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Ronzio M, Bernardini A, Taglietti V, Ceribelli M, Donati G, Gallo A, Pavesi G, Dellabona P, Casorati G, Messina G, Mantovani R, Dolfini D. Genomic binding of NF-Y in mouse and human cells. Genomics 2024; 116:110895. [PMID: 39025317 DOI: 10.1016/j.ygeno.2024.110895] [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: 04/21/2024] [Revised: 06/12/2024] [Accepted: 07/13/2024] [Indexed: 07/20/2024]
Abstract
NF-Y is a Transcription Factor that regulates transcription through binding to the CCAAT-box. To understand its strategy, we analyzed 16 ChIP-seq datasets from human and mouse cells. Shared loci, mostly located in promoters of expressed genes of cell cycle, metabolism and gene expression pathways, are associated with histone marks of active chromatin and specific modules of TFs. Other peaks are in enhancers and Transposable Elements -TE- of retroviral origin in human and mouse. We evaluated the relationship with USF1, a common synergistic partner in promoters and MLT1 TEs, upon NF-YB inactivation: USF1 binding decreases in promoters, modestly in MLT1, suggesting a pioneering role of NF-Y in formers, not in the latters. These data define a common set of NF-Y functional targets across different mammalian cell types, suggesting a pioneering role in promoters with respect to TEs.
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Affiliation(s)
- Mirko Ronzio
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Andrea Bernardini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | | | - Michele Ceribelli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Giacomo Donati
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di Torino, Torino, Italy
| | - Alberto Gallo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Giulio Pavesi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Paolo Dellabona
- Experimental Immunology Unit. Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milano, Italy
| | - Giulia Casorati
- Experimental Immunology Unit. Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milano, Italy
| | - Graziella Messina
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Diletta Dolfini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy.
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2
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Chen F, Xu T, Jin N, Li D, Ying Y, Wang C. Transcription factor NFYA inhibits ferroptosis in lung adenocarcinoma cells by regulating PEBP1. Mutat Res 2024; 829:111873. [PMID: 38996537 DOI: 10.1016/j.mrfmmm.2024.111873] [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: 03/26/2024] [Revised: 06/18/2024] [Accepted: 06/30/2024] [Indexed: 07/14/2024]
Abstract
BACKGROUND Ferroptosis is an iron-dependent programmed cell death mediated by lipid peroxidation. The purpose was to explore the molecular mechanism by which phosphatidylethanolamine-binding protein 1 (PEBP1) regulates ferroptosis in lung adenocarcinoma (LUAD), hoping to identify novel therapeutic targets for LUAD. METHODS The expression, enrichment pathways and upstream transcription factors of PEBP1 were analyzed using bioinformatics tools. Dual-luciferase reporter assay and chromatin immunoprecipitation (ChIP) experiments were conducted to validate the interaction and binding relationship between PEBP1 and the upstream transcription factor nuclear transcription factor Y subunit α (NFYA). Quantitative reverse transcription PCR (qRT-PCR) was conducted to measure the expression levels of PEBP1 and NFYA mRNA in LUAD cells. Cell viability was detected by cell counting kit-8 assay. In addition, levels of malondialdehyde (MDA), Fe2+, and lipid reactive oxygen species (ROS) were assessed to evaluate ferroptosis levels in LUAD cells. RESULTS PEBP1 was downregulated and significantly enriched in the ferroptosis signaling pathway in LUAD. Overexpression of PEBP1 suppressed cell viability remarkably, while levels of MDA, Fe2+, and lipid ROS were increased. Conversely, knockdown of PEBP1 produced the opposite effects. The upstream transcription factor NFYA, predicted to be involved in the regulation of PEBP1, was also upregulated in LUAD. Dual-luciferase reporter assay, ChIP, and molecular experiments revealed that NFYA transcriptionally suppressed the expression of PEBP1, and overexpression of NFYA could reverse the effects caused by PEBP1 overexpression. CONCLUSION PEBP1 regulated ferroptosis in LUAD, and the transcription factor NFYA inhibited ferroptosis in LUAD cells by transcriptionally downregulating PEBP1 expression.
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Affiliation(s)
- Feng Chen
- Department of Respirotory Medicine, Taizhou Municipal Hospital, Taizhou City 318000, China.
| | - Tingting Xu
- Department of Respirotory Medicine, Taizhou Municipal Hospital, Taizhou City 318000, China
| | - Ni Jin
- Department of Respirotory Medicine, Taizhou Municipal Hospital, Taizhou City 318000, China
| | - Digeng Li
- Department of Respirotory Medicine, Taizhou Municipal Hospital, Taizhou City 318000, China
| | - Yanfu Ying
- Department of Respirotory Medicine, Taizhou Municipal Hospital, Taizhou City 318000, China
| | - Chen Wang
- Department of Respirotory Medicine, Taizhou Municipal Hospital, Taizhou City 318000, China
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3
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Wang R, Cheng Y, Jiang N, Jiang T, Wei Z. Overexpression of the PtrNF-YA6 gene inhibits secondary cell wall thickening in poplar. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 343:112058. [PMID: 38447913 DOI: 10.1016/j.plantsci.2024.112058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/20/2024] [Accepted: 03/03/2024] [Indexed: 03/08/2024]
Abstract
The NF-Y gene family in plants plays a crucial role in numerous biological processes, encompassing hormone response, stress response, as well as growth and development. In this study, we first used bioinformatics techniques to identify members of the NF-YA family that may function in wood formation. We then used molecular biology techniques to investigate the role and molecular mechanism of PtrNF-YA6 in secondary cell wall (SCW) formation in Populus trichocarpa. We found that PtrNF-YA6 protein was localized in the nucleus and had no transcriptional activating activity. Overexpression of PtrNF-YA6 had an inhibitory effect on plant growth and development and significantly suppressed hemicellulose synthesis and SCW thickening in transgenic plants. Yeast one-hybrid and ChIP-PCR assays revealed that PtrNF-YA6 directly regulated the expression of hemicellulose synthesis genes (PtrGT47A-1, PtrGT8C, PtrGT8F, PtrGT43B, PtrGT47C, PtrGT8A and PtrGT8B). In conclusion, PtrNF-YA6 can inhibit plant hemicellulose synthesis and SCW thickening by regulating the expression of downstream SCW formation-related target genes.
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Affiliation(s)
- Ruiqi Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang 150040, China
| | - Yujia Cheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang 150040, China
| | - Nan Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang 150040, China
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang 150040, China.
| | - Zhigang Wei
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang 150040, China; Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China.
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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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Cui M, Bezprozvannaya S, Hao T, Elnwasany A, Szweda LI, Liu N, Bassel-Duby R, Olson EN. Transcription factor NFYa controls cardiomyocyte metabolism and proliferation during mouse fetal heart development. Dev Cell 2023; 58:2867-2880.e7. [PMID: 37972593 PMCID: PMC11000264 DOI: 10.1016/j.devcel.2023.10.012] [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: 05/31/2023] [Revised: 08/22/2023] [Accepted: 10/24/2023] [Indexed: 11/19/2023]
Abstract
Cardiomyocytes are highly metabolic cells responsible for generating the contractile force in the heart. During fetal development and regeneration, these cells actively divide but lose their proliferative activity in adulthood. The mechanisms that coordinate their metabolism and proliferation are not fully understood. Here, we study the role of the transcription factor NFYa in developing mouse hearts. Loss of NFYa alters cardiomyocyte composition, causing a decrease in immature regenerative cells and an increase in trabecular and mature cardiomyocytes, as identified by spatial and single-cell transcriptome analyses. NFYa-deleted cardiomyocytes exhibited reduced proliferation and impaired mitochondrial metabolism, leading to cardiac growth defects and embryonic death. NFYa, interacting with cofactor SP2, activates genes linking metabolism and proliferation at the transcription level. Our study identifies a nodal role of NFYa in regulating prenatal cardiac growth and a previously unrecognized transcriptional control mechanism of heart metabolism, highlighting the importance of mitochondrial metabolism during heart development and regeneration.
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Affiliation(s)
- Miao Cui
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
| | - Svetlana Bezprozvannaya
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine and Sen. Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Tian Hao
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA 02115, USA
| | - Abdallah Elnwasany
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Luke I Szweda
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Ning Liu
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine and Sen. Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Rhonda Bassel-Duby
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine and Sen. Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Eric N Olson
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine and Sen. Paul D. Wellstone Muscular Dystrophy Specialized Research Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.
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Sroka MW, Skopelitis D, Vermunt MW, Preall JB, El Demerdash O, de Almeida LMN, Chang K, Utama R, Gryder B, Caligiuri G, Ren D, Nalbant B, Milazzo JP, Tuveson DA, Dobin A, Hiebert SW, Stengel KR, Mantovani R, Khan J, Kohli RM, Shi J, Blobel GA, Vakoc CR. Myo-differentiation reporter screen reveals NF-Y as an activator of PAX3-FOXO1 in rhabdomyosarcoma. Proc Natl Acad Sci U S A 2023; 120:e2303859120. [PMID: 37639593 PMCID: PMC10483665 DOI: 10.1073/pnas.2303859120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 07/11/2023] [Indexed: 08/31/2023] Open
Abstract
Recurrent chromosomal rearrangements found in rhabdomyosarcoma (RMS) produce the PAX3-FOXO1 fusion protein, which is an oncogenic driver and a dependency in this disease. One important function of PAX3-FOXO1 is to arrest myogenic differentiation, which is linked to the ability of RMS cells to gain an unlimited proliferation potential. Here, we developed a phenotypic screening strategy for identifying factors that collaborate with PAX3-FOXO1 to block myo-differentiation in RMS. Unlike most genes evaluated in our screen, we found that loss of any of the three subunits of the Nuclear Factor Y (NF-Y) complex leads to a myo-differentiation phenotype that resembles the effect of inactivating PAX3-FOXO1. While the transcriptomes of NF-Y- and PAX3-FOXO1-deficient RMS cells bear remarkable similarity to one another, we found that these two transcription factors occupy nonoverlapping sites along the genome: NF-Y preferentially occupies promoters, whereas PAX3-FOXO1 primarily binds to distal enhancers. By integrating multiple functional approaches, we map the PAX3 promoter as the point of intersection between these two regulators. We show that NF-Y occupies CCAAT motifs present upstream of PAX3 to function as a transcriptional activator of PAX3-FOXO1 expression in RMS. These findings reveal a critical upstream role of NF-Y in the oncogenic PAX3-FOXO1 pathway, highlighting how a broadly essential transcription factor can perform tumor-specific roles in governing cellular state.
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Affiliation(s)
| | | | - Marit W. Vermunt
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | | | | | | | - Kenneth Chang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
| | - Raditya Utama
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
| | - Berkley Gryder
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH44106
| | | | - Diqiu Ren
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Benan Nalbant
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724
| | | | | | | | - Scott W. Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37232
| | - Kristy R. Stengel
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY10461
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133Milano, Italy
| | - Javed Khan
- Genetics Branch, National Cancer Institute, NIH, Bethesda, MD20892
| | - Rahul M. Kohli
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA19104
| | - Junwei Shi
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Gerd A. Blobel
- Division of Hematology, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
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Mahajan M, Sarkar A, Mondal S. Cell cycle protein BORA is associated with colorectal cancer progression by AURORA-PLK1 cascades: a bioinformatics analysis. J Cell Commun Signal 2023; 17:773-791. [PMID: 36538275 PMCID: PMC10409947 DOI: 10.1007/s12079-022-00719-6] [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: 07/25/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is the third most diagnosed cancer in the world. A better understanding of the molecular mechanism of CRC is essential for making novel strategies for the CRC management and its prevention. The present study aims to explore the molecular mechanism through integrated bioinformatics analysis by analyzing genes and their co-expression pattern in normal and CRC states. GSE110223, GSE110224 and GSE113513 gene expression profiles were analyzed in this study. The co-expression networks for normal and tumor samples were constructed separately and analyzed to identify the modules, sub-networks and key genes. Gene regulatory network analysis was done to understand the regulatory mechanism of selected genes. Survival analysis was performed for the identified sub-networks and key genes to understand their role in CRC progression. A total of seven modules were detected and the KEGG pathway analysis revealed these modules were mainly enriched with cell cycle, metabolism and signaling-related pathways. E2F6 and ETV4 transcription factors regulating the activity of multiple genes of identified modules were found to be up-regulated in CRC. Six Sub-networks and seven key genes, BORA, CCT7, DTL, RUVBL1, RUVBL2, THEM6 and TMEM97 associated with the CRC progression were identified. Disease-gene association analysis identified a novel association of the BORA gene with CRC that activates and regulates the AURORA-PLK1 cascades in the cell cycle. Survival analysis indicates that the overexpressed BORA is associated with unfavourable overall survival in CRC. The mechanistic role of BORA in the regulation of cell cycle progression suggests that BORA might act as a potential therapeutic target for CRC.
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Affiliation(s)
- Mohita Mahajan
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, K.K. Birla Goa Campus, Zuarinagar, Goa 403726 India
| | - Angshuman Sarkar
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, K.K. Birla Goa Campus, Zuarinagar, Goa 403726 India
| | - Sukanta Mondal
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, K.K. Birla Goa Campus, Zuarinagar, Goa 403726 India
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8
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Rani V, Joshi DC, Joshi P, Singh R, Yadav D. "Millet Models" for harnessing nuclear factor-Y transcription factors to engineer stress tolerance in plants: current knowledge and emerging paradigms. PLANTA 2023; 258:29. [PMID: 37358736 DOI: 10.1007/s00425-023-04186-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/17/2023] [Indexed: 06/27/2023]
Abstract
MAIN CONCLUSION The main purpose of this review is to shed light on the role of millet models in imparting climate resilience and nutritional security and to give a concrete perspective on how NF-Y transcription factors can be harnessed for making cereals more stress tolerant. Agriculture faces significant challenges from climate change, bargaining, population, elevated food prices, and compromises with nutritional value. These factors have globally compelled scientists, breeders, and nutritionists to think of some options that can combat the food security crisis and malnutrition. To address these challenges, mainstreaming the climate-resilient and nutritionally unparalleled alternative crops like millet is a key strategy. The C4 photosynthetic pathway and adaptation to low-input marginal agricultural systems make millets a powerhouse of important gene and transcription factor families imparting tolerance to various kinds of biotic and abiotic stresses. Among these, the nuclear factor-Y (NF-Y) is one of the prominent transcription factor families that regulate diverse genes imparting stress tolerance. The primary purpose of this article is to shed light on the role of millet models in imparting climate resilience and nutritional security and to give a concrete perspective on how NF-Y transcription factors can be harnessed for making cereals more stress tolerant. Future cropping systems could be more resilient to climate change and nutritional quality if these practices were implemented.
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Affiliation(s)
- Varsha Rani
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh, 273009, India
| | - D C Joshi
- ICAR-Vivekananda Institute of Hill Agriculture, Almora, Uttarakhand, 263601, India
| | - Priyanka Joshi
- Plant and Environmental Sciences, 113 Biosystems Research Complex, Clemson University, Clemson, South Carolina, 29634, USA
| | - Rajesh Singh
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Dinesh Yadav
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh, 273009, India.
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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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10
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Okada N, Ueki C, Shimazaki M, Tsujimoto G, Kohno S, Muranaka H, Yoshikawa K, Takahashi C. NFYA promotes malignant behavior of triple-negative breast cancer in mice through the regulation of lipid metabolism. Commun Biol 2023; 6:596. [PMID: 37268670 DOI: 10.1038/s42003-023-04987-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 05/26/2023] [Indexed: 06/04/2023] Open
Abstract
Two splicing variants exist in NFYA that exhibit high expression in many human tumour types. The balance in their expression correlates with prognosis in breast cancer, but functional differences remain unclear. Here, we demonstrate that NFYAv1, a long-form variant, upregulates the transcription of essential lipogenic enzymes ACACA and FASN to enhance the malignant behavior of triple-negative breast cancer (TNBC). Loss of the NFYAv1-lipogenesis axis strongly suppresses malignant behavior in vitro and in vivo, indicating that the NFYAv1-lipogenesis axis is essential for TNBC malignant behavior and that the axis might be a potential therapeutic target for TNBC. Furthermore, mice deficient in lipogenic enzymes, such as Acly, Acaca, and Fasn, exhibit embryonic lethality; however, Nfyav1-deficient mice exhibited no apparent developmental abnormalities. Our results indicate that the NFYAv1-lipogenesis axis has tumour-promoting effects and that NFYAv1 may be a safe therapeutic target for TNBC.
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Affiliation(s)
- Nobuhiro Okada
- Graduate School of Interdisciplinary Science & Engineering in Health Systems, Okayama University, Okayama, 700-8530, Japan.
- Department of Pharmacology, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan.
| | - Chihiro Ueki
- Graduate School of Interdisciplinary Science & Engineering in Health Systems, Okayama University, Okayama, 700-8530, Japan
| | - Masahiro Shimazaki
- Laboratory for Malignancy Control Research, Medical Innovation Center, Kyoto University, Kyoto, 606-8501, Japan
| | - Goki Tsujimoto
- Graduate School of Interdisciplinary Science & Engineering in Health Systems, Okayama University, Okayama, 700-8530, Japan
| | - Susumu Kohno
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, 920-1192, Japan
| | - Hayato Muranaka
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, 920-1192, Japan
- Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Kiyotsugu Yoshikawa
- Faculty of Pharmaceutical Sciences, Doshisha Women's College of Liberal Arts, Kyoto, 610-0395, Japan
| | - Chiaki Takahashi
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, 920-1192, Japan
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Peng J, Chan C, Zhang S, Sklavounos AA, Olson ME, Scott EY, Hu Y, Rajesh V, Li BB, Chamberlain MD, Zhang S, Peng H, Wheeler AR. All-in-One digital microfluidics pipeline for proteomic sample preparation and analysis. Chem Sci 2023; 14:2887-2900. [PMID: 36937585 PMCID: PMC10016607 DOI: 10.1039/d3sc00560g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 02/24/2023] Open
Abstract
Highly sensitive and reproducible analysis of samples containing low amounts of protein is restricted by sample loss and the introduction of contaminants during processing. Here, we report an All-in-One digital microfluidic (DMF) pipeline for proteomic sample reduction, alkylation, digestion, isotopic labeling and analysis. The system features end-to-end automation, with integrated thermal control for digestion, optimized droplet additives for sample manipulation and analysis, and an automated interface to liquid chromatography with tandem mass spectrometry (HPLC-MS/MS). Dimethyl labeling was integrated into the pipeline to allow for relative quantification of the trace samples at the nanogram level, and the new pipeline was applied to evaluating cancer cell lines and cancer tissue samples. Several known proteins (including HSP90AB1, HSPB1, LDHA, ENO1, PGK1, KRT18, and AKR1C2) and pathways were observed between model breast cancer cell lines related to hormone response, cell metabolism, and cell morphology. Furthermore, differentially quantified proteins (such as PGS2, UGDH, ASPN, LUM, COEA1, and PRELP) were found in comparisons of healthy and cancer breast tissues, suggesting potential utility of the All-in-One pipeline for the emerging application of proteomic cancer sub-typing. In sum, the All-in-One pipeline represents a powerful new tool for automated proteome processing and analysis, with the potential to be useful for evaluating mass-limited samples for a wide range of applications.
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Affiliation(s)
- Jiaxi Peng
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto 160 College Street Toronto ON M5S 3E1 Canada
- Institute of Biomedical Engineering, University of Toronto 164 College Street Toronto ON M5S 3G9 Canada
| | - Calvin Chan
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
| | - Shuailong Zhang
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
- School of Mechatronical Engineering, Beijing Institute of Technology Beijing 100081 China
- Beijing Advanced Innovation Center for Intelligent Robots and Systems, Beijing Institute of Technology Beijing 100081 China
| | - Alexandros A Sklavounos
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto 160 College Street Toronto ON M5S 3E1 Canada
| | - Maxwell E Olson
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
| | - Erica Y Scott
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto 160 College Street Toronto ON M5S 3E1 Canada
- Institute of Biomedical Engineering, University of Toronto 164 College Street Toronto ON M5S 3G9 Canada
| | - Yechen Hu
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto 160 College Street Toronto ON M5S 3E1 Canada
- Institute of Biomedical Engineering, University of Toronto 164 College Street Toronto ON M5S 3G9 Canada
| | - Vigneshwar Rajesh
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
| | - Bingyu B Li
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto 160 College Street Toronto ON M5S 3E1 Canada
- Institute of Biomedical Engineering, University of Toronto 164 College Street Toronto ON M5S 3G9 Canada
| | - M Dean Chamberlain
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto 160 College Street Toronto ON M5S 3E1 Canada
- Institute of Biomedical Engineering, University of Toronto 164 College Street Toronto ON M5S 3G9 Canada
- Saskatchewan Cancer Agency, University of Saskatchewan 107 Wiggins Road Saskatoon SK S7N 5E5 Canada
| | - Shen Zhang
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital 600 University Avenue Toronto ON M5G 1X5 Canada
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA Changsha Hunan 410000 China
| | - Hui Peng
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
- School of Environment, University of Toronto 33 Willcocks Street Toronto ON M5S 3E8 Canada
| | - Aaron R Wheeler
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto 160 College Street Toronto ON M5S 3E1 Canada
- Institute of Biomedical Engineering, University of Toronto 164 College Street Toronto ON M5S 3G9 Canada
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12
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Heo W, Hwang H, Kim J, Oh SH, Yu Y, Lee JH, Kim K. The CCAAT-box transcription factor, NF-Y complex, mediates the specification of the IL1 neurons in C. elegans. BMB Rep 2023; 56:153-159. [PMID: 36330709 PMCID: PMC10068339 DOI: 10.5483/bmbrep.2022-0146] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/07/2022] [Accepted: 10/27/2022] [Indexed: 09/16/2023] Open
Abstract
Neuronal differentiation is highly coordinated through a cascade of gene expression, mediated via interactions between transacting transcription factors and cis-regulatory elements of their target genes. However, the mechanisms of transcriptional regulation that determine neuronal cell-fate are not fully understood. Here, we show that the nuclear transcription factor Y (NF-Y) subunit, NFYA-1, is necessary and sufficient to express the flp-3 neuropeptide gene in the IL1 neurons of C. elegans. flp-3 expression is decreased in dorsal and lateral, but not ventral IL1s of nfya-1 mutants. The expression of another terminally differentiated gene, eat-4 vesicular glutamate transporter, is abolished, whereas the unc-8 DEG/ENaC gene and pan-neuronal genes are expressed normally in IL1s of nfya-1 mutants. nfya-1 is expressed in and acts in IL1s to regulate flp-3 and eat-4 expression. Ectopic expression of NFYA-1 drives the expression of flp-3 gene in other cell-types. Promoter analysis of IL1-expressed genes results in the identification of several cisregulatory motifs which are necessary for IL1 expression, including a putative CCAAT-box located in the flp-3 promoter that NFYA-1 directly interacts with. NFYA-1 and NFYA-2, together with NFYB-1 and NFYC-1, exhibit partly or fully redundant roles in the regulation of flp-3 or unc-8 expression, respectively. Taken together, our data indicate that the NF-Y complex regulates neuronal subtype-specification via regulating a set of terminal-differentiation genes. [BMB Reports 2023; 56(3): 153-159].
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Affiliation(s)
- Woojung Heo
- Department of Brain Sciences, DGIST, Daegu 42988, Korea
| | | | - Jimin Kim
- Department of Brain Sciences, DGIST, Daegu 42988, Korea
| | - Seung Hee Oh
- Department of Brain Sciences, DGIST, Daegu 42988, Korea
| | - Youngseok Yu
- Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Korea
| | - Jae-Hyung Lee
- Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Korea
- Department of Oral Microbiology, College of Dentistry, Kyung Hee University, Seoul 02447, Korea
| | - Kyuhyung Kim
- Department of Brain Sciences, DGIST, Daegu 42988, Korea
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Heo W, Hwang H, Kim J, Oh SH, Yu Y, Lee JH, Kim K. The CCAAT-box transcription factor, NF-Y complex, mediates the specification of the IL1 neurons in C. elegans. BMB Rep 2023; 56:153-159. [PMID: 36330709 PMCID: PMC10068339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/07/2022] [Accepted: 10/27/2022] [Indexed: 03/29/2023] Open
Abstract
Neuronal differentiation is highly coordinated through a cascade of gene expression, mediated via interactions between transacting transcription factors and cis-regulatory elements of their target genes. However, the mechanisms of transcriptional regulation that determine neuronal cell-fate are not fully understood. Here, we show that the nuclear transcription factor Y (NF-Y) subunit, NFYA-1, is necessary and sufficient to express the flp-3 neuropeptide gene in the IL1 neurons of C. elegans. flp-3 expression is decreased in dorsal and lateral, but not ventral IL1s of nfya-1 mutants. The expression of another terminally differentiated gene, eat-4 vesicular glutamate transporter, is abolished, whereas the unc-8 DEG/ENaC gene and pan-neuronal genes are expressed normally in IL1s of nfya-1 mutants. nfya-1 is expressed in and acts in IL1s to regulate flp-3 and eat-4 expression. Ectopic expression of NFYA-1 drives the expression of flp-3 gene in other cell-types. Promoter analysis of IL1-expressed genes results in the identification of several cisregulatory motifs which are necessary for IL1 expression, including a putative CCAAT-box located in the flp-3 promoter that NFYA-1 directly interacts with. NFYA-1 and NFYA-2, together with NFYB-1 and NFYC-1, exhibit partly or fully redundant roles in the regulation of flp-3 or unc-8 expression, respectively. Taken together, our data indicate that the NF-Y complex regulates neuronal subtype-specification via regulating a set of terminal-differentiation genes. [BMB Reports 2023; 56(3): 153-159].
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Affiliation(s)
- Woojung Heo
- Department of Brain Sciences, DGIST, Daegu 42988, Korea
| | | | - Jimin Kim
- Department of Brain Sciences, DGIST, Daegu 42988, Korea
| | - Seung Hee Oh
- Department of Brain Sciences, DGIST, Daegu 42988, Korea
| | - Youngseok Yu
- Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Korea
| | - Jae-Hyung Lee
- Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul 02447, Korea
- Department of Oral Microbiology, College of Dentistry, Kyung Hee University, Seoul 02447, Korea
| | - Kyuhyung Kim
- Department of Brain Sciences, DGIST, Daegu 42988, Korea
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14
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Alwadi D, Felty Q, Yoo C, Roy D, Deoraj A. Endocrine Disrupting Chemicals Influence Hub Genes Associated with Aggressive Prostate Cancer. Int J Mol Sci 2023; 24:ijms24043191. [PMID: 36834602 PMCID: PMC9959535 DOI: 10.3390/ijms24043191] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/25/2023] [Accepted: 01/30/2023] [Indexed: 02/08/2023] Open
Abstract
Prostate cancer (PCa) is one of the most frequently diagnosed cancers among men in the world. Its prevention has been limited because of an incomplete understanding of how environmental exposures to chemicals contribute to the molecular pathogenesis of aggressive PCa. Environmental exposures to endocrine-disrupting chemicals (EDCs) may mimic hormones involved in PCa development. This research aims to identify EDCs associated with PCa hub genes and/or transcription factors (TF) of these hub genes in addition to their protein-protein interaction (PPI) network. We are expanding upon the scope of our previous work, using six PCa microarray datasets, namely, GSE46602, GSE38241, GSE69223, GSE32571, GSE55945, and GSE26126, from the NCBI/GEO, to select differentially expressed genes based on |log2FC| (fold change) ≥ 1 and an adjusted p-value < 0.05. An integrated bioinformatics analysis was used for enrichment analysis (using DAVID.6.8, GO, KEGG, STRING, MCODE, CytoHubba, and GeneMANIA). Next, we validated the association of these PCa hub genes in RNA-seq PCa cases and controls from TCGA. The influence of environmental chemical exposures, including EDCs, was extrapolated using the chemical toxicogenomic database (CTD). A total of 369 overlapping DEGs were identified associated with biological processes, such as cancer pathways, cell division, response to estradiol, peptide hormone processing, and the p53 signaling pathway. Enrichment analysis revealed five up-regulated (NCAPG, MKI67, TPX2, CCNA2, CCNB1) and seven down-regulated (CDK1, CCNB2, AURKA, UBE2C, BUB1B, CENPF, RRM2) hub gene expressions. Expression levels of these hub genes were significant in PCa tissues with high Gleason scores ≥ 7. These identified hub genes influenced disease-free survival and overall survival of patients 60-80 years of age. The CTD studies showed 17 recognized EDCs that affect TFs (NFY, CETS1P54, OLF1, SRF, COMP1) that are known to bind to our PCa hub genes, namely, NCAPG, MKI67, CCNA2, CDK1, UBE2C, and CENPF. These validated differentially expressed hub genes can be potentially developed as molecular biomarkers with a systems perspective for risk assessment of a wide-ranging list of EDCs that may play overlapping and important role(s) in the prognosis of aggressive PCa.
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Affiliation(s)
- Diaaidden Alwadi
- Department of Environmental Health Sciences, Florida International University, Miami, FL 33199, USA
| | - Quentin Felty
- Department of Environmental Health Sciences, Florida International University, Miami, FL 33199, USA
| | - Changwon Yoo
- Department of Biostatistics, Florida International University, Miami, FL 33199, USA
| | - Deodutta Roy
- Department of Environmental Health Sciences, Florida International University, Miami, FL 33199, USA
| | - Alok Deoraj
- Department of Environmental Health Sciences, Florida International University, Miami, FL 33199, USA
- Correspondence:
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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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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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [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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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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Drosophila transcription factor NF-Y suppresses transcription of the lipase 4 gene, a key gene for lipid storage. Exp Cell Res 2022; 420:113307. [PMID: 36028059 DOI: 10.1016/j.yexcr.2022.113307] [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: 03/01/2022] [Revised: 07/31/2022] [Accepted: 08/04/2022] [Indexed: 11/23/2022]
Abstract
The CCAAT motif-binding factor NF-Y consists of three different subunits, NF-YA, NF-YB, and NF-YC. Although it is suggested that NF-Y activity is essential for normal tissue homeostasis, survival, and metabolic function, its precise role in lipid metabolism is not clarified yet. In Drosophila, eye disc specific knockdown of Drosophila NF-YA (dNF-YA) induced aberrant morphology of the compound eye, the rough eye phenotype in adults and mutation of the lipase 4 (lip4) gene suppressed the rough eye phenotype. RNA-seq analyses with dNF-YA knockdown third instar larvae identified the lip4 gene as one of the genes that are up-regulated by the dNF-YA knockdown. We identified three dNF-Y-binding consensuses in the 5'flanking region of the lip4 gene, and a chromatin immunoprecipitation assay with the specific anti-dNF-YA IgG demonstrated dNF-Y binding to this genomic region. The luciferase transient expression assay with cultured Drosophila S2 cells and the lip4 promoter-luciferase fusion genes with and without mutations in the dNF-Y-binding consensuses showed that each of the three dNF-Y consensus sequences negatively regulated lip4 gene promoter activity. Consistent with these results, qRT-PCR analysis with the dNF-YA knockdown third instar larvae revealed that endogenous lip4 mRNA levels were increased by the knockdown of dNF-YA in vivo. The specific knockdown of dNF-YA in the fat body with the collagen-GAL4 driver resulted in smaller oil droplets in the fat body cells. Collectively, these results suggest that dNF-Y is involved in lipid storage through its negative regulation of lip4 gene transcription.
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de Toledo VHC, Feltrin AS, Barbosa AR, Tahira AC, Brentani H. Sex differences in gene regulatory networks during mid-gestational brain development. Front Hum Neurosci 2022; 16:955607. [PMID: 36061507 PMCID: PMC9428411 DOI: 10.3389/fnhum.2022.955607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Neurodevelopmental disorders differ considerably between males and females, and fetal brain development is one of the most critical periods to determine risk for these disorders. Transcriptomic studies comparing male and female fetal brain have demonstrated that the highest difference in gene expression occurs in sex chromosomes, but several autossomal genes also demonstrate a slight difference that has not been yet explored. In order to investigate biological pathways underlying fetal brain sex differences, we applied medicine network principles using integrative methods such as co-expression networks (CEMiTool) and regulatory networks (netZoo). The pattern of gene expression from genes in the same pathway tend to reflect biologically relevant phenomena. In this study, network analysis of fetal brain expression reveals regulatory differences between males and females. Integrating two different bioinformatics tools, our results suggest that biological processes such as cell cycle, cell differentiation, energy metabolism and extracellular matrix organization are consistently sex-biased. MSET analysis demonstrates that these differences are relevant to neurodevelopmental disorders, including autism.
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Affiliation(s)
- Victor Hugo Calegari de Toledo
- Departamento e Instituto de Psiquiatria, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Psicopatologia e Terapêutica Psiquiátrica (LIM23), Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, Brazil
| | | | | | - Ana Carolina Tahira
- Laboratório de Expressão Gênica, Departamento de Parasitologia, Instituto Butantan, São Paulo, Brazil
| | - Helena Brentani
- Departamento e Instituto de Psiquiatria, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Psicopatologia e Terapêutica Psiquiátrica (LIM23), Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, Brazil
- *Correspondence: Helena Brentani
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Murugan NJ, Voutsadakis IA. Proteasome regulators in pancreatic cancer. World J Gastrointest Oncol 2022; 14:38-54. [PMID: 35116102 PMCID: PMC8790418 DOI: 10.4251/wjgo.v14.i1.38] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/14/2021] [Accepted: 12/02/2021] [Indexed: 02/06/2023] Open
Abstract
Pancreatic adenocarcinoma is one of the most lethal cancers with rising incidence. Despite progress in its treatment, with the introduction of more effective chemotherapy regimens in the last decade, prognosis of metastatic disease remains inferior to other cancers with long term survival being the exception. Molecular characterization of pancreatic cancer has elucidated the landscape of the disease and has revealed common lesions that contribute to pancreatic carcinogenesis. Regulation of proteostasis is critical in cancers due to increased protein turnover required to support the intense metabolism of cancer cells. The proteasome is an integral part of this regulation and is regulated, in its turn, by key transcription factors, which induce transcription of proteasome structural units. These include FOXO family transcription factors, NFE2L2, hHSF1 and hHSF2, and NF-Y. Networks that encompass proteasome regulators and transduction pathways dysregulated in pancreatic cancer such as the KRAS/ BRAF/MAPK and the Transforming growth factor beta/SMAD pathway contribute to pancreatic cancer progression. This review discusses the proteasome and its transcription factors within the pancreatic cancer cellular micro-environment. We also consider the role of stemness in carcinogenesis and the use of proteasome inhibitors as therapeutic agents.
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Affiliation(s)
- Nirosha J Murugan
- Department of Biology, Algoma University, Sault Sainte Marie P6A3T6, ON, Canada
| | - Ioannis A Voutsadakis
- Department of Medical Oncology, Sault Area Hospital, Sault Sainte Marie P6A3T6, ON, Canada
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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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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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Xu X, Xu J, Yuan C, Hu Y, Liu Q, Chen Q, Zhang P, Shi N, Qin C. Characterization of genes associated with TGA7 during the floral transition. BMC PLANT BIOLOGY 2021; 21:367. [PMID: 34380420 PMCID: PMC8359562 DOI: 10.1186/s12870-021-03144-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 07/14/2021] [Indexed: 05/30/2023]
Abstract
BACKGROUND The TGACG-binding (TGA) family has 10 members that play vital roles in Arabidopsis thaliana defense responses and development. However, their involvement in controlling flowering time remains largely unknown and requires further investigation. RESULTS To study the role of TGA7 during floral transition, we first investigated the tga7 mutant, which displayed a delayed-flowering phenotype under both long-day and short-day conditions. We then performed a flowering genetic pathway analysis and found that both autonomous and thermosensory pathways may affect TGA7 expression. Furthermore, to reveal the differential gene expression profiles between wild-type (WT) and tga7, cDNA libraries were generated for WT and tga7 mutant seedlings at 9 days after germination. For each library, deep-sequencing produced approximately 6.67 Gb of high-quality sequences, with the majority (84.55 %) of mRNAs being between 500 and 3,000 nt. In total, 325 differentially expressed genes were identified between WT and tga7 mutant seedlings. Among them, four genes were associated with flowering time control. The differential expression of these four flowering-related genes was further validated by qRT-PCR. CONCLUSIONS Among these four differentially expressed genes associated with flowering time control, FLC and MAF5 may be mainly responsible for the delayed-flowering phenotype in tga7, as TGA7 expression was regulated by autonomous pathway genes. These results provide a framework for further studying the role of TGA7 in promoting flowering.
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Affiliation(s)
- Xiaorui Xu
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, 311121, Hangzhou, China
| | - Jingya Xu
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, 311121, Hangzhou, China
| | - Chen Yuan
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, 311121, Hangzhou, China
| | - Yikai Hu
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, 311121, Hangzhou, China
| | - Qinggang Liu
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, 311121, Hangzhou, China
| | - Qianqian Chen
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, 311121, Hangzhou, China
| | - Pengcheng Zhang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, 311121, Hangzhou, China
| | - Nongnong Shi
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, 311121, Hangzhou, China.
| | - Cheng Qin
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, 311121, Hangzhou, China.
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Ershov P, Kaluzhskiy L, Mezentsev Y, Yablokov E, Gnedenko O, Ivanov A. Enzymes in the Cholesterol Synthesis Pathway: Interactomics in the Cancer Context. Biomedicines 2021; 9:biomedicines9080895. [PMID: 34440098 PMCID: PMC8389681 DOI: 10.3390/biomedicines9080895] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 02/06/2023] Open
Abstract
A global protein interactome ensures the maintenance of regulatory, signaling and structural processes in cells, but at the same time, aberrations in the repertoire of protein-protein interactions usually cause a disease onset. Many metabolic enzymes catalyze multistage transformation of cholesterol precursors in the cholesterol biosynthesis pathway. Cancer-associated deregulation of these enzymes through various molecular mechanisms results in pathological cholesterol accumulation (its precursors) which can be disease risk factors. This work is aimed at systematization and bioinformatic analysis of the available interactomics data on seventeen enzymes in the cholesterol pathway, encoded by HMGCR, MVK, PMVK, MVD, FDPS, FDFT1, SQLE, LSS, DHCR24, CYP51A1, TM7SF2, MSMO1, NSDHL, HSD17B7, EBP, SC5D, DHCR7 genes. The spectrum of 165 unique and 21 common protein partners that physically interact with target enzymes was selected from several interatomic resources. Among them there were 47 modifying proteins from different protein kinases/phosphatases and ubiquitin-protein ligases/deubiquitinases families. A literature search, enrichment and gene co-expression analysis showed that about a quarter of the identified protein partners was associated with cancer hallmarks and over-represented in cancer pathways. Our results allow to update the current fundamental view on protein-protein interactions and regulatory aspects of the cholesterol synthesis enzymes and annotate of their sub-interactomes in term of possible involvement in cancers that will contribute to prioritization of protein targets for future drug development.
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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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mTOR Driven Gene Transcription Is Required for Cholesterol Production in Neurons of the Developing Cerebral Cortex. Int J Mol Sci 2021; 22:ijms22116034. [PMID: 34204880 PMCID: PMC8199781 DOI: 10.3390/ijms22116034] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/15/2021] [Accepted: 05/28/2021] [Indexed: 12/13/2022] Open
Abstract
Dysregulated mammalian target of rapamycin (mTOR) activity is associated with various neurodevelopmental disorders ranging from idiopathic autism spectrum disorders (ASD) to syndromes caused by single gene defects. This suggests that maintaining mTOR activity levels in a physiological range is essential for brain development and functioning. Upon activation, mTOR regulates a variety of cellular processes such as cell growth, autophagy, and metabolism. On a molecular level, however, the consequences of mTOR activation in the brain are not well understood. Low levels of cholesterol are associated with a wide variety of neurodevelopmental disorders. We here describe numerous genes of the sterol/cholesterol biosynthesis pathway to be transcriptionally regulated by mTOR complex 1 (mTORC1) signaling in vitro in primary neurons and in vivo in the developing cerebral cortex of the mouse. We find that these genes are shared targets of the transcription factors SREBP, SP1, and NF-Y. Prenatal as well as postnatal mTORC1 inhibition downregulated expression of these genes which directly translated into reduced cholesterol levels, pointing towards a substantial metabolic function of the mTORC1 signaling cascade. Altogether, our results indicate that mTORC1 is an essential transcriptional regulator of the expression of sterol/cholesterol biosynthesis genes in the developing brain. Altered expression of these genes may be an important factor contributing to the pathogenesis of neurodevelopmental disorders associated with dysregulated mTOR signaling.
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Ronzio M, Bernardini A, Pavesi G, Mantovani R, Dolfini D. On the NF-Y regulome as in ENCODE (2019). PLoS Comput Biol 2020; 16:e1008488. [PMID: 33370256 PMCID: PMC7793273 DOI: 10.1371/journal.pcbi.1008488] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 01/08/2021] [Accepted: 11/04/2020] [Indexed: 11/19/2022] Open
Abstract
NF-Y is a trimeric Transcription Factor -TF- which binds with high selectivity to the conserved CCAAT element. Individual ChIP-seq analysis as well as ENCODE have progressively identified locations shared by other TFs. Here, we have analyzed data introduced by ENCODE over the last five years in K562, HeLa-S3 and GM12878, including several chromatin features, as well RNA-seq profiling of HeLa cells after NF-Y inactivation. We double the number of sequence-specific TFs and co-factors reported. We catalogue them in 4 classes based on co-association criteria, infer target genes categorizations, identify positional bias of binding sites and gene expression changes. Larger and novel co-associations emerge, specifically concerning subunits of repressive complexes as well as RNA-binding proteins. On the one hand, these data better define NF-Y association with single members of major classes of TFs, on the other, they suggest that it might have a wider role in the control of mRNA production. The ongoing ENCODE consortium represents a useful compendium of locations of TFs, chromatin marks, gene expression data. In previous reports, we identified modules of CCAAT-binding NF-Y with individual TFs. Here, we analyzed all 363 factors currently present: 68 with enrichment of CCAAT in their locations, 38 with overlap of peaks. New sequence-specific TFs, co-activators and co-repressors are reported. Co-association patterns correspond to specific targeted genes categorizations and gene expression changes, as assessed by RNA-seq after NF-Y inactivation. These data widen and better define a coherent model of synergy of NF-Y with selected groups of TFs and co-factors.
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Affiliation(s)
- Mirko Ronzio
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Andrea Bernardini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Giulio Pavesi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Diletta Dolfini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
- * E-mail:
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Bezzecchi E, Ronzio M, Mantovani R, Dolfini D. NF-Y Overexpression in Liver Hepatocellular Carcinoma (HCC). Int J Mol Sci 2020; 21:E9157. [PMID: 33271832 PMCID: PMC7731131 DOI: 10.3390/ijms21239157] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 11/24/2020] [Accepted: 11/24/2020] [Indexed: 12/24/2022] Open
Abstract
NF-Y is a pioneer trimeric transcription factor formed by the Histone Fold Domain (HFD) NF-YB/NF-YC subunits and NF-YA. Three subunits are required for DNA binding. CCAAT-specificity resides in NF-YA and transactivation resides in Q-rich domains of NF-YA and NF-YC. They are involved in alternative splicing (AS). We recently showed that NF-YA is overexpressed in breast and lung carcinomas. We report here on the overexpression of all subunits in the liver hepatocellular carcinoma (HCC) TCGA database, specifically the short NF-YAs and NF-YC2 (37 kDa) isoforms. This is observed at all tumor stages, in viral-infected samples and independently from the inflammatory status. Up-regulation of NF-YAs and NF-YC, but not NF-YB, is associated to tumors with mutant p53. We used a deep-learning-based method (DeepCC) to extend the partitioning of the three molecular clusters to all HCC TCGA tumors. In iCluster3, CCAAT is a primary matrix found in promoters of up-regulated genes, and cell-cycle pathways are enriched. Finally, clinical data indicate that, globally, only NF-YAs, but not HFD subunits, correlate with the worst prognosis; in iCluster1 patients, however, all subunits correlate. The data show a difference with other epithelial cancers, in that global overexpression of the three subunits is reported and clinically relevant in a subset of patients; yet, they further reinstate the regulatory role of the sequence-specific subunit.
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Affiliation(s)
| | | | | | - Diletta Dolfini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy; (E.B.); (M.R.); (R.M.)
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Nardone V, Chaves-Sanjuan A, Lapi M, Airoldi C, Saponaro A, Pasqualato S, Dolfini D, Camilloni C, Bernardini A, Gnesutta N, Mantovani R, Nardini M. Structural Basis of Inhibition of the Pioneer Transcription Factor NF-Y by Suramin. Cells 2020; 9:E2370. [PMID: 33138093 PMCID: PMC7692634 DOI: 10.3390/cells9112370] [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: 09/28/2020] [Revised: 10/25/2020] [Accepted: 10/26/2020] [Indexed: 12/27/2022] Open
Abstract
NF-Y is a transcription factor (TF) comprising three subunits (NF-YA, NF-YB, NF-YC) that binds with high specificity to the CCAAT sequence, a widespread regulatory element in gene promoters of prosurvival, cell-cycle-promoting, and metabolic genes. Tumor cells undergo "metabolic rewiring" through overexpression of genes involved in such pathways, many of which are under NF-Y control. In addition, NF-YA appears to be overexpressed in many tumor types. Thus, limiting NF-Y activity may represent a desirable anti-cancer strategy, which is an ongoing field of research. With virtual-screening docking simulations on a library of pharmacologically active compounds, we identified suramin as a potential NF-Y inhibitor. We focused on suramin given its high water-solubility that is an important factor for in vitro testing, since NF-Y is sensitive to DMSO. By electrophoretic mobility shift assays (EMSA), isothermal titration calorimetry (ITC), STD NMR, X-ray crystallography, and molecular dynamics (MD) simulations, we showed that suramin binds to the histone fold domains (HFDs) of NF-Y, preventing DNA-binding. Our analyses, provide atomic-level detail on the interaction between suramin and NF-Y and reveal a region of the protein, nearby the suramin-binding site and poorly conserved in other HFD-containing TFs, that may represent a promising starting point for rational design of more specific and potent inhibitors with potential therapeutic applications.
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Affiliation(s)
- Valentina Nardone
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy; (V.N.); (A.C.-S.); (M.L.); (A.S.); (D.D.); (C.C.); (A.B.); (N.G.); (R.M.)
| | - Antonio Chaves-Sanjuan
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy; (V.N.); (A.C.-S.); (M.L.); (A.S.); (D.D.); (C.C.); (A.B.); (N.G.); (R.M.)
| | - Michela Lapi
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy; (V.N.); (A.C.-S.); (M.L.); (A.S.); (D.D.); (C.C.); (A.B.); (N.G.); (R.M.)
| | - Cristina Airoldi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy;
| | - Andrea Saponaro
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy; (V.N.); (A.C.-S.); (M.L.); (A.S.); (D.D.); (C.C.); (A.B.); (N.G.); (R.M.)
| | - Sebastiano Pasqualato
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy;
| | - Diletta Dolfini
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy; (V.N.); (A.C.-S.); (M.L.); (A.S.); (D.D.); (C.C.); (A.B.); (N.G.); (R.M.)
| | - Carlo Camilloni
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy; (V.N.); (A.C.-S.); (M.L.); (A.S.); (D.D.); (C.C.); (A.B.); (N.G.); (R.M.)
| | - Andrea Bernardini
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy; (V.N.); (A.C.-S.); (M.L.); (A.S.); (D.D.); (C.C.); (A.B.); (N.G.); (R.M.)
| | - Nerina Gnesutta
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy; (V.N.); (A.C.-S.); (M.L.); (A.S.); (D.D.); (C.C.); (A.B.); (N.G.); (R.M.)
| | - Roberto Mantovani
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy; (V.N.); (A.C.-S.); (M.L.); (A.S.); (D.D.); (C.C.); (A.B.); (N.G.); (R.M.)
| | - Marco Nardini
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy; (V.N.); (A.C.-S.); (M.L.); (A.S.); (D.D.); (C.C.); (A.B.); (N.G.); (R.M.)
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Tian R, Zhou P, Li M, Tan J, Cui Z, Xu W, Wei J, Zhu J, Jin Z, Cao C, Fan W, Xie W, Huang Z, Xie H, You Z, Niu G, Wu C, Guo X, Weng X, Tian X, Yu F, Yu Z, Liang J, Hu Z. DeepHPV: a deep learning model to predict human papillomavirus integration sites. Brief Bioinform 2020; 22:5924410. [PMID: 33059369 DOI: 10.1093/bib/bbaa242] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/26/2020] [Accepted: 08/28/2020] [Indexed: 01/09/2023] Open
Abstract
Human papillomavirus (HPV) integrating into human genome is the main cause of cervical carcinogenesis. HPV integration selection preference shows strong dependence on local genomic environment. Due to this theory, it is possible to predict HPV integration sites. However, a published bioinformatic tool is not available to date. Thus, we developed an attention-based deep learning model DeepHPV to predict HPV integration sites by learning environment features automatically. In total, 3608 known HPV integration sites were applied to train the model, and 584 reviewed HPV integration sites were used as the testing dataset. DeepHPV showed an area under the receiver-operating characteristic (AUROC) of 0.6336 and an area under the precision recall (AUPR) of 0.5670. Adding RepeatMasker and TCGA Pan Cancer peaks improved the model performance to 0.8464 and 0.8501 in AUROC and 0.7985 and 0.8106 in AUPR, respectively. Next, we tested these trained models on independent database VISDB and found the model adding TCGA Pan Cancer performed better (AUROC: 0.7175, AUPR: 0.6284) than the model adding RepeatMasker peaks (AUROC: 0.6102, AUPR: 0.5577). Moreover, we introduced attention mechanism in DeepHPV and enriched the transcription factor binding sites including BHLHA15, CHR, COUP-TFII, DMRTA2, E2A, HIC1, INR, NPAS, Nr5a2, RARa, SCL, Snail1, Sox10, Sox3, Sox4, Sox6, STAT6, Tbet, Tbx5, TEAD, Tgif2, ZNF189, ZNF416 near attention intensive sites. Together, DeepHPV is a robust and explainable deep learning model, providing new insights into HPV integration preference and mechanism. Availability: DeepHPV is available as an open-source software and can be downloaded from https://github.com/JiuxingLiang/DeepHPV.git, Contact: huzheng1998@163.com, liangjiuxing@m.scnu.edu.cn, lizheyzy@163.com.
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Affiliation(s)
- Rui Tian
- Translational Medicine of the First Affiliated Hospital, Sun Yat-sen University
| | - Ping Zhou
- Dongguan Maternal and Child Health Care Hospital
| | - Mengyuan Li
- Department of Obstetrics and Gynecology at the First Affiliated Hospital, Sun Yat-sen University
| | - Jinfeng Tan
- First Affiliated Hospital, Sun Yat-sen University
| | - Zifeng Cui
- First Affiliated Hospital, Sun Yat-sen University
| | - Wei Xu
- Department of Obstetrics and Gynecology at the First Affiliated Hospital, Sun Yat-sen University
| | - Jingyue Wei
- Department of Obstetrics and Gynecology at the First Affiliated Hospital, Sun Yat-sen University
| | - Jingjing Zhu
- Department of Obstetrics and Gynecology of the First Affiliated Hospital, Sun Yat-sen University
| | - Zhuang Jin
- First Affiliated Hospital, Sun Yat-sen University
| | - Chen Cao
- Central Hospital of Wuhan, China
| | - Weiwen Fan
- College of Medicine at the Sun Yat-sen University
| | - Weiling Xie
- First Affiliated Hospital, Sun Yat-sen University
| | | | | | - Zeshan You
- First Affiliated Hospital, Sun Yat-sen University
| | - Gang Niu
- Department of Obstetrics and Gynecology of the First Affiliated Hospital, Sun Yat-sen University
| | - Canbiao Wu
- Institute for Brain Research and Rehabilitation at the South China Normal University
| | - Xiaofang Guo
- Department of Medical Oncology of the Eastern Hospital at the First Affiliated Hospital, Sun Yat-sen University
| | - Xuchu Weng
- Institute for Brain Research and Rehabilitation at the South China Normal University
| | | | - Fubing Yu
- Dongguan Maternal and Child Health Care Hospital
| | - Zhiying Yu
- Department of Gynecology, Shenzhen Second People's Hospital/the First Affiliated Hospital of Shenzhen University Health Science Center
| | - Jiuxing Liang
- Institute for Brain Research and Rehabilitation at the South China Normal University
| | - Zheng Hu
- Gynecological Oncology of the First Affiliated Hospital, Precision Medicine Institute, Sun Yat-sen University
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31
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Tharyan RG, Annibal A, Schiffer I, Laboy R, Atanassov I, Weber AL, Gerisch B, Antebi A. NFYB-1 regulates mitochondrial function and longevity via lysosomal prosaposin. Nat Metab 2020; 2:387-396. [PMID: 32694663 DOI: 10.1038/s42255-020-0200-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 03/26/2020] [Indexed: 12/24/2022]
Abstract
Mitochondria are multidimensional organelles whose activities are essential to cellular vitality and organismal longevity, yet underlying regulatory mechanisms spanning these different levels of organization remain elusive1-5. Here we show that Caenorhabditis elegans nuclear transcription factor Y, beta subunit (NFYB-1), a subunit of the NF-Y transcriptional complex6-8, is a crucial regulator of mitochondrial function. Identified in RNA interference (RNAi) screens, NFYB-1 loss leads to perturbed mitochondrial gene expression, reduced oxygen consumption, mitochondrial fragmentation, disruption of mitochondrial stress pathways, decreased mitochondrial cardiolipin levels and abolition of organismal longevity triggered by mitochondrial impairment. Multi-omics analysis reveals that NFYB-1 is a potent repressor of lysosomal prosaposin, a regulator of glycosphingolipid metabolism. Limiting prosaposin expression unexpectedly restores cardiolipin production, mitochondrial function and longevity in the nfyb-1 background. Similarly, cardiolipin supplementation rescues nfyb-1 phenotypes. These findings suggest that the NFYB-1-prosaposin axis coordinates lysosomal to mitochondria signalling via lipid pools to enhance cellular mitochondrial function and organismal health.
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Affiliation(s)
| | - Andrea Annibal
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Isabelle Schiffer
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- CECAD, University of Cologne, Cologne, Germany
| | - Raymond Laboy
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- CECAD, University of Cologne, Cologne, Germany
| | - Ilian Atanassov
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Birgit Gerisch
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Adam Antebi
- Max Planck Institute for Biology of Ageing, Cologne, Germany.
- CECAD, University of Cologne, Cologne, Germany.
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32
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Demin DE, Uvarova AN, Klepikova AV, Schwartz AM. The Influence of the Minor Short Isoform of Securin (PTTG1) on Transcription is Significantly Different from the Impact of the Full Isoform. Mol Biol 2020. [DOI: 10.1134/s0026893320010045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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33
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Dolfini D, Minuzzo M, Sertic S, Mantovani R. NF-YA overexpression protects from glutamine deprivation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1867:118571. [PMID: 31706909 DOI: 10.1016/j.bbamcr.2019.118571] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 09/20/2019] [Accepted: 10/03/2019] [Indexed: 12/20/2022]
Abstract
The heterotrimeric transcription factor NF-Y binds to CCAAT boxes of genes of glutamine metabolism. We set out to study the role of the regulatory NF-YA subunit in this pathway. We produced U2OS and A549 clones stably overexpressing -OE- the two splicing isoforms of NF-YA. NF-YA OE cells show normal growth and colony formation rates, but they become resistant to cell death upon glutamine deprivation. Increased mRNA and protein expression of the key biosynthetic enzyme GLUL in U2OS entails increased production of endogenous glutamine upon deprivation. The use of GLUL inhibitors dampens the NF-YA-mediated effect. NF-YA OE prevents activation of the pro-apoptotic transcription factor CHOP/DDIT3. Elevated basal levels of SERCA1/2, coding for the molecular target of Thapsigargin, correlate with resistance of NF-YA OE cells to the drug. The work represents a proof-of-principle that elevated levels of NF-YA, as found in some tumor types, helps altering cancer metabolic pathways.
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Affiliation(s)
- Diletta Dolfini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
| | - Mario Minuzzo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Sarah Sertic
- 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.
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34
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Overexpression and alternative splicing of NF-YA in breast cancer. Sci Rep 2019; 9:12955. [PMID: 31506469 PMCID: PMC6736888 DOI: 10.1038/s41598-019-49297-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/30/2019] [Indexed: 12/11/2022] Open
Abstract
NF-Y is a CCAAT-binding trimeric transcription factor, whose regulome, interactome and oncogenic potential point to direct involvement in cellular transformation. Yet little is known about the levels of NF-Y subunits in tumors. We focused on breast carcinomas, and analyzed RNA-Seq datasets of TCGA and 54 BRCA cell lines at gene and isoforms level. We partitioned all tumors in the four major subclasses. NF-YA, but not histone-fold subunits NF-YB/NF-YC, is globally overexpressed, correlating with the proliferative Ki67 marker and a common set of 840 genes, with cell-cycle, metabolism GO terms. Their promoters are enriched in NF-Y, GC-rich and E2F sites. Surprisingly, there is an isoform switch, with the “short” isoform -NF-YAs- becoming predominant in tumors. E2F genes are also overexpressed in BRCA, but no switch in isoforms is observed. In Basal-like Claudinlow cell lines and tumors, expression of NF-YAl -long- isoform is high, together with 11 typical EMT markers and low levels of basal Keratins. Analysis of Progression-Free-Intervals indicates that tumors with unbalance of NF-YA isoforms ratios have worst clinical outcomes. The data suggest that NF-YA overexpression increases CCAAT-dependent, pro-growth genes in BRCA. NF-YAs is associated with a proliferative signature, but high levels of NF-YAl signal loss of epithelial features, EMT and acquisition of a more aggressive behavior in a subset of Claudinlow Basal-like tumors.
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35
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Zhao Z, Dong Q, Liu X, Wei L, Liu L, Li Y, Wang X. Dynamic transcriptome profiling in DNA damage-induced cellular senescence and transient cell-cycle arrest. Genomics 2019; 112:1309-1317. [PMID: 31376528 DOI: 10.1016/j.ygeno.2019.07.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 04/14/2019] [Accepted: 07/30/2019] [Indexed: 12/13/2022]
Abstract
Cellular senescence is an irreversible cell cycle arrest process associated with aging and senescence-related diseases. DNA damage is an extensive feature of cellular senescence and aging. Different levels of DNA damage could lead to cellular senescence or transient cell-cycle arrest, but the genetic regulatory mechanisms determining cell fate are still not clear. In this work, high-resolution time course analysis of gene expression in DNA damage-induced cellular senescence and transient cell-cycle arrest was used to explore the transcriptomic differences between different cell fates after DNA damage response and to investigate the key regulatory factors affecting senescent cell fates. Pathways such as the cell cycle, DNA repair and cholesterol metabolism showed characteristic differential response. A number of key transcription factors were predicted to regulating cell cycle and DNA repair. Our study provides genome-wide insights into the molecular-level mechanisms of senescent cell fate decisions after DNA damage response.
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Affiliation(s)
- Zhen Zhao
- Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, BNRist, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Qiongye Dong
- Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, BNRist, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Xuehui Liu
- Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, BNRist, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Lei Wei
- Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, BNRist, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Liyang Liu
- Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, BNRist, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Yanda Li
- Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, BNRist, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Xiaowo Wang
- Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and System Biology, BNRist, Department of Automation, Tsinghua University, Beijing 100084, China.
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36
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Charitou T, Srihari S, Lynn MA, Jarboui MA, Fasterius E, Moldovan M, Shirasawa S, Tsunoda T, Ueffing M, Xie J, Xin J, Wang X, Proud CG, Boldt K, Al-Khalili Szigyarto C, Kolch W, Lynn DJ. Transcriptional and metabolic rewiring of colorectal cancer cells expressing the oncogenic KRAS G13D mutation. Br J Cancer 2019; 121:37-50. [PMID: 31133691 PMCID: PMC6738113 DOI: 10.1038/s41416-019-0477-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 04/22/2019] [Accepted: 04/25/2019] [Indexed: 12/16/2022] Open
Abstract
Background Activating mutations in KRAS frequently occur in colorectal cancer (CRC) patients, leading to resistance to EGFR-targeted therapies. Methods To better understand the cellular reprogramming which occurs in mutant KRAS cells, we have undertaken a systems-level analysis of four CRC cell lines which express either wild type (wt) KRAS or the oncogenic KRASG13D allele (mtKRAS). Results RNAseq revealed that genes involved in ribosome biogenesis, mRNA translation and metabolism were significantly upregulated in mtKRAS cells. Consistent with the transcriptional data, protein synthesis and cell proliferation were significantly higher in the mtKRAS cells. Targeted metabolomics analysis also confirmed the metabolic reprogramming in mtKRAS cells. Interestingly, mtKRAS cells were highly transcriptionally responsive to EGFR activation by TGFα stimulation, which was associated with an unexpected downregulation of genes involved in a range of anabolic processes. While TGFα treatment strongly activated protein synthesis in wtKRAS cells, protein synthesis was not activated above basal levels in the TGFα-treated mtKRAS cells. This was likely due to the defective activation of the mTORC1 and other pathways by TGFα in mtKRAS cells, which was associated with impaired activation of PKB signalling and a transient induction of AMPK signalling. Conclusions We have found that mtKRAS cells are substantially rewired at the transcriptional, translational and metabolic levels and that this rewiring may reveal new vulnerabilities in oncogenic KRAS CRC cells that could be exploited in future.
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Affiliation(s)
- Theodosia Charitou
- EMBL Australia Group, South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA, 5000, Australia
| | - Sriganesh Srihari
- EMBL Australia Group, South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA, 5000, Australia
| | - Miriam A Lynn
- EMBL Australia Group, South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA, 5000, Australia
| | - Mohamed-Ali Jarboui
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany.,Werner Siemens Imaging Center, University of Tübingen, Tübingen, Germany
| | - Erik Fasterius
- School of Biotechnology, Royal Institute of Technology, Stockholm, Sweden
| | - Max Moldovan
- EMBL Australia Group, South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA, 5000, Australia
| | - Senji Shirasawa
- Faculty of Medicine, Fukuoka University, Fukuoka, Fukuoka Prefecture, 814-0133, Japan
| | - Toshiyuki Tsunoda
- Faculty of Medicine, Fukuoka University, Fukuoka, Fukuoka Prefecture, 814-0133, Japan
| | - Marius Ueffing
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Jianling Xie
- Nutrition, Diabetes & Metabolism, South Australian Health & Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Jin Xin
- Nutrition, Diabetes & Metabolism, South Australian Health & Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Xuemin Wang
- Nutrition, Diabetes & Metabolism, South Australian Health & Medical Research Institute, Adelaide, SA, 5000, Australia.,School of Biological Sciences, University of Adelaide, Adelaide, SA, 5000, Australia
| | - Christopher G Proud
- Nutrition, Diabetes & Metabolism, South Australian Health & Medical Research Institute, Adelaide, SA, 5000, Australia.,School of Biological Sciences, University of Adelaide, Adelaide, SA, 5000, Australia
| | - Karsten Boldt
- Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | | | - Walter Kolch
- Systems Biology Ireland, University College Dublin, Dublin, Ireland.,School of Medicine, University College Dublin, Dublin, Ireland.,Conway Institute, University College Dublin, Dublin, Ireland
| | - David J Lynn
- EMBL Australia Group, South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA, 5000, Australia. .,School of Medicine, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia.
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37
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Janker L, Mayer RL, Bileck A, Kreutz D, Mader JC, Utpatel K, Heudobler D, Agis H, Gerner C, Slany A. Metabolic, Anti-apoptotic and Immune Evasion Strategies of Primary Human Myeloma Cells Indicate Adaptations to Hypoxia. Mol Cell Proteomics 2019; 18:936-953. [PMID: 30792264 PMCID: PMC6495257 DOI: 10.1074/mcp.ra119.001390] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Indexed: 12/26/2022] Open
Abstract
Multiple Myeloma (MM) is an incurable plasma cell malignancy primarily localized within the bone marrow (BM). It develops from a premalignant stage, monoclonal gammopathy of undetermined significance (MGUS), often via an intermediate stage, smoldering MM (SMM). The mechanisms of MM progression have not yet been fully understood, all the more because patients with MGUS and SMM already carry similar initial mutations as found in MM cells. Over the last years, increased importance has been attributed to the tumor microenvironment and its role in the pathophysiology of the disease. Adaptations of MM cells to hypoxic conditions in the BM have been shown to contribute significantly to MM progression, independently from the genetic predispositions of the tumor cells. Searching for consequences of hypoxia-induced adaptations in primary human MM cells, CD138-positive plasma cells freshly isolated from BM of patients with different disease stages, comprising MGUS, SMM, and MM, were analyzed by proteome profiling, which resulted in the identification of 6218 proteins. Results have been made fully accessible via ProteomeXchange with identifier PXD010600. Data previously obtained from normal primary B cells were included for comparative purposes. A principle component analysis revealed three clusters, differentiating B cells as well as MM cells corresponding to less and more advanced disease stages. Comparing these three clusters pointed to the alteration of pathways indicating adaptations to hypoxic stress in MM cells on disease progression. Protein regulations indicating immune evasion strategies of MM cells were determined, supported by immunohistochemical staining, as well as transcription factors involved in MM development and progression. Protein regulatory networks related to metabolic adaptations of the cells became apparent. Results were strengthened by targeted analyses of a selected panel of metabolites in MM cells and MM-associated fibroblasts. Based on our data, new opportunities may arise for developing therapeutic strategies targeting myeloma disease progression.
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Affiliation(s)
- Lukas Janker
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Rupert L Mayer
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Andrea Bileck
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Dominique Kreutz
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Johanna C Mader
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Kirsten Utpatel
- Department of Pathology, University Regensburg, Regensburg, Germany
| | - Daniel Heudobler
- Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, Regensburg, Germany
| | - Hermine Agis
- Department of Oncology, University Clinic for Internal Medicine I, Medical University of Vienna, Vienna, Austria
| | - Christopher Gerner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Astrid Slany
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria;.
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38
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Smieszek S, Jia P, Samuels DC, Zhao Z, Barnholtz-Sloan J, Kaur H, Letendre S, Ellis R, Franklin DR, Hulgan T, Kallianpur A, Bush WS. Nuclear-Mitochondrial interactions influence susceptibility to HIV-associated neurocognitive impairment. Mitochondrion 2019; 46:247-255. [PMID: 30026132 PMCID: PMC6336535 DOI: 10.1016/j.mito.2018.07.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 06/30/2018] [Accepted: 07/13/2018] [Indexed: 12/26/2022]
Abstract
HIV-associated neurocognitive impairment (NCI) is a term established to capture a wide spectrum of HIV related neurocognitive deficits ranging in severity from asymptomatic to dementia. The genetic underpinnings of this complex phenotype are incompletely understood. Mitochondrial function has long been thought to play a role in neurodegeneration, along with iron metabolism and transport. In this work, we aimed to characterize the interplay of mitochondrial DNA (mtDNA) haplogroup and nuclear genetic associations to NCI phenotypes in the CHARTER cohort, encompassing 1025 individuals of European-descent, African-descent, or admixed Hispanic. We first employed a polygenic modeling approach to investigate the global effect of previous marginally associated nuclear SNPs, and to examine how the polygenic effect of these SNPs is influenced by mtDNA haplogroups. We see evidence of a significant interaction between nuclear SNPs en masse and mtDNA haplogroups within European-descent and African-descent individuals. Subsequently, we performed an analysis of each SNP by mtDNA haplogroup, and detected significant interactions between two nuclear SNPs (rs17160128 and rs12460243) and European haplogroups. These findings, which require validation in larger cohorts, indicate a potential new role for nuclear-mitochondrial DNA interactions in susceptibility to NCI and shed light onto the pathophysiology of this neurocognitive phenotype.
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Affiliation(s)
- S Smieszek
- Department of Population and Quantitative Health Sciences, and Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, United States.
| | - P Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - D C Samuels
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Z Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - J Barnholtz-Sloan
- Department of Population and Quantitative Health Sciences, and Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, United States
| | - H Kaur
- Department of Genomic Medicine, Lerner Research Institute and Department of Medicine, Cleveland Clinic, Cleveland, OH, United States
| | - S Letendre
- Department of Medicine, University of California San Diego, San Diego, CA, United States
| | - R Ellis
- Department of Medicine, University of California San Diego, San Diego, CA, United States
| | - D R Franklin
- Department of Medicine, University of California San Diego, San Diego, CA, United States
| | - T Hulgan
- School of Medicine, Vanderbilt University, Nashville, TN, United States
| | - A Kallianpur
- Department of Genomic Medicine, Lerner Research Institute and Department of Medicine, Cleveland Clinic, Cleveland, OH, United States; Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - W S Bush
- Department of Population and Quantitative Health Sciences, and Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, United States; Department of Genomic Medicine, Lerner Research Institute and Department of Medicine, Cleveland Clinic, Cleveland, OH, United States
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Donato L, Scimone C, Nicocia G, D'Angelo R, Sidoti A. Role of oxidative stress in Retinitis pigmentosa: new involved pathways by an RNA-Seq analysis. Cell Cycle 2018; 18:84-104. [PMID: 30569795 DOI: 10.1080/15384101.2018.1558873] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Retinitis pigmentosa (RP) is a very heterogeneous inherited ocular disorder group characterized by progressive retinal disruption. Retinal pigment epithelium (RPE) degeneration, due to oxidative stress which arrests the metabolic support to photoreceptors, represents one of the principal causes of RP. Here, the role of oxidative stress in RP onset and progression was analyzed by a comparative whole transcriptome analysis of human RPE cells, treated with 100 µg/ml of oxLDL and untreated, at different time points. Experiment was thrice repeated and performed on Ion ProtonTM sequencing system. Data analysis, including low quality reads trimming and gene expression quantification, was realized by CLC Genomics Workbench software. The whole analysis highlighted 14 clustered "macro-pathways" and many sub-pathways, classified by selection of 5271 genes showing the highest alteration of expression. Among them, 23 genes were already known to be RP causative ones (15 over-expressed and 8 down-expressed), and their enrichment and intersection analyses highlighted new 77 candidate related genes (49 over-expressed and 28 down-expressed). A final filtering analysis then highlighted 29 proposed candidate genes. This data suggests that many new genes, not yet associated with RP, could influence its etiopathogenesis.
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Affiliation(s)
- Luigi Donato
- a Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine , University of Messina , Messina , Italy.,b Department of Cutting-Edge Medicine and Therapies, Biomolecular Strategies and Neuroscience, Section of Applied Neuroscience, Molecular Genetics and Predictive Medicine , I.E.ME.S.T. ., Palermo , Italy
| | - Concetta Scimone
- a Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine , University of Messina , Messina , Italy.,b Department of Cutting-Edge Medicine and Therapies, Biomolecular Strategies and Neuroscience, Section of Applied Neuroscience, Molecular Genetics and Predictive Medicine , I.E.ME.S.T. ., Palermo , Italy
| | - Giacomo Nicocia
- c Department of Clinical and Experimental Medicine , University of Messina , Messina , Italy
| | - Rosalia D'Angelo
- a Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine , University of Messina , Messina , Italy.,b Department of Cutting-Edge Medicine and Therapies, Biomolecular Strategies and Neuroscience, Section of Applied Neuroscience, Molecular Genetics and Predictive Medicine , I.E.ME.S.T. ., Palermo , Italy
| | - Antonina Sidoti
- a Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine , University of Messina , Messina , Italy.,b Department of Cutting-Edge Medicine and Therapies, Biomolecular Strategies and Neuroscience, Section of Applied Neuroscience, Molecular Genetics and Predictive Medicine , I.E.ME.S.T. ., Palermo , Italy
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40
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Perez-Gomez A, Carretero M, Weber N, Peterka V, To A, Titova V, Solis G, Osborn O, Petrascheck M. A phenotypic Caenorhabditis elegans screen identifies a selective suppressor of antipsychotic-induced hyperphagia. Nat Commun 2018; 9:5272. [PMID: 30532051 PMCID: PMC6288085 DOI: 10.1038/s41467-018-07684-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 11/12/2018] [Indexed: 12/30/2022] Open
Abstract
Antipsychotic (AP) drugs are used to treat psychiatric disorders but are associated with significant weight gain and metabolic disease. Increased food intake (hyperphagia) appears to be a driving force by which APs induce weight gain but the mechanisms are poorly understood. Here we report that administration of APs to C. elegans induces hyperphagia by a mechanism that is genetically distinct from basal food intake. We exploit this finding to screen for adjuvant drugs that suppress AP-induced hyperphagia in C. elegans and mice. In mice AP-induced hyperphagia is associated with a unique hypothalamic gene expression signature that is abrogated by adjuvant drug treatment. Genetic analysis of this signature using C. elegans identifies two transcription factors, nhr-25/Nr5a2 and nfyb-1/NFYB to be required for AP-induced hyperphagia. Our study reveals that AP-induced hyperphagia can be selectively suppressed without affecting basal food intake allowing for novel drug discovery strategies to combat AP-induced metabolic side effects.
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Affiliation(s)
- Anabel Perez-Gomez
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
- Department of Neuroscience, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Maria Carretero
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
- Department of Neuroscience, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Natalie Weber
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Veronika Peterka
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Alan To
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
- Department of Neuroscience, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Viktoriya Titova
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
- Department of Neuroscience, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Gregory Solis
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
- Department of Neuroscience, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Olivia Osborn
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
| | - Michael Petrascheck
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.
- Department of Neuroscience, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.
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Cao B, Zhao Y, Zhang Z, Li H, Xing J, Guo S, Qiu X, Zhang S, Min L, Zhu S. Gene regulatory network construction identified NFYA as a diffuse subtype-specific prognostic factor in gastric cancer. Int J Oncol 2018; 53:1857-1868. [PMID: 30106137 PMCID: PMC6192729 DOI: 10.3892/ijo.2018.4519] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/07/2018] [Indexed: 12/20/2022] Open
Abstract
Lauren classification is a pathology-based gastric cancer (GC) subtyping system, which is widely used in the clinical treatment of patients with GC. However, genome-scale molecular characteristics to distinguish between diffuse (DF) and intestinal (IT) GC remain incompletely characterized, particularly at the transcriptional regulatory level. In the present study, gene regulatory networks were constructed using the Passing Attributes between Networks for Data Assimilation (PANDA) algorithm for DF, IT and mixed GC. The results indicated that >85% of transcription factor (TF)-target edges were shared among all three GC subtypes. In TF enrichment analysis, 13 TFs, including nuclear transcription factor Y subunit α (NFYA) and forkhead box L1, were activated in DF GC, whereas 8 TFs, including RELA proto-oncogene and T-cell leukemia homeobox 1 (TLX1), were activated in IT GC. Out of these identified TFs, NFYA [Hazard ratio (HR) (95% confidence interval, CI)=0.560 (0.349, 0.900), P=0.017] and sex determining region Y [HR (95% CI)=0.603 (0.375, 0.969), P=0.037] were identified as independent prognostic factors in DF GC, but not in IT GC, whereas TLX1 [HR (95% CI)=0.547 (0.321, 0.9325), P=0.027] was identified as an independent prognostic factor in IT GC, but not in DF GC. Verification at the cellular level was also performed; interference of NFYA expression using small interfering RNA in MGC803 cells (DF GC-derived cells) markedly inhibited cell growth and colony formation. Similar effects were also detected in SGC-7901 cells (IT GC-derived cells), but to a lesser extent. In conclusion, identified gene regulatory networks differed between distinct GC subtypes, in which the same TFs had different biological effects. Specifically, NFYA was identified as a DF subtype-specific independent prognostic factor in GC.
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Affiliation(s)
- Bin Cao
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing 100050, P.R. China
| | - Yu Zhao
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing 100050, P.R. China
| | - Zheng Zhang
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing 100050, P.R. China
| | - Hengcun Li
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing 100050, P.R. China
| | - Jie Xing
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing 100050, P.R. China
| | - Shuilong Guo
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing 100050, P.R. China
| | - Xintao Qiu
- Department of Biomedical Informatics, Harvard School of Public Health, Boston, MA 02115, USA
| | - Shutian Zhang
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing 100050, P.R. China
| | - Li Min
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing 100050, P.R. China
| | - Shengtao Zhu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing 100050, P.R. China
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Zhang H, Liu J, Fu X, Yang A. Identification of Key Genes and Pathways in Tongue Squamous Cell Carcinoma Using Bioinformatics Analysis. Med Sci Monit 2017; 23:5924-5932. [PMID: 29240723 PMCID: PMC5738838 DOI: 10.12659/msm.905035] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Tongue squamous cell carcinoma (TSCC) is a major type of oral cancers and has remained an intractable cancer over the past decades. The aim of this study was to identify differentially expressed genes (DEGs) during TSCC and reveal their potential mechanisms. MATERIAL AND METHODS The gene expression profiles of GSE13601 were downloaded from the GEO database. The GSE13601 dataset contains 57 samples, including 31 tongue SCC samples and 26 matched normal mucosa samples. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses were performed; Cytoscape software was used for the protein-protein interaction (PPI) network and module analysis of the DEGs. RESULTS We identified a total of 1,050 upregulated DEGs (uDEGs) and 702 downregulated DEGs (dDEGs) of TSCC. The GO analysis results showed that uDEGs were significantly enriched in the following biological processes (BP): signal transduction, positive or negative regulation of cell proliferation, and negative regulation of cell proliferation. The dDEGs were significantly enriched in the following biological processes: signal transduction, cell adhesion, and apoptotic process. The KEGG pathway analysis showed that uDEGs were enriched in metabolic pathways, pathways in cancer, and PI3K-Akt signaling pathway, while the dDEGs were enriched in focal adhesion and ECM-receptor interaction. The top centrality hub genes RAC1, APP, EGFR, KNG1, AGT, and HRAS were identified from the PPI network. Module analysis revealed that TSCC was associated with significant pathways, including neuroactive ligand-receptor interaction, calcium signaling pathway, and chemokine signaling pathway. CONCLUSIONS The present study identified key genes and signal pathways, which deepen our understanding of the molecular mechanisms of carcinogenesis and development of the disease, and might be used as diagnostic and therapeutic molecular biomarkers for TSCC.
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Affiliation(s)
- Huayong Zhang
- Department of Head and Neck Surgery, Sun Yan-sen University Cancer Centre, Guangzhou, Guangdong, China (mainland).,Department of Cardiothoracic Surgery, The Fifth Affiliated Hospital of Sun Yan-sen University, Zhuhai, Guangdong, China (mainland)
| | - Jianmin Liu
- Department of Otorhinolaryngology and Head and Neck Surgery, People's Hospital of Deyang City, Deyang, Sichuan, China (mainland)
| | - Xiaoyan Fu
- Department of Head and Neck Surgery, Sun Yan-sen University Cancer Centre, Guangzhou, Guangdong, China (mainland)
| | - Ankui Yang
- Department of Head and Neck Surgery, Sun Yan-sen University Cancer Centre, Guangzhou, Guangdong, China (mainland)
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Ma S, Snyder M, Dinesh-Kumar SP. Discovery of Novel Human Gene Regulatory Modules from Gene Co-expression and Promoter Motif Analysis. Sci Rep 2017; 7:5557. [PMID: 28717181 PMCID: PMC5514134 DOI: 10.1038/s41598-017-05705-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/24/2017] [Indexed: 12/21/2022] Open
Abstract
Deciphering gene regulatory networks requires identification of gene expression modules. We describe a novel bottom-up approach to identify gene modules regulated by cis-regulatory motifs from a human gene co-expression network. Target genes of a cis-regulatory motif were identified from the network via the motif's enrichment or biased distribution towards transcription start sites in the promoters of co-expressed genes. A gene sub-network containing the target genes was extracted and used to derive gene modules. The analysis revealed known and novel gene modules regulated by the NF-Y motif. The binding of NF-Y proteins to these modules' gene promoters were verified using ENCODE ChIP-Seq data. The analyses also identified 8,048 Sp1 motif target genes, interestingly many of which were not detected by ENCODE ChIP-Seq. These target genes assemble into house-keeping, tissues-specific developmental, and immune response modules. Integration of Sp1 modules with genomic and epigenomic data indicates epigenetic control of Sp1 targets' expression in a cell/tissue specific manner. Finally, known and novel target genes and modules regulated by the YY1, RFX1, IRF1, and 34 other motifs were also identified. The study described here provides a valuable resource to understand transcriptional regulation of various human developmental, disease, or immunity pathways.
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Affiliation(s)
- Shisong Ma
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China.
- Department of Plant Biology and the Genome Center, College of Biological Sciences, University of California, Davis, CA, 95616, USA.
| | - Michael Snyder
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Savithramma P Dinesh-Kumar
- Department of Plant Biology and the Genome Center, College of Biological Sciences, University of California, Davis, CA, 95616, USA.
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Nishi-Tatsumi M, Yahagi N, Takeuchi Y, Toya N, Takarada A, Murayama Y, Aita Y, Sawada Y, Piao X, Oya Y, Shikama A, Masuda Y, Kubota M, Izumida Y, Matsuzaka T, Nakagawa Y, Sekiya M, Iizuka Y, Kawakami Y, Kadowaki T, Yamada N, Shimano H. A key role of nuclear factor Y in the refeeding response of fatty acid synthase in adipocytes. FEBS Lett 2017; 591:965-978. [PMID: 28281280 DOI: 10.1002/1873-3468.12620] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 03/02/2017] [Accepted: 03/04/2017] [Indexed: 11/10/2022]
Abstract
Fatty acid synthase (Fasn) is a key component of energy metabolism that is dynamically induced by food intake. Although extensive studies have revealed a number of transcription factors involved in the fasting/refeeding transition of Fasn expression in hepatocytes, much less evidence is available for adipocytes. Using the in vivo Ad-luc analytical system, we identified the inverted CCAAT element (ICE) around -100 nucleotides in the Fasn promoter as a critical cis-element for the refeeding response in adipocytes. Electrophoretic mobility shift assays and chromatin immunoprecipitation show that nuclear factor Y (NF-Y) binds to ICE specifically in refeeding states. Notably, the NF-Y binding to ICE is differently regulated between adipocytes and hepatocytes. These findings provide insights into the specific mechanisms controlling energy metabolism in adipocytes.
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Affiliation(s)
- Makiko Nishi-Tatsumi
- Nutrigenomics Research Group, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Naoya Yahagi
- Nutrigenomics Research Group, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Yoshinori Takeuchi
- Nutrigenomics Research Group, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Naoki Toya
- Nutrigenomics Research Group, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Ayako Takarada
- Nutrigenomics Research Group, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Yuki Murayama
- Nutrigenomics Research Group, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Yuichi Aita
- Nutrigenomics Research Group, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Yoshikazu Sawada
- Nutrigenomics Research Group, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Xiaoying Piao
- Nutrigenomics Research Group, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Yukari Oya
- Nutrigenomics Research Group, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Akito Shikama
- Nutrigenomics Research Group, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Yukari Masuda
- Nutrigenomics Research Group, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Midori Kubota
- Nutrigenomics Research Group, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Yoshihiko Izumida
- Nutrigenomics Research Group, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Takashi Matsuzaka
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Yoshimi Nakagawa
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Motohiro Sekiya
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Yoko Iizuka
- Department of Internal Medicine, Graduate School of Medicine, University of Tokyo, Japan
| | - Yasushi Kawakami
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Takashi Kadowaki
- Department of Internal Medicine, Graduate School of Medicine, University of Tokyo, Japan
| | - Nobuhiro Yamada
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Hitoshi Shimano
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
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Gurtner A, Manni I, Piaggio G. NF-Y in cancer: Impact on cell transformation of a gene essential for proliferation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:604-616. [PMID: 27939755 DOI: 10.1016/j.bbagrm.2016.12.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 11/30/2016] [Accepted: 12/05/2016] [Indexed: 12/17/2022]
Abstract
NF-Y is a ubiquitous heterotrimeric transcription factor with a binding affinity for the CCAAT consensus motif, one of the most common cis-acting element in the promoter and enhancer regions of eukaryote genes in direct (CCAAT) or reverse (ATTGG) orientation. NF-Y consists of three subunits, NF-YA, the regulatory subunit of the trimer, NF-YB, and NF-YC, all required for CCAAT binding. Growing evidence in cells and animal models support the notion that NF-Y, driving transcription of a plethora of cell cycle regulatory genes, is a key player in the regulation of proliferation. Proper control of cellular growth is critical for cancer prevention and uncontrolled proliferation is a hallmark of cancer cells. Indeed, during cell transformation aberrant molecular pathways disrupt mechanisms controlling proliferation and many growth regulatory genes are altered in tumors. Here, we review bioinformatics, molecular and functional evidence indicating the involvement of the cell cycle regulator NF-Y in cancer-associated pathways. This article is part of a Special Issue entitled: Nuclear Factor Y in Development and Disease, edited by Prof. Roberto Mantovani.
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Affiliation(s)
- Aymone Gurtner
- Department of Research, Advanced Diagnostics and Technological Innovation, UOSD SAFU, Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - Isabella Manni
- Department of Research, Advanced Diagnostics and Technological Innovation, UOSD SAFU, Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - Giulia Piaggio
- Department of Research, Advanced Diagnostics and Technological Innovation, UOSD SAFU, Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy.
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Hortschansky P, Haas H, Huber EM, Groll M, Brakhage AA. The CCAAT-binding complex (CBC) in Aspergillus species. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:560-570. [PMID: 27939757 DOI: 10.1016/j.bbagrm.2016.11.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/25/2016] [Accepted: 11/26/2016] [Indexed: 11/30/2022]
Abstract
BACKGROUND The CCAAT binding complex (CBC), consisting of a heterotrimeric core structure, is highly conserved in eukaryotes and constitutes an important general transcriptional regulator. Scope of the review. In this review we discuss the scientific history and the current state of knowledge of the multiple gene regulatory functions, protein motifs and structure of the CBC in fungi with a special focus on Aspergillus species. Major conclusions and general significance. Initially identified as a transcriptional activator of respiration in Saccharomyces cerevisiae, in other fungal species the CBC was found to be involved in highly diverse pathways, but a general rationale for its involvement was missing. Subsequently, the CBC was found to sense reactive oxygen species through oxidative modifications of cysteine residues in order to mediate redox regulation. Moreover, via interaction with the iron-sensing bZIP transcription factor HapX, the CBC was shown to mediate adaptation to both iron starvation and iron excess. Due to the control of various pathways in primary and secondary metabolism the CBC is of crucial importance for fungal virulence in both animal and plant hosts as well as antifungal resistance. Consequently, CBC-mediated control affects biological processes that are of high interest in biotechnology, agriculture and infection medicine. This article is part of a Special Issue entitled: Nuclear Factor Y in Development and Disease, edited by Prof. Roberto Mantovani.
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Affiliation(s)
- Peter Hortschansky
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, D-07745, Jena, Germany
| | - Hubertus Haas
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, A6020 Innsbruck, Austria
| | - Eva M Huber
- Center for Integrated Protein Science Munich at the Department Chemistry, Technische Universität München, Lichtenbergstr. 4, D-85748, Garching, Germany
| | - Michael Groll
- Center for Integrated Protein Science Munich at the Department Chemistry, Technische Universität München, Lichtenbergstr. 4, D-85748, Garching, Germany
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, D-07745, Jena, Germany; Department of Microbiology and Molecular Biology, Friedrich Schiller University (FSU), D-07745 Jena, Germany.
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Zhao H, Wu D, Kong F, Lin K, Zhang H, Li G. The Arabidopsis thaliana Nuclear Factor Y Transcription Factors. FRONTIERS IN PLANT SCIENCE 2016; 7:2045. [PMID: 28119722 PMCID: PMC5222873 DOI: 10.3389/fpls.2016.02045] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 12/21/2016] [Indexed: 05/03/2023]
Abstract
Nuclear factor Y (NF-Y) is an evolutionarily conserved trimeric transcription factor complex present in nearly all eukaryotes. The heterotrimeric NF-Y complex consists of three subunits, NF-YA, NF-YB, and NF-YC, and binds to the CCAAT box in the promoter regions of its target genes to regulate their expression. Yeast and mammal genomes generally have single genes with multiple splicing isoforms that encode each NF-Y subunit. By contrast, plant genomes generally have multi-gene families encoding each subunit and these genes are differentially expressed in various tissues or stages. Therefore, different subunit combinations can lead to a wide variety of NF-Y complexes in various tissues, stages, and growth conditions, indicating the potentially diverse functions of this complex in plants. Indeed, many recent studies have proved that the NF-Y complex plays multiple essential roles in plant growth, development, and stress responses. In this review, we highlight recent progress on NF-Y in Arabidopsis thaliana, including NF-Y protein structure, heterotrimeric complex formation, and the molecular mechanism by which NF-Y regulates downstream target gene expression. We then focus on its biological functions and underlying molecular mechanisms. Finally, possible directions for future research on NF-Y are also presented.
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