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg. Cancer Progression and Metastasis Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - D W Litchfield
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, Canada
| | - A F Castro
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile.
- Laboratorio de Transducción de Señales y Cáncer, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile.
| | - R Pincheira
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile.
- Laboratorio de Transducción de Señales y Cáncer, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile.
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Hu Y, Luo M. Cinobufotalin regulates the USP36/c-Myc axis to suppress malignant phenotypes of colon cancer cells in vitro and in vivo. Aging (Albany NY) 2024; 16:5526-5544. [PMID: 38517383 PMCID: PMC11006458 DOI: 10.18632/aging.205661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 01/04/2024] [Indexed: 03/23/2024]
Abstract
Ubiquitin-specific protease 36 (USP36) has been reported to exhibit oncogenic effects in various malignancies, but the function of USP36 in colon cancer progression remains indefinite. Herein, we aimed to determine the role and mechanism of USP36 in malignant phenotypes of colon cancer cells and explore the potential drug targeting USP36. Bioinformatics analyses indicated that USP36 is highly expressed and significantly related to tumor stages in colon cancer. Besides, USP36 was further up-regulated in oxaliplatin (Oxa)-resistant colon cancer cells. Colony formation, Edu staining, Transwell, wound healing, sphere formation, and CCK-8 assays were conducted and showed that the proliferation, Oxa-resistance, migration, stemness, and invasion of HCT116 cells were promoted after overexpressing USP36, while suppressed by USP36 knockdown. Mechanically, USP36 enhances c-Myc protein stabilization in HCT116 cells via deubiquitination. AutoDock tool and ubiquitin-AMC hydrolysis assay identified cinobufotalin (CBF), an anti-tumor drug, maybe a USP36 inhibitor by inhibiting its deubiquitination activity. CBF significantly prohibited proliferation, migration, invasion, and stemness of HCT116 cells and reversed Oxa-resistance, whereas enforced expression of USP36 blocked these effects. Moreover, in vivo analyses confirmed the oncogenic role of USP36 and the therapeutic potential of CBF in the malignancy of colon cancer. In conclusion, CBF may be a promising therapeutic agent for colon cancer due to its regulation of the USP36/c-Myc axis.
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Affiliation(s)
- Yongjun Hu
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Ming Luo
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha 410011, China
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Solar Vasconcelos JP, Chen N, Titmuss E, Tu D, Brule SY, Goodwin R, Jonker DJ, Price T, Zalcberg JR, Moore MJ, Karapetis CS, Siu L, Shapiro J, Simes J, Gill S, O'Callaghan CJ, Loree JM. Transverse Colon Primary Tumor Location as a Biomarker in Metastatic Colorectal Cancer: A Pooled Analysis of CCTG/AGITG CO.17 and CO.20 Randomized Clinical Trials. Clin Cancer Res 2024; 30:1121-1130. [PMID: 38170586 PMCID: PMC10940852 DOI: 10.1158/1078-0432.ccr-23-3275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/29/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024]
Abstract
PURPOSE Sidedness is prognostic and predictive of anti-EGFR efficacy in metastatic colorectal cancer (mCRC). Transverse colon has been historically excluded from several analyses of sidedness and the optimal division between left- and right-sided colorectal cancer is unclear. We investigated transverse colon primary tumor location as a biomarker in mCRC. EXPERIMENTAL DESIGN Pooled analysis of CCTG/AGITG CO.17 and CO.20 trials of cetuximab in chemotherapy-refractory mCRC. Outcomes of patients with RAS/BRAF wild-type (WT) mCRC from CO.17 and KRAS WT mCRC from CO.20 were analyzed according to location. RESULTS A total of 553 patients were analyzed, 32 (5.8%) with cancers from the transverse, 101 (18.3%) from right, and 420 from (75.9%) left colon. Transverse mCRC failed to reach significant benefit from cetuximab versus best supportive care (BSC) for overall survival [OS; median, 5.9 vs. 2.1 months; HR, 0.63; 95% confidence interval (CI), 0.28-1.42; P=0.26] and progression-free survival (PFS; median, 1.8 vs. 1.3 months; HR, 0.57; 95% CI, 0.26-1.28; P=0.16). Analyzing exclusively patients randomized to cetuximab, right-sided and transverse had comparable outcomes for OS (median, 5.6 vs. 5.9 months; HR, 0.82; 95% CI, 0.50-1.34; P=0.43) and PFS (median, 1.9 vs. 1.8 months; HR, 0.78; 95% CI, 0.49-1.26; P=0.31). Patients with left-sided mCRC had superior outcomes with cetuximab compared with transverse for OS (median, 9.7 vs. 5.9 months; HR, 0.42; 95% CI, 0.27-0.67; P=0.0002) and PFS (median, 3.8 vs. 1.8 months; HR, 0,49; 95% CI, 0.31-0.76; P=0.001). Location was not prognostic in patients treated with BSC alone. CONCLUSIONS Transverse mCRC has comparable prognostic and predictive features with right-sided mCRC.
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Affiliation(s)
| | - Nan Chen
- Department of Public Health Sciences, Queen's University, Kingston, Ontario, Canada
| | - Emma Titmuss
- BC Cancer, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dongsheng Tu
- Canadian Cancer Trials Group, Kingston, Ontario, Canada
| | | | - Rachel Goodwin
- The Ottawa Hospital, University of Ottawa, Ottawa, Ontario, Canada
| | - Derek J. Jonker
- The Ottawa Hospital, University of Ottawa, Ottawa, Ontario, Canada
| | - Timothy Price
- Queen Elizabeth Hospital, Adelaide, South Australia, Australia
| | - John R. Zalcberg
- Department of Medical Oncology, Alfred Health and School of Public Health, Faculty of Medicine, Monash University, Melbourne, Victoria, Australia
| | - Malcolm J. Moore
- Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
| | | | - Lillian Siu
- Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
| | - Jeremy Shapiro
- Department of Medical Oncology, Alfred Health and School of Public Health, Faculty of Medicine, Monash University, Melbourne, Victoria, Australia
| | - John Simes
- The University of Sydney, Sydney, New South Wales, Australia
| | - Sharlene Gill
- BC Cancer, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Jonathan M. Loree
- BC Cancer, University of British Columbia, Vancouver, British Columbia, Canada
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da Silva WN, Carvalho Costa PA, Scalzo Júnior SRA, Ferreira HAS, Prazeres PHDM, Campos CLV, Rodrigues Alves MT, Alves da Silva NJ, de Castro Santos AL, Guimarães LC, Chen Ferris ME, Thatte A, Hamilton A, Bicalho KA, Lobo AO, Santiago HDC, da Silva Barcelos L, Figueiredo MM, Teixeira MM, Vasconcelos Costa V, Mitchell MJ, Frézard F, Pires Goulart Guimaraes P. Ionizable Lipid Nanoparticle-Mediated TRAIL mRNA Delivery in the Tumor Microenvironment to Inhibit Colon Cancer Progression. Int J Nanomedicine 2024; 19:2655-2673. [PMID: 38500680 PMCID: PMC10946446 DOI: 10.2147/ijn.s452896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 03/05/2024] [Indexed: 03/20/2024] Open
Abstract
Introduction Immunotherapy has revolutionized cancer treatment by harnessing the immune system to enhance antitumor responses while minimizing off-target effects. Among the promising cancer-specific therapies, tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) has attracted significant attention. Methods Here, we developed an ionizable lipid nanoparticle (LNP) platform to deliver TRAIL mRNA (LNP-TRAIL) directly to the tumor microenvironment (TME) to induce tumor cell death. Our LNP-TRAIL was formulated via microfluidic mixing and the induction of tumor cell death was assessed in vitro. Next, we investigated the ability of LNP-TRAIL to inhibit colon cancer progression in vivo in combination with a TME normalization approach using Losartan (Los) or angiotensin 1-7 (Ang(1-7)) to reduce vascular compression and deposition of extracellular matrix in mice. Results Our results demonstrated that LNP-TRAIL induced tumor cell death in vitro and effectively inhibited colon cancer progression in vivo, particularly when combined with TME normalization induced by treatment Los or Ang(1-7). In addition, potent tumor cell death as well as enhanced apoptosis and necrosis was found in the tumor tissue of a group treated with LNP-TRAIL combined with TME normalization. Discussion Together, our data demonstrate the potential of the LNP to deliver TRAIL mRNA to the TME and to induce tumor cell death, especially when combined with TME normalization. Therefore, these findings provide important insights for the development of novel therapeutic strategies for the immunotherapy of solid tumors.
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Affiliation(s)
- Walison Nunes da Silva
- Department of Physiology and Biophysics, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | | | | | - Heloísa A S Ferreira
- Department of Physiology and Biophysics, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | | | | | | | | | | | - Lays Cordeiro Guimarães
- Department of Physiology and Biophysics, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Maria Eduarda Chen Ferris
- Department of Physiology and Biophysics, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Ajay Thatte
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Alex Hamilton
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Helton da Costa Santiago
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Lucíola da Silva Barcelos
- Department of Physiology and Biophysics, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Mauro Martins Teixeira
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | | | - Michael J Mitchell
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Frédéric Frézard
- Department of Physiology and Biophysics, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
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Tan L, Wu X, Tang Z, Chen H, Cao W, Wen C, Zou G, Zou H. The tsRNAs (tRFdb-3013a/b) serve as novel biomarkers for colon adenocarcinomas. Aging (Albany NY) 2024; 16:4299-4326. [PMID: 38451187 DOI: 10.18632/aging.205590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 01/24/2024] [Indexed: 03/08/2024]
Abstract
The tsRNAs (tRNA-derived small RNAs) are a novel class of small non-coding RNAs derived from transfer-RNAs. Colon adenocarcinoma (COAD) is the most malignant intestinal tumor. This study focused on the identification and characterization of tsRNA biomarkers in colon adenocarcinomas. Data processing and bioinformatic analyses were performed with the packages of R and Python software. The cell proliferation, migration and invasion abilities were determined by CCK-8 and transwell assays. Luciferase reporter assay was used to test the binding of tsRNA with its target genes. With computational methods, we identified the tRNA fragments profiles within COAD datasets, and discriminated forty-two differentially expressed tsRNAs between paired colon adenocarcinomas and non-tumor controls. Among the fragments derived from the 3' end of tRNA-His-GUG (a histidyl-transfer-RNA), tRFdb-3013a and tRFdb-3013b (tRFdb-3013a/b) were notably decreased in colon and rectum adenocarcinomas, especially, tRFdb-3013a/b might tend to be down-regulated in patients with lymphatic or vascular invasion present. The clinical survival of colorectal adenocarcinoma patients with low tRFdb-3013a/b expression was significantly worse than that of high expression patients. In colon adenocarcinoma cells, tRFdb-3013a could have inhibited cell proliferations, and reduced cell migration and invasion abilities. The enrichment analyses showed that most of tRFdb-3013a correlated-genes were enriched in the extracellular matrix associated GO terms, phagosome pathway, and a GSEA molecular signature pathway. Additionally, the 3'UTR of ST3GAL1 mRNA was predicted to contain the binding site of tRFdb-3013a/b, tRFdb-3013a/b might directly target and regulate ST3GAL1 expression in colon adenocarcinomas. These results suggested that tRFdb-3013a/b might serve as novel biomarkers for diagnosis and prognosis of colon adenocarcinomas, and act a key player in the progression of colon adenocarcinomas.
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Affiliation(s)
- Lihong Tan
- Chongqing Medical and Pharmaceutical College, Chongqing 401331, China
| | - Xiaoling Wu
- Chongqing Medical and Pharmaceutical College, Chongqing 401331, China
| | - Zhurong Tang
- Chongqing Medical University, Chongqing 400016, China
| | - Huan Chen
- Yueyang Hospital of Traditional Chinese Medicine, Yueyang 414000, China
- Chongqing Medical University, Chongqing 400016, China
| | - Weiguo Cao
- Chongqing Medical University, Chongqing 400016, China
| | - Chunjie Wen
- Chongqing Medical University, Chongqing 400016, China
| | - Guojun Zou
- Yueyang Hospital of Traditional Chinese Medicine, Yueyang 414000, China
| | - Hecun Zou
- Chongqing Medical University, Chongqing 400016, China
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Liu Y, Wang Y, Feng H, Ma L, Liu Y. PANoptosis-related genes function as efficient prognostic biomarkers in colon adenocarcinoma. Front Endocrinol (Lausanne) 2024; 15:1344058. [PMID: 38501104 PMCID: PMC10944899 DOI: 10.3389/fendo.2024.1344058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 02/20/2024] [Indexed: 03/20/2024] Open
Abstract
Background PANoptosis is a newly discovered cell death type, and tightly associated with immune system activities. To date, the mechanism, regulation and application of PANoptosis in tumor is largely unknown. Our aim is to explore the prognostic value of PANoptosis-related genes in colon adenocarcinoma (COAD). Methods Analyzing data from The Cancer Genome Atlas-COAD (TCGA-COAD) involving 458 COAD cases, we concentrated on five PANoptosis pathways from the Molecular Signatures Database (MSigDB) and a comprehensive set of immune-related genes. Our approach involved identifying distinct genetic COAD subtype clusters and developing a prognostic model based on these parameters. Results The research successfully identified two genetic subtype clusters in COAD, marked by distinct profiles in PANoptosis pathways and immune-related gene expression. A prognostic model, incorporating these findings, demonstrated significant predictive power for survival outcomes, underscoring the interplay between PANoptosis and immune responses in COAD. Conclusion This study enhances our understanding of COAD's genetic framework, emphasizing the synergy between cell death pathways and the immune system. The development of a prognostic model based on these insights offers a promising tool for personalized treatment strategies. Future research should focus on validating and refining this model in clinical settings to optimize therapeutic interventions in COAD.
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Affiliation(s)
- Yang Liu
- Endoscopy Center, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Yizhao Wang
- Endoscopy Center, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Huijin Feng
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, United States
| | - Lianjun Ma
- Endoscopy Center, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Yanqing Liu
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, United States
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Contreras-Toledo D, Jiménez-Fonseca P, López CL, Montes AF, López Muñoz AM, Vázquez Rivera F, Alonso V, Alcaide J, Salvà F, Covela Rúa M, Guillot M, Martín Carnicero A, Jimeno Mate R, Cameselle García S, Asensio Martínez E, González Astorga B, Fernandez-Diaz AB, González Villaroel P, Virgili Manrique AC, Melián Sosa M, Alonso B, Cousillas Castiñeiras A, Castañón López C, Aparicio J, Carmona-Bayonas A. Dynamic nature of BRAF or KRAS p.G12C mutations in second-line therapy for advanced colorectal cancer patients: do early and late effects exist? Br J Cancer 2024; 130:777-787. [PMID: 38191609 PMCID: PMC10912758 DOI: 10.1038/s41416-023-02563-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 12/08/2023] [Accepted: 12/19/2023] [Indexed: 01/10/2024] Open
Abstract
INTRODUCTION The mitogen-activated protein kinase (MAPK) signalling network aberrations in metastatic colorectal cancer (mCRC) generate intrinsic dynamic effects and temporal variations that are crucial but often overlooked in clinical trial populations. Here, we investigate the time-varying impact of MAPK pathway mutation genotype on each treatment line's contribution to the overall clinical course. METHODS The PROMETEO study focused on mCRC patients undergoing second-line treatment at 20 hospitals. We evaluated genotypes and employed flexible models to analyse the dynamic effect of each mutation. RESULTS We examined data derived from 1160 patients. The effects of KRAS G12C or G12V, and BRAF V600E are clearly time-varying, with unexpected consequences such as the deleterious effect of BRAF V600E vs other genotypes dissipating over time when subjects receive antiangiogenics, or KRAS G12V and G12C showing increasing aggressiveness over time. Thus, contrary to expectations, the 12-month survival rate from the second line for those who survived >6 months was 49.9% (95% CI, 32.7-67.3) for KRAS G12C and 59% (95% CI, 38.5-80.6) for BRAF V600E. CONCLUSIONS The dynamic perspective is essential for understanding the behaviour of tumours with specific genotypes, especially from the second line onward. This may be relevant in patient monitoring and treatment decision-making, particularly in cases with distinct mutations.
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Affiliation(s)
- Débora Contreras-Toledo
- Department of Medical Oncology, Hospital Universitario Central de Asturias, ISPA, Universidad de Oviedo, Oviedo, Spain.
| | - Paula Jiménez-Fonseca
- Department of Medical Oncology, Hospital Universitario Central de Asturias, ISPA, Universidad de Oviedo, Oviedo, Spain
| | - Carlos López López
- Department of Medical Oncology, Hospital Universitario Marqués de Valdecilla, IDIVAL, Universidad de Cantabria (UNICAN), Santander, Spain
| | - Ana Fernández Montes
- Department of Medical Oncology, Complexo Hospitalario Universitario de Ourense, Ourense, Spain
| | | | - Francisca Vázquez Rivera
- Department of Medical Oncology, Hospital Universitario de Santiago, Santiago de Compostela, Spain
| | - Vicente Alonso
- Department of Medical Oncology, Hospital Universitario Miguel Servet, IISA, Zaragoza, Spain
| | - Julia Alcaide
- Department of Medical Oncology, Hospital Costa del Sol, Marbella, Medical Oncology Intercenter Unit, Hospital Universitario Regional y Virgen de la Victoria, IBIMA, Málaga, Spain
| | - Francesc Salvà
- Department of Medical Oncology, Hospital Universitario Vall D'Hebrón, Vall D´Hebrón Institute of Oncology (VHIO), Barcelona, Spain
| | - Marta Covela Rúa
- Department of Medical Oncology, Hospital Universitario Lucus Augusti, Lugo, Spain
| | - Mónica Guillot
- Department of Medical Oncology, Hospital Universitario Son Espases, Palma de Mallorca, Spain
| | | | - Raquel Jimeno Mate
- Department of Medical Oncology, Hospital Universitario Marqués de Valdecilla, IDIVAL, Santander, Spain
| | | | | | | | | | | | | | - Marcos Melián Sosa
- Department of Medical Oncology, Instituto Valenciano de Oncología (IVO), Valencia, Spain
| | - Beatriz Alonso
- Department of Medical Oncology, Hospital Universitario de Canarias, Tenerife, Spain
| | | | | | - Jorge Aparicio
- Department of Medical Oncology, Hospital Universitario y Politécnico La Fe de Valencia, Valencia, Spain
| | - Alberto Carmona-Bayonas
- Department of Medical Oncology, Hospital Universitario Morales Meseguer, Universidad de Murcia, IMIB, Murcia, Spain.
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Attia A, Lagha A, Mezlini A, Ghazouani E, Yacoubi-Loueslati B, Namouchi I. HLA class II polymorphisms as prognostic biomarkers for right and left-sided colon cancer. Int J Biol Markers 2024; 39:40-51. [PMID: 38179594 DOI: 10.1177/03936155231224469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
BACKGROUND Colon cancer (CC) is one of the most common malignancies worldwide. Characterization of new prognostic biomarkers for right-sided CC (RCC) and left-sided CC (LCC) may contribute to improving early detection. An association of human leukocyte antigens class II (HLA-II) with the predisposition to CC was suggested. AIM OF THE STUDY We evaluated the association of DRB1 and DQB1 with the risk of LCC and RCC. PATIENTS AND METHODS Our study comprised 93 CC patients and 100 healthy controls. Genotyping of HLA class II alleles were performed by the Polymerase Chain Reaction Sequence-Specific Primers (PCR-SSP). RESULTS DRB1*03 was positively associated with CC. In contrast, DRB1*11, DRB1*13, DQB1*03, and DQB1*05 were negatively linked to CC. Haplotype analysis revealed that DRB1*04-DQB1*04 and DRB1*09-DQB1*02 were positive, while DRB1*01-DQB1*05, DRB1*04-DQB1*03, DRB1*07-DQB1*02, DRB1*11-DQB1*03, DRB1*11-DQB1*05, and DRB1*13-DQB1*06 were negatively associated with CC. For sigmoid CC, DRB1*13, DRB1*11, and DQB1*05 were negative, while DRB1*04-DQB1*02, and DRB1*07-DQB1*03 were positively associated. DRB1*03 and DRB1*04-DQB1*04 were positive, while DRB1*11 and DQB1*03 were negatively linked to RCC. According to the LCC, DRB1*07, DRB1*11, DQB1*03, DQB1*05, and DRB1*07-DQB1*02 were negative. In contrast, DRB1*09-DQB1*02 was positively associated with LCC. Stratified analysis revealed that DRB1*11 is associated with higher risk of metastasis in CC and sigmoid CC, and tolerance to treatment in RCC. DQB1*03 was associated with lymph-node invasion in CC. CONCLUSION DRB1 and DQB1 polymorphisms could be used as future biomarkers for the early detection of subjects at a higher risk of developing RCC and LCC, metastasis in sigmoid CC, and tolerance to treatment in RCC.
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Affiliation(s)
- Amani Attia
- Laboratory of Mycology, Pathologies, and Biomarkers (LR16ES05), University of Tunis El Manar, (UTM), Faculty of Sciences of Tunis (FST), Tunis, Tunisia
| | - Awatef Lagha
- Laboratory of Mycology, Pathologies, and Biomarkers (LR16ES05), University of Tunis El Manar, (UTM), Faculty of Sciences of Tunis (FST), Tunis, Tunisia
- Laboratory of Immunology, Military Hospital of Tunis, Tunis, Tunisia
| | - Amel Mezlini
- Medical Oncology Department, Salah Azaiez Oncology Institute, Tunis, Tunisia
| | | | - Besma Yacoubi-Loueslati
- Laboratory of Mycology, Pathologies, and Biomarkers (LR16ES05), University of Tunis El Manar, (UTM), Faculty of Sciences of Tunis (FST), Tunis, Tunisia
| | - Imene Namouchi
- Laboratory of Mycology, Pathologies, and Biomarkers (LR16ES05), University of Tunis El Manar, (UTM), Faculty of Sciences of Tunis (FST), Tunis, Tunisia
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Xia C, Liang D, Liao C. Difference in gene expressions between left-sided and right-sided colon cancer. Asian J Surg 2024; 47:1673-1674. [PMID: 38160146 DOI: 10.1016/j.asjsur.2023.12.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 12/08/2023] [Indexed: 01/03/2024] Open
Affiliation(s)
- Chuqi Xia
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Kunming Medical University, No.374 Dianmian Avenue, Kunming, 650101, China.
| | - Daoming Liang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Kunming Medical University, No.374 Dianmian Avenue, Kunming, 650101, China.
| | - Chen Liao
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Kunming Medical University, No.374 Dianmian Avenue, Kunming, 650101, China.
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Rai S, Singh MP, Sinha A, Srivastava A, Datta D, Srivastava S. Unravelling a novel CTNND1-RAB6A fusion transcript: Implications in colon cancer cell migration. Int J Biol Macromol 2024; 262:129981. [PMID: 38336316 DOI: 10.1016/j.ijbiomac.2024.129981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 01/22/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024]
Abstract
The interchange of DNA sequences between genes may occur because of chromosomal rearrangements leading to the formation of chimeric genes. These chimeric genes have been linked to various cancers, accumulated significant interest in recent times. We used paired-end RNA-seq. data of four CRC and one normal sample generated from our previous study. The STAR-Fusion pipeline was utilized to identify the fusion genes unique to CRC. The in-silico identified fusion gene(s) were explored for their diagnostic, prognostic and therapeutic biomarker potential using TCGA-datasets, then validated through PCR and DNA sequencing. Further, cell line-based studies were performed to gain functional insights of the novel fusion transcript CTNND1-RAB6A, which was amplified in one sample. Sequencing revealed that there was a total loss of the CTNND1 gene, whereas RAB6A retained its coding sequence. Further, RAB6A was functionally characterized for its oncogenic potential in HCT116 cell line. RAB6A under-expression was found to be significantly associated with increased cell migration and is proposed to be regulated via the RAB6A-ECR1-Liprin-α axis. We conclude that RAB6A gene may play significant role in CRC oncogenesis, and could be used as a potential biomarker and therapeutic target in future for better management of a subset of CRCs harbouring this fusion.
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Affiliation(s)
- Sandhya Rai
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Teliyarganj-Prayagraj, U.P. 211004, India
| | - Manish Pratap Singh
- Department of Zoology, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, (U.P.) 273009, India
| | - Abhipsa Sinha
- Division of cancer biology, CSIR-Central Drug Research Institute, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226031, India
| | - Ankit Srivastava
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Teliyarganj-Prayagraj, U.P. 211004, India
| | - Dipak Datta
- Division of cancer biology, CSIR-Central Drug Research Institute, Jankipuram Extension, Sitapur Road, Lucknow, Uttar Pradesh 226031, India
| | - Sameer Srivastava
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Teliyarganj-Prayagraj, U.P. 211004, India.
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Ye C, Sun Q, Yan J, Xue D, Xu J, Ma H, Li F. Development of fatty acid metabolism score based on gene signature for predicting prognosis and immunotherapy response in colon cancer. Clin Transl Oncol 2024; 26:630-643. [PMID: 37480430 DOI: 10.1007/s12094-023-03282-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 07/11/2023] [Indexed: 07/24/2023]
Abstract
PURPOSE Metabolic reprogramming is a novel hallmark and therapeutic target of cancer. Our study aimed to establish fatty acid metabolism-associated scores based on gene signature and investigated its effects on immunotherapy in colon cancer. METHODS Gene expression and clinical information were collected from Gene Expression Omnibus (GEO) database to identify a gene signature by non-negative matrix factorization (NMF) clustering and Cox regression analysis. Subsequently, we constructed the fatty acid metabolism score (FA-score) model by principal component analysis (PCA) and explored its relativity of prognosis and the response to immunotherapy in colon cancer. Finally, the Cancer Genome Atlas (TCGA) database was introduced and in vitro study was performed for verification. RESULTS The FA-score-high group had a higher level of fatty acid metabolism and was associated with worse patient overall survival. Significantly, FA-score correlated closely with the biomarkers of immunotherapy, and the FA-score-high group had a poorer therapeutic efficacy of immune checkpoint blockade. In vitro experiments demonstrated that ACSL5 may be a critical metabolic regulatory target. CONCLUSIONS Our study provided a comprehensive analysis of the heterogeneity of fatty acid metabolism in colon cancer. We highlighted the potential clinical utility of fatty acid metabolism-related genes to be biomarkers of colon cancer prognosis and targets to improve the effect of immunotherapy.
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Affiliation(s)
- Changchun Ye
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Qi Sun
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jun Yan
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Dong Xue
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jiarui Xu
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Haiyun Ma
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Fanni Li
- Department of Talent Highland, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an 710061, Shaanxi, China.
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Yun ZY, Wu D, Wang X, Huang P, Li N. MiR-214-3p overexpression-triggered chondroitin polymerizing factor (CHPF) inhibition modulates the ferroptosis and metabolism in colon cancer. Kaohsiung J Med Sci 2024; 40:244-254. [PMID: 38190270 DOI: 10.1002/kjm2.12802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 11/25/2023] [Accepted: 12/07/2023] [Indexed: 01/10/2024] Open
Abstract
Colon cancer is a common cancer with high mortality globally. The role of chondroitin polymerizing factor (CHPF) has been elucidated in various cancers. However, its role and mechanism remain unknown in colon cancer. CHPF expression was examined by GEPIA database, reverse transcription-quantitative polymerase chain reaction and western blot. The relationship between CHPF expression and the clinicopathologic characteristics as well as miR-214-3p level was determined in colon cancer patients. The role and mechanism of CHPF in the growth, ferroptosis, and glycolysis of colon cancer cells were evaluated by cell counting kit-8, biochemical detections, luciferase, and western blot experiments. Additionally, the role of CHPF was explored in xenografted mice. CHPF expression was increased and was related to advanced TNM stage, poor differentiation and shorter overall survival in patients with colon cancer. Knockdown of CHPF inhibited colon cancer cell growth, and downregulated the expression of proteins involving in ferroptosis and glycolysis both in vitro and in vivo. Besides, CHPF silencing increased the levels of ferrous iron and ROS, but decreased glucose uptake, lactate product, and ATP level in vitro. Mechanically, miR-214-3p directly targeted CHPF and negatively regulated its expression. Upregulation of miR-214-3p reduced cell viability, glucose uptake, lactate product, and ATP level, but increased the levels of ferrous iron and ROS, which were reversed by the overexpression of CHPF. Upregulation of CHPF predicted poor prognosis, and miR-214-3p/CHPF axis inhibited growth, downregulated the levels of glycolysis-related indexes, and promoted ferroptosis in colon cancer cells.
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Affiliation(s)
- Zhi-Yuan Yun
- Department of Internal Medicine, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, Heilongjiang, China
| | - Di Wu
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, Heilongjiang, China
| | - Xin Wang
- Department of Internal Medicine, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, Heilongjiang, China
| | - Peng Huang
- Department of Gastrointestinal Oncology, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, Heilongjiang, China
| | - Na Li
- Department of Internal Medicine, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, Heilongjiang, China
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Peng Y, Ouyang C, Wu Y, Ma R, Li H, Li Y, Jing J, Sun L. A novel PCDscore based on programmed cell death-related genes can effectively predict prognosis and therapy responses of colon adenocarcinoma. Comput Biol Med 2024; 170:107933. [PMID: 38217978 DOI: 10.1016/j.compbiomed.2024.107933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 12/06/2023] [Accepted: 01/01/2024] [Indexed: 01/15/2024]
Abstract
Emerging evidence suggests a correlation between oncogenesis and programmed cell death (PCD). However, comprehensive studies that incorporate all identified PCD-related genes to guide colon adenocarcinoma (COAD) prognosis and precision treatment strategies are lacking. In this study, a series of bioinformatics analyses were comprehensively conducted using data from the TCGA-COAD, GSE17538, and GSE39582 cohorts. A total of 21 PCD-associated prognostic genes were identified through univariate Cox analysis. LASSO and multivariate Cox methods were employed to establish a prognostic gene signature (ALOX12, HSPA1A, IL13, MID2, RFFL, and SLC39A8) and the corresponding scoring system, termed PCDscore, which exhibited robust predictive ability. The ssGSEA and ESTIMATE algorithms were utilized to evaluate the tumor microenvironment of COAD. The high PCDscore group demonstrated a poorer prognosis, characterized by lower CD4+ T cell infiltration and a higher stromal score. In contrast, the low PCDscore group exhibited sensitivity to common chemotherapy drugs such as Cisplatin and 5-Fluorouracil. Single-cell sequencing analysis further revealed that the high-PCDscore group displayed a lower proportion of CD4+ T cells. Colorectal cancer samples from the years 2013-2017 were employed to validate the PCDscore, while those from 2018 to 2019 served as a temporal external validation set for the PCDscore. In vitro experimental results indicated that the overexpression of SLC39A8 inhibited the proliferation and invasion of colorectal cancer cells. The study developed a novel PCDscore system based on the analysis of genes related to all identified PCD types, providing valuable insights into clinical prognosis and drug sensitivity for patients with COAD.
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Affiliation(s)
- Yangjie Peng
- Key Laboratory of Gastrointestinal Cancer Etiology and Prevention, Shenyang 110001, Liaoning, China; Department of Anorectal Surgery, The First Hospital of China Medical University, Shenyang 110001, Liaoning, China
| | - Cheng Ouyang
- Key Laboratory of Gastrointestinal Cancer Etiology and Prevention, Shenyang 110001, Liaoning, China; Tumor Etiology and Screening Department of Cancer Institute, and Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang 110001, Liaoning, China
| | - Yijun Wu
- Key Laboratory of Gastrointestinal Cancer Etiology and Prevention, Shenyang 110001, Liaoning, China; Tumor Etiology and Screening Department of Cancer Institute, and Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang 110001, Liaoning, China
| | - Rui Ma
- Key Laboratory of Gastrointestinal Cancer Etiology and Prevention, Shenyang 110001, Liaoning, China; Tumor Etiology and Screening Department of Cancer Institute, and Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang 110001, Liaoning, China
| | - Hao Li
- Department of Clinical Laboratory, The First Hospital of China Medical University, Shenyang 110001, Liaoning, China
| | - Yanke Li
- Key Laboratory of Gastrointestinal Cancer Etiology and Prevention, Shenyang 110001, Liaoning, China; Department of Anorectal Surgery, The First Hospital of China Medical University, Shenyang 110001, Liaoning, China.
| | - Jingjing Jing
- Key Laboratory of Gastrointestinal Cancer Etiology and Prevention, Shenyang 110001, Liaoning, China; Tumor Etiology and Screening Department of Cancer Institute, and Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang 110001, Liaoning, China.
| | - Liping Sun
- Key Laboratory of Gastrointestinal Cancer Etiology and Prevention, Shenyang 110001, Liaoning, China; Tumor Etiology and Screening Department of Cancer Institute, and Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang 110001, Liaoning, China.
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Kaur E, Agrawal R, Arun R, Madhavan V, Srivastava V, Kumar D, Rath PP, Kumar N, Vedagopuram S, Pandey N, Priya S, Legembre P, Gourinath S, Bajaj A, Sengupta S. Small molecules that disrupt RAD54-BLM interaction hamper tumor proliferation in colon cancer chemoresistance models. J Clin Invest 2024; 134:e161941. [PMID: 38421735 PMCID: PMC11014671 DOI: 10.1172/jci161941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 02/27/2024] [Indexed: 03/02/2024] Open
Abstract
RAD54 and BLM helicase play pivotal roles during homologous recombination repair (HRR) to ensure genome maintenance. BLM amino acids (aa 181-212) interact with RAD54 and enhance its chromatin remodeling activity. Functionally, this interaction heightens HRR, leading to a decrease in residual DNA damage in colon cancer cells. This contributes to chemoresistance in colon cancer cells against cisplatin, camptothecin, and oxaliplatin, eventually promoting tumorigenesis in preclinical colon cancer mouse models. ChIP-Seq analysis and validation revealed increased BLM and RAD54 corecruitment on the MRP2 promoter in camptothecin-resistant colon cancer cells, leading to BLM-dependent enhancement of RAD54-mediated chromatin remodeling. We screened the Prestwick small-molecule library, with the intent to revert camptothecin- and oxaliplatin-induced chemoresistance by disrupting the RAD54-BLM interaction. Three FDA/European Medicines Agency-approved candidates were identified that could disrupt this interaction. These drugs bound to RAD54, altered its conformation, and abrogated RAD54-BLM-dependent chromatin remodeling on G5E4 and MRP2 arrays. Notably, the small molecules also reduced HRR efficiency in resistant lines, diminished anchorage-independent growth, and hampered the proliferation of tumors generated using camptothecin- and oxaliplatin-resistant colon cancer cells in both xenograft and syngeneic mouse models in BLM-dependent manner. Therefore, the 3 identified small molecules can serve as possible viable candidates for adjunct therapy in colon cancer treatment.
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Affiliation(s)
- Ekjot Kaur
- Biotechnology Research Innovation Council—National Institute of Immunology (BRIC-NII), New Delhi, India
| | - Ritu Agrawal
- Biotechnology Research Innovation Council—National Institute of Immunology (BRIC-NII), New Delhi, India
| | - Rimpy Arun
- Biotechnology Research Innovation Council—National Institute of Immunology (BRIC-NII), New Delhi, India
| | - Vinoth Madhavan
- Biotechnology Research Innovation Council—National Institute of Immunology (BRIC-NII), New Delhi, India
| | - Vivek Srivastava
- Biotechnology Research Innovation Council—National Institute of Immunology (BRIC-NII), New Delhi, India
| | - Dilip Kumar
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore
| | | | - Nitin Kumar
- Biotechnology Research Innovation Council—National Institute of Immunology (BRIC-NII), New Delhi, India
| | - Sreekanth Vedagopuram
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Nishant Pandey
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Swati Priya
- Biotechnology Research Innovation Council—National Institute of Immunology (BRIC-NII), New Delhi, India
| | - Patrick Legembre
- UMR CNRS 7276, INSERM U1262, CRIBL, Université Limoges, Limoges, France
| | | | - Avinash Bajaj
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Sagar Sengupta
- Biotechnology Research Innovation Council—National Institute of Immunology (BRIC-NII), New Delhi, India
- Biotechnology Research Innovation Council—National Institute of Biomedical Genomics (BRIC-NIBMG), Kalyani, India
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Yang Y, Mirzaei G. Performance analysis of data resampling on class imbalance and classification techniques on multi-omics data for cancer classification. PLoS One 2024; 19:e0293607. [PMID: 38422094 PMCID: PMC10903850 DOI: 10.1371/journal.pone.0293607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 10/17/2023] [Indexed: 03/02/2024] Open
Abstract
Cancer, in any of its forms, remains a significant public health concern worldwide. Advances in early detection and treatment could lead to a decline in the overall death rate from cancer in recent decades. Therefore, tumor prediction and classification play an important role in fighting cancer. This study built computational models for a joint analysis of RNA seq, copy number variation (CNV), and DNA methylation to classify normal and tumor samples across liver cancer, breast cancer, and colon adenocarcinoma from The Cancer Genome Atlas (TCGA) dataset. Total of 18 machine learning methods were evaluated based on the AUC, precision, recall, and F-measure. Besides, five techniques were compared to ameliorate problems of class imbalance in the cancer datasets. Synthetic Minority Oversampling Technique (SMOTE) demonstrated the best performance. The results indicate that the model applying Stochastic Gradient Descent (SGD) for learning binary class SVM with hinge loss has the highest classification results on liver cancer and breast cancer datasets, with accuracy over 99% and AUC greater than or equal to 0.999. For colon adenocarcinoma dataset, both SGD and Sequential Minimal Optimization (SMO) that implements John Platt's sequential minimal optimization algorithm for training a support vector machine shows an outstanding classification performance with accuracy of 100%, AUC, precision, recall, and F-measure all at 1.000.
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Affiliation(s)
- Yuting Yang
- Department of Computer Science and Engineering, The Ohio State University, Columbus, Ohio, United States of America
| | - Golrokh Mirzaei
- Department of Computer Science and Engineering, The Ohio State University, Marion, Ohio, United States of America
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Ma Y, Wang J, He X, Liu Y, Zhen S, An L, Yang Q, Niu F, Wang H, An B, Tai X, Yan Z, Wu C, Yang X, Liu X. Molecular mechanism of human ISG20L2 for the ITS1 cleavage in the processing of 18S precursor ribosomal RNA. Nucleic Acids Res 2024; 52:1878-1895. [PMID: 38153123 PMCID: PMC10899777 DOI: 10.1093/nar/gkad1210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/03/2023] [Accepted: 12/10/2023] [Indexed: 12/29/2023] Open
Abstract
The exonuclease ISG20L2 has been initially characterized for its role in the mammalian 5.8S rRNA 3' end maturation, specifically in the cleavage of ITS2 of 12S precursor ribosomal RNA (pre-rRNA). Here, we show that human ISG20L2 is also involved in 18S pre-rRNA maturation through removing the ITS1 region, and contributes to ribosomal biogenesis and cell proliferation. Furthermore, we determined the crystal structure of the ISG20L2 nuclease domain at 2.9 Å resolution. It exhibits the typical αβα fold of the DEDD 3'-5' exonuclease with a catalytic pocket located in the hollow near the center. The catalytic residues Asp183, Glu185, Asp267, His322 and Asp327 constitute the DEDDh motif in ISG20L2. The active pocket represents conformational flexibility in the absence of an RNA substrate. Using structural superposition and mutagenesis assay, we mapped RNA substrate binding residues in ISG20L2. Finally, cellular assays revealed that ISG20L2 is aberrantly up-regulated in colon adenocarcinoma and promotes colon cancer cell proliferation through regulating ribosome biogenesis. Together, these results reveal that ISG20L2 is a new enzymatic member for 18S pre-rRNA maturation, provide insights into the mechanism of ISG20L2 underlying pre-rRNA processing, and suggest that ISG20L2 is a potential therapeutic target for colon adenocarcinoma.
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Affiliation(s)
- Yinliang Ma
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Jiaxu Wang
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
- College of Life Sciences, State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453002 Henan, China
| | - Xingyi He
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Yuhang Liu
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Shuo Zhen
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Lina An
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Qian Yang
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Fumin Niu
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Hong Wang
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Boran An
- Affiliated Hospital of Hebei University, Hebei University, Baoding 071002 Hebei, China
| | - Xinyue Tai
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Zhenzhen Yan
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Chen Wu
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Xiaoyun Yang
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055 Guangdong, China
| | - Xiuhua Liu
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
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Jansen RA, Mainardi S, Dias MH, Bosma A, van Dijk E, Selig R, Albrecht W, Laufer SA, Zender L, Bernards R. Small-molecule inhibition of MAP2K4 is synergistic with RAS inhibitors in KRAS-mutant cancers. Proc Natl Acad Sci U S A 2024; 121:e2319492121. [PMID: 38377196 PMCID: PMC10907260 DOI: 10.1073/pnas.2319492121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/10/2024] [Indexed: 02/22/2024] Open
Abstract
The Kirsten rat sarcoma viral oncogene homologue KRAS is among the most commonly mutated oncogenes in human cancers, thus representing an attractive target for precision oncology. The approval for clinical use of the first selective inhibitors of G12C mutant KRAS therefore holds great promise for cancer treatment. However, despite initial encouraging clinical results, the overall survival benefit that patients experience following treatment with these inhibitors has been disappointing to date, pointing toward the need to develop more powerful combination therapies. Here, we show that responsiveness to KRASG12C and pan-RAS inhibitors in KRAS-mutant lung and colon cancer cells is limited by feedback activation of the parallel MAP2K4-JNK-JUN pathway. Activation of this pathway leads to elevated expression of receptor tyrosine kinases that reactivate KRAS and its downstream effectors in the presence of drug. We find that the combination of sotorasib, a drug targeting KRASG12C, and the MAP2K4 inhibitor HRX-0233 prevents this feedback activation and is highly synergistic in a panel of KRASG12C-mutant lung and colon cancer cells. Moreover, combining HRX-0233 and sotorasib is well-tolerated and resulted in durable tumor shrinkage in mouse xenografts of human lung cancer cells, suggesting a therapeutic strategy for KRAS-driven cancers.
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Affiliation(s)
- Robin A. Jansen
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam1066 CX, The Netherlands
| | - Sara Mainardi
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam1066 CX, The Netherlands
| | - Matheus Henrique Dias
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam1066 CX, The Netherlands
| | - Astrid Bosma
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam1066 CX, The Netherlands
| | - Emma van Dijk
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam1066 CX, The Netherlands
| | | | | | - Stefan A. Laufer
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen72074, Germany
- Tübingen Center for Academic Drug Discovery and Development, Tübingen72074, Germany
- Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies” (EXC 2180), Eberhard Karls Universität Tübingen, Tübingen72076, Germany
| | - Lars Zender
- Tübingen Center for Academic Drug Discovery and Development, Tübingen72074, Germany
- Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies” (EXC 2180), Eberhard Karls Universität Tübingen, Tübingen72076, Germany
- Department of Medical Oncology and Pneumology, University Hospital Tübingen, Tübingen72076, Germany
- German Cancer Research Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg69120, Germany
| | - René Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam1066 CX, The Netherlands
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Song HS, Ha SY, Kim JY, Kim M, Choi JH. The effect of genetic variants of SLC22A18 on proliferation, migration, and invasion of colon cancer cells. Sci Rep 2024; 14:3925. [PMID: 38366023 PMCID: PMC10873386 DOI: 10.1038/s41598-024-54658-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/15/2024] [Indexed: 02/18/2024] Open
Abstract
Solute carrier family (SLC) transporters are expressed in the digestive system and play important roles in maintaining physiological functions in the body. In addition, SLC transporters act as oncoproteins or tumor-suppressor proteins during the development, progression, and metastasis of various digestive system cancers. SLC22A18, a member of the SLC22 gene family, is an orphan transporter with an unknown endogenous substrate. Previous study revealed that SLC22A18 is downregulated in colorectal cancer tissues and that it acts as a suppressor in colorectal cancer, although the effects of SLC22A18 variants on colon cancer cell proliferation, migration, and invasion are unknown. Therefore, in this study, we identified SLC22A18 variants found in multiple populations by searching public databases and determined the in vitro effects of these missense variations on transporter expression and cancer progression. Our results indicated that three missense SLC22A18 variants-p.Ala6Thr, p.Arg12Gln, and p.Arg86His-had significantly lower cell expression than the wild type, possibly owing to intracellular degradation. Furthermore, these three variants caused significantly higher proliferation, migration, and invasion of colon cancer cells than the wild type. Our findings suggest that missense variants of SLC22A18 can potentially serve as biomarkers or prognostic tools that enable clinicians to predict colorectal cancer progression.
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Affiliation(s)
- Hyo Sook Song
- Department of Pharmacology, Inflammation-Cancer Microenvironment Research Center, College of Medicine, Ewha Womans University, 25 Magokdong-ro 2-gil, Gangseo-gu, Seoul, 07804, Republic of Korea
| | - Seung Yeon Ha
- Department of Pharmacology, Inflammation-Cancer Microenvironment Research Center, College of Medicine, Ewha Womans University, 25 Magokdong-ro 2-gil, Gangseo-gu, Seoul, 07804, Republic of Korea
| | - Jin-Young Kim
- Department of Pharmacology, Inflammation-Cancer Microenvironment Research Center, College of Medicine, Ewha Womans University, 25 Magokdong-ro 2-gil, Gangseo-gu, Seoul, 07804, Republic of Korea
| | - Minsuk Kim
- Department of Pharmacology, Inflammation-Cancer Microenvironment Research Center, College of Medicine, Ewha Womans University, 25 Magokdong-ro 2-gil, Gangseo-gu, Seoul, 07804, Republic of Korea
| | - Ji Ha Choi
- Department of Pharmacology, Inflammation-Cancer Microenvironment Research Center, College of Medicine, Ewha Womans University, 25 Magokdong-ro 2-gil, Gangseo-gu, Seoul, 07804, Republic of Korea.
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Yang L, Tu L, Bisht S, Mao Y, Petkovich D, Thursby SJ, Liang J, Patel N, Yen RWC, Largent T, Zahnow C, Brock M, Gabrielson K, Salimian KJ, Baylin SB, Easwaran H. Tissue-location-specific transcription programs drive tumor dependencies in colon cancer. Nat Commun 2024; 15:1384. [PMID: 38360902 PMCID: PMC10869357 DOI: 10.1038/s41467-024-45605-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 01/30/2024] [Indexed: 02/17/2024] Open
Abstract
Cancers of the same tissue-type but in anatomically distinct locations exhibit different molecular dependencies for tumorigenesis. Proximal and distal colon cancers exemplify such characteristics, with BRAFV600E predominantly occurring in proximal colon cancers along with increased DNA methylation phenotype. Using mouse colon organoids, here we show that proximal and distal colon stem cells have distinct transcriptional programs that regulate stemness and differentiation. We identify that the homeobox transcription factor, CDX2, which is silenced by DNA methylation in proximal colon cancers, is a key mediator of the differential transcriptional programs. Cdx2-mediated proximal colon-specific transcriptional program concurrently is tumor suppressive, and Cdx2 loss sufficiently creates permissive state for BRAFV600E-driven transformation. Human proximal colon cancers with CDX2 downregulation showed similar transcriptional program as in mouse proximal organoids with Cdx2 loss. Developmental transcription factors, such as CDX2, are thus critical in maintaining tissue-location specific transcriptional programs that create tissue-type origin specific dependencies for tumor development.
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Affiliation(s)
- Lijing Yang
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, PR China
| | - Lei Tu
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Shilpa Bisht
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Yiqing Mao
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Daniel Petkovich
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Sara-Jayne Thursby
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Jinxiao Liang
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Nibedita Patel
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Ray-Whay Chiu Yen
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Tina Largent
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Cynthia Zahnow
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Malcolm Brock
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Kathy Gabrielson
- Department of Comparative Medicine, Johns Hopkins Medical Institutions, 863 Broadway Research Building, 733 N. Broadway, Baltimore, MD, 21205-2196, USA
| | - Kevan J Salimian
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Stephen B Baylin
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Hariharan Easwaran
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA.
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Chang YM, Kang YR, Lee YG, Sung MK. Sex differences in colonic gene expression and fecal microbiota composition in a mouse model of obesity-associated colorectal cancer. Sci Rep 2024; 14:3576. [PMID: 38347027 PMCID: PMC10861586 DOI: 10.1038/s41598-024-53861-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 02/06/2024] [Indexed: 02/15/2024] Open
Abstract
This study investigated the sex-specific correlation between obesity and colorectal cancer emphasizing a more pronounced association in males. Estrogen, chromosomal genes, and gut bacteria were assessed in C57BL6/J male, female and ovariectomized (OVX) female mice, subjected to either a low-fat diet (LFD) or high-fat diet (HFD) for 14 weeks. Induction of colon tumor involved azoxymethane (10 mg/kg) administration, followed by three cycles of dextran sulfate sodium. Male mice on HFD exhibited higher final body weight and increased colon tumors compared to females. Colonic mucin 2 expression was significantly higher in females. HFD-modulated differentially expressed genes numbered 290 for males, 64 for females, and 137 for OVX females. Only one up-regulated gene (Gfra3) overlapped between females and OVX females, while two down-regulated genes (Thrsp and Gbp11) overlapped between males and OVX females. Genes up-regulated by HFD in males were linked to cytokine-cytokine interaction, HIF-1 signaling pathway, central carbon metabolism in cancer. Sex-specific changes in gut microbial composition in response to HFD were observed. These findings suggest a male-specific vulnerability to HFD-induced colon tumor formation, implicating key genes and colonic bacteria in colon tumorigenesis.
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Affiliation(s)
- Yoo-Mee Chang
- Department of Food and Nutrition, College of Human Ecology, Sookmyung Women's University, 100, Cheongpa-ro 47-gil, Yongsan-gu, Seoul, 04310, Republic of Korea
| | - Yoo-Ree Kang
- Department of Food and Nutrition, College of Human Ecology, Sookmyung Women's University, 100, Cheongpa-ro 47-gil, Yongsan-gu, Seoul, 04310, Republic of Korea
| | - Yu-Gyeong Lee
- Department of Food and Nutrition, College of Human Ecology, Sookmyung Women's University, 100, Cheongpa-ro 47-gil, Yongsan-gu, Seoul, 04310, Republic of Korea
| | - Mi-Kyung Sung
- Department of Food and Nutrition, College of Human Ecology, Sookmyung Women's University, 100, Cheongpa-ro 47-gil, Yongsan-gu, Seoul, 04310, Republic of Korea.
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Ramasamy D, Thippannah M, Maharajan HRP, Balaiah M, Seshadri RA, Kodous AS, Herceg Z, Mehta A, Rao AKDM, Mani S. Transcriptome-wide profiling identifies colon cancer-associated m6A transcripts and potential RNA methyl modifiers. Mol Biol Rep 2024; 51:299. [PMID: 38345740 DOI: 10.1007/s11033-024-09217-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/05/2024] [Indexed: 02/15/2024]
Abstract
BACKGROUND N6-methyladenosine (m6A) is a prevalent and crucial RNA methylation modification that plays a significant role in various biological and pathological processes. The dysregulation of m6A has been linked to the initiation, progression, and metastasis of several cancer types, including colon cancer. The transcriptome of colon cancer indeed provides insight into dysregulated coding and non-coding RNAs, but it does not reveal the mechanisms, such as m6A modifications, that determine post-transcriptional and pre-translational regulations. This study using MeRIP sequencing aims to explain the distribution of m6A modification across altered gene expression and its association with colon cancer. METHODS AND RESULTS The levels of m6A in different colon cancer cell lines were quantified and correlated with the expression of m6A modifiers such as writers, readers, and erasers. Our results showed that global m6A levels in colon cancer were associated with METTL14, YTHDF2, and YTHDC1. We performed Epi-transcriptome profiling of m6A in colon cancer cell lines using Methylated RNA Immunoprecipitation (MeRIP) sequencing. The differential methylation analysis revealed 7312 m6A regions among the colon cancer cell lines. Our findings indicated that the m6A RNA methylation modifications were mainly distributed in the last exonic and 3' untranslated regions. We also discovered that non-coding RNAs such as miRNA, lncRNA, and circRNA carry m6A marks. Gene set enrichment and motif analysis suggested a strong association of m6A with post-transcriptional events, particularly splicing control. Overall, our study sheds light on the potential role of m6A in colon cancer and highlights the importance of further investigation in this area. CONCLUSION This study reports m6A enrichment in the last exonic regions and 3' UTRs of mRNA transcripts in colon cancer. METTL14, YTHDF2, and YTHDC1 were the most significant modifiers in colon cancer cells. The functions of m6A-modified genes were found to be RNA methylation and RNA capping. Overall, the study illustrates the transcriptome-wide distribution of m6A and its eminent role in mRNA splicing and translation control of colon cancer.
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Affiliation(s)
- Deepa Ramasamy
- Department of Molecular Oncology, Cancer Institute (W.I.A), Chennai, Tamil Nadu, 600036, India
| | - Megha Thippannah
- Department of Molecular Oncology, Cancer Institute (W.I.A), Chennai, Tamil Nadu, 600036, India
| | | | - Meenakumari Balaiah
- Department of Molecular Oncology, Cancer Institute (W.I.A), Chennai, Tamil Nadu, 600036, India
| | | | - Ahmad S Kodous
- Department of Molecular Oncology, Cancer Institute (W.I.A), Chennai, Tamil Nadu, 600036, India
- Radiation Biology Department, National Centre for Radiation Research & Technology, Egyptian Atomic-Energy Authority, P.O. Box 8029, Cairo, Egypt
| | - Zdenko Herceg
- Epigenomics Group, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Anurag Mehta
- Department of Research, Rajiv Gandhi Cancer Institute and Research Centre, Sector 5, Rohini, Delhi, 110085, India
| | | | - Samson Mani
- Department of Molecular Oncology, Cancer Institute (W.I.A), Chennai, Tamil Nadu, 600036, India.
- Department of Research, Rajiv Gandhi Cancer Institute and Research Centre, Sector 5, Rohini, Delhi, 110085, India.
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Cheng C, Liu Z, Liu D, Chen H, Wang Y, Sun B. LncRNA CCAT1 participates in pancreatic ductal adenocarcinoma progression by forming a positive feedback loop with c-Myc. Carcinogenesis 2024; 45:69-82. [PMID: 37936306 DOI: 10.1093/carcin/bgad076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 10/29/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) play fundamental roles in cancer development; however, the underlying mechanisms for a large proportion of lncRNAs in pancreatic ductal adenocarcinoma (PDAC) have not been elucidated. The expression of colon cancer-associated transcript-1 (CCAT1) in PDAC specimens and cell lines was measured by quantitative real-time polymerase chain reaction (qRT-PCR). The function of CCAT1 was examined in vitro and in vivo. The interactions among CCAT1, miR-24-3p and c-Myc were determined by bioinformatics analysis, RNA immunoprecipitation (RIP), dual-luciferase reporter assay, and rescue experiments. CCAT1 was significantly increased in PDAC, positively correlated with PDAC progression and predicted a worse prognosis. Furthermore, CCAT1 enhanced Adenosine triphosphate (ATP) production to facilitate PDAC cell proliferation, colony formation and motility in vitro and tumor growth in vivo. CCAT1 may serve as an miR-24-3p sponge, thereby counteracting its repression by c-Myc expression. Reciprocally, c-Myc may act as a transcription factor to alter CCAT1 expression by directly targeting its promoter region, thus forming a positive feedback loop with CCAT1. Collectively, these results demonstrate that a positive feedback loop of CCAT1/miR-24-3p/c-Myc is involved in PDAC development, which may serve as a biomarker and therapeutic target for PDAC.
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Affiliation(s)
- Chundong Cheng
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, 23 Youzheng Street, Nangang District, Harbin 150001, Heilongjiang, China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, 23 Youzheng Street, Nangang District, Harbin 150001, Heilongjiang, China
| | - Zonglin Liu
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, 23 Youzheng Street, Nangang District, Harbin 150001, Heilongjiang, China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, 23 Youzheng Street, Nangang District, Harbin 150001, Heilongjiang, China
| | - Danxi Liu
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, 23 Youzheng Street, Nangang District, Harbin 150001, Heilongjiang, China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, 23 Youzheng Street, Nangang District, Harbin 150001, Heilongjiang, China
| | - Hua Chen
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, 23 Youzheng Street, Nangang District, Harbin 150001, Heilongjiang, China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, 23 Youzheng Street, Nangang District, Harbin 150001, Heilongjiang, China
| | - Yongwei Wang
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, 23 Youzheng Street, Nangang District, Harbin 150001, Heilongjiang, China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, 23 Youzheng Street, Nangang District, Harbin 150001, Heilongjiang, China
| | - Bei Sun
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, 23 Youzheng Street, Nangang District, Harbin 150001, Heilongjiang, China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, 23 Youzheng Street, Nangang District, Harbin 150001, Heilongjiang, China
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Wang Z, Burigotto M, Ghetti S, Vaillant F, Tan T, Capaldo BD, Palmieri M, Hirokawa Y, Tai L, Simpson DS, Chang C, Huang AS, Lieschke E, Diepstraten ST, Kaloni D, Riffkin C, Huang DC, Li Wai Suen CS, Garnham AL, Gibbs P, Visvader JE, Sieber OM, Herold MJ, Fava LL, Kelly GL, Strasser A. Loss-of-Function but Not Gain-of-Function Properties of Mutant TP53 Are Critical for the Proliferation, Survival, and Metastasis of a Broad Range of Cancer Cells. Cancer Discov 2024; 14:362-379. [PMID: 37877779 PMCID: PMC10850947 DOI: 10.1158/2159-8290.cd-23-0402] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 10/03/2023] [Accepted: 10/23/2023] [Indexed: 10/26/2023]
Abstract
Mutations in the tumor suppressor TP53 cause cancer and impart poor chemotherapeutic responses, reportedly through loss-of-function, dominant-negative effects and gain-of-function (GOF) activities. The relative contributions of these attributes is unknown. We found that removal of 12 different TP53 mutants with reported GOFs by CRISPR/Cas9 did not impact proliferation and response to chemotherapeutics of 15 human cancer cell lines and colon cancer-derived organoids in culture. Moreover, removal of mutant TP53/TRP53 did not impair growth or metastasis of human cancers in immune-deficient mice or growth of murine cancers in immune-competent mice. DepMap mining revealed that removal of 158 different TP53 mutants had no impact on the growth of 391 human cancer cell lines. In contrast, CRISPR-mediated restoration of wild-type TP53 extinguished the growth of human cancer cells in vitro. These findings demonstrate that LOF but not GOF effects of mutant TP53/TRP53 are critical to sustain expansion of many tumor types. SIGNIFICANCE This study provides evidence that removal of mutant TP53, thereby deleting its reported GOF activities, does not impact the survival, proliferation, metastasis, or chemotherapy responses of cancer cells. Thus, approaches that abrogate expression of mutant TP53 or target its reported GOF activities are unlikely to exert therapeutic impact in cancer. See related commentary by Lane, p. 211 . This article is featured in Selected Articles from This Issue, p. 201.
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Affiliation(s)
- Zilu Wang
- The Walter and Eliza Hall Institute (WEHI), Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Matteo Burigotto
- Armenise-Harvard Laboratory of Cell Division, Department of Cellular, Computational and Integrative Biology – CIBIO, University of Trento, Trento, Italy
| | - Sabrina Ghetti
- Armenise-Harvard Laboratory of Cell Division, Department of Cellular, Computational and Integrative Biology – CIBIO, University of Trento, Trento, Italy
| | - François Vaillant
- The Walter and Eliza Hall Institute (WEHI), Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Tao Tan
- The Walter and Eliza Hall Institute (WEHI), Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Bianca D. Capaldo
- The Walter and Eliza Hall Institute (WEHI), Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Michelle Palmieri
- The Walter and Eliza Hall Institute (WEHI), Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Yumiko Hirokawa
- The Walter and Eliza Hall Institute (WEHI), Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Lin Tai
- The Walter and Eliza Hall Institute (WEHI), Melbourne, Australia
| | - Daniel S. Simpson
- The Walter and Eliza Hall Institute (WEHI), Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Catherine Chang
- The Walter and Eliza Hall Institute (WEHI), Melbourne, Australia
| | - Allan Shuai Huang
- The Walter and Eliza Hall Institute (WEHI), Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Elizabeth Lieschke
- The Walter and Eliza Hall Institute (WEHI), Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Sarah T. Diepstraten
- The Walter and Eliza Hall Institute (WEHI), Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Deeksha Kaloni
- The Walter and Eliza Hall Institute (WEHI), Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Chris Riffkin
- The Walter and Eliza Hall Institute (WEHI), Melbourne, Australia
| | - David C.S. Huang
- The Walter and Eliza Hall Institute (WEHI), Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Connie S.N. Li Wai Suen
- The Walter and Eliza Hall Institute (WEHI), Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Alexandra L. Garnham
- The Walter and Eliza Hall Institute (WEHI), Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Peter Gibbs
- The Walter and Eliza Hall Institute (WEHI), Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Jane E. Visvader
- The Walter and Eliza Hall Institute (WEHI), Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Oliver M. Sieber
- The Walter and Eliza Hall Institute (WEHI), Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Marco J. Herold
- The Walter and Eliza Hall Institute (WEHI), Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Luca L. Fava
- Armenise-Harvard Laboratory of Cell Division, Department of Cellular, Computational and Integrative Biology – CIBIO, University of Trento, Trento, Italy
| | - Gemma L. Kelly
- The Walter and Eliza Hall Institute (WEHI), Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - Andreas Strasser
- The Walter and Eliza Hall Institute (WEHI), Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
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LIU GANG, SHI LEI, WANG BIN, WU ZEHUI, ZHAO HAIYUAN, ZHAO TIANYU, SHI LIANGHUI. Role of oncogenic long noncoding RNA KCNQ1OT1 in colon cancer. Oncol Res 2024; 32:585-596. [PMID: 38361755 PMCID: PMC10865742 DOI: 10.32604/or.2023.029349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 09/05/2023] [Indexed: 02/17/2024] Open
Abstract
The role of lncRNA KCNQ1 opposite strand/antisense transcript 1 (KCNQ1OT1) in colon cancer involves various tumorigenic processes and has been studied widely. However, the mechanism by which it promotes colon cancer remains unclear. Retroviral vector pSEB61 was retrofitted in established HCT116-siKCN and SW480-siKCN cells to silence KCNQ1OT1. Cellular proliferation was measured using CCK8 assay, and flow cytometry (FCM) detected cell cycle changes. RNA sequencing (RNA-Seq) analysis showed differentially expressed genes (DEGs). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were carried out to analyze enriched functions and signaling pathways. RT-qPCR, immunofluorescence, and western blotting were carried out to validate downstream gene expressions. The effects of tumorigenesis were evaluated in BALB/c nude mice by tumor xenografts. Our data revealed that the silencing of KCNQ1OT1 in HCT116 and SW480 cells slowed cell growth and decreased the number of cells in the G2/M phase. RNA-Seq analysis showed the data of DEGs enriched in various GO and KEGG pathways such as DNA replication and cell cycle. RT-qPCR, immunofluorescence, and western blotting confirmed downstream CCNE2 and PCNA gene expressions. HCT116-siKCN cells significantly suppressed tumorigenesis in BALB/c nude mice. Our study suggests that lncRNA KCNQ1OT1 may provide a promising therapeutic strategy for colon cancer.
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Affiliation(s)
- GANG LIU
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Wannan Medical College, Wuhu, 241001, China
| | - LEI SHI
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Wannan Medical College, Wuhu, 241001, China
| | - BIN WANG
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Wannan Medical College, Wuhu, 241001, China
| | - ZEHUI WU
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Wannan Medical College, Wuhu, 241001, China
| | - HAIYUAN ZHAO
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Wannan Medical College, Wuhu, 241001, China
| | - TIANYU ZHAO
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Stomatological Hospital of Chongqing Medical University, Chongqing, 401147, China
| | - LIANGHUI SHI
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Wannan Medical College, Wuhu, 241001, China
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Zou D, Xu T. Construction and validation of a colon cancer prognostic model based on tumor mutation burden-related genes. Sci Rep 2024; 14:2867. [PMID: 38311637 PMCID: PMC10838917 DOI: 10.1038/s41598-024-53257-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 01/30/2024] [Indexed: 02/06/2024] Open
Abstract
Currently, immunotherapy has entered the clinical diagnosis and treatment guidelines for colon cancer, but existing immunotherapy markers cannot predict the effectiveness of immunotherapy well. This study utilized the TCGA-COAD queue to perform differential gene analysis on high and low-mutation burden samples, and screen differentially expressed genes (DEGs). To explore new molecular markers or predictive models of immunotherapy by using DEGs for NMF classification and prognostic model construction. Through systematic bioinformatics analysis, the TCGA-COAD cohort was successfully divided into high mutation burden subtypes and low mutation burden subtypes by NMF typing using DEGs. The proportion of MSI-H between high mutation burden subtypes was significantly higher than that of low mutation burden subtypes, but there was no significant difference in immunotherapy efficacy between the two subtypes. Drug sensitivity analysis showed significant differences in drug sensitivity between the two subtypes. Subsequently, we constructed a prognostic model using DEGs, which can effectively predict patient survival and immunotherapy outcomes. The prognosis and immunotherapy outcomes of the low-risk group were significantly better than those of the high-risk group. The external dataset validation of the constructed prognostic model using the GSE39582 dataset from the GEO database yielded consistent results. At the same time, we also analyzed the TMB and MSI situation between the high and low-risk groups, and the results showed that there was no significant difference in TMB between the high and low-risk groups, but the proportion of MSI-H in the high-risk group was significantly higher than that in the low-risk group. Finally, we conclude that TMB is not a suitable molecular marker for predicting the efficacy of immunotherapy in colon cancer. The newly constructed prognostic model can effectively differentiate the prognosis of colon cancer patients and predict their immunotherapy efficacy.
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Affiliation(s)
- Daoyang Zou
- The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Tianwen Xu
- The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China.
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Liao L, Tang J, Hong Z, Jiang W, Li Y, Kong L, Han K, Hou Z, Zhang C, Zhou C, Zhang L, Sui Q, Xiao B, Mei W, Yu J, Yang W, Pan Z, Ding PR. The effects of oxaliplatin-based adjuvant chemotherapy in high-risk stage II colon cancer with mismatch repair-deficient: a retrospective study. BMC Cancer 2024; 24:164. [PMID: 38302968 PMCID: PMC10835817 DOI: 10.1186/s12885-024-11821-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND For high-risk stageIImismatch repair deficient (dMMR) colon cancers, the benefit of adjuvant chemotherapy remains debatable. The principal aim of this study was to evaluate the prognostic value of high-risk factors and the effect of oxaliplatin-based adjuvant chemotherapy among dMMR stageIIcolon cancers. METHODS Patients with stage II dMMR colon cancers diagnosed between June 2011 and May 2018 were enrolled in the study. Clinicopathological characteristics, treatment, and follow-up data were retrospectively collected. The high-risk group was defined as having one of the following factors: pT4 disease, fewer than twelve lymph nodes harvested (< 12 LNs), poorly differentiated histology, perineural invasion (PNI), lymphatic vascular invasion (LVI), or elevated preoperative carcinoembryonic antigen (CEA). The low-risk group did not have any risk factors above. Factors associated with disease-free survival (DFS) were included in univariate and multivariate Cox analyses. RESULTS We collected a total of 262 consecutive patients with stage II dMMR colon cancer. 179 patients (68.3%) have at least one high-risk factor. With a median follow-up of 50.1 months, the low-risk group was associated with a tended to have a better 3-year DFS than the high-risk group (96.4% vs 89.4%; P = 0.056). Both elevated preoperative CEA (HR 2.93; 95% CI 1.26-6.82; P = 0.013) and pT4 disease (HR 2.58; 95% CI 1.06-6.25; P = 0.037) were independent risk factors of recurrence. Then, the 3-year DFS was 92.6% for the surgery alone group and 88.1% for the adjuvant chemotherapy group (HR 1.64; 95% CI 0.67-4.02; P = 0.280). Furthermore, no survival benefit from oxaliplatin-based adjuvant chemotherapy was observed in the high-risk group and in the subgroups with pT4 disease or < 12 LNs. CONCLUSIONS These data suggests that not all high-risk factors have a similar impact on stage II dMMR colon cancers. Elevated preoperative CEA and pT4 tumor stage are associated with increased recurrence risk. However, oxaliplatin-based adjuvant chemotherapy shows no survival benefits in stage II dMMR colon cancers, either with or without high-risk factors.
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Affiliation(s)
- Leen Liao
- Department of Colorectal Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jinghua Tang
- Department of Colorectal Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zhigang Hong
- Department of Colorectal Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wu Jiang
- Department of Colorectal Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yuan Li
- Department of Colorectal Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Lingheng Kong
- Department of Colorectal Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Kai Han
- Department of Colorectal Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zhenlin Hou
- Department of Colorectal Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Chenzhi Zhang
- Department of Colorectal Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Chi Zhou
- Department of Colorectal Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Linjie Zhang
- Department of Colorectal Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Qiaoqi Sui
- Department of Colorectal Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Binyi Xiao
- Department of Colorectal Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Weijian Mei
- Department of Colorectal Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jiehai Yu
- Department of Colorectal Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wanjun Yang
- Department of Colorectal Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zhizhong Pan
- Department of Colorectal Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China.
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Pei-Rong Ding
- Department of Colorectal Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China.
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China.
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