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Bao Z, Yang M, Guo Y, Ge Q, Zhang H. MTFR2 accelerates hepatocellular carcinoma mediated by metabolic reprogramming via the Akt signaling pathway. Cell Signal 2024; 123:111366. [PMID: 39182591 DOI: 10.1016/j.cellsig.2024.111366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 08/13/2024] [Accepted: 08/22/2024] [Indexed: 08/27/2024]
Abstract
Metabolic reprogramming has recently been identified as a hallmark of malignancies. The shift from oxidative phosphorylation to glycolysis in hepatocellular carcinoma (HCC) meets the demands of rapid cell growth and provides a microenvironment for tumor progression. This study sought to uncover the function and mechanism of MTFR2 in the metabolic reprogramming of HCC. Elevated MTFR2 expression was associated with poor patient prognosis. Downregulation of MTFR2 blocked malignant behaviors, epithelial-to-mesenchymal transition (EMT), and glycolysis in HCC cells. Nuclear transcription factor Y subunit gamma (NFYC) was also associated with poor patient prognosis, and NFYC bound to the promoter of MTFR2 to activate transcription and promote Akt signaling. The repressive effects of NFYC knockdown on EMT and glycolysis in HCC cells were compromised by MTFR2 overexpression, elicited through the activation of the Akt signaling. Knockdown of NFYC slowed the growth and intrahepatic metastasis in vivo, which was reversed by MTFR2 overexpression. In conclusion, our work shows that activation of MTFR2 by the transcription factor NFYC promotes Akt signaling, thereby potentiating metabolic reprogramming in HCC development. Targeting the NFYC/MTFR2/Akt axis may represent a therapeutic strategy for HCC.
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Affiliation(s)
- Zhongming Bao
- Department of Hepatobiliary Surgery, Huai'an Hospital Affiliated to Yangzhou University (The Fifth People's Hospital of Huai'an), Huaiyin 223300, Jiangsu, PR China
| | - Ming Yang
- Department of Hepatobiliary Surgery, Huai'an Hospital Affiliated to Yangzhou University (The Fifth People's Hospital of Huai'an), Huaiyin 223300, Jiangsu, PR China
| | - Yunhu Guo
- Department of Hepatobiliary Surgery, Huai'an Hospital Affiliated to Yangzhou University (The Fifth People's Hospital of Huai'an), Huaiyin 223300, Jiangsu, PR China
| | - Qi Ge
- School of Biological Science and Food Engineering, Chuzhou University, Chuzhou 239000, Anhui, PR China.
| | - Huaguo Zhang
- Department of Hepatobiliary Surgery, Huai'an Hospital Affiliated to Yangzhou University (The Fifth People's Hospital of Huai'an), Huaiyin 223300, Jiangsu, PR China.
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2
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Yang YT, Yao CY, Kao CJ, Chiu PJ, Lin ME, Hou HA, Lin CC, Chou WC, Tien HF. Clinical relevance of NFYA splice variants in patients with acute myeloid leukaemia undergoing intensive chemotherapy. Br J Haematol 2024. [PMID: 39192759 DOI: 10.1111/bjh.19733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 08/14/2024] [Indexed: 08/29/2024]
Abstract
Aberrant alternative splicing (AS) contributes to leukemogenesis, but reports on the clinical and biological implications of aberrant AS in acute myeloid leukaemia (AML) remain limited. Here, we used RNA-seq to analyse AS in AML cells from 341 patients, comparing them to healthy CD34+ haematopoietic stem cells (HSCs). Our findings highlight distinct AS patterns in the nuclear transcription factor Y subunit alpha (NFYA) gene, with two main isoforms: NFYA-L (Long) and NFYA-S (Short), differing in exon 3 inclusion. Patients with lower NFYA-L but higher NFYA-S expression, termed NFYA-S predominance, displayed more favourable characteristics and better outcomes following intensive chemotherapy, regardless of age and European LeukemiaNet risk classification, compared to those with higher NFYA-L but lower NFYA-S expression, termed NFYA-L predominance. The prognostic effects were validated using The Cancer Genome Atlas cohort. Transcriptome analysis revealed upregulated cell cycle genes in NFYA-S predominant cases, resembling those of active HSCs, demonstrating relative chemosensitivity. Conversely, NFYA-L predominant cases, as observed in KMT2A-rearranged leukaemia, were associated with relative chemoresistance. NFYA-S overexpression in OCI-AML3 cells promoted cell proliferation, S-phase entry and increased cytarabine sensitivity, suggesting its clinical and therapeutic relevance in AML. Our study underscores NFYA AS as a potential prognostic biomarker in AML.
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Affiliation(s)
- Yi-Tsung Yang
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chi-Yuan Yao
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chein-Jun Kao
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Po-Ju Chiu
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Hematological Oncology, National Taiwan University Cancer Center, Taipei, Taiwan
| | - Ming-En Lin
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Hsin-An Hou
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chien-Chin Lin
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Wen-Chien Chou
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Hwei-Fang Tien
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Department of Internal Medicine, Far-Eastern Memorial Hospital, New Taipei City, Taiwan
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3
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Ramirez CFA, Taranto D, Ando-Kuri M, de Groot MHP, Tsouri E, Huang Z, de Groot D, Kluin RJC, Kloosterman DJ, Verheij J, Xu J, Vegna S, Akkari L. Cancer cell genetics shaping of the tumor microenvironment reveals myeloid cell-centric exploitable vulnerabilities in hepatocellular carcinoma. Nat Commun 2024; 15:2581. [PMID: 38519484 PMCID: PMC10959959 DOI: 10.1038/s41467-024-46835-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 03/12/2024] [Indexed: 03/25/2024] Open
Abstract
Myeloid cells are abundant and plastic immune cell subsets in the liver, to which pro-tumorigenic, inflammatory and immunosuppressive roles have been assigned in the course of tumorigenesis. Yet several aspects underlying their dynamic alterations in hepatocellular carcinoma (HCC) progression remain elusive, including the impact of distinct genetic mutations in shaping a cancer-permissive tumor microenvironment (TME). Here, in newly generated, clinically-relevant somatic female HCC mouse models, we identify cancer genetics' specific and stage-dependent alterations of the liver TME associated with distinct histopathological and malignant HCC features. Mitogen-activated protein kinase (MAPK)-activated, NrasG12D-driven tumors exhibit a mixed phenotype of prominent inflammation and immunosuppression in a T cell-excluded TME. Mechanistically, we report a NrasG12D cancer cell-driven, MEK-ERK1/2-SP1-dependent GM-CSF secretion enabling the accumulation of immunosuppressive and proinflammatory monocyte-derived Ly6Clow cells. GM-CSF blockade curbs the accumulation of these cells, reduces inflammation, induces cancer cell death and prolongs animal survival. Furthermore, GM-CSF neutralization synergizes with a vascular endothelial growth factor (VEGF) inhibitor to restrain HCC outgrowth. These findings underscore the profound alterations of the myeloid TME consequential to MAPK pathway activation intensity and the potential of GM-CSF inhibition as a myeloid-centric therapy tailored to subsets of HCC patients.
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Affiliation(s)
- Christel F A Ramirez
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daniel Taranto
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Masami Ando-Kuri
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marnix H P de Groot
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Efi Tsouri
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Zhijie Huang
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, 510060, PR China
| | - Daniel de Groot
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Roelof J C Kluin
- Genomics Core facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daan J Kloosterman
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Joanne Verheij
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Jing Xu
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, 510060, PR China
| | - Serena Vegna
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Leila Akkari
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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4
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Dolfini D, Gnesutta N, Mantovani R. Expression and function of NF-Y subunits in cancer. Biochim Biophys Acta Rev Cancer 2024; 1879:189082. [PMID: 38309445 DOI: 10.1016/j.bbcan.2024.189082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/05/2024]
Abstract
NF-Y is a Transcription Factor (TF) targeting the CCAAT box regulatory element. It consists of the NF-YB/NF-YC heterodimer, each containing an Histone Fold Domain (HFD), and the sequence-specific subunit NF-YA. NF-YA expression is associated with cell proliferation and absent in some post-mitotic cells. The review summarizes recent findings impacting on cancer development. The logic of the NF-Y regulome points to pro-growth, oncogenic genes in the cell-cycle, metabolism and transcriptional regulation routes. NF-YA is involved in growth/differentiation decisions upon cell-cycle re-entry after mitosis and it is widely overexpressed in tumors, the HFD subunits in some tumor types or subtypes. Overexpression of NF-Y -mostly NF-YA- is oncogenic and decreases sensitivity to anti-neoplastic drugs. The specific roles of NF-YA and NF-YC isoforms generated by alternative splicing -AS- are discussed, including the prognostic value of their levels, although the specific molecular mechanisms of activity are still to be deciphered.
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Affiliation(s)
- Diletta Dolfini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, Milano 20133, Italy
| | - Nerina Gnesutta
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, Milano 20133, Italy
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, Milano 20133, Italy.
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5
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Jing M, Xiong X, Mao X, Song Q, Zhang L, Ouyang Y, Pang Y, Fu Y, Yan W. HMGB1 promotes mitochondrial transfer between hepatocellular carcinoma cells through RHOT1 and RAC1 under hypoxia. Cell Death Dis 2024; 15:155. [PMID: 38378644 PMCID: PMC10879213 DOI: 10.1038/s41419-024-06536-6] [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: 09/12/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 02/22/2024]
Abstract
Mitochondrial transfer plays an important role in various diseases, and many mitochondrial biological functions can be regulated by HMGB1. To explore the role of mitochondrial transfer in hepatocellular carcinoma (HCC) and its relationship with HMGB1, field emission scanning electron microscopy, immunofluorescence, and flow cytometry were used to detect the mitochondrial transfer between HCC cells. We found that mitochondrial transfer between HCC cells was confirmed using tunnel nanotubes (TNTs). The transfer of mitochondria from the highly invasive HCC cells to the less invasive HCC cells could enhance the migration and invasion ability of the latter. The hypoxic conditions increased the mitochondrial transfer between HCC cells. Then the mechanism was identified using co-immunoprecipitation, luciferase reporter assay, and chromatin immunoprecipitation. We found that RHOT1, a mitochondrial transport protein, promoted mitochondrial transfer and the migration and metastasis of HCC cells during this process. Under hypoxia, HMGB1 further regulated RHOT1 expression by increasing the expression of NFYA and NFYC subunits of the NF-Y complex. RAC1, a protein associated with TNTs formation, promoted mitochondrial transfer and HCC development. Besides, HMGB1 regulated RAC1 aggregation to the cell membrane under hypoxia. Finally, the changes and significance of related molecules in clinical samples of HCC were analyzed using bioinformatics and tissue microarray analyses. We found that HCC patients with high HMGB1, RHOT1, or RAC1 expression exhibited a relatively shorter overall survival period. In conclusion, under hypoxic conditions, HMGB1 promoted mitochondrial transfer and migration and invasion of HCC cells by increasing the expression of mitochondrial transport protein RHOT1 and TNTs formation-related protein RAC1.
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Affiliation(s)
- Mengjia Jing
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiaofeng Xiong
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xin Mao
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Qianben Song
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Lumiao Zhang
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yiming Ouyang
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yingzhi Pang
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yu Fu
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Wei Yan
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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6
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Rigillo G, Belluti S, Campani V, Ragazzini G, Ronzio M, Miserocchi G, Bighi B, Cuoghi L, Mularoni V, Zappavigna V, Dolfini D, Mercatali L, Alessandrini A, Imbriano C. The NF-Y splicing signature controls hybrid EMT and ECM-related pathways to promote aggressiveness of colon cancer. Cancer Lett 2023:216262. [PMID: 37307894 DOI: 10.1016/j.canlet.2023.216262] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/24/2023] [Accepted: 06/04/2023] [Indexed: 06/14/2023]
Abstract
Aberrant splicing events are associated with colorectal cancer (CRC) and provide new opportunities for tumor diagnosis and treatment. The expression of the splice variants of NF-YA, the DNA binding subunit of the transcription factor NF-Y, is deregulated in multiple cancer types compared to healthy tissues. NF-YAs and NF-YAl isoforms differ in the transactivation domain, which may result in distinct transcriptional programs. In this study, we demonstrated that the NF-YAl transcript is higher in aggressive mesenchymal CRCs and predicts shorter patients' survival. In 2D and 3D conditions, CRC cells overexpressing NF-YAl (NF-YAlhigh) exhibit reduced cell proliferation, rapid single cell amoeboid-like migration, and form irregular spheroids with poor cell-to-cell adhesion. Compared to NF-YAshigh, NF-YAlhigh cells show changes in the transcription of genes involved in epithelial-mesenchymal transition, extracellular matrix and cell adhesion. NF-YAl and NF-YAs bind similarly to the promoter of the E-cadherin gene, but oppositely regulate its transcription. The increased metastatic potential of NF-YAlhigh cells in vivo was confirmed in zebrafish xenografts. These results suggest that the NF-YAl splice variant could be a new CRC prognostic factor and that splice-switching strategies may reduce metastatic CRC progression.
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Affiliation(s)
- Giovanna Rigillo
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 213/D, 41125, Modena, Italy
| | - Silvia Belluti
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 213/D, 41125, Modena, Italy
| | - Virginia Campani
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 213/D, 41125, Modena, Italy
| | - Gregorio Ragazzini
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, via Campi 213/A, 41125, Modena, Italy
| | - Mirko Ronzio
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
| | - Giacomo Miserocchi
- Preclinic and Osteoncology Unit, Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014, Meldola, Italy
| | - Beatrice Bighi
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, via Campi 213/A, 41125, Modena, Italy
| | - Laura Cuoghi
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 213/D, 41125, Modena, Italy
| | - Valentina Mularoni
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 213/D, 41125, Modena, Italy
| | - Vincenzo Zappavigna
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 213/D, 41125, Modena, Italy
| | - Diletta Dolfini
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
| | - Laura Mercatali
- Preclinic and Osteoncology Unit, Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014, Meldola, Italy
| | - Andrea Alessandrini
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, via Campi 213/A, 41125, Modena, Italy; CNR-Nanoscience Institute-S3, Modena, Italy
| | - Carol Imbriano
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 213/D, 41125, Modena, Italy.
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7
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Londero M, Gallo A, Cattaneo C, Ghilardi A, Ronzio M, Del Giacco L, Mantovani R, Dolfini D. NF-YAl drives EMT in Claudin low tumours. Cell Death Dis 2023; 14:65. [PMID: 36707502 PMCID: PMC9883497 DOI: 10.1038/s41419-023-05591-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/29/2023]
Abstract
NF-Y is a trimeric transcription factor whose binding site -the CCAAT box- is enriched in cancer-promoting genes. The regulatory subunit, the sequence-specificity conferring NF-YA, comes in two major isoforms, NF-YA long (NF-YAl) and short (NF-YAs). Extensive expression analysis in epithelial cancers determined two features: widespread overexpression and changes in NF-YAl/NF-YAs ratios (NF-YAr) in tumours with EMT features. We performed wet and in silico experiments to explore the role of the isoforms in breast -BRCA- and gastric -STAD- cancers. We generated clones of two Claudinlow BRCA lines SUM159PT and BT549 ablated of exon-3, thus shifting expression from NF-YAl to NF-YAs. Edited clones show normal growth but reduced migratory capacities in vitro and ability to metastatize in vivo. Using TCGA, including upon deconvolution of scRNA-seq data, we formalize the clinical importance of high NF-YAr, associated to EMT genes and cell populations. We derive a novel, prognostic 158 genes signature common to BRCA and STAD Claudinlow tumours. Finally, we identify splicing factors associated to high NF-YAr, validating RBFOX2 as promoting expression of NF-YAl. These data bring three relevant results: (i) the definition and clinical implications of NF-YAr and the 158 genes signature in Claudinlow tumours; (ii) genetic evidence of 28 amino acids in NF-YAl with EMT-promoting capacity; (iii) the definition of selected splicing factors associated to NF-YA isoforms.
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Affiliation(s)
- Michela Londero
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Alberto Gallo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Camilla Cattaneo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Anna Ghilardi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Mirko Ronzio
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Luca Del Giacco
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Diletta Dolfini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy.
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8
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Li Z, You C, Huang J, Zhang M. NFYAv1 is a Tumor-Promoting Transcript Associated with Poor Prognosis of Hepatocellular Carcinoma. Med Sci Monit 2023; 29:e938410. [PMID: 36680333 PMCID: PMC9875548 DOI: 10.12659/msm.938410] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 12/27/2022] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Nuclear Transcription Factor Y Subunit Alpha (NFYA), together with NFYB and NFYC, form a sequence-specific heterotrimeric nuclear transcription factor (NFY), but their functional role in hepatocellular carcinoma (HCC) is still unclear. In this study, we explored the association between the NFY subunit genes and the survival of primary hepatocellular carcinoma (HCC) patients in The Cancer Genome Atlas (TCGA). The transcript-specific effect on HCC cell growth was studied. MATERIAL AND METHODS RNA-seq data from the Genotype-Tissue Expression Project (GTEx) and TCGA were analyzed in combination. In vitro cellular and molecular studies were conducted using SK-Hep-1 and Hep3B cells. Pearson's correlation coefficients were calculated to assess correlations. Welch's unpaired t test and one-way ANOVA with post hoc Tukey's multiple comparisons were performed. Kaplan-Meier (K-M) survival curves were assessed by conducting log-rank (Mantel-Cox) test. RESULTS NFYA was the only prognosis-related gene. Among the 2 splicing transcripts of NFYA, the long isoform (NFYAv1, NM_002505.5) but not the short-form (NFYAv2, NM_021705.4) was significantly associated with worse progression-free survival (PFS) (high [n=179] vs low [n=179], HR: 1.657, 95% CI: 1.228-2.235, P<0.001) and disease-specific survival (DSS) (high [n=175] vs low [n=175], HR: 1.986, 95% CI: 1.269-3.108, P<0.001) in HCC patients. GO/KEGG analysis in TCGA confirmed that NFYAv1 and NFYAv2 co-expressed (|Pearson's r|≥0.6) genes in primary HCC patients were enriched in quite different GO/KEGG terms. NFYAv1 knockdown significantly decreased cell viability and increased G0/G1 cell cycle arrest. The shRNA only targeting NFYAv1 had a significantly stronger growth-inhibiting effect than the shRNA targeting both NFYAv1 and NFYAv2. CONCLUSIONS This study showed that NFYAv1 is a tumor-promoting transcript associated with poor prognosis of HCC.
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Affiliation(s)
- Zigang Li
- Department of Hepatobiliary Surgery, The First People’s Hospital of Yibin, Yibin, Sichuan, PR China
| | - Chengshan You
- Department of Endocrinology, The Second People’s Hospital of Yibin, Yibin, Sichuan, PR China
| | - Jun Huang
- Department of Hepatobiliary Surgery, The First People’s Hospital of Yibin, Yibin, Sichuan, PR China
| | - Ming Zhang
- Department of Hepatobiliary Surgery, The First People’s Hospital of Yibin, Yibin, Sichuan, PR China
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9
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Chen E, He Y, Jiang J, Yi J, Zou Z, Song Q, Ren Q, Lin Z, Lu Y, Liu J, Zhang J. CDCA8 induced by NF-YA promotes hepatocellular carcinoma progression by regulating the MEK/ERK pathway. Exp Hematol Oncol 2023; 12:9. [PMID: 36639822 PMCID: PMC9838039 DOI: 10.1186/s40164-022-00366-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 12/29/2022] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is one of the most lethal malignant tumors. Cell division cycle associated 8 (CDCA8) is an important multifactorial regulator in cancers. However, its up and downstream targets and effects in HCC are still unclear. METHODS A comprehensive bioinformatics analysis was performed using The Cancer Genome Atlas dataset (TCGA) to explore novel core oncogenes. We quantified CDCA8 levels in HCC tumors using qRT-PCR. HCC cell's proliferative, migratory, and invasive abilities were detected using a Cell Counting Kit-8 (CCK-8) assay, 5-ethynyl-2'-deoxyuridine (EdU) assay, clone formation, and a Transwell assay. An orthotopic tumor model and tail vein model were constructed to determine the effects of CDCA8 inhibition in vivo. The mechanism underlying CDCA8 was investigated using RNA sequencing. The prognostic value of CDCA8 was assessed with immunohistochemical staining of the tissue microarrays. RESULTS CDCA8 was identified as a novel oncogene during HCC development. The high expression of CDCA8 was an independent predictor for worse HCC outcomes both in publicly available datasets and in our cohort. We found that CDCA8 knockdown inhibited HCC cell proliferation, colony formation, and migration by suppressing the MEK/ERK pathway in vitro. Moreover, CDCA8 deficiency significantly inhibited tumorigenesis and metastasis. Next-generation sequencing and laboratory validation showed that CDCA8 silencing inhibited the expression of TPM3, NECAP2, and USP13. Furthermore, NA-YA overexpression upregulated the expression of CDCA8. CDCA8 knockdown could attenuate NF-YA-mediated cell invasion in vitro. The expression of NF-YA alone or in combined with CDCA8 were validated as significant independent risk factors for patient survival. CONCLUSION Our findings revealed that the expression of CDCA8 alone or in combined with NF-YA contributed to cancer progression, and could serve as novel potential therapeutic targets for HCC patients.
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Affiliation(s)
- Erbao Chen
- grid.440601.70000 0004 1798 0578Department of Hepatobiliary and Pancreatic Surgery, Peking University Shenzhen Hospital, Shenzhen, 518036 Guangdong China ,grid.263817.90000 0004 1773 1790School of Medicine, Southern University of Science and Technology, Shenzhen, 518055 Guangdong China
| | - Yu He
- grid.263817.90000 0004 1773 1790School of Medicine, Southern University of Science and Technology, Shenzhen, 518055 Guangdong China
| | - Jing Jiang
- grid.440601.70000 0004 1798 0578Department of Pathology, Peking University Shenzhen Hospital, Shenzhen, Guangdong China
| | - Jing Yi
- grid.440601.70000 0004 1798 0578Department of Hepatobiliary and Pancreatic Surgery, Peking University Shenzhen Hospital, Shenzhen, 518036 Guangdong China
| | - Zhilin Zou
- grid.414701.7Department of Ophthalmology, Affiliated Eye Hospital of Wenzhou Medical University, Wenzhou, Zhejiang China
| | - Qiuzi Song
- grid.440601.70000 0004 1798 0578Department of Hepatobiliary and Pancreatic Surgery, Peking University Shenzhen Hospital, Shenzhen, 518036 Guangdong China
| | - Qingqi Ren
- grid.440601.70000 0004 1798 0578Department of Hepatobiliary and Pancreatic Surgery, Peking University Shenzhen Hospital, Shenzhen, 518036 Guangdong China
| | - Zewei Lin
- grid.440601.70000 0004 1798 0578Department of Hepatobiliary and Pancreatic Surgery, Peking University Shenzhen Hospital, Shenzhen, 518036 Guangdong China
| | - Yi Lu
- grid.263817.90000 0004 1773 1790School of Medicine, Southern University of Science and Technology, Shenzhen, 518055 Guangdong China ,Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen, Guangdong China
| | - Jikui Liu
- grid.440601.70000 0004 1798 0578Department of Hepatobiliary and Pancreatic Surgery, Peking University Shenzhen Hospital, Shenzhen, 518036 Guangdong China
| | - Jian Zhang
- grid.263817.90000 0004 1773 1790School of Medicine, Southern University of Science and Technology, Shenzhen, 518055 Guangdong China ,Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen, Guangdong China
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10
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Construction of Oxidative Stress-Related Genes Risk Model Predicts the Prognosis of Uterine Corpus Endometrial Cancer Patients. Cancers (Basel) 2022; 14:cancers14225572. [PMID: 36428665 PMCID: PMC9688652 DOI: 10.3390/cancers14225572] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 11/01/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Oxidative stress contributes significantly to cancer development. Recent studies have demonstrated that oxidative stress could alter the epigenome and, in particular, DNA methylation. This study aimed to explore the potential link between oxidative stress and uterine corpus endometrial carcinoma (UCEC). An analysis of RNA-seq data and relevant clinical information was conducted with data from The Cancer Genome Atlas (TCGA), and oxidative stress genes were obtained from Gene Set Enrichment Analysis (GSEA). Differentially expressed genes (DEGs) in normal and tumor groups of UCEC were analyzed using GO and KEGG enrichment analysis. As a result of survival analysis, Lasso regression analysis of DEGs, a risk score model of oxidative stress-related genes (OSRGs) was constructed. Moreover, this study demonstrated that OSRGs are associated with immune cell infiltration in UCEC, suggesting oxidative stress may play a role in UCEC development by activating immune cells. We discovered 136 oxidative stress-related DEGs in UCEC, from which we screened 25 prognostic genes significantly related to the overall survival of UCEC patients. BCL2A1, CASP6, GPX2, HIC1, IL19, MSX1, RNF183, SFN, TRPM2 and HIST1H3C are associated with a good prognosis while CDKN2A, CHAC1, E2F1, GSDME, HMGA1, ITGA7, MCM4, MYBL2, PPIF, S100A1, S100A9, STK26 and TRIB3 are involved in a poor prognosis in UCEC. A 7-OSRGs-based risk score (H3C1, CDKN2A, STK26, TRPM2, E2F1, CHAC1, MSX1) was generated by Lasso regression. Further, an association was found between H3C1, CDKN2A, STK26, TRPM2, E2F1, CHAC1 and MSX1 expression levels and the immune infiltrating cells, including CD8 T cells, NK cells, and mast cells in UCEC. NFYA and RFX5 were speculated as common transcription factors of CDKN2A, TRPM2, E2F1, CHAC1, and MSX1 in UCEC.
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11
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Genetic Polymorphisms of lncRNA LINC00673 as Predictors of Hepatocellular Carcinoma Progression in an Elderly Population. Int J Mol Sci 2022; 23:ijms232112737. [PMID: 36361527 PMCID: PMC9654806 DOI: 10.3390/ijms232112737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/19/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
Long noncoding (lnc)RNAs are reported to be key regulators of tumor progression, including hepatocellular carcinoma (HCC). The lncRNA long intergenic noncoding RNA 00673 (LINC00673) was indicated to play an important role in HCC progression, but the impacts of genetic variants (single-nucleotide polymorphisms, SNPs) of LINC00673 on HCC remain unclear. A TaqMan allelic discrimination assay was performed to analyze the genotypes of three tagging SNPs, viz., rs9914618 G > A, rs6501551 A > G, and rs11655237 C > T, of LINC00673 in 783 HCC patients and 1197 healthy subjects. Associations of functional SNPs of LINC00673 with HCC susceptibility and clinicopathologic variables were analyzed by logistic regression models. After stratification by confounding factor, we observed that elderly patients (≥60 years) with the LINC00673 rs9914618 A allele had an increased risk of developing HCC under a codominant model (p = 0.025) and dominant model (p = 0.047). Moreover, elderly patients carrying the GA + AA genotype of rs9914618 exhibited a higher risk of having lymph node metastasis compared to those who were homozygous for the major allele (p = 0.013). Genotype screening of rs9914618 in HCC cell lines showed that cells carrying the AA genotype expressed higher LINC00673 levels compared to the cells carrying the GG genotype. Further analyses of clinical datasets from the Cancer Genome Atlas (TCGA) showed that LINC00673 expressions were upregulated in HCC tissues compared to normal tissues, and were correlated with advanced clinical stages and poorer prognoses. In conclusions, our results suggested that the LINC00673 rs9914618 polymorphism may be a promising HCC biomarker, especially in elderly populations.
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12
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Ventura I, Revert F, Revert-Ros F, Gómez-Tatay L, Prieto-Ruiz JA, Hernández-Andreu JM. SP1 and NFY Regulate the Expression of PNPT1, a Gene Encoding a Mitochondrial Protein Involved in Cancer. Int J Mol Sci 2022; 23:ijms231911399. [PMID: 36232701 PMCID: PMC9570217 DOI: 10.3390/ijms231911399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/13/2022] [Accepted: 09/23/2022] [Indexed: 11/26/2022] Open
Abstract
The Polyribonucleotide nucleotidyltransferase 1 gene (PNPT1) encodes polynucleotide phosphorylase (PNPase), a 3′-5′ exoribonuclease involved in mitochondrial RNA degradation and surveillance and RNA import into the mitochondrion. Here, we have characterized the PNPT1 promoter by in silico analysis, luciferase reporter assays, electrophoretic mobility shift assays (EMSA), chromatin immunoprecipitation (ChIP), siRNA-based mRNA silencing and RT-qPCR. We show that the Specificity protein 1 (SP1) transcription factor and Nuclear transcription factor Y (NFY) bind the PNPT1 promoter, and have a relevant role regulating the promoter activity, PNPT1 expression, and mitochondrial activity. We also found in Kaplan–Meier survival curves that a high expression of either PNPase, SP1 or NFY subunit A (NFYA) is associated with a poor prognosis in liver cancer. In summary, our results show the relevance of SP1 and NFY in PNPT1 expression, and point to SP1/NFY and PNPase as possible targets in anti-cancer therapy.
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13
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Lu T, Li C, Xiang C, Gong Y, Peng W, Hou F, Chen C. Over-expression of NFYB affects stromal cells reprogramming and predicts worse survival in gastric cancer patients. Aging (Albany NY) 2022; 14:7851-7865. [PMID: 36152055 PMCID: PMC9596197 DOI: 10.18632/aging.204294] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/29/2022] [Indexed: 11/25/2022]
Abstract
Gastric cancer (GC) is the fifth most common cancer worldwide and the third most fatal. Cancer-associated fibroblasts (CAFs) play an essential role in promoting the occurrence and development of gastric cancer in all stages. NFYB is highly expressed in multiple tumors and promotes tumor invasion, metastasis, and drug resistance, but its role in the occurrence and development of gastric cancer remains unclear. Hence, we used TCGA, TIMER, Kaplan-Meier Plot, and UALCAN databases to analyze the expression of NFYB in pan-cancers and assess its clinical prognostic value. We found that high expression of NFYB may be a promising prognostic biomarker in patients with gastric cancer. High expression of NFYB was associated with high T stage, high histological grade, diffuse gastric cancer, and early-onset GC. Moreover, High expression of NFYB was associated with CAFs infiltration in the GC microenvironment. The prognosis of GC patients with high expression of NFYB and high infiltration of CAFs was worse. Therefore, NFYB may serve as a potential prognostic biomarker in patients with GC.
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Affiliation(s)
- Tailiang Lu
- Department of General Surgery, Hunan Provincial People's Hospital, The First-Affiliated Hospital of Hunan Normal University, Changsha, Hunan Province, China
| | - Chenglong Li
- Department of General Surgery, Hunan Provincial People's Hospital, The First-Affiliated Hospital of Hunan Normal University, Changsha, Hunan Province, China
| | - Cailing Xiang
- Department of General Surgery, Hunan Provincial People's Hospital, The First-Affiliated Hospital of Hunan Normal University, Changsha, Hunan Province, China
| | - Yongqiang Gong
- Department of General Surgery, Hunan Provincial People's Hospital, The First-Affiliated Hospital of Hunan Normal University, Changsha, Hunan Province, China
| | - Wei Peng
- Department of General Surgery, Hunan Provincial People's Hospital, The First-Affiliated Hospital of Hunan Normal University, Changsha, Hunan Province, China
| | - Futao Hou
- Department of General Surgery, Hunan Provincial People's Hospital, The First-Affiliated Hospital of Hunan Normal University, Changsha, Hunan Province, China
| | - Chaowu Chen
- Department of General Surgery, Hunan Provincial People's Hospital, The First-Affiliated Hospital of Hunan Normal University, Changsha, Hunan Province, China
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14
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Zhao C, Sun J, Dang Z, Su Q, Yang J. Circ_0000775 Promotes the Migration, Invasion and EMT of Hepatic Carcinoma Cells by Recruiting IGF2BP2 to Stabilize CDC27. Pathol Res Pract 2022; 235:153908. [DOI: 10.1016/j.prp.2022.153908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 03/29/2022] [Accepted: 04/17/2022] [Indexed: 10/18/2022]
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15
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Gallo A, Ronzio M, Bezzecchi E, Mantovani R, Dolfini D. NF-Y subunits overexpression in gastric adenocarcinomas (STAD). Sci Rep 2021; 11:23764. [PMID: 34887475 PMCID: PMC8660849 DOI: 10.1038/s41598-021-03027-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 11/22/2021] [Indexed: 12/12/2022] Open
Abstract
NF-Y is a pioneer transcription factor-TF-formed by the Histone-like NF-YB/NF-YC subunits and the regulatory NF-YA. It binds to the CCAAT box, an element enriched in promoters of genes overexpressed in many types of cancer. NF-YA is present in two major isoforms-NF-YAs and NF-YAl-due to alternative splicing, overexpressed in epithelial tumors. Here we analyzed NF-Y expression in stomach adenocarcinomas (STAD). We completed the partitioning of all TCGA tumor samples (450) according to molecular subtypes proposed by TCGA and ACRG, using the deep learning tool DeepCC. We analyzed differentially expressed genes-DEG-for enriched pathways and TFs binding sites in promoters. CCAAT is the predominant element only in the core group of genes upregulated in all subtypes, with cell-cycle gene signatures. NF-Y subunits are overexpressed, particularly NF-YA. NF-YAs is predominant in CIN, MSI and EBV TCGA subtypes, NF-YAl is higher in GS and in the ACRG EMT subtypes. Moreover, NF-YAlhigh tumors correlate with a discrete Claudinlow cohort. Elevated NF-YB levels are protective in MSS;TP53+ patients, whereas high NF-YAl/NF-YAs ratios correlate with worse prognosis. We conclude that NF-Y isoforms are associated to clinically relevant features of gastric cancer.
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Affiliation(s)
- Alberto Gallo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Mirko Ronzio
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Eugenia Bezzecchi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Diletta Dolfini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy.
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16
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Li Y, Zou L, Liu X, Luo J, Liu H. Identification of Immune-Related Genes for Establishment of Prognostic Index in Hepatocellular Carcinoma. Front Cell Dev Biol 2021; 9:760079. [PMID: 34796177 PMCID: PMC8593215 DOI: 10.3389/fcell.2021.760079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/11/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Immune checkpoint inhibitor (ICI) therapy has been proved to be a promising therapy to many types of solid tumors. However, effective biomarker for estimating the response to ICI therapy and prognosis of hepatocellular carcinoma (HCC) patients remains underexplored. The aim of this study is to build a novel immune-related prognostic index based on transcriptomic profiles. Methods: Weighted gene co-expression network analysis (WGCNA) was conducted to identify immune-related hub genes that are differentially expressed in HCC cohorts. Next, univariate Cox regression analysis and least absolute shrinkage and selection operator (LASSO) analysis were used to detect hub genes associated to overall survival (OS). To validate the immune-related prognostic index, univariate and multivariate Cox regression analysis were performed. CIBERSORT and ESTIMATE were used to explore the tumor microenvironment and immune infiltration level. Results: The differential expression analysis detected a total of 148 immune-related genes, among which 25 genes were identified to be markedly related to overall survival in HCC patients. LASSO analysis yielded 10 genes used to construct the immune-related gene prognostic index (IRGPI), by which a risk score is computed to estimate low vs. high risk indicating the response to ICI therapy and prognosis. Further analysis confirmed that this immune-related prognostic index is an effective indicator to immune infiltration level, response to ICI treatment and OS. The IRGPI low-risk patients had better overall survival (OS) than IRGPI high-risk patients on two independent cohorts. Moreover, we found that IRGPI high-risk group was correlated with high TP53 mutation rate, immune-suppressing tumor microenvironment, and these patients acquired less benefit from ICI therapy. In contrast, IRGPI-low risk group was associated with low TP53 and PIK3CA mutation rate, high infiltration of naive B cells and T cells, and these patients gained relatively more benefit from ICI therapy.
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Affiliation(s)
- Yinfang Li
- Aliyun School of Big Data, Changzhou University, Changzhou, China
| | - Ling Zou
- Aliyun School of Big Data, Changzhou University, Changzhou, China
| | - Xuejun Liu
- School of Computer Science and Technology, Nanjing Tech University, Nanjing, China
| | - Judong Luo
- Department of Radiotherapy, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Hui Liu
- School of Computer Science and Technology, Nanjing Tech University, Nanjing, China
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17
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Belluti S, Semeghini V, Rigillo G, Ronzio M, Benati D, Torricelli F, Reggiani Bonetti L, Carnevale G, Grisendi G, Ciarrocchi A, Dominici M, Recchia A, Dolfini D, Imbriano C. Alternative splicing of NF-YA promotes prostate cancer aggressiveness and represents a new molecular marker for clinical stratification of patients. J Exp Clin Cancer Res 2021; 40:362. [PMID: 34782004 PMCID: PMC8594157 DOI: 10.1186/s13046-021-02166-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 11/02/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Approaches based on expression signatures of prostate cancer (PCa) have been proposed to predict patient outcomes and response to treatments. The transcription factor NF-Y participates to the progression from benign epithelium to both localized and metastatic PCa and is associated with aggressive transcriptional profile. The gene encoding for NF-YA, the DNA-binding subunit of NF-Y, produces two alternatively spliced transcripts, NF-YAs and NF-YAl. Bioinformatic analyses pointed at NF-YA splicing as a key transcriptional signature to discriminate between different tumor molecular subtypes. In this study, we aimed to determine the pathophysiological role of NF-YA splice variants in PCa and their association with aggressive subtypes. METHODS Data on the expression of NF-YA isoforms were extracted from the TCGA (The Cancer Genome Atlas) database of tumor prostate tissues and validated in prostate cell lines. Lentiviral transduction and CRISPR-Cas9 technology allowed the modulation of the expression of NF-YA splice variants in PCa cells. We characterized 3D cell cultures through in vitro assays and RNA-seq profilings. We used the rank-rank hypergeometric overlap approach to identify concordant/discordant gene expression signatures of NF-YAs/NF-YAl-overexpressing cells and human PCa patients. We performed in vivo studies in SHO-SCID mice to determine pathological and molecular phenotypes of NF-YAs/NF-YAl xenograft tumors. RESULTS NF-YA depletion affects the tumorigenic potential of PCa cells in vitro and in vivo. Elevated NF-YAs levels are associated to aggressive PCa specimens, defined by Gleason Score and TNM classification. NF-YAl overexpression increases cell motility, while NF-YAs enhances cell proliferation in PCa 3D spheroids and xenograft tumors. The transcriptome of NF-YAs-spheroids has an extensive overlap with localized and metastatic human PCa signatures. According to PCa PAM50 classification, NF-YAs transcript levels are higher in LumB, characterized by poor prognosis compared to LumA and basal subtypes. A significant decrease in NF-YAs/NF-YAl ratio distinguishes PCa circulating tumor cells from cancer cells in metastatic sites, consistently with pro-migratory function of NF-YAl. Stratification of patients based on NF-YAs expression is predictive of clinical outcome. CONCLUSIONS Altogether, our results indicate that the modulation of NF-YA isoforms affects prostate pathophysiological processes and contributes to cancer-relevant phenotype, in vitro and in vivo. Evaluation of NF-YA splicing may represent a new molecular strategy for risk assessment of PCa patients.
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Affiliation(s)
- Silvia Belluti
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 213/D, Modena, Italy
| | - Valentina Semeghini
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 213/D, Modena, Italy
| | - Giovanna Rigillo
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 213/D, Modena, Italy
| | - Mirko Ronzio
- Department of Biosciences, University of Milan, Milan, Italy
| | - Daniela Benati
- Centre for Regenerative Medicine, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Federica Torricelli
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Luca Reggiani Bonetti
- Department of Medical and Surgical Sciences for Children & Adults, Division of Pathology, University-Hospital of Modena and Reggio Emilia, Modena, Italy
| | - Gianluca Carnevale
- Surgical, Medical and Dental Department of Morphological Sciences Related to Transplant, Oncology and Regenerative Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - Giulia Grisendi
- Laboratory of Cellular Therapy, Program of Cell Therapy and Immuno-Oncology, Division of Oncology, Department of Medical and Surgical Sciences for Children & Adults, University-Hospital of Modena and Reggio Emilia, Modena, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Massimo Dominici
- Laboratory of Cellular Therapy, Program of Cell Therapy and Immuno-Oncology, Division of Oncology, Department of Medical and Surgical Sciences for Children & Adults, University-Hospital of Modena and Reggio Emilia, Modena, Italy
| | - Alessandra Recchia
- Centre for Regenerative Medicine, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Diletta Dolfini
- Department of Biosciences, University of Milan, Milan, Italy
| | - Carol Imbriano
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 213/D, Modena, Italy.
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18
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Chen L, Zhang M, Wang X, Liu Y, Bian J, Yan D, Yin W. Cardiac steroid ouabain transcriptionally increases human leukocyte antigen DR expression on monocytes. Steroids 2021; 175:108915. [PMID: 34508735 DOI: 10.1016/j.steroids.2021.108915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/31/2021] [Accepted: 08/30/2021] [Indexed: 01/18/2023]
Abstract
Sepsis is a life-threatening disease characterized by acute multiple organ dysfunction and immunosuppression that is also called as immunoparalysis. Increasing evidence suggests that immunoparalysis largely contributes to the high mortality of sepsis, but the effective remedies are lacking. As an important antigen presentation molecule, human leukocyte antigen DR (HLA-DR) is remarkably down-regulated in sepsis-induced immunoparalysis, therefore, re-stimulation of HLA-DR expression is expected to be useful in reversing immunoparalysis. We previously described that ouabain, as a Na+, K+-ATPase ligand, is able to counteract immunoparalysis by regulating TH1 cytokines expression. Here, we expanded the finding that ouabain not only prevents LPS-induced down-regulation of HLA-DR on monocytes, but also transcriptionally activates HLA-DR α/β expression mediated by CIITA4, IRF1, c-Src, and Stat1 phosphorylation. Since ouabain can improve sepsis-induced immunoparalysis by multiple mechanisms, we propose that ouabain may be a promising agent in septic therapy that deserves further investigation.
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Affiliation(s)
- Lili Chen
- State Key Lab of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, China
| | - Manli Zhang
- State Key Lab of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, China
| | - Xiya Wang
- State Key Lab of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, China
| | - Yongjian Liu
- State Key Lab of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, China
| | - Jinjun Bian
- Department of Anesthesiology and Critical Care, Changhai Hospital, Naval Medical University, Shanghai, China.
| | - Dong Yan
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, China.
| | - Wu Yin
- State Key Lab of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, China.
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19
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CK2α causes stemness and chemotherapy resistance in liver cancer through the Hedgehog signaling pathway. Hepatobiliary Pancreat Dis Int 2021:S1499-3872(21)00173-9. [PMID: 34548224 DOI: 10.1016/j.hbpd.2021.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 08/26/2021] [Indexed: 02/05/2023]
Abstract
BACKGROUND Liver cancer is one of the major causes of cancer-related deaths globally. Cancer cell stemness and chemotherapy resistance contribute to the high mortality. Although evidence indicates that the alpha subunit of protein kinase 2 (CK2α) is involved in several human cancers, its function in liver cancer remains unknown. In the present study, we aimed to elucidate the role of CK2α in liver cancer. METHODS We examined the role of CK2α regulation in stemness and chemotherapy resistance capacity of liver cancer cells. MTT assays, tumor sphere formation assays, RT-PCR, flow cytometry, Western blotting assay, clonogenicity assay, matrigel invasion assay and bioinformatics were conducted in this study. RESULTS CK2α expression in the liver cancer tissues was notably upregulated compared with that in the corresponding non-tumorous tissues. The overexpression of CK2α promoted tumor sphere formation, increased the percentage of CD133(+) and side population cells, caused the resistance of liver cancer cells to 5-FU treatment, increased the expression levels of NANOG, OCT4, SOX2, Gli1 and Ptch1, and enhanced the ability of CD133(+) cell clone formation and invasion. Consistently, the downregulation of CK2α had the opposite effects. CK2α silencing inhibited the Hedgehog pathway by reducing the expression of Gli1 and Ptch1. Mechanistically, CK2α regulation on liver cancer cell stemness and chemotherapy resistance was found to be involved in the Hedgehog signaling pathway. CONCLUSIONS Our study may bring some new insights into the occurrence of liver cancer. Furthermore, these findings suggest that targeting CK2α may be a novel therapeutic strategy for patients with liver cancer.
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20
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Transcription factors linked to the molecular signatures in the development of hepatocellular carcinoma on a cirrhotic background. Med Oncol 2021; 38:121. [PMID: 34468893 DOI: 10.1007/s12032-021-01567-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 08/19/2021] [Indexed: 02/06/2023]
Abstract
Mechanisms underlying the regulation of gene expression in cancer have been surveyed for decades to find novel prognostic factors and new targets for molecular targeted therapies in cancer. Because most cases of liver cancer are associated with liver cirrhosis, we aimed to analyze the gene expression signatures and the gene regulatory mechanism in hepatocellular carcinoma (HCC) on a cirrhotic background using high-throughput data analysis. In the present study, three valid array-based datasets containing HCC and liver cirrhosis samples were obtained to identify common differentially expressed genes (DEGs). Moreover, a comprehensive data analysis was conducted based on RNA-Seq data and using Kaplan-Meier curve analysis to find molecular signatures that reduce patients' survival rate. Furthermore, we proposed a gene regulatory network (GRN) to explore the possible regulatory mechanism of these molecular signatures by transcription factors in HCC progression from cirrhosis. Besides, we analyzed protein-protein interactions, gene ontology (GO), and pathway enrichment to elucidate the cellular and molecular function of the GRN elements in HCC. In this way, we found a list of 231 molecular signatures in HCC derived from cirrhosis. We also found the importance of TCF4, RUNX1, HINFP, KDM2B, MAF, JUN, NR5A2, NFYA, and AR as key differentially expressed transcription factors (DETFs) in the progression of HCC from cirrhosis. In conclusion, the identified molecular signatures and their transcription factors propose candidate prognostic markers and possible molecular targets in the progression of HCC.
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21
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NF-Y Subunits Overexpression in HNSCC. Cancers (Basel) 2021; 13:cancers13123019. [PMID: 34208636 PMCID: PMC8234210 DOI: 10.3390/cancers13123019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/31/2021] [Accepted: 06/06/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Cancer cells have altered gene expression profiles. This is ultimately elicited by altered structure, expression or binding of transcription factors to regulatory regions of genomes. The CCAAT-binding trimer is a pioneer transcription factor involved in the activation of “cancer” genes. We and others have shown that the regulatory NF-YA subunit is overexpressed in epithelial cancers. Here, we examined large datasets of bulk gene expression profiles, as well as single-cell data, in head and neck squamous cell carcinomas by bioinformatic methods. We partitioned tumors according to molecular subtypes, mutations and positivity for HPV. We came to the conclusion that high levels of the histone-like subunits and the “short” NF-YAs isoform are protective in HPV-positive tumors. On the other hand, high levels of the “long” NF-YAl were found in the recently identified aggressive and metastasis-prone cell population undergoing partial epithelial to mesenchymal transition, p-EMT. Abstract NF-Y is the CCAAT-binding trimer formed by the histone fold domain (HFD), NF-YB/NF-YC and NF-YA. The CCAAT box is generally prevalent in promoters of “cancer” genes. We reported the overexpression of NF-YA in BRCA, LUAD and LUSC, and of all subunits in HCC. Altered splicing of NF-YA was found in breast and lung cancer. We analyzed RNA-seq datasets of TCGA and cell lines of head and neck squamous cell carcinomas (HNSCC). We partitioned all TCGA data into four subtypes, deconvoluted single-cell RNA-seq of tumors and derived survival curves. The CCAAT box was enriched in the promoters of overexpressed genes. The “short” NF-YAs was overexpressed in all subtypes and the “long” NF-YAl in Mesenchymal. The HFD subunits are overexpressed, except Basal (NF-YB) and Atypical (NF-YC); NF-YAl is increased in p53 mutated tumors. In HPV-positive tumors, high levels of NF-YAs, p16 and ΔNp63 correlate with better prognosis. Deconvolution of single cell RNA-seq (scRNA-seq) found a correlation of NF-YAl with Cancer Associated Fibroblasts (CAFs) and p-EMT cells, a population endowed with metastatic potential. We conclude that overexpression of HFD subunits and NF-YAs is protective in HPV-positive tumors; expression of NF-YAl is largely confined to mutp53 tumors and malignant p-EMT cells.
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