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Dong Y, Hu K, Zhang J, Zhu M, Liu M, Yuan Y, Sun X, Xu Z, Li S, Zhu Y, Zhang C, Zhang P, Liu T. ScRNA-seq of gastric cancer tissues reveals differences in the immune microenvironment of primary tumors and metastases. Oncogene 2024; 43:1549-1564. [PMID: 38555278 DOI: 10.1038/s41388-024-03012-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 03/12/2024] [Accepted: 03/15/2024] [Indexed: 04/02/2024]
Abstract
Gastric carcinoma (GC) is regarded as one of the deadliest cancer characterized by diversity and haste metastasis and suffers limited understanding of the spatial variation between primary and metastatic GC tumors. In this project, transcriptome analysis on 46 primary tumorous, adjacent non-tumorous, and metastatic GC tissues was performed. The results demonstrated that metastatic tumorous tissues had diminished CD8+ T cells compared to primary tumors, which is mechanistically attributed to being due to innate immunity differences represented by marked differences in macrophages between metastatic and primary tumors, particularly those expressing ApoE, where their abundance is linked to unfavorable prognoses. Examining variations in gene expression and interactions indicated possible strategies of immune evasion hindering the growth of CD8+ T cells in metastatic tumor tissues. More insights could be gained into the immune evasion mechanisms by portraying information about the GC ecosystem.
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Affiliation(s)
- Yu Dong
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Keshu Hu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Jiayu Zhang
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Mengxuan Zhu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Mengling Liu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Yitao Yuan
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Xun Sun
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Zhenghang Xu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Suyao Li
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Yanjing Zhu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Chi Zhang
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Pengfei Zhang
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
| | - Tianshu Liu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
- Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, 20032, China.
- Center of Evidence-based Medicine, Fudan University, Shanghai, China.
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2
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Shi Y, Yao M, Shen S, Wang L, Yao D. Abnormal expression of Krüppel-like transcription factors and their potential values in lung cancer. Heliyon 2024; 10:e28292. [PMID: 38560274 PMCID: PMC10979174 DOI: 10.1016/j.heliyon.2024.e28292] [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: 07/27/2023] [Revised: 03/15/2024] [Accepted: 03/15/2024] [Indexed: 04/04/2024] Open
Abstract
Lung cancer still is one of the most common malignancy tumors in the world. However, the mechanisms of its occurrence and development have not been fully elucidated. Zinc finger protein family (ZNFs) is the largest transcription factor family in human genome. Recently, the more and more basic and clinical evidences have confirmed that ZNFs/Krüppel-like factors (KLFs) refer to a group of conserved zinc finger-containing transcription factors that are involved in lung cancer progression, with the functions of promotion, inhibition, dual roles and unknown classifications. Based on the recent literature, some of the oncogenic KLFs are promising molecular biomarkers for diagnosis, prognosis or therapeutic targets of lung cancer. Interestingly, a novel computational approach has been proposed by using machine learning on features calculated from primary sequences, the XGBoost-based model with accuracy of 96.4 % is efficient in identifying KLF proteins. This paper reviews the recent some progresses of the oncogenic KLFs with their potential values for diagnosis, prognosis and molecular target in lung cancer.
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Affiliation(s)
- Yang Shi
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University & Department of Medical Immunology, Medical School of Nantong University, Nantong 226001, China
- Department of Thoracic Surgery, First People's Hospital of Yancheng, Yancheng 224001, China
| | - Min Yao
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University & Department of Medical Immunology, Medical School of Nantong University, Nantong 226001, China
| | - Shuijie Shen
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University & Department of Medical Immunology, Medical School of Nantong University, Nantong 226001, China
| | - Li Wang
- Research Center for Intelligent Information Technology, Nantong University, Nantong 226019, Jiangsu, China
| | - Dengfu Yao
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University & Department of Medical Immunology, Medical School of Nantong University, Nantong 226001, China
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3
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Yaseen U, Hwang S, Park S, Kim SB, Lee HJ, Cha JY. New Insights into the Role of KLF10 in Tissue Fibrosis. Int J Mol Sci 2024; 25:1276. [PMID: 38279278 PMCID: PMC10816924 DOI: 10.3390/ijms25021276] [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: 12/14/2023] [Revised: 01/14/2024] [Accepted: 01/18/2024] [Indexed: 01/28/2024] Open
Abstract
Fibrosis, characterized by excessive extracellular matrix accumulation, disrupts normal tissue architecture, causes organ dysfunction, and contributes to numerous chronic diseases. This review focuses on Krüppel-like factor 10 (KLF10), a transcription factor significantly induced by transforming growth factor-β (TGF-β), and its role in fibrosis pathogenesis and progression across various tissues. KLF10, initially identified as TGF-β-inducible early gene-1 (TIEG1), is involved in key biological processes including cell proliferation, differentiation, apoptosis, and immune responses. Our analysis investigated KLF10 gene and protein structures, interaction partners, and context-dependent functions in fibrotic diseases. This review highlights recent findings that underscore KLF10 interaction with pivotal signaling pathways, such as TGF-β, and the modulation of gene expression in fibrotic tissues. We examined the dual role of KLF10 in promoting and inhibiting fibrosis depending on tissue type and fibrotic context. This review also discusses the therapeutic potential of targeting KLF10 in fibrotic diseases, based on its regulatory role in key pathogenic mechanisms. By consolidating current research, this review aims to enhance the understanding of the multifaceted role of KLF10 in fibrosis and stimulate further research into its potential as a therapeutic target in combating fibrotic diseases.
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Affiliation(s)
- Uzma Yaseen
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon 21999, Republic of Korea; (U.Y.); (S.P.); (S.-B.K.)
| | - Soonjae Hwang
- Department of Biochemistry, Lee Gil Ya Cancer and Diabetes Institute, College of Medicine, Gachon University, Incheon 21999, Republic of Korea;
| | - Sangbin Park
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon 21999, Republic of Korea; (U.Y.); (S.P.); (S.-B.K.)
| | - Soo-Bin Kim
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon 21999, Republic of Korea; (U.Y.); (S.P.); (S.-B.K.)
| | - Ho-Jae Lee
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon 21999, Republic of Korea; (U.Y.); (S.P.); (S.-B.K.)
- Department of Biochemistry, Lee Gil Ya Cancer and Diabetes Institute, College of Medicine, Gachon University, Incheon 21999, Republic of Korea;
| | - Ji-Young Cha
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon 21999, Republic of Korea; (U.Y.); (S.P.); (S.-B.K.)
- Department of Biochemistry, Lee Gil Ya Cancer and Diabetes Institute, College of Medicine, Gachon University, Incheon 21999, Republic of Korea;
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4
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Zhu Y, Song Z, Wang Z. A Prediction Model for Deciphering Intratumoral Heterogeneity Derived from the Microglia/Macrophages of Glioma Using Non-Invasive Radiogenomics. Brain Sci 2023; 13:1667. [PMID: 38137116 PMCID: PMC10742081 DOI: 10.3390/brainsci13121667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/25/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
Microglia and macrophages play a major role in glioma immune responses within the glioma microenvironment. We aimed to construct a prognostic prediction model for glioma based on microglia/macrophage-correlated genes. Additionally, we sought to develop a non-invasive radiogenomics approach for risk stratification evaluation. Microglia/macrophage-correlated genes were identified from four single-cell datasets. Hub genes were selected via lasso-Cox regression, and risk scores were calculated. The immunological characteristics of different risk stratifications were assessed, and radiomics models were constructed using corresponding MRI imaging to predict risk stratification. We identified eight hub genes and developed a relevant risk score formula. The risk score emerged as a significant prognostic predictor correlated with immune checkpoints, and a relevant nomogram was drawn. High-risk groups displayed an active microenvironment associated with microglia/macrophages. Furthermore, differences in somatic mutation rates, such as IDH1 missense variant and TP53 missense variant, were observed between high- and low-risk groups. Lastly, a radiogenomics model utilizing five features from magnetic resonance imaging (MRI) T2 fluid-attenuated inversion recovery (Flair) effectively predicted the risk groups under a random forest model. Our findings demonstrate that risk stratification based on microglia/macrophages can effectively predict prognosis and immune functions in glioma. Moreover, we have shown that risk stratification can be non-invasively predicted using an MRI-T2 Flair-based radiogenomics model.
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Affiliation(s)
| | | | - Zhong Wang
- Department of Neurosurgery, The First Affifiliated Hospital of Soochow University, No. 899, Pinghai Road, Suzhou 215006, China
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5
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Wara AK, Rawal S, Yang X, Pérez-Cremades D, Sachan M, Chen J, Feinberg MW. KLF10 deficiency in CD4 + T cells promotes atherosclerosis progression by altering macrophage dynamics. Atherosclerosis 2022; 359:27-41. [PMID: 36174463 DOI: 10.1016/j.atherosclerosis.2022.08.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 08/24/2022] [Accepted: 08/31/2022] [Indexed: 11/02/2022]
Abstract
BACKGROUND AND AIMS Accumulating evidence supports a critical role for CD4+ T cells as drivers and modifiers of the chronic inflammatory response in atherosclerosis. Effector T cells have pro-atherogenic properties, whereas CD4+ regulatory T cells (Tregs) exert suppressive activity in atherosclerosis through increased secretion of inhibitory cytokines such as transforming growth factor-β or interleukin-10. In addition, Tregs have been shown to suppress inflammatory macrophages and promote the resolution of atherosclerosis plaques. Impaired Treg numbers and function have been associated with atherosclerosis plaque development. However, the underlying mechanisms remain unclear. METHODS AND RESULTS Here, we investigated a cell-autonomous role of a transcription factor, Krüppel-like factor 10 (KLF10), in CD4+ T cells in regulating atherosclerosis progression. Using CD4+ T-cell-specific KLF10 knockout (TKO) mice, we identified exaggerated plaque progression due to defects in immunosuppressive functions of Tregs on macrophages. TKO mice exhibited increased lesion size as well as higher CD4+ T cells and macrophage content compared to WT mice. TKO plaques also showed increased necrotic cores along with defective macrophage efferocytosis. In contrast, adoptive cellular therapy using WT Tregs abrogated the accelerated lesion progression and deleterious effects in TKO mice. Intriguingly, RNA-seq analyses of TKO lesions revealed increased chemotaxis and cell proliferation, and reduced phagocytosis compared to WT lesions. Mechanistically, TKO-Tregs impaired the efferocytosis capacity of macrophages in vitro and promoted a pro-inflammatory macrophage phenotype via increased IFN-γ and decreased TGF-β secretion. CONCLUSIONS Taken together, these findings establish a critical role for KLF10 in regulating CD4+ Treg-macrophage interactions and atherosclerosis.
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Affiliation(s)
- Akm Khyrul Wara
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Shruti Rawal
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Xilan Yang
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA; Department of General Practice, The Fourth Affiliated Hospital of Nanjing Medical University, Nanjing, 210031, China
| | - Daniel Pérez-Cremades
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA; Department of Physiology, University of Valencia, and INCLIVA Biomedical Research Institute, Valencia, 46010, Spain
| | - Madhur Sachan
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Jingshu Chen
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Mark W Feinberg
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
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6
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Kulkarni A, Pandey A, Trainor P, Carlisle S, Yu W, Kukutla P, Xu J. Aryl hydrocarbon receptor and Krüppel like factor 10 mediate a transcriptional axis modulating immune homeostasis in mosquitoes. Sci Rep 2022; 12:6005. [PMID: 35397616 PMCID: PMC8994780 DOI: 10.1038/s41598-022-09817-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/21/2022] [Indexed: 11/25/2022] Open
Abstract
Immune responses require delicate controls to maintain homeostasis while executing effective defense. Aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor. The Krüppel-like factor 10 (KLF10) is a C2H2 zinc-finger containing transcription factor. The functions of mosquito AhR and KLF10 have not been characterized. Here we show that AhR and KLF10 constitute a transcriptional axis to modulate immune responses in mosquito Anopheles gambiae. The manipulation of AhR activities via agonists or antagonists repressed or enhanced the mosquito antibacterial immunity, respectively. KLF10 was recognized as one of the AhR target genes in the context. Phenotypically, silencing KLF10 reversed the immune suppression caused by the AhR agonist. The transcriptome comparison revealed that silencing AhR and KLF10 plus challenge altered the expression of 2245 genes in the same way. The results suggest that KLF10 is downstream of AhR in a transcriptional network responsible for immunomodulation. This AhR–KLF10 axis regulates a set of genes involved in metabolism and circadian rhythms in the context. The axis was required to suppress the adverse effect caused by the overactivation of the immune pathway IMD via the inhibitor gene Caspar silencing without a bacterial challenge. These results demonstrate that the AhR–KLF10 axis mediates an immunoregulatory transcriptional network as a negative loop to maintain immune homeostasis.
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Affiliation(s)
- Aditi Kulkarni
- Biology Department, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Ashmita Pandey
- Biology Department, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Patrick Trainor
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Samantha Carlisle
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Wanqin Yu
- Biology Department, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Phanidhar Kukutla
- Biology Department, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Jiannong Xu
- Biology Department, New Mexico State University, Las Cruces, NM, 88003, USA.
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7
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S E, K V, W C, T R, FAM K, C S, H C, J N, J Z, R M, P M. Lymphopenia-induced lymphoproliferation drives activation of naive T cells and expansion of regulatory populations. iScience 2021; 24:102164. [PMID: 33665580 PMCID: PMC7907823 DOI: 10.1016/j.isci.2021.102164] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 10/15/2020] [Accepted: 02/04/2021] [Indexed: 11/23/2022] Open
Abstract
Chemotherapy pre-conditioning is an essential component of chimeric antigen receptor transduced cell therapy. Acute lymphopenia-induced proliferation (LIP) is known to be driven primarily by homeostatic cytokines, but little is known on the underlying mechanisms in humans. We undertook phenotypic and transcriptional analysis of T cells undergoing LIP two weeks post-myeloablative autograft stem cell transplantation. Strong IL-7 signaling was reflected in downregulated IL-7R expression on all T cells, including naive cells, along with parallel increased IL-2Rα expression. Notably, activated residual naive cells expressed Fas indicating recent TCR engagement. Moreover, proportion of Ki67 + FoxP3+ Tregs was almost doubled. Transcriptional analysis revealed increased fatty acid metabolism and interferon signaling responses. In contrast, TGF-β signaling was strongly suppressed. Thus, human LIP response is characterized by cytokine and TCR-driven proliferation which drives global T cell activation but also preferentially triggers regulatory cell expansion which may limit tumor-specific immunity. These features indicate potential therapeutic opportunities to manipulate immunotherapy regimens incorporating LIP conditioning protocols.
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Affiliation(s)
- Eldershaw S
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Verma K
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Croft W
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
- Centre for Computational Biology, University of Birmingham, Birmingham, UK
| | - Rai T
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Kinsella FAM
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
- Center for clinical Haematology, Queen Elizabeth Hospital, Birmingham, UK
| | - Stephens C
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Chen H
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Nunnick J
- Center for clinical Haematology, Queen Elizabeth Hospital, Birmingham, UK
| | - Zuo J
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Malladi R
- Center for clinical Haematology, Queen Elizabeth Hospital, Birmingham, UK
| | - Moss P
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
- Centre for Computational Biology, University of Birmingham, Birmingham, UK
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8
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Yeh CM, Lee YJ, Ko PY, Lin YM, Sung WW. High Expression of KLF10 Is Associated with Favorable Survival in Patients with Oral Squamous Cell Carcinoma. ACTA ACUST UNITED AC 2020; 57:medicina57010017. [PMID: 33379261 PMCID: PMC7824494 DOI: 10.3390/medicina57010017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 12/02/2022]
Abstract
Background and Objectives: Krüppel-like transcription factor 10 (KLF10) plays a vital role in regulating cell proliferation, including the anti-proliferative process, activation of apoptosis, and differentiation control. KLF10 may also act as a protective factor against oral cancer. We studied the impact of KLF10 expression on the clinical outcomes of oral cancer patients to identify its role as a prognostic factor in oral cancer. Materials and Methods: KLF10 immunoreactivity was analyzed by immunohistochemical (IHC) stain analysis in 286 cancer specimens from primary oral cancer patients. The prognostic value of KLF10 on overall survival was determined by Kaplan–Meier analysis and the Cox proportional hazard model. Results: High KLF10 expression was significantly associated with male gender and betel quid chewing. The 5-year survival rate was greater for patients with high KLF10 expression than for those with low KLF10 expression (62.5% vs. 51.3%, respectively; p = 0.005), and multivariate analyses showed that high KLF10 expression was the only independent factor correlated with greater overall patient survival. The significant correlation between high KLF10 expression and a higher 5-year survival rate was observed in certain subgroups of clinical parameters, including female gender, non-smokers, cancer stage T1, and cancer stage N0. Conclusions: KLF10 expression, detected by IHC staining, could be an independent prognostic marker for oral cancer patients.
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Affiliation(s)
- Chung-Min Yeh
- Department of Pathology, Changhua Christian Hospital, Changhua 50006, Taiwan;
- Department of Medical Technology, Jen-Teh Junior College of Medicine, Nursing and Management, Miaoli 35664, Taiwan
| | - Yi-Ju Lee
- Department of Pathology, Chung Shan Medical University, Taichung 40201, Taiwan;
- Department of Pathology, Chung Shan Medical University Hospital, Taichung 40201, Taiwan
- School of Medicine, Chung Shan Medical University, Taichung 40201, Taiwan;
| | - Po-Yun Ko
- School of Medicine, Chung Shan Medical University, Taichung 40201, Taiwan;
- Department of Medical Education, MacKay Memorial Hospital, Taipei 10491, Taiwan
| | - Yueh-Min Lin
- Department of Pathology, Changhua Christian Hospital, Changhua 50006, Taiwan;
- School of Medicine, Chung Shan Medical University, Taichung 40201, Taiwan;
- Correspondence: (Y.-M.L.); or (W.-W.S.); Tel.: +886-4-723-8595 (Y.-M.L.); +886-4-2473-9595 (ext. 10646) (W.-W.S.)
| | - Wen-Wei Sung
- School of Medicine, Chung Shan Medical University, Taichung 40201, Taiwan;
- Institute of Medicine, Chung Shan Medical University, Taichung 40201, Taiwan
- Department of Urology, Chung Shan Medical University Hospital, Taichung 40201, Taiwan
- Correspondence: (Y.-M.L.); or (W.-W.S.); Tel.: +886-4-723-8595 (Y.-M.L.); +886-4-2473-9595 (ext. 10646) (W.-W.S.)
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9
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Sun Y, Wu L, Zhong Y, Zhou K, Hou Y, Wang Z, Zhang Z, Xie J, Wang C, Chen D, Huang Y, Wei X, Shi Y, Zhao Z, Li Y, Guo Z, Yu Q, Xu L, Volpe G, Qiu S, Zhou J, Ward C, Sun H, Yin Y, Xu X, Wang X, Esteban MA, Yang H, Wang J, Dean M, Zhang Y, Liu S, Yang X, Fan J. Single-cell landscape of the ecosystem in early-relapse hepatocellular carcinoma. Cell 2020; 184:404-421.e16. [PMID: 33357445 DOI: 10.1016/j.cell.2020.11.041] [Citation(s) in RCA: 365] [Impact Index Per Article: 91.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 08/24/2020] [Accepted: 11/20/2020] [Indexed: 02/08/2023]
Abstract
Hepatocellular carcinoma (HCC) has high relapse and low 5-year survival rates. Single-cell profiling in relapsed HCC may aid in the design of effective anticancer therapies, including immunotherapies. We profiled the transcriptomes of ∼17,000 cells from 18 primary or early-relapse HCC cases. Early-relapse tumors have reduced levels of regulatory T cells, increased dendritic cells (DCs), and increased infiltrated CD8+ T cells, compared with primary tumors, in two independent cohorts. Remarkably, CD8+ T cells in recurrent tumors overexpressed KLRB1 (CD161) and displayed an innate-like low cytotoxic state, with low clonal expansion, unlike the classical exhausted state observed in primary HCC. The enrichment of these cells was associated with a worse prognosis. Differential gene expression and interaction analyses revealed potential immune evasion mechanisms in recurrent tumor cells that dampen DC antigen presentation and recruit innate-like CD8+ T cells. Our comprehensive picture of the HCC ecosystem provides deeper insights into immune evasion mechanisms associated with tumor relapse.
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Affiliation(s)
- Yunfan Sun
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China; Zhong-Hua Precision Medical Center, Zhongshan Hospital, Fudan University-BGI, Shanghai 200032, China
| | - Liang Wu
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China; Zhong-Hua Precision Medical Center, Zhongshan Hospital, Fudan University-BGI, Shanghai 200032, China; BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
| | - Yu Zhong
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China; School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510640, China
| | - Kaiqian Zhou
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China; Zhong-Hua Precision Medical Center, Zhongshan Hospital, Fudan University-BGI, Shanghai 200032, China
| | - Yong Hou
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China; Zhong-Hua Precision Medical Center, Zhongshan Hospital, Fudan University-BGI, Shanghai 200032, China; BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, Shenzhen 518100, China
| | - Zifei Wang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China; BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Zefan Zhang
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China; Zhong-Hua Precision Medical Center, Zhongshan Hospital, Fudan University-BGI, Shanghai 200032, China
| | - Jiarui Xie
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China; School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510640, China
| | - Chunqing Wang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China; BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Dandan Chen
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Yaling Huang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Xiaochan Wei
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Yinghong Shi
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China
| | - Zhikun Zhao
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Yuehua Li
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Ziwei Guo
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Qichao Yu
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Liqin Xu
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Giacomo Volpe
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Shuangjian Qiu
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China; Zhong-Hua Precision Medical Center, Zhongshan Hospital, Fudan University-BGI, Shanghai 200032, China
| | - Jian Zhou
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China; Zhong-Hua Precision Medical Center, Zhongshan Hospital, Fudan University-BGI, Shanghai 200032, China
| | - Carl Ward
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Huichuan Sun
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China; Zhong-Hua Precision Medical Center, Zhongshan Hospital, Fudan University-BGI, Shanghai 200032, China
| | - Ye Yin
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China
| | - Xun Xu
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen 518120, China
| | - Xiangdong Wang
- Zhong-Hua Precision Medical Center, Zhongshan Hospital, Fudan University-BGI, Shanghai 200032, China
| | - Miguel A Esteban
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China; Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Institute for Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Huanming Yang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China; BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen 518120, China
| | - Jian Wang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China; James D. Watson Institute of Genome Science, Hangzhou 310008, China
| | - Michael Dean
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute Rockville, MD 20850, USA
| | - Yaguang Zhang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Shiping Liu
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China; BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, Shenzhen 518100, China.
| | - Xinrong Yang
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China; Zhong-Hua Precision Medical Center, Zhongshan Hospital, Fudan University-BGI, Shanghai 200032, China.
| | - Jia Fan
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China; Zhong-Hua Precision Medical Center, Zhongshan Hospital, Fudan University-BGI, Shanghai 200032, China.
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10
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Abstract
Viral RNAs can perturb the miRNA regulatory network, competing with host RNAs as part of their infective process. An in silico competing endogenous RNA (ceRNA) analysis has been carried on SARS-CoV-2. The results suggest that, in humans, the decrease of microRNA activity caused by viral RNAs can lead to a perturbation of vesicle trafficking and the inflammatory response, in particular by enhancing KLF10 activity. The results suggest also that, during the study of the mechanics of viral infections, it could be of general interest to investigate the competition of viral RNA with cellular transcripts for shared microRNAs.
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Affiliation(s)
- Walter Arancio
- University of Palermo, Viale delle Scienze, 90127, Palermo, Italy. .,Scuola "Borgese XXVII Maggio", Piazza Contardo Ferrini, 13, 90146, Palermo, Italy. .,Advanced data analysis group, Fondazione Ri.MED, Via Bandiera 11, 90133, Palermo, Italy.
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11
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Shi A, Kasumova GG, Michaud WA, Cintolo-Gonzalez J, Díaz-Martínez M, Ohmura J, Mehta A, Chien I, Frederick DT, Cohen S, Plana D, Johnson D, Flaherty KT, Sullivan RJ, Kellis M, Boland GM. Plasma-derived extracellular vesicle analysis and deconvolution enable prediction and tracking of melanoma checkpoint blockade outcome. SCIENCE ADVANCES 2020; 6:6/46/eabb3461. [PMID: 33188016 PMCID: PMC7673759 DOI: 10.1126/sciadv.abb3461] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 09/28/2020] [Indexed: 05/02/2023]
Abstract
Immune checkpoint inhibitors (ICIs) show promise, but most patients do not respond. We identify and validate biomarkers from extracellular vesicles (EVs), allowing non-invasive monitoring of tumor- intrinsic and host immune status, as well as a prediction of ICI response. We undertook transcriptomic profiling of plasma-derived EVs and tumors from 50 patients with metastatic melanoma receiving ICI, and validated with an independent EV-only cohort of 30 patients. Plasma-derived EV and tumor transcriptomes correlate. EV profiles reveal drivers of ICI resistance and melanoma progression, exhibit differentially expressed genes/pathways, and correlate with clinical response to ICI. We created a Bayesian probabilistic deconvolution model to estimate contributions from tumor and non-tumor sources, enabling interpretation of differentially expressed genes/pathways. EV RNA-seq mutations also segregated ICI response. EVs serve as a non-invasive biomarker to jointly probe tumor-intrinsic and immune changes to ICI, function as predictive markers of ICI responsiveness, and monitor tumor persistence and immune activation.
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Affiliation(s)
- Alvin Shi
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - William A Michaud
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Jacqueline Ohmura
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Arnav Mehta
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Isabel Chien
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | | | - Sonia Cohen
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Deborah Plana
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Douglas Johnson
- Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | | | - Ryan J Sullivan
- Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Genevieve M Boland
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
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12
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MondoA:MLX complex regulates glucose-dependent gene expression and links to circadian rhythm in liver and brain of the freeze-tolerant wood frog, Rana sylvatica. Mol Cell Biochem 2020; 473:203-216. [PMID: 32638259 DOI: 10.1007/s11010-020-03820-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/27/2020] [Indexed: 10/23/2022]
Abstract
The wood frog, Rana sylvatica, is one of only a few vertebrate species that display natural freeze tolerance. Frogs survive the freezing of about two-thirds of their body water as extracellular ice over the winter months. Multiple adaptations support freeze tolerance including metabolic rate depression and the production of huge amounts of glucose (often 200 mM or more) as a cryoprotectant that protects cells from freeze damage. To understand how high glucose levels affect gene expression, we studied MondoA, a glucose sensing transcription factor, and its partner MLX (Max-like protein) to assess their ability to modulate the expression of genes involved in glucose metabolism and circadian rhythm. Wood frog liver and brain tissues were analyzed, assessing protein levels, nuclear distribution, and DNA binding activity of MondoA:MLX during freezing (24 h at - 2.5 °C) and subsequent thawing (8 h returned to 5 °C), as compared with 5 °C controls. Downstream targets of MondoA:MLX were also evaluated: TXNIP (thioredoxin interacting protein), ARRDC4 (arrestin domain containing 4), HK-2 (hexokinase-2), PFKFB-3 (6-phosphofructo-2-kinase isozyme 3) and KLF-10 (Kruppel-like factor-10). Both KLF-10 and PFKFB-3 are also involved in circadian dependant regulation which was also explored in the current study via analysis of BMAL-1 (aryl hydrocarbon receptor nuclear translocator-like protein 1) and CLOCK (circadian locomotor output cycles kaput) proteins. Our data establish the MondoA-MLX complex as active under the hyperglycemic conditions in liver to regulate glucose metabolism and may also link to circadian rhythm in liver via KLF-10 and PFKFB-3 but not in brain.
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13
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Chen X, Shi W, Zhang H. The role of KLF14 in multiple disease processes. Biofactors 2020; 46:276-282. [PMID: 31925990 DOI: 10.1002/biof.1612] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/31/2019] [Indexed: 12/13/2022]
Abstract
Kruppel-like factor 14 (KLF14) is a newly identified member of the KLF family. Expression of KLF14 is induced by TGF-β in intrauterine and ectodermal tissue. Initial researches on KLF14 focused on its role in lipid and glucose metabolism. In recent years, however, the role of KLF14 in regulating cell signaling pathways, cell proliferation and differentiation has been explored. Moreover, the research has gradually extended into the field of tumorigenesis and immune regulation. This paper aims to briefly review the functions of KLF14 in physiologyical and pathological process.
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Affiliation(s)
- Xiaoyan Chen
- Department of Gastroenterology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenjie Shi
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Heng Zhang
- Department of Gastroenterology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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14
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The Use of Genetically Engineered Mouse Models for Studying the Function of Mutated Driver Genes in Pancreatic Cancer. J Clin Med 2019; 8:jcm8091369. [PMID: 31480737 PMCID: PMC6780401 DOI: 10.3390/jcm8091369] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 02/06/2023] Open
Abstract
Pancreatic cancer is often treatment-resistant, with the emerging standard of care, gemcitabine, affording only a few months of incrementally-deteriorating survival. Reflecting on the history of failed clinical trials, genetically engineered mouse models (GEMMs) in oncology research provides the inspiration to discover new treatments for pancreatic cancer that come from better knowledge of pathogenesis mechanisms, not only of the derangements in and consequently acquired capabilities of the cancer cells, but also in the aberrant microenvironment that becomes established to support, sustain, and enhance neoplastic progression. On the other hand, the existing mutational profile of pancreatic cancer guides our understanding of the disease, but leaves many important questions of pancreatic cancer biology unanswered. Over the past decade, a series of transgenic and gene knockout mouse modes have been produced that develop pancreatic cancers with features reflective of metastatic pancreatic ductal adenocarcinoma (PDAC) in humans. Animal models of PDAC are likely to be essential to understanding the genetics and biology of the disease and may provide the foundation for advances in early diagnosis and treatment.
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15
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Chokeshaiusaha K, Sananmuang T, Puthier D, Nguyen C. An innovative approach to predict immune-associated genes mutually targeted by cow and human milk microRNAs expression profiles. Vet World 2018; 11:1203-1209. [PMID: 30410222 PMCID: PMC6200572 DOI: 10.14202/vetworld.2018.1203-1209] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 07/16/2018] [Indexed: 12/21/2022] Open
Abstract
Aim: Milk is rich in miRNAs - the endogenous small non-coding RNA responsible for gene post-transcriptional silencing. Milk miRNAs were previously evidenced to affect consumer’s immune response. While most studies relied on a few well-characterized milk miRNAs to relate their immunoregulatory roles on target genes among mammals, this study introduced a procedure to predict the target genes based on overall milk miRNA expression profiles - the miRNome data of cow and human. Materials and Methods: Cow and human milk miRNome expression datasets of cow and human milk lipids at 2, 4, and 6 months of lactation periods were preprocessed and predicted for their target genes using TargetScanHuman. Enrichment analysis was performed using target genes to extract the immune-associated gene ontology (GO) terms shared between the two species. The genes within these terms with more than 50 different miRNAs of each species targeting were selected and reviewed for their immunological functions. Results: A total of 146 and 129 miRNAs were identified in cow and human milk with several miRNAs reproduced from other previous reports. Enrichment analysis revealed nine immune-related GO terms shared between cow and human (adjusted p≤0.01). There were 14 genes related to these terms with more than 50 miRNA genes of each species targeting them. These genes were evidenced for their major roles in lymphocyte stimulation and differentiation. Conclusion: A novel procedure to determine mutual immune-associated genes targeted by milk miRNAs was demonstrated using cow and human milk miRNome data. As far as we know, this was the 1st time that milk miRNA target genes had been identified based on such cross-species approach. Hopefully, the introduced strategy should hereby facilitate a variety of cross-species miRNA studies in the future.
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Affiliation(s)
- Kaj Chokeshaiusaha
- Department of Veterinary Science, Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-OK, Chonburi, Thailand
| | - Thanida Sananmuang
- Department of Veterinary Science, Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-OK, Chonburi, Thailand
| | - Denis Puthier
- Aix-Marseille Université, INSERM UMR 1090, TAGC, Marseille, France
| | - Catherine Nguyen
- Aix-Marseille Université, INSERM UMR 1090, TAGC, Marseille, France
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16
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Muñoz-Soriano V, Belacortu Y, Sanz FJ, Solana-Manrique C, Dillon L, Suay-Corredera C, Ruiz-Romero M, Corominas M, Paricio N. Cbt modulates Foxo activation by positively regulating insulin signaling in Drosophila embryos. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2018; 1861:S1874-9399(18)30034-8. [PMID: 30055320 DOI: 10.1016/j.bbagrm.2018.07.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 07/10/2018] [Accepted: 07/19/2018] [Indexed: 01/05/2023]
Abstract
In late Drosophila embryos, the epidermis exhibits a dorsal hole as a consequence of germ band retraction. It is sealed during dorsal closure (DC), a morphogenetic process in which the two lateral epidermal layers converge towards the dorsal midline and fuse. We previously demonstrated the involvement of the Cbt transcription factor in Drosophila DC. However its molecular role in the process remained obscure. In this study, we used genomic approaches to identify genes regulated by Cbt as well as its direct targets during late embryogenesis. Our results reveal a complex transcriptional circuit downstream of Cbt and evidence that it is functionally related with the Insulin/insulin-like growth factor signaling pathway. In this context, Cbt may act as a positive regulator of the pathway, leading to the repression of Foxo activity. Our results also suggest that the DC defects observed in cbt embryos could be partially due to Foxo overactivation and that a regulatory feedback loop between Foxo and Cbt may be operating in the DC context.
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Affiliation(s)
- Verónica Muñoz-Soriano
- Departamento de Genética, Facultad CC Biológicas, Universitat de València, 46100 Burjasot, Spain; Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València, Dr Moliner 50, 46100 Burjassot, Spain
| | - Yaiza Belacortu
- Departamento de Genética, Facultad CC Biológicas, Universitat de València, 46100 Burjasot, Spain
| | - Francisco José Sanz
- Departamento de Genética, Facultad CC Biológicas, Universitat de València, 46100 Burjasot, Spain; Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València, Dr Moliner 50, 46100 Burjassot, Spain
| | - Cristina Solana-Manrique
- Departamento de Genética, Facultad CC Biológicas, Universitat de València, 46100 Burjasot, Spain; Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València, Dr Moliner 50, 46100 Burjassot, Spain
| | - Luke Dillon
- Departamento de Genética, Facultad CC Biológicas, Universitat de València, 46100 Burjasot, Spain
| | - Carmen Suay-Corredera
- Departamento de Genética, Facultad CC Biológicas, Universitat de València, 46100 Burjasot, Spain
| | - Marina Ruiz-Romero
- Departament de Genètica, Facultat de Biologia, and Institut de Biomedicina (IBUB) de la Universitat de Barcelona, Barcelona, Spain
| | - Montserrat Corominas
- Departament de Genètica, Facultat de Biologia, and Institut de Biomedicina (IBUB) de la Universitat de Barcelona, Barcelona, Spain
| | - Nuria Paricio
- Departamento de Genética, Facultad CC Biológicas, Universitat de València, 46100 Burjasot, Spain; Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València, Dr Moliner 50, 46100 Burjassot, Spain.
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17
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Xu YL, Zhang MH, Guo W, Xue Y, Du X, Zhang T, Wu N, Wu Y. MicroRNA-19 restores vascular endothelial cell function in lower limb ischemia-reperfusion injury through the KLF10-dependent TGF-β1/Smad signaling pathway in rats. J Cell Biochem 2018; 119:9303-9315. [PMID: 29953651 DOI: 10.1002/jcb.27207] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 05/24/2018] [Indexed: 12/25/2022]
Abstract
Ischemia-reperfusion injury (IRI) is a severe problem patients diagnosed with acute limb ischemia. Recently, microRNAs (miR) have emerged as regulators of IRI as well as ischemic preconditioning and ischemic postconditioning. Therefore, using rat models, this study aims to explore all of the possible mechanisms that miR-19 exhibits with its relation to the transforming growth factor beta (TGF-β1)/Smad signaling pathway in the lower limb IRI. An immunofluorescence staining method was used to identify the Krueppel-like factor 10 (KLF10) positive expression and the location of KLF10 expression. The targeting relationship that miR-19 has with KLF10 was verified by the dual-luciferase reporter gene assay. Vascular endothelial cells (VECs) were treated with elevated or suppressed miR-19 or KLF10 knockdown. A 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide assay was used to test cell proliferation, and flow cytometry was employed to detect both cell cycle and apoptosis. The KLF10-positive expression in the VECs (both in cytoplasm and nucleus) was found to be elevated in the IRI rats. We found that miR-19 was downregulated, KLF10 upregulated, and the TGF-β1/Smad signaling pathway activated in the vascular epithelial tissues of IRI rats. KLF10 is a target gene of miR-19. Overexpression of miR-19 decreased the expression of KLF10, TGF-β1, and Smad2/3. Decreased miR-19 inhibited VEC proliferation, arrested VECs at the G1 phase, and promoted the apoptosis of VECs following their lower limb I/R injury. These results indicate miR-19 as being an inhibitor in the VEC injury of IRI via the TGF-β1/Smad signaling pathway by suppression of KLF10.
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Affiliation(s)
- Yong-Le Xu
- Department of Vascular Surgery, Chinese PLA General Hospital, Beijing, China
| | - Min-Hong Zhang
- Department of Vascular Surgery, Chinese PLA General Hospital, Beijing, China
| | - Wei Guo
- Department of Cardiovascular Surgery, Chinese PLA Rocket Force General Hospital, Beijing, China
| | - Yan Xue
- Department of Vascular Surgery, Chinese PLA General Hospital, Beijing, China.,Department of Cardiovascular Surgery, General Hospital of Armed Police Force, Beijing, China
| | - Xin Du
- Department of Vascular Surgery, Chinese PLA General Hospital, Beijing, China
| | - Tao Zhang
- Department of Vascular Surgery, Peking University People's Hospital, Beijing, China
| | - Na Wu
- Department of Central Laboratory & Institute of Clinical Molecular Biology, Peking University People's Hospital, Beijing, China
| | - Ye Wu
- Department of Vascular Surgery, Chinese PLA General Hospital, Beijing, China
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18
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Kim G, Gu MJ, Kim SJ, Ko KH, Kye YC, Kim CG, Cho JH, Lee WK, Song KD, Chu H, Park YM, Han SH, Yun CH. Transcription Factor KLF10 Constrains IL-17-Committed Vγ4 + γδ T Cells. Front Immunol 2018. [PMID: 29541070 PMCID: PMC5835516 DOI: 10.3389/fimmu.2018.00196] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
γδ T cells, known to be an important source of innate IL-17 in mice, provide critical contributions to host immune responses. Development and function of γδ T cells are directed by networks of diverse transcription factors (TFs). Here, we examine the role of the zinc finger TFs, Kruppel-like factor 10 (KLF10), in the regulation of IL-17-committed CD27- γδ T (γδ27--17) cells. We found selective augmentation of Vγ4+ γδ27- cells with higher IL-17 production in KLF10-deficient mice. Surprisingly, KLF10-deficient CD127hi Vγ4+ γδ27--17 cells expressed higher levels of CD5 than their wild-type counterparts, with hyper-responsiveness to cytokine, but not T-cell receptor, stimuli. Thymic maturation of Vγ4+ γδ27- cells was enhanced in newborn mice deficient in KLF10. Finally, a mixed bone marrow chimera study indicates that intrinsic KLF10 signaling is requisite to limit Vγ4+ γδ27--17 cells. Collectively, these findings demonstrate that KLF10 regulates thymic development of Vγ4+ γδ27- cells and their peripheral homeostasis at steady state.
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Affiliation(s)
- Girak Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Min Jeong Gu
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Soo Ji Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Kwang Hyun Ko
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Yoon-Chul Kye
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Cheol Gyun Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Jae-Ho Cho
- Academy of Immunology and Microbiology, Institute for Basic Science, Pohang, South Korea
| | - Woon-Kyu Lee
- College of Medicine, Inha University, Incheon, South Korea
| | - Ki-Duk Song
- Department of Animal Biotechnology, Chonbuk National University, Jeonju, South Korea
| | - Hyuk Chu
- Division of Bacterial Disease Research, Center for Infectious Disease Research, National Institute of Health, Korea Centers for Disease Control and Prevention, Osong, South Korea
| | - Yeong-Min Park
- Department of Immunology, Laboratory of Dendritic Cell Differentiation and Regulation, School of Medicine, Konkuk University, Chungju, South Korea
| | - Seung Hyun Han
- Department of Oral Microbiology and Immunology, DRI and BK21 Plus Program, School of Dentistry, Seoul National University, Seoul, South Korea
| | - Cheol-Heui Yun
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.,Center for Food Bioconvergence, Seoul National University, Seoul, South Korea.,Institute of Green Bio Science Technology, Seoul National University, Pyeongchang, South Korea
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19
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Cousin MA, Zimmermann MT, Mathison AJ, Blackburn PR, Boczek NJ, Oliver GR, Lomberk GA, Urrutia RA, Deyle DR, Klee EW. Functional validation reveals the novel missense V419L variant in TGFBR2 associated with Loeys-Dietz syndrome (LDS) impairs canonical TGF-β signaling. Cold Spring Harb Mol Case Stud 2017; 3:mcs.a001727. [PMID: 28679693 PMCID: PMC5495030 DOI: 10.1101/mcs.a001727] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 04/12/2017] [Indexed: 12/31/2022] Open
Abstract
TGF-β-related heritable connective tissue disorders are characterized by a similar pattern of cardiovascular defects, including aortic root dilatation, mitral valve prolapse, vascular aneurysms, and vascular dissections and exhibit incomplete penetrance and variable expressivity. Because of the phenotypic overlap of these disorders, panel-based genetic testing is frequently used to confirm the clinical findings. Unfortunately in many cases, variants of uncertain significance (VUSs) obscure the genetic diagnosis until more information becomes available. Here, we describe and characterize the functional impact of a novel VUS in the TGFBR2 kinase domain (c.1255G>T; p.Val419Leu), in a patient with the clinical diagnosis of Marfan syndrome spectrum. We assessed the structural and functional consequence of this VUS using molecular modeling, molecular dynamic simulations, and in vitro cell-based assays. A high-quality homology-based model of TGFBR2 was generated and computational mutagenesis followed by refinement and molecular dynamics simulations were used to assess structural and dynamic changes. Relative to wild type, the V419L induced conformational and dynamic changes that may affect ATP binding, increasing the likelihood of adopting an inactive state, and, we hypothesize, alter canonical signaling. Experimentally, we tested this by measuring the canonical TGF-β signaling pathway activation at two points; V419L significantly delayed SMAD2 phosphorylation by western blot and significantly decreased TGF-β-induced gene transcription by reporter assays consistent with known pathogenic variants in this gene. Thus, our results establish that the V419L variant leads to aberrant TGF-β signaling and confirm the diagnosis of Loeys-Dietz syndrome in this patient.
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Affiliation(s)
- Margot A Cousin
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Michael T Zimmermann
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Angela J Mathison
- Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Department of Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Patrick R Blackburn
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, Florida 32224, USA.,Center for Individualized Medicine, Mayo Clinic, Jacksonville, Florida 32224, USA
| | - Nicole J Boczek
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Gavin R Oliver
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Gwen A Lomberk
- Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Department of Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Raul A Urrutia
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Department of Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - David R Deyle
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Clinic Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Eric W Klee
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.,Department of Clinic Genomics, Mayo Clinic, Rochester, Minnesota 55905, USA
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Jonsson S, Sveinbjornsson G, de Lapuente Portilla AL, Swaminathan B, Plomp R, Dekkers G, Ajore R, Ali M, Bentlage AEH, Elmér E, Eyjolfsson GI, Gudjonsson SA, Gullberg U, Gylfason A, Halldorsson BV, Hansson M, Holm H, Johansson Å, Johnsson E, Jonasdottir A, Ludviksson BR, Oddsson A, Olafsson I, Olafsson S, Sigurdardottir O, Sigurdsson A, Stefansdottir L, Masson G, Sulem P, Wuhrer M, Wihlborg AK, Thorleifsson G, Gudbjartsson DF, Thorsteinsdottir U, Vidarsson G, Jonsdottir I, Nilsson B, Stefansson K. Identification of sequence variants influencing immunoglobulin levels. Nat Genet 2017. [DOI: 10.1038/ng.3897] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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KLF10 loss in the pancreas provokes activation of SDF-1 and induces distant metastases of pancreatic ductal adenocarcinoma in the Kras G12D p53 flox/flox model. Oncogene 2017; 36:5532-5543. [PMID: 28581520 DOI: 10.1038/onc.2017.155] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 02/15/2017] [Accepted: 03/23/2017] [Indexed: 12/12/2022]
Abstract
Krüppel-like transcription factor 10 (KLF10), also named as TIEG1, plays essential roles in mediating transforming growth factor beta (TGFβ) signaling and has been shown to function as a tumor suppressor in multiple cancer types. However, its roles in mediating cancer progression in vivo have yet to be fully characterized. Here, we have employed two well-characterized Pdx-1CreLSL-KrasG12D and Pdx-1CreLSL-KrasG12Dp53L/L pancreatic cancer models to ablate KLF10 expression and determine the impact of KLF10 deletion on tumor development and progression. We show that loss of KLF10 cooperates with KrasG12D leading to an invasive and widely metastatic phenotype of pancreatic ductal adenocarcinoma (PDAC). Mechanistically, loss of KLF10 in PDAC is shown to increase distant metastases and cancer stemness through activation of SDF-1/CXCR4 and AP-1 pathways. Furthermore, we demonstrate that targeting the SDF-1/CXCR4 pathway in the context of KLF10 deletion substantially suppresses PDAC progression suggesting that inhibition of this pathway represents a novel therapeutic strategy for PDAC treatment.
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Knoedler JR, Subramani A, Denver RJ. The Krüppel-like factor 9 cistrome in mouse hippocampal neurons reveals predominant transcriptional repression via proximal promoter binding. BMC Genomics 2017; 18:299. [PMID: 28407733 PMCID: PMC5390390 DOI: 10.1186/s12864-017-3640-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 03/17/2017] [Indexed: 12/22/2022] Open
Abstract
Background Krüppel-like factor 9 (Klf9) is a zinc finger transcription factor that functions in neural cell differentiation, but little is known about its genomic targets or mechanism of action in neurons. Results We used the mouse hippocampus-derived neuronal cell line HT22 to identify genes regulated by Klf9, and we validated our findings in mouse hippocampus. We engineered HT22 cells to express a Klf9 transgene under control of the tetracycline repressor, and used RNA sequencing to identify genes modulated by Klf9. We found 217 genes repressed and 21 induced by Klf9. We also engineered HT22 cells to co-express biotin ligase and a Klf9 fusion protein containing an N-terminal biotin ligase recognition peptide. Using chromatin-streptavidin precipitation (ChSP) sequencing we identified 3,514 genomic regions where Klf9 associated. Seventy-five percent of these were within 1 kb of transcription start sites, and Klf9 associated in chromatin with 60% of the repressed genes. We analyzed the promoters of several repressed genes containing Klf9 ChSP peaks using transient transfection reporter assays and found that Klf9 repressed promoter activity, which was abolished after mutation of Sp/Klf-like motifs. Knockdown or knockout of Klf9 in HT22 cells caused dysregulation of Klf9 target genes. Chromatin immunoprecipitation assays showed that Klf9 associated in chromatin from mouse hippocampus with genes identified by ChSP sequencing on HT22 cells, and expression of Klf9 target genes was dysregulated in the hippocampus of neonatal Klf9-null mice. Gene ontology analysis revealed that Klf9 genomic targets include genes involved in cystokeletal remodeling, Wnt signaling and inflammation. Conclusions We have identified genomic targets of Klf9 in hippocampal neurons and created a foundation for future studies on how it functions in chromatin, and regulates neuronal morphology and survival across the lifespan. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3640-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joseph R Knoedler
- Neuroscience Graduate Program, The University of Michigan, Ann Arbor, MI, 48109, USA.,Current address: Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Arasakumar Subramani
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, 3065C Kraus Natural Science Building, Ann Arbor, MI, 48109, USA
| | - Robert J Denver
- Neuroscience Graduate Program, The University of Michigan, Ann Arbor, MI, 48109, USA. .,Department of Molecular, Cellular and Developmental Biology, The University of Michigan, 3065C Kraus Natural Science Building, Ann Arbor, MI, 48109, USA.
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Papadakis KA, Krempski J, Svingen P, Xiong Y, Sarmento OF, Lomberk GA, Urrutia RA, Faubion WA. Krüppel-like factor KLF10 deficiency predisposes to colitis through colonic macrophage dysregulation. Am J Physiol Gastrointest Liver Physiol 2015; 309:G900-9. [PMID: 26472224 PMCID: PMC4669350 DOI: 10.1152/ajpgi.00309.2015] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 10/13/2015] [Indexed: 01/31/2023]
Abstract
Krüppel-like factor (KLF)-10 is an important transcriptional regulator of TGF-β1 signaling in both CD8(+) and CD4(+) T lymphocytes. In the present study, we demonstrate a novel role for KLF10 in the regulation of TGFβRII expression with functional relevance in macrophage differentiation and activation. We first show that transfer of KLF10(-/-) bone marrow-derived macrophages into wild-type (WT) mice leads to exacerbation of experimental colitis. At the cell biological level, using two phenotypic strategies, we show that KLF10-deficient mice have an altered colonic macrophage phenotype with higher frequency of proinflammatory LyC6(+)MHCII(+) cells and a reciprocal decrease of the anti-inflammatory LyC6(-)MHCII(+) subset. Additionally, the anti-inflammatory CD11b(+)CX3CR1(hi) subset of colonic macrophages is significantly decreased in KLF10(-/-) compared with WT mice under inflammatory conditions. Molecularly, CD11b(+) colonic macrophages from KLF10(-/-) mice exhibit a proinflammatory cytokine profile with increased production of TNF-α and lower production of IL-10 in response to LPS stimulation. Because KLF10 is a transcription factor, we explored how this protein may regulate macrophage function. Consequently, we analyzed the expression of TGFβRII expression in colonic macrophages and found that, in the absence of KLF10, macrophages express lower levels of TGFβRII and display an attenuated Smad-2 phosphorylation following TGF-β1 stimulation. We further show that KLF10 directly binds to the TGFβRII promoter in macrophages, leading to enhanced gene expression through histone H3 acetylation. Collectively, our data reveal a critical role for KLF10 in the epigenetic regulation of TGFβRII expression in macrophages and the acquisition of a "regulatory" phenotype that contributes to intestinal mucosal homeostasis.
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Affiliation(s)
| | - James Krempski
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; and
| | - Phyllis Svingen
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; and
| | - Yuning Xiong
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; and
| | - Olga F Sarmento
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; and
| | - Gwen A Lomberk
- Epigenetics and Chromatin Dynamics Laboratory, Departments of Medicine and Biochemistry and Molecular Biology, Epigenetic Translational Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Raul A Urrutia
- Epigenetics and Chromatin Dynamics Laboratory, Departments of Medicine and Biochemistry and Molecular Biology, Epigenetic Translational Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - William A Faubion
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota; and
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Feinberg MW. Fine-tuning innate and adaptive immune responses: another KLFhanger. Focus on "Krüppel-like factor KLF10 regulates transforming growth factor receptor II expression and TGF-β signaling in CD8+ T lymphocytes". Am J Physiol Cell Physiol 2015; 308:C359-61. [PMID: 25567811 DOI: 10.1152/ajpcell.00418.2014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Mark W Feinberg
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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