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Daly AC, Cambuli F, Äijö T, Lötstedt B, Marjanovic N, Kuksenko O, Smith-Erb M, Fernandez S, Domovic D, Van Wittenberghe N, Drokhlyansky E, Griffin GK, Phatnani H, Bonneau R, Regev A, Vickovic S. Tissue and cellular spatiotemporal dynamics in colon aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.22.590125. [PMID: 38712088 PMCID: PMC11071407 DOI: 10.1101/2024.04.22.590125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Tissue structure and molecular circuitry in the colon can be profoundly impacted by systemic age-related effects, but many of the underlying molecular cues remain unclear. Here, we built a cellular and spatial atlas of the colon across three anatomical regions and 11 age groups, encompassing ~1,500 mouse gut tissues profiled by spatial transcriptomics and ~400,000 single nucleus RNA-seq profiles. We developed a new computational framework, cSplotch, which learns a hierarchical Bayesian model of spatially resolved cellular expression associated with age, tissue region, and sex, by leveraging histological features to share information across tissue samples and data modalities. Using this model, we identified cellular and molecular gradients along the adult colonic tract and across the main crypt axis, and multicellular programs associated with aging in the large intestine. Our multi-modal framework for the investigation of cell and tissue organization can aid in the understanding of cellular roles in tissue-level pathology.
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Affiliation(s)
- Aidan C. Daly
- New York Genome Center, New York, NY, USA
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
| | | | - Tarmo Äijö
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
| | - Britta Lötstedt
- New York Genome Center, New York, NY, USA
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Nemanja Marjanovic
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Olena Kuksenko
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | | | | | | | | | - Eugene Drokhlyansky
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gabriel K Griffin
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Hemali Phatnani
- New York Genome Center, New York, NY, USA
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Richard Bonneau
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
- Center for Data Science, New York University, New York, NY, USA
- Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - Aviv Regev
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA
| | - Sanja Vickovic
- New York Genome Center, New York, NY, USA
- Klarman Cell Observatory Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Engineering and Herbert Irving Institute for Cancer Dynamics, Columbia University, New York, NY, USA
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Beijer Laboratory for Gene and Neuro Research, Uppsala University, Uppsala, Sweden
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Chang Y, Chen L, Tang J, Chen G, Ji J, Xu M. USP7-mediated JUND suppresses RCAN2 transcription and elevates NFATC1 to enhance stem cell property in colorectal cancer. Cell Biol Toxicol 2023; 39:3121-3140. [PMID: 37535148 DOI: 10.1007/s10565-023-09822-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/13/2023] [Indexed: 08/04/2023]
Abstract
Cancer stem cells (CSCs) encompass a subset of highly aggressive tumor cells that are involved in tumor initiation and progression. This study investigates the function of regulator of calcineurin 2 (RCAN2) in the stem cell property in colorectal cancer (CRC). By analyzing four GEO datasets, we obtained RCAN2 as a stemness-related gene in CRC. RCAN2 was poorly expressed in CRC tissues and cells, especially in CSCs. RCAN2 restoration reduced calcineurin activity and promoted phosphorylation and degradation of nuclear factor of activated T cells 1 (NFATC1) protein, leading to reduced stemness of CSCs. JunD proto-oncogene (JUND), whose protein level was increased in CRC samples and CRC stem cells, bound to RCAN2 and suppressed its transcription. The abundant ubiquitin specific peptidase 7 (USP7) in CSCs enhanced JUND protein stability through deubiquitination modification. Lentivirus-mediated knockdown of USP7 or JUND also blocked the calcineurin-NFATC1 signaling and reduced the protein levels of stemness-related proteins. Moreover, the USP7 knockdown weakened the colony/sphere formation ability as well as the tumorigenicity of CSCs, and it reduced the CSC content in xenograft tumors. However, further restoration of JUND rescued the stemness of the CSCs. Overall, this study demonstrates that USP7-mediated JUND suppresses RCAN2 transcription and activates NFATC1 to enhance stem cell property in CRC. 1. RCAN2 is poorly expressed in CRC tissues and cells and especially in CSCs. 2. RCAN2 reduces stemness of CSCs by blocking calcineurin-NFATC1 signal transduction. 3. JUND binds to RCAN2 promoter to suppresses RCAN2 transcription. 4. USP7 enhances JUND protein stability via deubiquitination modification. 5. Downregulation of USP7 or JUND restores RCAN2 level and suppresses stemness of CSCs.
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Affiliation(s)
- Yunli Chang
- Department of Gastroenterology, Pudong New Area People's Hospital, No. 490, Chuanhuan South Road, Pudong New Area, Shanghai, 201299, People's Republic of China
| | - Lingling Chen
- Department of Gastroenterology, Pudong New Area People's Hospital, No. 490, Chuanhuan South Road, Pudong New Area, Shanghai, 201299, People's Republic of China
| | - Jie Tang
- Department of Gastroenterology, Pudong New Area People's Hospital, No. 490, Chuanhuan South Road, Pudong New Area, Shanghai, 201299, People's Republic of China
| | - Guoyu Chen
- Department of Gastroenterology, Pudong New Area People's Hospital, No. 490, Chuanhuan South Road, Pudong New Area, Shanghai, 201299, People's Republic of China
| | - Jieru Ji
- Department of Gastroenterology, Pudong New Area People's Hospital, No. 490, Chuanhuan South Road, Pudong New Area, Shanghai, 201299, People's Republic of China
| | - Ming Xu
- Department of Gastroenterology, Pudong New Area People's Hospital, No. 490, Chuanhuan South Road, Pudong New Area, Shanghai, 201299, People's Republic of China.
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Zhang L, Xu C, Wang SH, Ge QW, Wang XW, Xiao P, Yao QH. Cancer-associated fibroblast-related gene signatures predict survival and drug response in patients with colorectal cancer. Front Genet 2022; 13:1054152. [PMID: 36506313 PMCID: PMC9732269 DOI: 10.3389/fgene.2022.1054152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/14/2022] [Indexed: 11/27/2022] Open
Abstract
Background: Cancer-associated fibroblasts (CAFs) play an important role in the tumorigenesis, immunosuppression and metastasis of colorectal cancer (CRC), and can predict poor prognosis in patients with CRC. The present study aimed to construct a CAFs-related prognostic signature for CRC. Methods: The clinical information and corresponding RNA data of CRC patients were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The Estimation of STromal and Immune cells in MAlignant Tumor tissues (ESTIMATES) and xCell methods were applied to evaluate the tumor microenvironment infiltration from bulk gene expression data. Weighted gene co-expression network analysis (WGCNA) was used to construct co-expression modules. The key module was identified by calculating the module-trait correlations. The univariate Cox regression and least absolute shrinkage operator (LASSO) analyses were combined to develop a CAFs-related signature for the prognostic model. Moreover, pRRophetic and Tumor Immune Dysfunction and Exclusion (TIDE) algorithms were utilized to predict chemosensitivity and immunotherapy response. Human Protein Atlas (HPA) databases were employed to evaluate the protein expressions. Results: ESTIMATES and xCell analysis showed that high CAFs infiltration was associated with adverse prognoses. A twenty-gene CAFs-related prognostic signature (CAFPS) was established in the training cohort. Kaplan-Meier survival analyses reveled that CRC patients with higher CAFs risk scores were associated with poor prognosis in each cohort. Univariate and multivariate Cox regression analyses verified that CAFPS was as an independent prognostic factor in predicting overall survival, and a nomogram was built for clinical utility in predicting CRC prognosis. Patients with higher CAFs risk scores tended to not respond to immunotherapy, but were more sensitive to five conventional chemotherapeutic drugs. Conclusion: In summary, the CAFPS could serve as a robust prognostic indicator in CRC patients, which might help to optimize risk stratification and provide a new insight into individual treatments for CRC.
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Affiliation(s)
- Lei Zhang
- Department of Integrated Chinese and Western Medicine, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Chao Xu
- Department of Integrated Chinese and Western Medicine, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Si-Han Wang
- The Second College of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - Qin-Wen Ge
- The First College of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xiao-Wei Wang
- Department of Plastic Surgery, Zhejiang Hospital, Hangzhou, China
| | - Pan Xiao
- Department of Integrated Chinese and Western Medicine, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Qing-Hua Yao
- Department of Integrated Chinese and Western Medicine, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China,Integrated Traditional Chinese and Western Medicine Oncology Laboratory, Key Laboratory of Traditional Chinese Medicine of Zhejiang Province, Hangzhou, China,Key Laboratory of Head and Neck Cancer Translational Research of Zhejiang Province, Hangzhou, China,*Correspondence: Qing-Hua Yao,
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Løvestad AH, Repesa A, Costanzi JM, Lagström S, Christiansen IK, Rounge TB, Ambur OH. Differences in integration frequencies and APOBEC3 profiles of five high-risk HPV types adheres to phylogeny. Tumour Virus Res 2022; 14:200247. [PMID: 36100161 PMCID: PMC9485212 DOI: 10.1016/j.tvr.2022.200247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 02/06/2023] Open
Abstract
Persistent infection with Human Papillomavirus (HPV) is responsible for almost all cases of cervical cancers, and HPV16 and HPV18 associated with the majority of these. These types differ in the proportion of viral minor nucleotide variants (MNVs) caused by APOBEC3 mutagenesis as well as integration frequencies. Whether these traits extend to other types remains uncertain. This study aimed to investigate and compare genomic variability and chromosomal integration in the two phylogenetically distinct Alpha-7 and Alpha-9 clades of carcinogenic HPV types. The TaME-seq protocol was employed to sequence cervical cell samples positive for HPV31, HPV33 or HPV45 and combine these with data from a previous study on HPV16 and HPV18. APOBEC3 mutation signatures were found in Alpha-9 (HPV16/31/33) but not in Alpha-7 (HPV18/45). HPV45 had significantly more MNVs compared to the other types. Alpha-7 had higher integration frequency compared to Alpha-9. An increase in integration frequency with increased diagnostic severity was found for Alpha-7. The results highlight important differences and broaden our understanding of the molecular mechanisms behind cervical cancer induced by high-risk HPV types from the Alpha-7 and Alpha-9 clades.
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Affiliation(s)
- Alexander Hesselberg Løvestad
- Department of Life Sciences and Health, Faculty of Health Sciences, OsloMet - Oslo Metropolitan University, Oslo, Norway
| | - Adina Repesa
- Department of Life Sciences and Health, Faculty of Health Sciences, OsloMet - Oslo Metropolitan University, Oslo, Norway
| | - Jean-Marc Costanzi
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
| | - Sonja Lagström
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway,Department of Research, Cancer Registry of Norway, Oslo, Norway,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Irene Kraus Christiansen
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway,Department of Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus University Hospital and University of Oslo, Lørenskog, Norway
| | - Trine B. Rounge
- Department of Research, Cancer Registry of Norway, Oslo, Norway,Centre for Bioinformatics, Department of Pharmacy, University of Oslo, Oslo, Norway,Corresponding author. Department of Research, Cancer Registry of Norway, Oslo, Norway
| | - Ole Herman Ambur
- Department of Life Sciences and Health, Faculty of Health Sciences, OsloMet - Oslo Metropolitan University, Oslo, Norway,Corresponding authors.
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Fang X, Wang H, Tan X, Ye T, Xu Y, Fan J. Elevated Serum Regulator of Calcineurin 2 is Associated With an Increased Risk of Non-Alcoholic Fatty Liver Disease. Front Pharmacol 2022; 13:840764. [PMID: 35370729 PMCID: PMC8967172 DOI: 10.3389/fphar.2022.840764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/24/2022] [Indexed: 11/13/2022] Open
Abstract
Background: The promoting effect of the regulator of calcineurin 2 (RCAN2) in hepatic steatosis has been observed in animal studies. However, the association of RCAN2 with non-alcoholic fatty liver disease (NAFLD) in humans remains unclear. This study aimed to evaluate the expression of RCAN2 in the liver of mice with hepatic steatosis and in the serum of NAFLD patients and to explore the relationship between serum RCAN2 levels and NAFLD. Methods: The mRNA and protein expression of RCAN2 were detected by quantitative real-time PCR (qRT-PCR) and Western blot. NAFLD was diagnosed by abdominal ultrasonography. Circulating RCAN2 levels were measured by ELISA kits. The relationship between serum RCAN2 levels and NAFLD was assessed. Results: qRT-PCR and Western blot analysis showed that compared with the corresponding controls, the mRNA and protein expression of RCAN2 were significantly increased in the liver tissues of db/db and mice on a high-fat diet. Serum RCAN2 levels were markedly elevated in NAFLD patients compared with non-NAFLD subjects. Binary logistic regression analysis showed that serum RCAN2 levels were significantly associated with NAFLD. Receiver operation characteristic (ROC) curve analysis showed that serum RCAN2 might act as a predictive biomarker for NAFLD [area under the curve (AUC) = 0.663, 95% CI = 0.623–0.702], and the serum RCAN2/(AST/ALT) ratio displayed improved predictive accuracy (AUC = 0.816, 95% CI = 0.785–0.846). Conclusion: Elevated serum RCAN2 levels were associated with an increased risk of NAFLD. Serum RCAN2, especially the serum RCAN2/(AST/ALT) ratio, might be a candidate diagnostic marker for NAFLD.
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Affiliation(s)
- Xia Fang
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Metabolic Vascular Disease Key Laboratory of Sichuan Province, Luzhou, China.,Sichuan Clinical Research Center for Nephropathy, Luzhou, China.,Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, Luzhou, China
| | - Hongya Wang
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Metabolic Vascular Disease Key Laboratory of Sichuan Province, Luzhou, China.,Sichuan Clinical Research Center for Nephropathy, Luzhou, China.,Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, Luzhou, China
| | - Xiaozhen Tan
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Metabolic Vascular Disease Key Laboratory of Sichuan Province, Luzhou, China.,Sichuan Clinical Research Center for Nephropathy, Luzhou, China.,Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, Luzhou, China
| | - Ting Ye
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Yong Xu
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Metabolic Vascular Disease Key Laboratory of Sichuan Province, Luzhou, China.,Sichuan Clinical Research Center for Nephropathy, Luzhou, China.,Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, Luzhou, China
| | - Jiahao Fan
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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6
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Wang H, Fang X, Ren Q, Zeng Y, Tan X, Ye T, Fan J, Xu Y. Association Between Circulating Regulator of Calcineurin 2 Concentrations With Overweight and Obesity. Front Endocrinol (Lausanne) 2022; 13:857841. [PMID: 35733783 PMCID: PMC9208054 DOI: 10.3389/fendo.2022.857841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 04/28/2022] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Regulator of calcineurin 2 (RCAN2) has been reported to promote food intake and weight gain in animal studies. However, its effect on body weight in humans is unclear. OBJECTIVE This study aimed to investigate the relationship between serum RCAN2 concentrations and participants with overweight/obesity. METHODS A cross-sectional study was performed in 872 Chinese adults, including 348 participants with normal weight (NW), 397 participants with overweight (OW), and 127 participants with obesity (OB). All participants were divided into NW, OW and OB groups according to their body mass index (BMI). Serum RCAN2 concentrations were determined by enzyme-linked immunosorbent assay. RESULTS Serum RCAN2 concentrations gradually increased with the increase of BMI (p < 0.001). The percentages of OW/OB gradually increased in tandem with increasing tertiles of RCAN2 (p < 0.001). Additionally, serum RCAN2 concentrations were significantly correlated with a series of anthropometric and metabolic parameters, predominantly including body weight, BMI, SBP, DBP, total cholesterol, triglycerides, HDL-C, LDL-C (all p < 0.05). Furthermore, logistic regression analysis showed that the risk of OW/OB was significantly increased with the increase of serum RCAN2 concentrations. Receiver operation characteristic (ROC) curve analysis revealed that serum RCAN2, especially serum RCAN2/(AST/ALT) ratio, might serve as a candidate biomarker for obesity. CONCLUSION Serum RCAN2 concentrations were increased in subjects with OW/OB. The increased serum RCAN2 concentrations were associated with the increased risks of OW/OB.
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Affiliation(s)
- Hongya Wang
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, Luzhou, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, Luzhou, China
| | - Xia Fang
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, Luzhou, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, Luzhou, China
| | - Qian Ren
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, Luzhou, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, Luzhou, China
| | - Yan Zeng
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, Luzhou, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, Luzhou, China
| | - Xiaozhen Tan
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, Luzhou, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, Luzhou, China
| | - Ting Ye
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jiahao Fan
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- *Correspondence: Jiahao Fan, ; Yong Xu,
| | - Yong Xu
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, Luzhou, China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, Luzhou, China
- *Correspondence: Jiahao Fan, ; Yong Xu,
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7
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Xu YJ, He MK, Liu S, Huang LC, Bu XY, Kan A, Shi M. Construction of a single nucleotide variant score-related gene-based prognostic model in hepatocellular carcinoma: analysis of multi-independent databases and validation in vitro. Cancer Cell Int 2021; 21:610. [PMID: 34794449 PMCID: PMC8600893 DOI: 10.1186/s12935-021-02321-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/05/2021] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND The accumulation of single nucleotide variants (SNVs) and the emergence of neoantigens can affect tumour proliferation and the immune microenvironment. However, the SNV-related immune microenvironment characteristics and key genes involved in hepatocellular carcinoma (HCC) are still unclear. We aimed to evaluate differences in the SNV-related immune microenvironment, construct a prognostic model and validate the key genes in vitro. METHODS The categories of samples were defined by the expression of SNV score-related genes to evaluate the differences in mutational features, immune environment and prognosis. The survival model was constructed with survival-associated genes and verified in two independent test datasets. RCAN2, the key gene screened out for biofunction, was validated in vitro. RESULTS IC2, among the three integrated clusters (IC1, IC2, IC3) classified by the 82 SNV score-related genes, was distinct from the rest in SNV score and immune cell infiltration, showing a better prognosis. Seven prognostic markers, HTRA3, GGT5, RCAN2, LGALS3, CXCL1, CLEC3B, and CTHRC1, were screened to construct a prognostic model. The survival model distinguished high-risk patients with poor prognoses in three independent datasets (log-rank P < 0.0001, 0.011, and 0.0068, respectively) with acceptable sensitivity and specificity. RCAN2 was inversely correlated with NK cell infiltration, and knockdown of RCAN2 promoted proliferation in HCC. CONCLUSIONS This study revealed the characteristics of the HCC SNV-associated subgroup and screened seven latent markers for their accuracy of prognosis. Additionally, RCAN2 was preliminarily proven to influence proliferation in HCC and it had a close relationship with NK cell infiltration in vitro. With the capability to predict HCC outcomes, the model constructed with seven key differentially expressed genes offers new insights into individual therapy.
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Affiliation(s)
- Yu-Jie Xu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China.,Department of Hepatic Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Min-Ke He
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China.,Department of Hepatic Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Shuang Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China.,Department of Hepatic Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Li-Chang Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China.,Department of Hepatic Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Xiao-Yun Bu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China.,Department of Hepatic Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Anna Kan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China.,Department of Hepatic Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Ming Shi
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China. .,Department of Hepatic Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China.
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Mammarella E, Zampieri C, Panatta E, Melino G, Amelio I. NUAK2 and RCan2 participate in the p53 mutant pro-tumorigenic network. Biol Direct 2021; 16:11. [PMID: 34348766 PMCID: PMC8335924 DOI: 10.1186/s13062-021-00296-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 07/29/2021] [Indexed: 02/04/2023] Open
Abstract
Most inactivating mutations in TP53 gene generates neomorphic forms of p53 proteins that experimental evidence and clinical observations suggest to exert gain-of-function effects. While massive effort has been deployed in the dissection of wild type p53 transcriptional programme, p53 mutant pro-tumorigenic gene network is still largely elusive. To help dissecting the molecular basis of p53 mutant GOF, we performed an analysis of a fully annotated genomic and transcriptomic human pancreatic adenocarcinoma to select candidate players of p53 mutant network on the basis their differential expression between p53 mutant and p53 wild-type cohorts and their prognostic value. We identified NUAK2 and RCan2 whose p53 mutant GOF-dependent regulation was further validated in pancreatic cancer cellular model. Our data demonstrated that p53R270H can physically bind RCan2 gene locus in regulatory regions corresponding to the chromatin permissive areas where known binding partners of p53 mutant, such as p63 and Srebp, bind. Overall, starting from clinically relevant data and progressing into experimental validation, our work suggests NUAK2 and RCan2 as novel candidate players of the p53 mutant pro-tumorigenic network whose prognostic and therapeutic interest might attract future studies.
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Affiliation(s)
- Eleonora Mammarella
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Carlotta Zampieri
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Emanuele Panatta
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Gerry Melino
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Ivano Amelio
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133 Rome, Italy
- School of Life Sciences, University of Nottingham, Nottingham, UK
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9
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Cui C, Zhou Y, Cui Q. Defining the functional divergence of orthologous genes between human and mouse in the context of miRNA regulation. Brief Bioinform 2021; 22:6314723. [PMID: 34226920 DOI: 10.1093/bib/bbab253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/10/2021] [Accepted: 06/15/2021] [Indexed: 11/13/2022] Open
Abstract
Animal models have a certain degree of similarity with human in genes and physiological processes, which leads them to be valuable tools for studying human diseases and for assisting drug development. However, translational researches adopting animal models are largely restricted by the species heterogeneity, which is also a major reason for the failure of drug research. Currently, computational method for exploring the functional differences between orthologous genes is still insufficient. For this purpose, here, we presented an algorithm, functional divergence score (FDS), by comprehensively evaluating the functional differences between the microRNAs regulating the paired orthologous genes. Given that mouse is one of the most popular model animals, currently, FDS was designed to dissect the functional divergence of orthologous genes between human and mouse. The results showed that gene FDS value is significantly associated with gene evolutionary characteristics and can discover expression divergence of human-mouse orthologous genes. Moreover, FDS performed well in distinguishing the targets of approved drugs and the failed ones. These results suggest that FDS is a valuable tool to evaluate the functional divergence of paired human and mouse orthologous genes. In addition, for each orthologous gene pair, FDS can provide detailed differences in functions and phenotypes. Our study provided a useful tool for quantifying the functional difference between human and mouse, and the presented framework is easily to be extended to the orthologous genes between human and other species. An online server of FDS is available at http://www.cuilab.cn/fds/.
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Affiliation(s)
- Chunmei Cui
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Yuan Zhou
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Qinghua Cui
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing, China
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10
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Jang HJ, Yang JH, Hong E, Jo E, Lee S, Lee S, Choi JS, Yoo HS, Kang H. Chelidonine Induces Apoptosis via GADD45a-p53 Regulation in Human Pancreatic Cancer Cells. Integr Cancer Ther 2021; 20:15347354211006191. [PMID: 33884928 PMCID: PMC8077490 DOI: 10.1177/15347354211006191] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Chelidonium majus has been used as a traditional medicine in China and western countries for various diseases, including inflammation and cancer. However, the anti-cancer effect of chelidonine, a major compound of C. majus extracts, on pancreatic cancer remains poorly understood. In this study, we found that treatment with chelidonine inhibited proliferation of BxPC-3 and MIA PaCa-2 human pancreatic cancer cells. Annexin-V/propidium iodide staining assay showed that this growth inhibitory effect of chelidonine was induced through apoptosis. We found that chelidonine treatment upregulated mRNA levels and transcription factor activity in both cell lines. Increases in protein expression levels of p53, GADD45A, p21 and cleaved caspase-3 were also observed, with more distinct changes in MIA PaCa-2 cells compared to the BxPC-3 cells. These results suggest that chelidonine induces pancreatic cancer apoptosis through the p53 and GADD45A pathways. Our findings provide new insights into the use of chelidonine for the treatment of pancreatic cancer.
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Affiliation(s)
- Hyun-Jin Jang
- Korea Basic Science Institute, Daejeon,
Republic of Korea
- Sungkyunkwan University, Suwon,
Republic of Korea
| | - Jae Ho Yang
- Daejeon Korean Medicine Hospital of
Daejeon University, Seoul, Republic of Korea
| | - Eunmi Hong
- Korea Basic Science Institute, Daejeon,
Republic of Korea
| | - Eunbi Jo
- Korea Basic Science Institute, Daejeon,
Republic of Korea
- Hanyang University, Seoul, Republic of
Korea
| | - Soon Lee
- Korea Basic Science Institute, Daejeon,
Republic of Korea
- University of Science and Technology,
Daejeon, Republic of Korea
| | - Sanghun Lee
- Korea Institute of Oriental Medicine,
Daejeon, Republic of Korea
| | - Jong Soon Choi
- Korea Basic Science Institute, Daejeon,
Republic of Korea
| | - Hwa Seung Yoo
- Daejeon Korean Medicine Hospital of
Daejeon University, Seoul, Republic of Korea
- Hwa Seung Yoo, East West Cancer Center,
Seoul Korean Medicine Hospital of Daejeon University, Seoul 05836, Rep. of
Korea.
| | - Hyuno Kang
- Korea Basic Science Institute, Daejeon,
Republic of Korea
- Hyuno Kang, Division of Analytical Science,
Korea Basic Science Institute, 169-148, Gwahak-ro, Yuseong-gu, Daejeon 34133,
Republic of Korea.
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11
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Kochi M, Hinoi T, Niitsu H, Miguchi M, Saito Y, Sada H, Sentani K, Sakamoto N, Oue N, Tashiro H, Sotomaru Y, Yasui W, Ohdan H. Oncogenic mutation in RAS-RAF axis leads to increased expression of GREB1, resulting in tumor proliferation in colorectal cancer. Cancer Sci 2020; 111:3540-3549. [PMID: 32629543 PMCID: PMC7541019 DOI: 10.1111/cas.14558] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/27/2020] [Accepted: 06/30/2020] [Indexed: 12/22/2022] Open
Abstract
BRAFV600E mutation accounts for up to 90% of all BRAF mutations in human colorectal cancer (CRC), and constitutively activates the MEK‐MAPK pathway. It is recognized that neutralizing mAbs for epidermal growth factor receptor alone are not effective for CRC with BRAFV600E mutation. Therefore, there is increasing interest in identification of the possible therapeutic targets in downstream of BRAF mutation in CRCs. To address this, we studied genome engineered mouse models for colonic neoplasia that has BrafV600E mutation on the basis of Apc inactivation, induced in 2 distinct Cre mouse models, CDX2P‐G22Cre and CDX2P‐CreERT2 mice. We carried out oligonucleotide microarray analysis for colonic neoplasia generated in these mouse models, and compared gene expression profiles among Kras/Braf WT, Kras‐mutated, and Braf‐mutated mouse colon tumors to seek new molecular targets corresponding to the KRAS‐BRAF‐MAPK axis. We found that the expression of the growth regulation by estrogen in breast cancer protein 1 (Greb1) was the most upregulated gene in Braf‐mutated mouse tumors compared to Kras/Braf WT counterparts. The silencing of GREB1 significantly reduced the proliferation and tumorigenesis of CRC cell lines, whereas the overexpression of GREB1 promoted cell proliferation. Although GREB1 was first identified as a hormone‐responsive gene mediating estrogen‐stimulated cell proliferation in endometriosis, breast, and ovarian cancers, these results suggest that RAS‐RAF‐MAPK signaling upregulates GREB1 expression in CRC, resulting in cellular proliferation. Thus, GREB1 is a possible therapeutic target for CRCs with BrafV600E mutation.
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Affiliation(s)
- Masatoshi Kochi
- Department of Gastroenterological and Transplant Surgery, Applied Life Sciences, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Takao Hinoi
- Department of Gastroenterological and Transplant Surgery, Applied Life Sciences, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.,Department of Surgery, National Hospital Organization Kure Medical Center and Chugoku Cancer Center, Hiroshima, Japan.,Department of Clinical and Molecular Genetics, Hiroshima University Hospital, Hiroshima, Japan
| | - Hiroaki Niitsu
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Masashi Miguchi
- Department of Gastroenterological, Breast and Transplant Surgery, Hiroshima Prefectural Hospital, Hiroshima, Japan
| | - Yasufumi Saito
- Department of Surgery, Chugoku Rosai Hospital, Hiroshima, Japan
| | - Haruki Sada
- Department of Gastroenterological and Transplant Surgery, Applied Life Sciences, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.,Department of Surgery, National Hospital Organization Kure Medical Center and Chugoku Cancer Center, Hiroshima, Japan
| | - Kazuhiro Sentani
- Department of Molecular Pathology, Hiroshima University Institute of Biomedical and Health Sciences, Hiroshima, Japan
| | - Naoya Sakamoto
- Department of Molecular Pathology, Hiroshima University Institute of Biomedical and Health Sciences, Hiroshima, Japan
| | - Naohide Oue
- Department of Molecular Pathology, Hiroshima University Institute of Biomedical and Health Sciences, Hiroshima, Japan
| | - Hirotaka Tashiro
- Department of Surgery, National Hospital Organization Kure Medical Center and Chugoku Cancer Center, Hiroshima, Japan
| | - Yusuke Sotomaru
- Natural Science Center for Basic Research and Development, Hiroshima University, Hiroshima, Japan
| | - Wataru Yasui
- Department of Molecular Pathology, Hiroshima University Institute of Biomedical and Health Sciences, Hiroshima, Japan
| | - Hideki Ohdan
- Department of Gastroenterological and Transplant Surgery, Applied Life Sciences, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
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12
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Lee SK, Ahnn J. Regulator of Calcineurin (RCAN): Beyond Down Syndrome Critical Region. Mol Cells 2020; 43:671-685. [PMID: 32576715 PMCID: PMC7468584 DOI: 10.14348/molcells.2020.0060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/23/2020] [Accepted: 05/25/2020] [Indexed: 12/19/2022] Open
Abstract
The regulator of calcineurin (RCAN) was first reported as a novel gene called DSCR1, encoded in a region termed the Down syndrome critical region (DSCR) of human chromosome 21. Genome sequence comparisons across species using bioinformatics revealed three members of the RCAN gene family, RCAN1, RCAN2, and RCAN3, present in most jawed vertebrates, with one member observed in most invertebrates and fungi. RCAN is most highly expressed in brain and striated muscles, but expression has been reported in many other tissues, as well, including the heart and kidneys. Expression levels of RCAN homologs are responsive to external stressors such as reactive oxygen species, Ca2+, amyloid β, and hormonal changes and upregulated in pathological conditions, including Alzheimer's disease, cardiac hypertrophy, diabetes, and degenerative neuropathy. RCAN binding to calcineurin, a Ca2+/calmodulin-dependent phosphatase, inhibits calcineurin activity, thereby regulating different physiological events via dephosphorylation of important substrates. Novel functions of RCANs have recently emerged, indicating involvement in mitochondria homeostasis, RNA binding, circadian rhythms, obesity, and thermogenesis, some of which are calcineurin-independent. These developments suggest that besides significant contributions to DS pathologies and calcineurin regulation, RCAN is an important participant across physiological systems, suggesting it as a favorable therapeutic target.
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Affiliation(s)
- Sun-Kyung Lee
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
- Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Joohong Ahnn
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
- Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
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13
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Liu Y, Cao J, Zhu YN, Ma Y, Murtaza G, Li Y, Wang JH, Pu YS. C1222C Deletion in Exon 8 of ABL1 Is Involved in Carcinogenesis and Cell Cycle Control of Colorectal Cancer Through IRS1/PI3K/Akt Pathway. Front Oncol 2020; 10:1385. [PMID: 32850446 PMCID: PMC7433659 DOI: 10.3389/fonc.2020.01385] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 06/30/2020] [Indexed: 12/16/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most commonly diagnosed cancers worldwide. ABL1 (c-Abl) is a non-receptor tyrosine kinase, whose role, and molecular mechanism in CRC remain largely unclear. The aim of this study was to elucidate the role of ABL1 to obtain information on colon cancer gene mutation. We analyzed the tissue samples obtained from patients with CRC, CRC cell lines, and the immunodeficient mice. The proliferation, cell cycle, and apoptosis of CRC cells were examined. IPA software was used to analyze the molecules involved in CRC after ABL1 RNA interference. We found ABL1 was highly expressed in CRC tissues and cells. This high expression was associated with the TNM stage of CRC patients. In exon 8 of the ABL1 gene, we identified a novel mutation of C1222C deletion, which was related to the CRC stage. Depletion of ABL1 resulted in the inhibition of proliferation and escalation of apoptosis in two CRC cell lines, SW480, and HCT-116. Our in vivo study also demonstrated that depletion of ABL1 reduced CRC tumor progression. The results of the ingenuity pathway analysis indicated that the expression of 732 genes was upregulated and that of 691 genes was downregulated in mice transplanted with ABL1-downregulated CRC cells, among which we confirmed that depletion of ABL1 inhibited TGF-β1 via IRS1/PI3K/AKT pathway in CRC progression. These findings demonstrated that ABL1 plays an important role and that it can be a potential molecular target for CRC therapy.
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Affiliation(s)
- Yi Liu
- Department of Oncology, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Jian Cao
- Department of Pharmacy, Xijing Hospital, Air Force Military Medical University, Xi'an, China
| | - Ya-Ning Zhu
- Department of Pharmacy, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Yu Ma
- Department of Pathology, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Ghulam Murtaza
- Department of Pharmacy, COMSATS University Islamabad, Lahore Campus, Lahore, Pakistan
| | - Yu Li
- Department of Oncology, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Jian-Hua Wang
- The Second Department of General Surgery, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Yan-Song Pu
- The Second Department of General Surgery, Shaanxi Provincial People's Hospital, Xi'an, China
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14
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Cholesterol and beyond - The role of the mevalonate pathway in cancer biology. Biochim Biophys Acta Rev Cancer 2020; 1873:188351. [PMID: 32007596 DOI: 10.1016/j.bbcan.2020.188351] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 01/14/2020] [Accepted: 01/30/2020] [Indexed: 02/07/2023]
Abstract
Cancer is a multifaceted global disease. Transformation of a normal to a malignant cell takes several steps, including somatic mutations, epigenetic alterations, metabolic reprogramming and loss of cell growth control. Recently, the mevalonate pathway has emerged as a crucial regulator of tumor biology and a potential therapeutic target. This pathway controls cholesterol production and posttranslational modifications of Rho-GTPases, both of which are linked to several key steps of tumor progression. Inhibitors of the mevalonate pathway induce pleiotropic antitumor-effects in several human malignancies, identifying the pathway as an attractive candidate for novel therapies. In this review, we will provide an overview about the role and regulation of the mevalonate pathway in certain aspects of cancer initiation and progression and its potential for therapeutic intervention in oncology.
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15
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Gang W, Yu-Zhu W, Yang Y, Feng S, Xing-Li F, Heng Z. The critical role of calcineurin/NFAT (C/N) pathways and effective antitumor prospect for colorectal cancers. J Cell Biochem 2019; 120:19254-19273. [PMID: 31489709 DOI: 10.1002/jcb.29243] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 06/10/2019] [Indexed: 12/11/2022]
Abstract
Transcription factors (TFs) like a nuclear factor of activated T-cells (NFAT) and its controller calcineurin are highly expressed in primary intestinal epithelial cells (IECs) due to delamination, damage by tumor-associated flora and selective activation in the intestinal tract tumor are crucial in the progression and growth of colorectal cancer (CRC). This study sought to summarize the current findings concerning the dysregulated calcineurin/NFAT (C/N) signaling involved in CRC initiation and progression. These signalings include proliferation, T-cell functions, and glycolysis with high lactate production that remodels the acidosis, which genes in tumor cells provide an evolutionary advantage, or even increased their attack phenotype. Moreover, the relationship between C/N and gut microbiome in CRC, especially role of NFAT and toll-like receptor signaling in regulating intestinal microbiota are also discussed. Furthermore, this review will discuss the proteins and genes relating to C/N induced acidosis in CRC, which includes ASIC2 regulated C/N1 and TFs associated with the glycolytic by-product that affect T-cell functions and CRC cell growth. It is revealed that calcineurin or NFAT targeting to antitumor, selective calcineurin inhibition or targets in NFAT signaling may be useful for clinical treatment of CRC. This can further aid in the identification of specific targets via cancer patient-personalized approach. Future studies should be focused on targeting to C/N or TLR signaling by the combination of therapeutic agents to regulate T-cell functions and gut microbiome for activating potent anticancer property with the prospect of potentiating the antitumor therapy for CRC.
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Affiliation(s)
- Wang Gang
- Department of Pharmaceutics, Shanghai Eight People's Hospital, Jiangsu University, Shanghai, China
| | - Wang Yu-Zhu
- Department of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yu Yang
- Department of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Shi Feng
- Department of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Fu Xing-Li
- Department of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Zhang Heng
- Department of General Surgery, Nanjing Lishui District People's Hospital, Zhongda Hospital Lishui Branch, Southeast University, Nanjing, China
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16
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Gao W, Xu Y, Chen T, Du Z, Liu X, Hu Z, Wei D, Gao C, Zhang W, Li Q. Targeting oxidative pentose phosphate pathway prevents recurrence in mutant Kras colorectal carcinomas. PLoS Biol 2019; 17:e3000425. [PMID: 31461438 PMCID: PMC6736310 DOI: 10.1371/journal.pbio.3000425] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 09/10/2019] [Accepted: 08/09/2019] [Indexed: 12/17/2022] Open
Abstract
Recurrent tumors originate from cancer stem cells (CSCs) that survive conventional treatments. CSCs consist of heterogeneous subpopulations that display distinct sensitivity to anticancer drugs. Such a heterogeneity presents a significant challenge in preventing tumor recurrence. In the current study, we observed that quiescent CUB-domain–containing protein 1 (CDCP1)+ CSCs are enriched after chemotherapy in mutant Kirsten rat sarcoma viral oncogene homolog (Kras) colorectal carcinomas (CRCs) and serve as a reservoir for recurrence. Mechanistically, glucose catabolism in CDCP1+ CSCs is routed to the oxidative pentose phosphate pathway (PPP); multiple cycling of carbon backbones in the oxidative PPP potentially maximizes NADPH reduction to counteract chemotherapy-induced reactive oxygen species (ROS) formation, thereby allowing CDCP1+ CSCs to survive chemotherapeutic attack. This is dependent on silent mating type information regulation 2 homolog 5 (Sirt5)-mediated inhibition of the glycolytic enzyme triosephosphate isomerase (TPI) through demalonylation of Lys56. Blocking demalonylation of TPI at Lys56 increases chemosensitivity of CDCP1+ CSCSs and delays recurrence of mutant Kras CRCs in vivo. These findings pinpoint a new therapeutic approach for combating mutant Kras CRCs. This study shows that CDCP1-positive cancer stem cells represent a critical driving force behind tumor relapse in colorectal tumors that have mutant Kras and reveals a unique role for the oxidative pentose phosphate pathway in this process.
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Affiliation(s)
- WenChao Gao
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Department of General Surgery, ChangZheng Hospital, Second Military Medical University, Shanghai, China
| | - YuTing Xu
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Tao Chen
- Endoscopy Center, ZhongShan Hospital, Fudan University, Shanghai, China
| | - ZunGuo Du
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Department of Pathology, HuaShan Hospital, Fudan University, Shanghai, China
| | - XiuJuan Liu
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Department of Pathology, HuaShan Hospital, Fudan University, Shanghai, China
| | - ZhiQian Hu
- Department of General Surgery, ChangZheng Hospital, Second Military Medical University, Shanghai, China
| | - Dong Wei
- Department of Anus and Intestine Surgery, PLA Central Hospital 150, Luoyang, China
| | - ChunFang Gao
- Department of Anus and Intestine Surgery, PLA Central Hospital 150, Luoyang, China
| | - Wei Zhang
- Department of Cancer Biology, Cancer Center of Wake Forest Baptist Medical Center, Winston-Salem, North Carolina, United States of America
| | - QingQuan Li
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai, China
- * E-mail:
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17
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Hattori Y, Sentani K, Shinmei S, Oo HZ, Hattori T, Imai T, Sekino Y, Sakamoto N, Oue N, Niitsu H, Hinoi T, Ohdan H, Yasui W. Clinicopathological significance of RCAN2 production in gastric carcinoma. Histopathology 2019; 74:430-442. [DOI: 10.1111/his.13764] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 09/29/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Yui Hattori
- Department of Molecular Pathology; Graduate School of Biomedical and Health Sciences; Hiroshima University; Hiroshima Japan
| | - Kazuhiro Sentani
- Department of Molecular Pathology; Graduate School of Biomedical and Health Sciences; Hiroshima University; Hiroshima Japan
| | - Shunsuke Shinmei
- Department of Urology; Graduate School of Biomedical and Health Sciences; Hiroshima University; Hiroshima Japan
| | - Htoo Zarni Oo
- Department of Urologic Sciences; University of British Columbia; Vancouver Prostate Centre; Vancouver British Columbia Canada
| | - Takuya Hattori
- Department of Molecular Pathology; Graduate School of Biomedical and Health Sciences; Hiroshima University; Hiroshima Japan
| | - Takeharu Imai
- Department of Surgical Oncology; Gifu University Graduate School of Medicine; Gifu Japan
| | - Yohei Sekino
- Department of Molecular Pathology; Graduate School of Biomedical and Health Sciences; Hiroshima University; Hiroshima Japan
- Department of Urology; Graduate School of Biomedical and Health Sciences; Hiroshima University; Hiroshima Japan
| | - Naoya Sakamoto
- Department of Molecular Pathology; Graduate School of Biomedical and Health Sciences; Hiroshima University; Hiroshima Japan
| | - Naohide Oue
- Department of Molecular Pathology; Graduate School of Biomedical and Health Sciences; Hiroshima University; Hiroshima Japan
| | - Hiroaki Niitsu
- Department of Gastroenterological Transplant Surgery; Graduate School of Biomedical and Health Sciences; Hiroshima University; Hiroshima Japan
| | - Takao Hinoi
- Department of Gastroenterological Transplant Surgery; Graduate School of Biomedical and Health Sciences; Hiroshima University; Hiroshima Japan
- Department of Surgery; National Hospital Organisation Kure Medical Centre; Kure Japan
| | - Hideki Ohdan
- Department of Gastroenterological Transplant Surgery; Graduate School of Biomedical and Health Sciences; Hiroshima University; Hiroshima Japan
| | - Wataru Yasui
- Department of Molecular Pathology; Graduate School of Biomedical and Health Sciences; Hiroshima University; Hiroshima Japan
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18
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Pi H, Li M, Zou L, Yang M, Deng P, Fan T, Liu M, Tian L, Tu M, Xie J, Chen M, Li H, Xi Y, Zhang L, He M, Lu Y, Chen C, Zhang T, Wang Z, Yu Z, Gao F, Zhou Z. AKT inhibition-mediated dephosphorylation of TFE3 promotes overactive autophagy independent of MTORC1 in cadmium-exposed bone mesenchymal stem cells. Autophagy 2018; 15:565-582. [PMID: 30324847 DOI: 10.1080/15548627.2018.1531198] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Cadmium (Cd) is a toxic metal that is widely found in numerous environmental matrices and induces serious adverse effects in various organs and tissues. Bone tissue seems to be a crucial target of Cd contamination. Macroautophagy/autophagy has been proposed to play a pivotal role in Cd-mediated bone toxicity. However, the mechanisms that underlie Cd-induced autophagy are not yet completely understood. We demonstrated that Cd treatment increased autophagic flux and inhibition of the autophagic process using Atg7 gene silencing blocked the Cd-induced mesenchymal stem cell death. Mechanistically, Cd activated nuclear translocation of TFE3 but not that of TFEB or MITF, which contributed to the expression of autophagy-related genes and lysosomal biogenesis. Specifically, Cd decreased expression of phospho-AKT (Ser473). The reduction in AKT activity led to dephosphorylation of cytosolic TFE3 at Ser565 and promoted TFE3 nuclear translocation independently of MTORC1. Notably, Cd treatment increased the activity of PPP3/calcineurin, and pharmacological inhibition of PPP3/calcineurin with FK506 suppressed AKT dephosphorylation and TFE3 activity. These results suggest that PPP3/calcineurin negatively regulates AKT phosphorylation and is involved in Cd-induced TFE3-dependent autophagy. Modulation of the PPP3/calcineurin-AKT-TFE3 autophagic-lysosomal machinery may offer novel therapeutic approaches for the treatment of Cd-induced bone damage. Abbreviations: ACTB: actin: beta; AKT: thymoma viral proto-oncogene; AMPK: AMP-activated protein kinase; ATG: autophagy related; Baf A1: bafilomycin A1; Cd: cadmium; FOXO3: forkhead box O3; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MITF: melanogenesis associated transcription factor; MSC: mesenchymal stem sell; MTORC1: mechanistic target of rapamycin kinase complex 1; RPS6KB1: ribosomal protein S6 kinase: polypeptide 1; SGK1: serum/glucocorticoid regulated kinase 1; SQSTM1/p62: sequestosome 1;TFE3: transcription factor E3; TFEB: transcription factor EB; TFEC: transcription factor EC.
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Affiliation(s)
- Huifeng Pi
- b Department of Occupational Health , Third Military Medical University , Chongqing , China.,c Department of Aerospace Medicine , Fourth Military Medical University , Xi'an , China
| | - Min Li
- b Department of Occupational Health , Third Military Medical University , Chongqing , China.,d Wuhan General Hospital of Guangzhou Military Region , Wuhan , China
| | - Lingyun Zou
- e Bao'an Maternal and Child Health Hospital , Jinan University , Shenzhen , China
| | - Min Yang
- b Department of Occupational Health , Third Military Medical University , Chongqing , China.,f Department of Gastroenterology, XinQiao Hospital , Third Military Medical University , Chongqing , China
| | - Ping Deng
- b Department of Occupational Health , Third Military Medical University , Chongqing , China
| | - Tengfei Fan
- g Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital , Central South University , Changsha , China
| | - Menyu Liu
- b Department of Occupational Health , Third Military Medical University , Chongqing , China
| | - Li Tian
- b Department of Occupational Health , Third Military Medical University , Chongqing , China
| | - Manyu Tu
- b Department of Occupational Health , Third Military Medical University , Chongqing , China
| | - Jia Xie
- b Department of Occupational Health , Third Military Medical University , Chongqing , China
| | - Mengyan Chen
- b Department of Occupational Health , Third Military Medical University , Chongqing , China
| | - Huijuan Li
- b Department of Occupational Health , Third Military Medical University , Chongqing , China
| | - Yu Xi
- a Department of Environmental Medicine, and Department of Critical Care Medicine of the First Affiliated Hospital , Zhejiang University School of Medicine , Hangzhou , China
| | - Lei Zhang
- b Department of Occupational Health , Third Military Medical University , Chongqing , China
| | - Mindi He
- b Department of Occupational Health , Third Military Medical University , Chongqing , China
| | - Yonghui Lu
- b Department of Occupational Health , Third Military Medical University , Chongqing , China
| | - Chunhai Chen
- b Department of Occupational Health , Third Military Medical University , Chongqing , China
| | - Tao Zhang
- b Department of Occupational Health , Third Military Medical University , Chongqing , China
| | - Zheng Wang
- c Department of Aerospace Medicine , Fourth Military Medical University , Xi'an , China
| | - Zhengping Yu
- b Department of Occupational Health , Third Military Medical University , Chongqing , China
| | - Feng Gao
- c Department of Aerospace Medicine , Fourth Military Medical University , Xi'an , China
| | - Zhou Zhou
- a Department of Environmental Medicine, and Department of Critical Care Medicine of the First Affiliated Hospital , Zhejiang University School of Medicine , Hangzhou , China.,b Department of Occupational Health , Third Military Medical University , Chongqing , China
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19
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Wei R, Wong JPC, Lyu P, Xi X, Tong O, Zhang SD, Yuen HF, Shirasawa S, Kwok HF. In vitro and clinical data analysis of Osteopontin as a prognostic indicator in colorectal cancer. J Cell Mol Med 2018; 22:4097-4105. [PMID: 29851214 PMCID: PMC6111822 DOI: 10.1111/jcmm.13686] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 04/21/2018] [Indexed: 12/25/2022] Open
Abstract
Osteopontin (OPN) has been shown to promote colorectal cancer (CRC) progression; however, the mechanism of OPN-induced CRC progression is largely unknown. In this study, we found that OPN overexpression led to enhanced anchorage-independent growth, cell migration and invasion in KRAS gene mutant cells but to a lesser extent in KRAS wild-type cells. OPN overexpression also induced PI3K signalling, expression of Snail and Matrix metallopeptidase 9 (MMP9), and suppressed the expression of E-cadherin in KRAS mutant cells. In human CRC specimens, a high-level expression of OPN significantly predicted poorer survival in CRC patients and OPN expression was positively correlated with MMP9 expression, and negatively correlated with E-cadherin expression. Furthermore, we have found that 15 genes were co-upregulated in OPN highly expression CRC and a list of candidate drugs that may have potential to reverse the secreted phosphoprotein 1 (SPP1) gene signature by connectivity mapping. In summary, OPN is a potential prognostic indicator and therapeutic target for colon cancer.
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Affiliation(s)
- Ran Wei
- Faculty of Health Sciences, University of Macau, Taipa, Macau
| | | | - Peng Lyu
- Faculty of Health Sciences, University of Macau, Taipa, Macau
| | - Xinping Xi
- Faculty of Health Sciences, University of Macau, Taipa, Macau
| | - Olivia Tong
- Faculty of Health Sciences, University of Macau, Taipa, Macau
| | - Shu-Dong Zhang
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, University of Ulster, Londonderry, UK
| | - Hiu Fung Yuen
- Institute of Molecular and Cell Biology, A*STAR, Singapore City, Singapore
| | - Senji Shirasawa
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka, Japan
| | - Hang Fai Kwok
- Faculty of Health Sciences, University of Macau, Taipa, Macau
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20
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Wong HL, Ng LPW, Koh SP, Chan LWC, Wong EYK, Xue VW, Tsang HFA, Chan AKC, Chiu KY, Cheuk W, Wong SCC. Hotspot KRAS exon 2 mutations in CD166 positive colorectal cancer and colorectal adenoma cells. Oncotarget 2018; 9:20426-20438. [PMID: 29755662 PMCID: PMC5945530 DOI: 10.18632/oncotarget.24921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 01/20/2018] [Indexed: 12/19/2022] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer and the fourth leading cause of cancer deaths worldwide. Recent studies have shown that cancer stem cells (CSCs) are an important cause of tumor recurrence and metastasis. We hypothesized that CSCs marker CD166-positive CRC and colorectal adenoma (CAD) cells consist of more hotspot mutations than CD166-negative CRC and colorectal adenoma cells. To verify this, formalin fixed paraffin embedded tissue specimens from 42 patients each with CRC and CAD were recruited and CD166 immunohistochemical (IHC) staining followed by macrodissection was performed. DNA extracted was used for quantitative polymerase chain reaction detection on a somatic mutation array. Results showed that the immunoreactivity of CD166 protein had significant difference among CRC, CAD, and normal colorectal epithelial tissues (NCET) (P < 0.0001, Kruskal-Wallis test). Moreover, nucleotide changes were found in APC, KRAS, P53, PIK3CA, FBXW7 and SRC genes. Among those genes, KRAS exon 2 mutations were validated in another cohort of 70 CRC and 72 CAD specimens. Results showed that the difference in percentage of KRAS exon 2 mutations between CD166 positive and CD166 negative CRC specimens was significant (P < 0.05, chi-square test). Long term follow-up of the CRC patients showed that CD166-positive KRAS exon 2 mutations was useful in discriminating CRC patients with worse outcome. This study has provided evidence that KRAS exon 2 mutations are concentrated in CD166-positive cancer cells, with prognostic significance in CRC, and those mutations are also detected in CAD.
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Affiliation(s)
- Hung Lai Wong
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region
| | - Lawrence Po Wah Ng
- Department of Pathology, Queen Elizabeth Hospital, Kowloon Central Cluster, Hospital Authority, Hong Kong Special Administrative Region
| | - Su Pin Koh
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region
| | - Lawrence Wing Chi Chan
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region
| | - Evelyn Yin Kwan Wong
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region
| | - Vivian Weiwen Xue
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region
| | - Hin Fung Andy Tsang
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region
| | - Amanda Kit Ching Chan
- Department of Pathology, Queen Elizabeth Hospital, Kowloon Central Cluster, Hospital Authority, Hong Kong Special Administrative Region
| | - Ka Yue Chiu
- Department of Pathology, Queen Elizabeth Hospital, Kowloon Central Cluster, Hospital Authority, Hong Kong Special Administrative Region
| | - Wah Cheuk
- Department of Pathology, Queen Elizabeth Hospital, Kowloon Central Cluster, Hospital Authority, Hong Kong Special Administrative Region
| | - Sze Chuen Cesar Wong
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region
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21
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Ishida R, Koyanagi-Aoi M, Oshima N, Kakeji Y, Aoi T. The Tissue-Reconstructing Ability of Colon CSCs Is Enhanced by FK506 and Suppressed by GSK3 Inhibition. Mol Cancer Res 2017; 15:1455-1466. [DOI: 10.1158/1541-7786.mcr-17-0071] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 06/06/2017] [Accepted: 07/11/2017] [Indexed: 11/16/2022]
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22
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Peterson LE, Kovyrshina T. Progression inference for somatic mutations in cancer. Heliyon 2017; 3:e00277. [PMID: 28492066 PMCID: PMC5415494 DOI: 10.1016/j.heliyon.2017.e00277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 03/08/2017] [Accepted: 03/23/2017] [Indexed: 01/05/2023] Open
Abstract
Computational methods were employed to determine progression inference of genomic alterations in commonly occurring cancers. Using cross-sectional TCGA data, we computed evolutionary trajectories involving selectivity relationships among pairs of gene-specific genomic alterations such as somatic mutations, deletions, amplifications, downregulation, and upregulation among the top 20 driver genes associated with each cancer. Results indicate that the majority of hierarchies involved TP53, PIK3CA, ERBB2, APC, KRAS, EGFR, IDH1, VHL, etc. Research into the order and accumulation of genomic alterations among cancer driver genes will ever-increase as the costs of nextgen sequencing subside, and personalized/precision medicine incorporates whole-genome scans into the diagnosis and treatment of cancer.
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Affiliation(s)
- Leif E. Peterson
- Center for Biostatistics, Houston Methodist Research Institute, Houston, TX 77030, USA
- Dept. of Healthcare Policy and Research, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
- Dept. of Biostatistics, School of Public Health, University of Texas – Health Science Center, Houston, TX 77030, USA
- Dept. of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Dept. of Neuroscience and Experimental Therapeutics, Texas A&M University Health Science Center, College Station, TX 77843, USA
| | - Tatiana Kovyrshina
- Center for Biostatistics, Houston Methodist Research Institute, Houston, TX 77030, USA
- Dept. of Mathematics and Statistics, University of Houston – Downtown, Houston, TX 77002, USA
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