1
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Polacchini G, Venerando A, Colitti M. Antioxidant and anti-ageing effects of oleuropein aglycone in canine skeletal muscle cells. Tissue Cell 2024; 88:102369. [PMID: 38555794 DOI: 10.1016/j.tice.2024.102369] [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: 01/22/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/02/2024]
Abstract
Reactive oxygen species (ROS) are normally produced in skeletal muscle. However, an imbalance in their regulatory systems can lead to their accumulation and ultimately to oxidative stress, which is one of the causes of the ageing process. Companion dogs share the same environment and lifestyle as humans, making them an excellent comparative model for the study of ageing, as well as they constitute a growing market for bioactive molecules that improve the quality of life of pets. The anti-ageing properties of oleuropein aglycone (OLE), a bioactive compound from olive leaves known for its antioxidant properties, were investigated in Myok9 canine muscle cell model. After incubation with OLE, senescence was induced in the canine cellular model by hydrogen peroxide (H2O2). Analyses were performed on cells after seven days of differentiation. The oxidative stress induced by H2O2 treatment on differentiated canine muscle cells led to a significant increase in ROS formation, which was reduced by OLE pretreatment alone or in combination with H2O2 by about 34% and 32%, respectively. Cells treated with H2O2 showed a 48% increase the area of senescent cells stained by SA-β-gal, while OLE significantly reduced the coloured area by 52%. OLE, alone or in combination with H2O2, showed a significant antioxidant activity, possibly through autophagy activation, as indicated by the expression of autophagic markers.
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Affiliation(s)
- Giulia Polacchini
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Italy
| | - Andrea Venerando
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Italy
| | - Monica Colitti
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Italy.
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2
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Zhu J, Wang L. The Role of lncRNA-miR-26a-mRNA Network in Cancer Progression and Treatment. Biochem Genet 2024; 62:1443-1461. [PMID: 37730965 DOI: 10.1007/s10528-023-10475-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 07/24/2023] [Indexed: 09/22/2023]
Abstract
The role of non-coding RNAs in regulating biological processes associated with cancer progression, such as proliferation, migration, and apoptosis, has been extensively studied. Long non-coding RNAs (lncRNAs) play a role in regulating these processes through various mechanisms, including transcriptional and post-transcriptional modifications. In post-transcriptional regulation, lncRNAs can bind to specific miRNAs and affect their function, which can either promote or inhibit cancer development. The interaction between lncRNAs, miRNAs, and mRNAs forms a network known as competitive endogenous RNA (ceRNA), which is involved in cancer progression or inhibition. One specific miRNA called miR-26a-5p has been identified as having tumor-suppressive properties. However, when lncRNAs bind to and inhibit miR-26a-5p, it can lead to cancer progression. Therefore, targeting this ceRNA network could be a promising strategy for preventing cancer development. This review will first discuss the anticancer effects of miR-26a-5p and then explore the involvement of the lncRNA-miR26a-5p-mRNA axis in cancer progression and potential targeted therapies.
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Affiliation(s)
- Jun Zhu
- Department of Oncology, Daye People's Hospital, Daye, Hubei, 435100, China.
| | - Liya Wang
- Department of Obstetrics and Gynecology, Pengren Hospital, Daye, Hubei, 435100, China
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3
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Wang X, Shen H, Chen Y, Zhang Y, Wang J, Liu S, Xu B, Wang H, Frangou C, Zhang J. MEF2D Functions as a Tumor Suppressor in Breast Cancer. Int J Mol Sci 2024; 25:5207. [PMID: 38791246 PMCID: PMC11121549 DOI: 10.3390/ijms25105207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/05/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
The myocyte enhancer factor 2 (MEF2) gene family play fundamental roles in the genetic programs that control cell differentiation, morphogenesis, proliferation, and survival in a wide range of cell types. More recently, these genes have also been implicated as drivers of carcinogenesis, by acting as oncogenes or tumor suppressors depending on the biological context. Nonetheless, the molecular programs they regulate and their roles in tumor development and progression remain incompletely understood. The present study evaluated whether the MEF2D transcription factor functions as a tumor suppressor in breast cancer. The knockout of the MEF2D gene in mouse mammary epithelial cells resulted in phenotypic changes characteristic of neoplastic transformation. These changes included enhanced cell proliferation, a loss of contact inhibition, and anchorage-independent growth in soft agar, as well as the capacity for tumor development in mice. Mechanistically, the knockout of MEF2D induced the epithelial-to-mesenchymal transition (EMT) and activated several oncogenic signaling pathways, including AKT, ERK, and Hippo-YAP. Correspondingly, a reduced expression of MEF2D was observed in human triple-negative breast cancer cell lines, and a low MEF2D expression in tissue samples was found to be correlated with a worse overall survival and relapse-free survival in breast cancer patients. MEF2D may, thus, be a putative tumor suppressor, acting through selective gene regulatory programs that have clinical and therapeutic significance.
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Affiliation(s)
- Xiaoxia Wang
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA; (X.W.); (H.S.); (Y.C.)
| | - He Shen
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA; (X.W.); (H.S.); (Y.C.)
| | - Yanmin Chen
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA; (X.W.); (H.S.); (Y.C.)
| | - Yali Zhang
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA; (Y.Z.); (J.W.); (S.L.)
| | - Jianmin Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA; (Y.Z.); (J.W.); (S.L.)
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA; (Y.Z.); (J.W.); (S.L.)
| | - Bo Xu
- Department of Pathology, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA;
| | - Hai Wang
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA;
| | - Costa Frangou
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA;
| | - Jianmin Zhang
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, 665 Elm Street, Buffalo, NY 14203, USA; (X.W.); (H.S.); (Y.C.)
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4
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Chinellato M, Perin S, Carli A, Lastella L, Biondi B, Borsato G, Di Giorgio E, Brancolini C, Cendron L, Angelini A. Folding of Class IIa HDAC Derived Peptides into α-helices Upon Binding to Myocyte Enhancer Factor-2 in Complex with DNA. J Mol Biol 2024; 436:168541. [PMID: 38492719 DOI: 10.1016/j.jmb.2024.168541] [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: 10/15/2023] [Revised: 02/27/2024] [Accepted: 03/11/2024] [Indexed: 03/18/2024]
Abstract
Interaction of transcription factor myocyte enhancer factor-2 (MEF2) family members with class IIa histone deacetylases (HDACs) has been implicated in a wide variety of diseases. Though considerable knowledge on this topic has been accumulated over the years, a high resolution and detailed analysis of the binding mode of multiple class IIa HDAC derived peptides with MEF2D is still lacking. To fulfil this gap, we report here the crystal structure of MEF2D in complex with double strand DNA and four different class IIa HDAC derived peptides, namely HDAC4, HDAC5, HDAC7 and HDAC9. All class IIa HDAC derived peptides form extended amphipathic α-helix structures that fit snugly in the hydrophobic groove of MEF2D domain. Binding mode of class IIa HDAC derived peptides to MEF2D is very similar and occur primarily through nonpolar interactions mediated by highly conserved branched hydrophobic amino acids. Further studies revealed that class IIa HDAC derived peptides are unstructured in solution and appear to adopt a folded α-helix structure only upon binding to MEF2D. Comparison of our peptide-protein complexes with previously characterized structures of MEF2 bound to different co-activators and co-repressors, highlighted both differences and similarities, and revealed the adaptability of MEF2 in protein-protein interactions. The elucidation of the three-dimensional structure of MEF2D in complex with multiple class IIa HDAC derived peptides provide not only a better understanding of the molecular basis of their interactions but also have implications for the development of novel antagonist.
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Affiliation(s)
- Monica Chinellato
- Department of Biology, University of Padua, Via U. Bassi 58, 35131 Padova, Italy
| | - Stefano Perin
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Mestre, Italy
| | - Alberto Carli
- Department of Biology, University of Padua, Via U. Bassi 58, 35131 Padova, Italy
| | - Luana Lastella
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Via Marzolo 1, 35131 Padova, Italy
| | - Barbara Biondi
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Via Marzolo 1, 35131 Padova, Italy
| | - Giuseppe Borsato
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Mestre, Italy
| | - Eros Di Giorgio
- Department of Medicine, Università Degli Studi di Udine, P.le Kolbe 4, 33100 Udine, Italy
| | - Claudio Brancolini
- Department of Medicine, Università Degli Studi di Udine, P.le Kolbe 4, 33100 Udine, Italy
| | - Laura Cendron
- Department of Biology, University of Padua, Via U. Bassi 58, 35131 Padova, Italy.
| | - Alessandro Angelini
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Mestre, Italy; European Centre for Living Technology (ECLT), Ca' Bottacin, Dorsoduro 3911, Calle Crosera, 30123 Venice, Italy.
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Ojo OA, Shen H, Ingram JT, Bonner JA, Welner RS, Lacaud G, Zajac AJ, Shi LZ. Gfi1 controls the formation of effector CD8 T cells during chronic infection and cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.579535. [PMID: 38659890 PMCID: PMC11042319 DOI: 10.1101/2024.04.18.579535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
During chronic infections and tumor progression, CD8 T cells gradually lose their effector functions and become exhausted. These exhausted CD8 T cells are heterogeneous and comprised of different subsets, including self-renewing progenitors that give rise to Ly108 - CX3CR1 + effector-like cells. Generation of these effector-like cells is essential for the control of chronic infections and tumors, albeit limited. However, the precise cues and mechanisms directing the formation and maintenance of exhausted effector-like are incompletely understood. Using genetic mouse models challenged with LCMV Clone 13 or syngeneic tumors, we show that the expression of a transcriptional repressor, growth factor independent 1 (Gfi1) is dynamically regulated in exhausted CD8 T cells, which in turn regulates the formation of exhausted effector-like cells. Gfi1 deletion in T cells dysregulates the chromatin accessibility and transcriptomic programs associated with the differentiation of LCMV Clone 13-specific CD8 T cell exhaustion, preventing the formation of effector-like and terminally exhausted cells while maintaining progenitors and a newly identified Ly108 + CX3CR1 + state. These Ly108 + CX3CR1 + cells have a distinct chromatin profile and may represent an alternative target for therapeutic interventions to combat chronic infections and cancer. In sum, we show that Gfi1 is a critical regulator of the formation of exhausted effector-like cells.
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6
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Zhang G, Fu Y, Yang L, Ye F, Zhang P, Zhang S, Ma L, Li J, Wu H, Han X, Wang J, Guo G. Construction of single-cell cross-species chromatin accessibility landscapes with combinatorial-hybridization-based ATAC-seq. Dev Cell 2024; 59:793-811.e8. [PMID: 38330939 DOI: 10.1016/j.devcel.2024.01.015] [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: 06/01/2023] [Revised: 11/03/2023] [Accepted: 01/18/2024] [Indexed: 02/10/2024]
Abstract
Despite recent advances in single-cell genomics, the lack of maps for single-cell candidate cis-regulatory elements (cCREs) in non-mammal species has limited our exploration of conserved regulatory programs across vertebrates and invertebrates. Here, we developed a combinatorial-hybridization-based method for single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) named CH-ATAC-seq, enabling the construction of single-cell accessible chromatin landscapes for zebrafish, Drosophila, and earthworms (Eisenia andrei). By integrating scATAC censuses of humans, monkeys, and mice, we systematically identified 152 distinct main cell types and around 0.8 million cell-type-specific cCREs. Our analysis provided insights into the conservation of neural, muscle, and immune lineages across species, while epithelial cells exhibited a higher organ-origin heterogeneity. Additionally, a large-scale gene regulatory network (GRN) was constructed in four vertebrates by integrating scRNA-seq censuses. Overall, our study provides a valuable resource for comparative epigenomics, identifying the evolutionary conservation and divergence of gene regulation across different species.
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Affiliation(s)
- Guodong Zhang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China; Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Yuting Fu
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Lei Yang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Fang Ye
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China; Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Peijing Zhang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Shuang Zhang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Lifeng Ma
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Jiaqi Li
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Hanyu Wu
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Xiaoping Han
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China; Zhejiang Provincial Key Laboratory for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou 310058, China.
| | - Jingjing Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China; Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China.
| | - Guoji Guo
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou 310000, China; Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China; Zhejiang Provincial Key Laboratory for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou 310058, China; Institute of Hematology, Zhejiang University, Hangzhou, China.
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7
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Xia L, Nie T, Lu F, Huang L, Shi X, Ren D, Lu J, Li X, Xu T, Cui B, Wang Q, Gao G, Yang Q. Direct regulation of FNIP1 and FNIP2 by MEF2 sustains MTORC1 activation and tumor progression in pancreatic cancer. Autophagy 2024; 20:505-524. [PMID: 37772772 PMCID: PMC10936626 DOI: 10.1080/15548627.2023.2259735] [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: 01/12/2023] [Accepted: 09/12/2023] [Indexed: 09/30/2023] Open
Abstract
MTOR (mechanistic target of rapamycin kinase) complex 1 (MTORC1) orchestrates diverse environmental signals to facilitate cell growth and is frequently activated in cancer. Translocation of MTORC1 from the cytosol to the lysosomal surface by the RRAG GTPases is the key step in MTORC1 activation. Here, we demonstrated that transcription factors MEF2A and MEF2D synergistically regulated MTORC1 activation via modulating its cyto-lysosome shutting. Mechanically, MEF2A and MEF2D controlled the transcription of FNIP1 and FNIP2, the components of the FLCN-FNIP1 or FNIP2 complex that acts as a RRAGC-RRAGD GTPase-activating element to promote the recruitment of MTORC1 to lysosome and its activation. Furthermore, we determined that the pro-oncogenic protein kinase SRC/c-Src directly phosphorylated MEF2D at three conserved tyrosine residues. The tyrosine phosphorylation enhanced MEF2D transcriptional activity and was indispensable for MTORC1 activation. Finally, both the protein and tyrosine phosphorylation levels of MEF2D are elevated in human pancreatic cancers, positively correlating with MTORC1 activity. Depletion of both MEF2A and MEF2D or expressing the unphosphorylatable MEF2D mutant suppressed tumor cell growth. Thus, our study revealed a transcriptional regulatory mechanism of MTORC1 that promoted cell anabolism and proliferation and uncovered its critical role in pancreatic cancer progression.Abbreviation: ACTB: actin beta; ChIP: chromatin immunoprecipitation; EGF: epidermal growth factor; EIF4EBP1: eukaryotic translation initiation factor 4E binding protein 1; FLCN: folliculin; FNIP1: folliculin interacting protein 1; FNIP2: folliculin interacting protein 2; GAP: GTPase activator protein; GEF: guanine nucleotide exchange factors; GTPase: guanosine triphosphatase; LAMP2: lysosomal associated membrane protein 2; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MEF2: myocyte enhancer factor 2; MEF2A: myocyte enhancer factor 2A; MEF2D: myocyte enhancer factor 2D; MEF2D-3YF: Y131F, Y333F, Y337F mutant; MTOR: mechanistic target of rapamycin kinase; MTORC1: MTOR complex 1; NR4A1: nuclear receptor subfamily 4 group A member 1; RPTOR: regulatory associated protein of MTOR complex 1; RHEB: Ras homolog, mTORC1 binding; RPS6KB1: ribosomal protein S6 kinase B1; RRAG: Ras related GTP binding; RT-qPCR: real time-quantitative PCR; SRC: SRC proto-oncogene, non-receptor tyrosine kinase; TMEM192: transmembrane protein 192; WT: wild-type.
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Affiliation(s)
- Li Xia
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
- Department of Neurosurgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Tiejian Nie
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Fangfang Lu
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Lu Huang
- Department of Anesthesiology, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Xiaolong Shi
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Dongni Ren
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Jianjun Lu
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Xiaobin Li
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Tuo Xu
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Bozhou Cui
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Qing Wang
- Department of General Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Guodong Gao
- Department of Neurosurgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Qian Yang
- Department of Experimental Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi, China
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8
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Casillo SM, Gatesman TA, Chilukuri A, Varadharajan S, Johnson BJ, David Premkumar DR, Jane EP, Plute TJ, Koncar RF, Stanton ACJ, Biagi-Junior CAO, Barber CS, Halbert ME, Golbourn BJ, Halligan K, Cruz AF, Mansi NM, Cheney A, Mullett SJ, Land CV, Perez JL, Myers MI, Agrawal N, Michel JJ, Chang YF, Vaske OM, MichaelRaj A, Lieberman FS, Felker J, Shiva S, Bertrand KC, Amankulor N, Hadjipanayis CG, Abdullah KG, Zinn PO, Friedlander RM, Abel TJ, Nazarian J, Venneti S, Filbin MG, Gelhaus SL, Mack SC, Pollack IF, Agnihotri S. An ERK5-PFKFB3 axis regulates glycolysis and represents a therapeutic vulnerability in pediatric diffuse midline glioma. Cell Rep 2024; 43:113557. [PMID: 38113141 DOI: 10.1016/j.celrep.2023.113557] [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: 08/14/2022] [Revised: 07/28/2023] [Accepted: 11/22/2023] [Indexed: 12/21/2023] Open
Abstract
Metabolic reprogramming in pediatric diffuse midline glioma is driven by gene expression changes induced by the hallmark histone mutation H3K27M, which results in aberrantly permissive activation of oncogenic signaling pathways. Previous studies of diffuse midline glioma with altered H3K27 (DMG-H3K27a) have shown that the RAS pathway, specifically through its downstream kinase, extracellular-signal-related kinase 5 (ERK5), is critical for tumor growth. Further downstream effectors of ERK5 and their role in DMG-H3K27a metabolic reprogramming have not been explored. We establish that ERK5 is a critical regulator of cell proliferation and glycolysis in DMG-H3K27a. We demonstrate that ERK5 mediates glycolysis through activation of transcription factor MEF2A, which subsequently modulates expression of glycolytic enzyme PFKFB3. We show that in vitro and mouse models of DMG-H3K27a are sensitive to the loss of PFKFB3. Multi-targeted drug therapy against the ERK5-PFKFB3 axis, such as with small-molecule inhibitors, may represent a promising therapeutic approach in patients with pediatric diffuse midline glioma.
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Affiliation(s)
- Stephanie M Casillo
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Taylor A Gatesman
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Akanksha Chilukuri
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Srinidhi Varadharajan
- Department of Pediatric Hematology and Oncology, St Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Brenden J Johnson
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Daniel R David Premkumar
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Esther P Jane
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Tritan J Plute
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Robert F Koncar
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Ann-Catherine J Stanton
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Carlos A O Biagi-Junior
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Callie S Barber
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Matthew E Halbert
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Brian J Golbourn
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Katharine Halligan
- Division of Hematology Oncology, University of Pittsburgh School of Medicine, Pittsburgh, Pittsburgh, PA 15261, USA; Division of Hematology Oncology, Department of Pediatrics, Albany Medical College, Albany, NY 12208, USA
| | - Andrea F Cruz
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Neveen M Mansi
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Allison Cheney
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; University of California, Santa Cruz Genomics Institute, Santa Cruz, CA 95064, USA
| | - Steven J Mullett
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Clinton Van't Land
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15261, USA; Rangos Metabolic Core Facility, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Jennifer L Perez
- Department of Neurological Surgery, Mayo Clinic Alix School of Medicine, Rochester, MN 55905, USA
| | - Max I Myers
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Nishant Agrawal
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Joshua J Michel
- Rangos Flow Cytometry Core Laboratory, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Yue-Fang Chang
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Olena M Vaske
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; University of California, Santa Cruz Genomics Institute, Santa Cruz, CA 95064, USA
| | - Antony MichaelRaj
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Frank S Lieberman
- Adult Neuro-Oncology Program, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - James Felker
- Pediatric Neuro-Oncology Program, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Sruti Shiva
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Heart, Lung, Blood, and Vascular Medicine Institute, Department of Internal Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Kelsey C Bertrand
- Department of Pediatric Hematology and Oncology, St Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Nduka Amankulor
- Department of Neurosurgery, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Costas G Hadjipanayis
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Kalil G Abdullah
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Pascal O Zinn
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Robert M Friedlander
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Taylor J Abel
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Javad Nazarian
- Brain Tumor Institute, Children's National Hospital, Washington, DC 20010, USA
| | - Sriram Venneti
- Laboratory of Brain Tumor Metabolism and Epigenetics, Department of Pathology, University of Michigan Medical School, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Stacy L Gelhaus
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA; Health Sciences Mass Spectrometry Core, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Stephen C Mack
- Department of Pediatric Hematology and Oncology, St Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ian F Pollack
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Sameer Agnihotri
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA; Pediatric Neuro-Oncology Program, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA.
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9
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Zhao Y, Su J, Xu CY, Li YB, Hu T, Li Y, Yang L, Zhao Q, Zhang WY. Establishment of a mandible defect model in rabbits infected with multiple bacteria and bioinformatics analysis. Front Bioeng Biotechnol 2024; 12:1350024. [PMID: 38282893 PMCID: PMC10811100 DOI: 10.3389/fbioe.2024.1350024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/04/2024] [Indexed: 01/30/2024] Open
Abstract
Objective: A model of chronic infectious mandibular defect (IMD) caused by mixed infection with Staphylococcus aureus and Pseudomonas aeruginosa was established to explore the occurrence and development of IMD and identify key genes by transcriptome sequencing and bioinformatics analysis. Methods: S. aureus and P. aeruginosa were diluted to 3 × 108 CFU/mL, and 6 × 3 × 3 mm defects lateral to the Mandibular Symphysis were induced in 28 New Zealand rabbits. Sodium Morrhuate (0.5%) and 50 μL bacterial solution were injected in turn. The modeling was completed after the bone wax closed; the effects were evaluated through postoperative observations, imaging and histological analyses. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and protein‒protein interaction (PPI) network analyses were performed to investigate the function of the differentially expressed genes (DEGs). Results: All rabbits showed characteristics of infection. The bacterial cultures were positive, and polymerase chain reaction (PCR) was used to identify S. aureus and P. aeruginosa. Cone beam CT and histological analyses showed inflammatory cell infiltration, pus formation in the medullary cavity, increased osteoclast activity in the defect area, and blurring at the edge of the bone defect. Bioinformatics analysis showed 1,804 DEGs, 743 were upregulated and 1,061 were downregulated. GO and KEGG analyses showed that the DEGs were enriched in immunity and osteogenesis inhibition, and the core genes identified by the PPI network were enriched in the Hedgehog pathway, which plays a role in inflammation and tissue repair; the MEF2 transcription factor family was predicted by IRegulon. Conclusion: By direct injection of bacterial solution into the rabbit mandible defect area, the rabbit chronic IMD model was successfully established. Based on the bioinformatics analysis, we speculate that the Hedgehog pathway and the MEF2 transcription factor family may be potential intervention targets for repairing IMD.
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Affiliation(s)
- Yuan Zhao
- Department of Stomatology, 920th Hospital of Joint Logistics Support Force of People’s Liberation Army of China, Kunming, China
- Postgraduate Research Institute, Kunming Medical University, Kunming, China
| | - Jun Su
- Department of Stomatology, 920th Hospital of Joint Logistics Support Force of People’s Liberation Army of China, Kunming, China
| | - Chong-yan Xu
- Department of Stomatology, 920th Hospital of Joint Logistics Support Force of People’s Liberation Army of China, Kunming, China
- Postgraduate Research Institute, Kunming Medical University, Kunming, China
| | - Yan-bo Li
- Postgraduate Research Institute, Kunming Medical University, Kunming, China
| | - Tong Hu
- Department of Stomatology, 920th Hospital of Joint Logistics Support Force of People’s Liberation Army of China, Kunming, China
- Postgraduate Research Institute, Kunming Medical University, Kunming, China
| | - Yi Li
- Department of Stomatology, 920th Hospital of Joint Logistics Support Force of People’s Liberation Army of China, Kunming, China
- Postgraduate Research Institute, Kunming Medical University, Kunming, China
| | - Li Yang
- Department of Stomatology, 920th Hospital of Joint Logistics Support Force of People’s Liberation Army of China, Kunming, China
| | - Qiang Zhao
- Department of Stomatology, 920th Hospital of Joint Logistics Support Force of People’s Liberation Army of China, Kunming, China
| | - Wen-yun Zhang
- Department of Stomatology, 920th Hospital of Joint Logistics Support Force of People’s Liberation Army of China, Kunming, China
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10
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Wellman R, Jacobson D, Secrier M, Labbadia J. Distinct patterns of proteostasis network gene expression are associated with different prognoses in melanoma patients. Sci Rep 2024; 14:198. [PMID: 38167612 PMCID: PMC10761826 DOI: 10.1038/s41598-023-50640-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/22/2023] [Indexed: 01/05/2024] Open
Abstract
The proteostasis network (PN) is a collection of protein folding and degradation pathways that spans cellular compartments and acts to preserve the integrity of the proteome. The differential expression of PN genes is a hallmark of many cancers, and the inhibition of protein quality control factors is an effective way to slow cancer cell growth. However, little is known about how the expression of PN genes differs between patients and how this impacts survival outcomes. To address this, we applied unbiased hierarchical clustering to gene expression data obtained from primary and metastatic cutaneous melanoma (CM) samples and found that two distinct groups of individuals emerge across each sample type. These patient groups are distinguished by the differential expression of genes encoding ATP-dependent and ATP-independent chaperones, and proteasomal subunits. Differences in PN gene expression were associated with increased levels of the transcription factors, MEF2A, SP4, ZFX, CREB1 and ATF2, as well as markedly different survival outcomes. However, surprisingly, similar PN alterations in primary and metastatic samples were associated with discordant survival outcomes in patients. Our findings reveal that the expression of PN genes demarcates CM patients and highlights several new proteostasis sub-networks that could be targeted for more effective suppression of CM within specific individuals.
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Affiliation(s)
- Rachel Wellman
- Division of Biosciences, Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London, UK
- Division of Biosciences, Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, UK
| | - Daniel Jacobson
- Division of Biosciences, Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, UK
- UCL Cancer Institute, University College London, London, UK
| | - Maria Secrier
- Division of Biosciences, Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, UK.
| | - John Labbadia
- Division of Biosciences, Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London, UK.
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11
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de Barros JW, Joule Pierre K, Kempinas WDG, Tremblay JJ. Ethylene dimethanesulfonate effects on gene promoter activities related to the endocrine function of immortalized Leydig cell lines R2C and MA-10. Curr Res Toxicol 2023; 6:100147. [PMID: 38234696 PMCID: PMC10792691 DOI: 10.1016/j.crtox.2023.100147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/12/2023] [Accepted: 12/21/2023] [Indexed: 01/19/2024] Open
Abstract
Ethylene dimethanesulfonate (EDS) is a molecule with known selective cytotoxicity on adult Leydig cells. A single intraperitoneal injection in rats but not mice, leads to male androgen deprivation and infertility. In vitro studies using rat and mouse immortalized Leydig cell lines, showed similar effects of cell death promoted by EDS in rat cells as seen in vivo, and suggest that EDS affects gene transcription, which could firstly compromise steroidogenesis before the apoptosis process. Using gene reporter assay, this study aimed to investigate EDS effects on the promoter activity of genes important for endocrine function (Star, Insl3) and response to toxic agents (Gsta3) in immortalized Leydig cell lines (rat R2C and mouse MA-10 cells), as well as identify possible EDS-responsive elements in the Star gene promoter. EDS exposure of R2C and MA-10 Leydig cells increased Gsta3 promoter activity after 4 h of treatment and decreased Insl3 promoter activity only in R2C cells after 24 h of treatment. EDS also decreased Star promoter activity in both Leydig cell lines. Using R2C cells, the EDS-responsive region in the Star promoter was located between -400 and -195 bp. This suggests that this region and the associated transcription factors, which include MEF2, might be targeted by EDS. Additional somatic gonadal cell lines expressing Star were used and EDS did not affect Star promoter activity in DC3 granulosa cells while Star promoter activity was increased in MSC-1 Sertoli cells after 24 h of treatment. This study contributes to the knowledge regarding the mechanism of EDS action in Leydig cells, and in other gonadal cell lineages, and brings new light regarding the rats and mice differential susceptibility to EDS effects, in addition to providing new avenues for experimental approaches to better understand Leydig cell function and dynamics in different rodent species.
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Affiliation(s)
- Jorge W.F. de Barros
- Laboratory of Reproductive and Developmental Biology and Toxicology, São Paulo State University (Unesp), Department of Structural and Functional Biology, Institute of Biosciences, Botucatu, SP, Brazil
- Reproduction, Mother and Child Health, Centre de Recherche du Centre Hospitalier Universitaire de Québec – Université Laval, Québec City, Canada
| | - Kenley Joule Pierre
- Reproduction, Mother and Child Health, Centre de Recherche du Centre Hospitalier Universitaire de Québec – Université Laval, Québec City, Canada
| | - Wilma De G. Kempinas
- Laboratory of Reproductive and Developmental Biology and Toxicology, São Paulo State University (Unesp), Department of Structural and Functional Biology, Institute of Biosciences, Botucatu, SP, Brazil
| | - Jacques J. Tremblay
- Reproduction, Mother and Child Health, Centre de Recherche du Centre Hospitalier Universitaire de Québec – Université Laval, Québec City, Canada
- Department of Obstetrics, Gynecology, and Reproduction, Faculty of Medicine, Centre for Research in Reproduction, Development and Intergenerational Health, Université Laval, Québec City, Canada
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12
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Lambo S, Trinh DL, Ries RE, Jin D, Setiadi A, Ng M, Leblanc VG, Loken MR, Brodersen LE, Dai F, Pardo LM, Ma X, Vercauteren SM, Meshinchi S, Marra MA. A longitudinal single-cell atlas of treatment response in pediatric AML. Cancer Cell 2023; 41:2117-2135.e12. [PMID: 37977148 DOI: 10.1016/j.ccell.2023.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/15/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023]
Abstract
Pediatric acute myeloid leukemia (pAML) is characterized by heterogeneous cellular composition, driver alterations and prognosis. Characterization of this heterogeneity and how it affects treatment response remains understudied in pediatric patients. We used single-cell RNA sequencing and single-cell ATAC sequencing to profile 28 patients representing different pAML subtypes at diagnosis, remission and relapse. At diagnosis, cellular composition differed between genetic subgroups. Upon relapse, cellular hierarchies transitioned toward a more primitive state regardless of subtype. Primitive cells in the relapsed tumor were distinct compared to cells at diagnosis, with under-representation of myeloid transcriptional programs and over-representation of other lineage programs. In some patients, this was accompanied by the appearance of a B-lymphoid-like hierarchy. Our data thus reveal the emergence of apparent subtype-specific plasticity upon treatment and inform on potentially targetable processes.
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Affiliation(s)
- Sander Lambo
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Diane L Trinh
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Rhonda E Ries
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Dan Jin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Audi Setiadi
- British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Pathology & Laboratory Medicine, Division of Hematopathology, Children's and Women's Health Centre of British Columbia, Vancouver, BC, Canada; Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Michelle Ng
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada; Department of Medical Genetics and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Veronique G Leblanc
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | | | | | - Fangyan Dai
- Hematologics, Incorporated, Seattle, WA, USA
| | | | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Suzanne M Vercauteren
- British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Pathology & Laboratory Medicine, Division of Hematopathology, Children's and Women's Health Centre of British Columbia, Vancouver, BC, Canada; Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada; Department of Medical Genetics and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.
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13
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Roth JF, Braunschweig U, Wu M, Li JD, Lin ZY, Larsen B, Weatheritt RJ, Gingras AC, Blencowe BJ. Systematic analysis of alternative exon-dependent interactome remodeling reveals multitasking functions of gene regulatory factors. Mol Cell 2023; 83:4222-4238.e10. [PMID: 38065061 DOI: 10.1016/j.molcel.2023.10.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 08/09/2023] [Accepted: 10/24/2023] [Indexed: 12/18/2023]
Abstract
Alternative splicing significantly expands biological complexity, particularly in the vertebrate nervous system. Increasing evidence indicates that developmental and tissue-dependent alternative exons often control protein-protein interactions; yet, only a minor fraction of these events have been characterized. Using affinity purification-mass spectrometry (AP-MS), we show that approximately 60% of analyzed neural-differential exons in proteins previously implicated in transcriptional regulation result in the gain or loss of interaction partners, which in some cases form unexpected links with coupled processes. Notably, a neural exon in Chtop regulates its interaction with the Prmt1 methyltransferase and DExD-Box helicases Ddx39b/a, affecting its methylation and activity in promoting RNA export. Additionally, a neural exon in Sap30bp affects interactions with RNA processing factors, modulating a critical function of Sap30bp in promoting the splicing of <100 nt "mini-introns" that control nuclear RNA levels. AP-MS is thus a powerful approach for elucidating the multifaceted functions of proteins imparted by context-dependent alternative exons.
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Affiliation(s)
- Jonathan F Roth
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | | | - Mingkun Wu
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jack Daiyang Li
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Brett Larsen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada
| | - Robert J Weatheritt
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; EMBL Australia, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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14
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Fadaka AO, Akinsoji T, Klein A, Madiehe AM, Meyer M, Keyster M, Sikhwivhilu LM, Sibuyi NRS. Stage-specific treatment of colorectal cancer: A microRNA-nanocomposite approach. J Pharm Anal 2023; 13:1235-1251. [PMID: 38174117 PMCID: PMC10759263 DOI: 10.1016/j.jpha.2023.07.008] [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] [Received: 02/16/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 01/05/2024] Open
Abstract
Colorectal cancer (CRC) is among the leading causes of cancer mortality. The lifetime risk of developing CRC is about 5% in adult males and females. CRC is usually diagnosed at an advanced stage, and at this point therapy has a limited impact on cure rates and long-term survival. Novel and/or improved CRC therapeutic options are needed. The involvement of microRNAs (miRNAs) in cancer development has been reported, and their regulation in many oncogenic pathways suggests their potent tumor suppressor action. Although miRNAs provide a promising therapeutic approach for cancer, challenges such as biodegradation, specificity, stability and toxicity, impede their progression into clinical trials. Nanotechnology strategies offer diverse advantages for the use of miRNAs for CRC-targeted delivery and therapy. The merits of using nanocarriers for targeted delivery of miRNA-formulations are presented herein to highlight the role they can play in miRNA-based CRC therapy by targeting different stages of the disease.
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Affiliation(s)
- Adewale Oluwaseun Fadaka
- Department of Anesthesia, Division of Pain Management, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, 7535, South Africa
| | - Taiwo Akinsoji
- School of Medicine, Southern Illinois University, Springfield, IL, 62702, USA
| | - Ashwil Klein
- Plant Omics Laboratory, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, 7535, South Africa
| | - Abram Madimabe Madiehe
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, 7535, South Africa
- Nanobiotechnology Research Group, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, 7535, South Africa
| | - Mervin Meyer
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, 7535, South Africa
| | - Marshall Keyster
- Environmental Biotechnology Laboratory, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, 7535, South Africa
| | - Lucky Mashudu Sikhwivhilu
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Advanced Materials Division, Mintek, Johannesburg, 2125, South Africa
- Department of Chemistry, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou, 0950, South Africa
| | - Nicole Remaliah Samantha Sibuyi
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Biolabels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, 7535, South Africa
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Advanced Materials Division, Mintek, Johannesburg, 2125, South Africa
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15
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Wang Z, Luo M, Liang Q, Zhao K, Hu Y, Wang W, Feng X, Hu B, Teng J, You T, Li R, Bao Z, Pan W, Yang T, Zhang C, Li T, Dong X, Yi X, Liu B, Zhao L, Li M, Chen K, Song W, Yang J, Li MJ. Landscape of enhancer disruption and functional screen in melanoma cells. Genome Biol 2023; 24:248. [PMID: 37904237 PMCID: PMC10614365 DOI: 10.1186/s13059-023-03087-5] [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: 08/18/2022] [Accepted: 10/12/2023] [Indexed: 11/01/2023] Open
Abstract
BACKGROUND The high mutation rate throughout the entire melanoma genome presents a major challenge in stratifying true driver events from the background mutations. Numerous recurrent non-coding alterations, such as those in enhancers, can shape tumor evolution, thereby emphasizing the importance in systematically deciphering enhancer disruptions in melanoma. RESULTS Here, we leveraged 297 melanoma whole-genome sequencing samples to prioritize highly recurrent regions. By performing a genome-scale CRISPR interference (CRISPRi) screen on highly recurrent region-associated enhancers in melanoma cells, we identified 66 significant hits which could have tumor-suppressive roles. These functional enhancers show unique mutational patterns independent of classical significantly mutated genes in melanoma. Target gene analysis for the essential enhancers reveal many known and hidden mechanisms underlying melanoma growth. Utilizing extensive functional validation experiments, we demonstrate that a super enhancer element could modulate melanoma cell proliferation by targeting MEF2A, and another distal enhancer is able to sustain PTEN tumor-suppressive potential via long-range interactions. CONCLUSIONS Our study establishes a catalogue of crucial enhancers and their target genes in melanoma growth and progression, and illuminates the identification of novel mechanisms of dysregulation for melanoma driver genes and new therapeutic targeting strategies.
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Affiliation(s)
- Zhao Wang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China.
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China.
| | - Menghan Luo
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Qian Liang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
- Scientific Research Center, Wenzhou Medical University, Wenzhou, China
| | - Ke Zhao
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yuelin Hu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Wei Wang
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xiangling Feng
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Bolang Hu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Jianjin Teng
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Tianyi You
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Ran Li
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Zhengkai Bao
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Wenhao Pan
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Tielong Yang
- Department of Bone and Soft Tissue Tumor, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Chao Zhang
- Department of Bone and Soft Tissue Tumor, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Ting Li
- Department of Bone and Soft Tissue Tumor, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xiaobao Dong
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xianfu Yi
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Ben Liu
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Li Zhao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Miaoxin Li
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Weihong Song
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, The Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, China.
| | - Jilong Yang
- Department of Bone and Soft Tissue Tumor, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China.
| | - Mulin Jun Li
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China.
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.
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16
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Szczepanek J, Tretyn A. MicroRNA-Mediated Regulation of Histone-Modifying Enzymes in Cancer: Mechanisms and Therapeutic Implications. Biomolecules 2023; 13:1590. [PMID: 38002272 PMCID: PMC10669115 DOI: 10.3390/biom13111590] [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: 09/21/2023] [Revised: 10/22/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
In the past decade, significant advances in molecular research have provided a deeper understanding of the intricate regulatory mechanisms involved in carcinogenesis. MicroRNAs, short non-coding RNA sequences, exert substantial influence on gene expression by repressing translation or inducing mRNA degradation. In the context of cancer, miRNA dysregulation is prevalent and closely associated with various stages of carcinogenesis, including initiation, progression, and metastasis. One crucial aspect of the cancer phenotype is the activity of histone-modifying enzymes that govern chromatin accessibility for transcription factors, thus impacting gene expression. Recent studies have revealed that miRNAs play a significant role in modulating these histone-modifying enzymes, leading to significant implications for genes related to proliferation, differentiation, and apoptosis in cancer cells. This article provides an overview of current research on the mechanisms by which miRNAs regulate the activity of histone-modifying enzymes in the context of cancer. Both direct and indirect mechanisms through which miRNAs influence enzyme expression are discussed. Additionally, potential therapeutic implications arising from miRNA manipulation to selectively impact histone-modifying enzyme activity are presented. The insights from this analysis hold significant therapeutic promise, suggesting the utility of miRNAs as tools for the precise regulation of chromatin-related processes and gene expression. A contemporary focus on molecular regulatory mechanisms opens therapeutic pathways that can effectively influence the control of tumor cell growth and dissemination.
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Affiliation(s)
- Joanna Szczepanek
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, ul. Wilenska 4, 87-100 Torun, Poland
| | - Andrzej Tretyn
- Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, ul. Lwowska 1, 87-100 Torun, Poland;
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Song X, Dong C, Man X. Phosphorylated MAPK11 promotes the progression of clear cell renal cell carcinoma by maintaining RUNX2 protein abundance. J Cell Mol Med 2023; 27:2583-2593. [PMID: 37525479 PMCID: PMC10468653 DOI: 10.1111/jcmm.17870] [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: 11/28/2022] [Revised: 06/20/2023] [Accepted: 07/16/2023] [Indexed: 08/02/2023] Open
Abstract
Previous studies have demonstrated that mitogen-activated protein kinase 11 (MAPK11) functions as an important point of integration in signalling transduction pathways and controlling endocellular processes, including viability of cells, differentiation, proliferation and apoptosis, through the sequence phosphorylation of the substrate protein Ser/Thr kinase protein cascade. Though MAPK 11 plays an important role in various tumours, especially in the invasive and metastatic processes, its expression and molecular mechanism in clear cell renal cell carcinoma (ccRCC) remain unclear. Runt-associated transcription factor 2 (RUNX2), a main transcription factor for osteoblast differentiation and chondrocyte maturation, has high expression in a number of tumours. In this study, the mRNA and protein levels of targeted genes in ccRCC tissues and adjacent tissues are analysed using the Cancer Genome Atlas (TCGA) database and western blotting. The ccRCC cell proliferation was measured with colony formation and EdU assay, and cell migration was examined through transwell assay. The interactive behaviour between proteins was detected with immunoprecipitation. Half-life period of RUNX2 protein was measured with cycloheximide chase assay. The results of the study indicated overexpression of MAPK11 and RUNX2 in ccRCC tissues and cell lines. MAPK11 and RUNX2 promoted the ccRCC cell proliferation and migration. Additionally, physical interaction took place between RUNX2 and P-MAPK11, which functioned to sustain the stability of RUNX2 protein. The high expression of RUNX2 could neutralize the functional degradation in MAPK11. And the outcomes of the study suggest that the P-MAPK11/RUNX2 axis may be used as a potential therapeutic target of ccRCC.
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Affiliation(s)
- Xiandong Song
- Department of UrologyThe First Hospital of China Medical UniversityShenyangLiaoningChina
| | - Changming Dong
- Department of UrologyThe First Hospital of China Medical UniversityShenyangLiaoningChina
| | - Xiaojun Man
- Department of UrologyThe First Hospital of China Medical UniversityShenyangLiaoningChina
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18
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Maisuria R, Norton A, Shao C, Bradley EW, Mansky K. Conditional Loss of MEF2C Expression in Osteoclasts Leads to a Sex-Specific Osteopenic Phenotype. Int J Mol Sci 2023; 24:12686. [PMID: 37628864 PMCID: PMC10454686 DOI: 10.3390/ijms241612686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Myocyte enhancement factor 2C (MEF2C) is a transcription factor studied in the development of skeletal and smooth muscles. Bone resorption studies have exhibited that the reduced expression of MEF2C contributes to osteopetrosis and the dysregulation of pathological bone remodeling. Our current study aims to determine how MEF2C contributes to osteoclast differentiation and to analyze the skeletal phenotype of Mef2c-cKO mice (Cfms-cre; Mef2cfl/fl). qRT-PCR and Western blot demonstrated that Mef2c expression is highest during the early days of osteoclast differentiation. Osteoclast genes, including c-Fos, c-Jun, Dc-stamp, Cathepsin K, and Nfatc1, had a significant reduction in expression, along with a reduction in osteoclast size. Despite reduced CTX activity, female Mef2c cKO mice were osteopenic, with decreased bone formation as determined via a P1NP ELISA, and a reduced number of osteoblasts. There was no difference between male WT and Mef2c-cKO mice. Our results suggest that Mef2c is critical for osteoclastogenesis, and that its dysregulation leads to a sex-specific osteopenic phenotype.
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Affiliation(s)
- Ravi Maisuria
- Department of Developmental and Surgical Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA; (R.M.); (A.N.)
| | - Andrew Norton
- Department of Developmental and Surgical Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA; (R.M.); (A.N.)
| | - Cynthia Shao
- College of Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Elizabeth W. Bradley
- Department of Orthopedics, School of Medicine and Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Kim Mansky
- Department of Developmental and Surgical Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA; (R.M.); (A.N.)
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19
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de Mattos K, Dumas FO, Campolina-Silva GH, Belleannée C, Viger RS, Tremblay JJ. ERK5 Cooperates With MEF2C to Regulate Nr4a1 Transcription in MA-10 and MLTC-1 Leydig Cells. Endocrinology 2023; 164:bqad120. [PMID: 37539861 PMCID: PMC10435423 DOI: 10.1210/endocr/bqad120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/30/2023] [Accepted: 08/02/2023] [Indexed: 08/05/2023]
Abstract
Leydig cells produce hormones required for the development and maintenance of sex characteristics and fertility in males. MEF2 transcription factors are important regulators of Leydig cell gene expression and steroidogenesis. ERK5 is an atypical member of the MAP kinase family that modulates transcription factor activity, either by direct phosphorylation or by acting as a transcriptional coactivator. While MEF2 and ERK5 are known to cooperate transcriptionally, the presence and role of ERK5 in Leydig cells remained unknown. Our goal was to determine whether ERK5 is present in Leydig cells and whether it cooperates with MEF2 to regulate gene expression. We found that ERK5 is present in Leydig cells in testicular tissue and immortalized cell lines. ERK5 knockdown in human chorionic gonadotrophin-treated MA-10 Leydig cells reduced steroidogenesis and decreased Star and Nr4a1 expression. Luciferase assays using a synthetic reporter plasmid containing 3 MEF2 elements revealed that ERK5 enhances MEF2-dependent promoter activation. Although ERK5 did not cooperate with MEF2 on the Star promoter in Leydig cell lines, we found that ERK5 and MEF2C do cooperate on the Nr4a1 promoter, which contains 2 adjacent MEF2 elements. Mutation of each MEF2 element in a short version of the Nr4a1 promoter significantly decreased the ERK5/MEF2C cooperation, indicating that both MEF2 elements need to be intact. The ERK5/MEF2C cooperation did not require phosphorylation of MEF2C on Ser387. Taken together, our data identify ERK5 as a new regulator of MEF2 activity in Leydig cells and provide potential new insights into mechanisms that regulate Leydig cell gene expression and function.
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Affiliation(s)
- Karine de Mattos
- Reproduction, Mother and Child Health, Centre de recherche du centre hospitalier universitaire de Québec, Université Laval, Québec City, QC, G1V 4G2, Canada
| | - Félix-Olivier Dumas
- Reproduction, Mother and Child Health, Centre de recherche du centre hospitalier universitaire de Québec, Université Laval, Québec City, QC, G1V 4G2, Canada
| | - Gabriel Henrique Campolina-Silva
- Reproduction, Mother and Child Health, Centre de recherche du centre hospitalier universitaire de Québec, Université Laval, Québec City, QC, G1V 4G2, Canada
| | - Clémence Belleannée
- Reproduction, Mother and Child Health, Centre de recherche du centre hospitalier universitaire de Québec, Université Laval, Québec City, QC, G1V 4G2, Canada
- Centre de recherche en Reproduction, Développement et Santé Intergénérationnelle, Department of Obstetrics, Gynecology, and Reproduction, Faculty of Medicine, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Robert S Viger
- Reproduction, Mother and Child Health, Centre de recherche du centre hospitalier universitaire de Québec, Université Laval, Québec City, QC, G1V 4G2, Canada
- Centre de recherche en Reproduction, Développement et Santé Intergénérationnelle, Department of Obstetrics, Gynecology, and Reproduction, Faculty of Medicine, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Jacques J Tremblay
- Reproduction, Mother and Child Health, Centre de recherche du centre hospitalier universitaire de Québec, Université Laval, Québec City, QC, G1V 4G2, Canada
- Centre de recherche en Reproduction, Développement et Santé Intergénérationnelle, Department of Obstetrics, Gynecology, and Reproduction, Faculty of Medicine, Université Laval, Québec City, QC, G1V 0A6, Canada
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20
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Padilla-Benavides T, Olea-Flores M, Sharma T, Syed SA, Witwicka H, Zuñiga-Eulogio MD, Zhang K, Navarro-Tito N, Imbalzano AN. Differential Contributions of mSWI/SNF Chromatin Remodeler Sub-Families to Myoblast Differentiation. Int J Mol Sci 2023; 24:11256. [PMID: 37511016 PMCID: PMC10378909 DOI: 10.3390/ijms241411256] [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: 05/30/2023] [Revised: 07/03/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Mammalian SWI/SNF (mSWI/SNF) complexes are ATP-dependent chromatin remodeling enzymes that are critical for normal cellular functions. mSWI/SNF enzymes are classified into three sub-families based on the presence of specific subunit proteins. The sub-families are Brm- or Brg1-associated factor (BAF), ncBAF (non-canonical BAF), and polybromo-associated BAF (PBAF). The biological roles for the different enzyme sub-families are poorly described. We knocked down the expression of genes encoding unique subunit proteins for each sub-family, Baf250A, Brd9, and Baf180, which mark the BAF, ncBAF, and PBAF sub-families, respectively, and examined the requirement for each in myoblast differentiation. We found that Baf250A and the BAF complex were required to drive lineage-specific gene expression. KD of Brd9 delayed differentiation. However, while the Baf250A-dependent gene expression profile included myogenic genes, the Brd9-dependent gene expression profile did not, suggesting Brd9 and the ncBAF complex indirectly contributed to differentiation. Baf180 was dispensable for myoblast differentiation. The results distinguish between the roles of the mSWI/SNF enzyme sub-families during myoblast differentiation.
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Affiliation(s)
- Teresita Padilla-Benavides
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA; (M.O.-F.); (M.D.Z.-E.); (K.Z.)
| | - Monserrat Olea-Flores
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA; (M.O.-F.); (M.D.Z.-E.); (K.Z.)
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; (T.S.); (S.A.S.); (H.W.)
| | - Tapan Sharma
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; (T.S.); (S.A.S.); (H.W.)
| | - Sabriya A. Syed
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; (T.S.); (S.A.S.); (H.W.)
| | - Hanna Witwicka
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; (T.S.); (S.A.S.); (H.W.)
| | - Miriam D. Zuñiga-Eulogio
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA; (M.O.-F.); (M.D.Z.-E.); (K.Z.)
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39086, GRO, Mexico;
| | - Kexin Zhang
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA; (M.O.-F.); (M.D.Z.-E.); (K.Z.)
| | - Napoleon Navarro-Tito
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39086, GRO, Mexico;
| | - Anthony N. Imbalzano
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; (T.S.); (S.A.S.); (H.W.)
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21
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Myers PJ, Lee SH, Lazzara MJ. An integrated mechanistic and data-driven computational model predicts cell responses to high- and low-affinity EGFR ligands. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.25.543329. [PMID: 37425852 PMCID: PMC10327094 DOI: 10.1101/2023.06.25.543329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The biophysical properties of ligand binding heavily influence the ability of receptors to specify cell fates. Understanding the rules by which ligand binding kinetics impact cell phenotype is challenging, however, because of the coupled information transfers that occur from receptors to downstream signaling effectors and from effectors to phenotypes. Here, we address that issue by developing an integrated mechanistic and data-driven computational modeling platform to predict cell responses to different ligands for the epidermal growth factor receptor (EGFR). Experimental data for model training and validation were generated using MCF7 human breast cancer cells treated with the high- and low-affinity ligands epidermal growth factor (EGF) and epiregulin (EREG), respectively. The integrated model captures the unintuitive, concentration-dependent abilities of EGF and EREG to drive signals and phenotypes differently, even at similar levels of receptor occupancy. For example, the model correctly predicts the dominance of EREG over EGF in driving a cell differentiation phenotype through AKT signaling at intermediate and saturating ligand concentrations and the ability of EGF and EREG to drive a broadly concentration-sensitive migration phenotype through cooperative ERK and AKT signaling. Parameter sensitivity analysis identifies EGFR endocytosis, which is differentially regulated by EGF and EREG, as one of the most important determinants of the alternative phenotypes driven by different ligands. The integrated model provides a new platform to predict how phenotypes are controlled by the earliest biophysical rate processes in signal transduction and may eventually be leveraged to understand receptor signaling system performance depends on cell context. One-sentence summary Integrated kinetic and data-driven EGFR signaling model identifies the specific signaling mechanisms that dictate cell responses to EGFR activation by different ligands.
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22
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Nandanpawar P, Sahoo L, Sahoo B, Murmu K, Chaudhari A, Pavan kumar A, Das P. Identification of differentially expressed genes and SNPs linked to harvest body weight of genetically improved rohu carp, Labeo rohita. Front Genet 2023; 14:1153911. [PMID: 37359361 PMCID: PMC10285081 DOI: 10.3389/fgene.2023.1153911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
In most of the aquaculture selection programs, harvest body weight has been a preferred performance trait for improvement. Molecular interplay of genes linked to higher body weight is not elucidated in major carp species. The genetically improved rohu carp with 18% average genetic gain per generation with respect to harvest body weight is a promising candidate for studying genes' underlying performance traits. In the present study, muscle transcriptome sequencing of two groups of individuals, with significant difference in breeding value, belonging to the tenth generation of rohu carp was performed using the Illumina HiSeq 2000 platform. A total of 178 million paired-end raw reads were generated to give rise to 173 million reads after quality control and trimming. The genome-guided transcriptome assembly and differential gene expression produced 11,86,119 transcripts and 451 upregulated and 181 downregulated differentially expressed genes (DEGs) between high-breeding value and low-breeding value (HB & LB) groups, respectively. Similarly, 39,158 high-quality coding SNPs were identified with the Ts/Tv ratio of 1.23. Out of a total of 17 qPCR-validated transcripts, eight were associated with cellular growth and proliferation and harbored 13 SNPs. The gene expression pattern was observed to be positively correlated with RNA-seq data for genes such as myogenic factor 6, titin isoform X11, IGF-1 like, acetyl-CoA, and thyroid receptor hormone beta. A total of 26 miRNA target interactions were also identified to be associated with significant DETs (p-value < 0.05). Genes such as Myo6, IGF-1-like, and acetyl-CoA linked to higher harvest body weight may serve as candidate genes in marker-assisted breeding and SNP array construction for genome-wide association studies and genomic selection.
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Affiliation(s)
- P. Nandanpawar
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - L. Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - B. Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - K. Murmu
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - A. Chaudhari
- ICAR-Central Institute of Fisheries Education, Mumbai, Maharashtra, India
| | - A. Pavan kumar
- ICAR-Central Institute of Fisheries Education, Mumbai, Maharashtra, India
| | - P. Das
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
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23
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Wang Y, Abrol R, Mak JYW, Das Gupta K, Ramnath D, Karunakaran D, Fairlie DP, Sweet MJ. Histone deacetylase 7: a signalling hub controlling development, inflammation, metabolism and disease. FEBS J 2023; 290:2805-2832. [PMID: 35303381 PMCID: PMC10952174 DOI: 10.1111/febs.16437] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/02/2022] [Accepted: 03/16/2022] [Indexed: 12/20/2022]
Abstract
Histone deacetylases (HDACs) catalyse removal of acetyl groups from lysine residues on both histone and non-histone proteins to control numerous cellular processes. Of the 11 zinc-dependent classical HDACs, HDAC4, 5, 7 and 9 are class IIa HDAC enzymes that regulate cellular and developmental processes through both enzymatic and non-enzymatic mechanisms. Over the last two decades, HDAC7 has been associated with key roles in numerous physiological and pathological processes. Molecular, cellular, in vivo and disease association studies have revealed that HDAC7 acts through multiple mechanisms to control biological processes in immune cells, osteoclasts, muscle, the endothelium and epithelium. This HDAC protein regulates gene expression, cell proliferation, cell differentiation and cell survival and consequently controls development, angiogenesis, immune functions, inflammation and metabolism. This review focuses on the cell biology of HDAC7, including the regulation of its cellular localisation and molecular mechanisms of action, as well as its associative and causal links with cancer and inflammatory, metabolic and fibrotic diseases. We also review the development status of small molecule inhibitors targeting HDAC7 and their potential for intervention in different disease contexts.
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Affiliation(s)
- Yizhuo Wang
- Institute for Molecular Bioscience (IMB)The University of QueenslandSt. LuciaAustralia
- IMB Centre for Inflammation and Disease ResearchThe University of QueenslandSt. LuciaAustralia
| | - Rishika Abrol
- Institute for Molecular Bioscience (IMB)The University of QueenslandSt. LuciaAustralia
- IMB Centre for Inflammation and Disease ResearchThe University of QueenslandSt. LuciaAustralia
| | - Jeffrey Y. W. Mak
- Institute for Molecular Bioscience (IMB)The University of QueenslandSt. LuciaAustralia
| | - Kaustav Das Gupta
- Institute for Molecular Bioscience (IMB)The University of QueenslandSt. LuciaAustralia
- IMB Centre for Inflammation and Disease ResearchThe University of QueenslandSt. LuciaAustralia
| | - Divya Ramnath
- Institute for Molecular Bioscience (IMB)The University of QueenslandSt. LuciaAustralia
- IMB Centre for Inflammation and Disease ResearchThe University of QueenslandSt. LuciaAustralia
| | - Denuja Karunakaran
- Institute for Molecular Bioscience (IMB)The University of QueenslandSt. LuciaAustralia
- IMB Centre for Inflammation and Disease ResearchThe University of QueenslandSt. LuciaAustralia
| | - David P. Fairlie
- Institute for Molecular Bioscience (IMB)The University of QueenslandSt. LuciaAustralia
- IMB Centre for Inflammation and Disease ResearchThe University of QueenslandSt. LuciaAustralia
- Australian Infectious Diseases Research CentreThe University of QueenslandSt. LuciaAustralia
| | - Matthew J. Sweet
- Institute for Molecular Bioscience (IMB)The University of QueenslandSt. LuciaAustralia
- IMB Centre for Inflammation and Disease ResearchThe University of QueenslandSt. LuciaAustralia
- Australian Infectious Diseases Research CentreThe University of QueenslandSt. LuciaAustralia
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24
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Wood S, Ishida K, Hagerty JR, Karahodza A, Dennis JN, Jolly ER. Characterization of Schistosome Sox Genes and Identification of a Flatworm Class of Sox Regulators. Pathogens 2023; 12:690. [PMID: 37242360 PMCID: PMC10222431 DOI: 10.3390/pathogens12050690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
Schistosome helminths infect over 200 million people across 78 countries and are responsible for nearly 300,000 deaths annually. However, our understanding of basic genetic pathways crucial for schistosome development is limited. The sex determining region Y-box 2 (Sox2) protein is a Sox B type transcriptional activator that is expressed prior to blastulation in mammals and is necessary for embryogenesis. Sox expression is associated with pluripotency and stem cells, neuronal differentiation, gut development, and cancer. Schistosomes express a Sox-like gene expressed in the schistosomula after infecting a mammalian host when schistosomes have about 900 cells. Here, we characterized and named this Sox-like gene SmSOXS1. SmSoxS1 protein is a developmentally regulated activator that localizes to the anterior and posterior ends of the schistosomula and binds to Sox-specific DNA elements. In addition to SmSoxS1, we have also identified an additional six Sox genes in schistosomes, two Sox B, one SoxC, and three Sox genes that may establish a flatworm-specific class of Sox genes with planarians. These data identify novel Sox genes in schistosomes to expand the potential functional roles for Sox2 and may provide interesting insights into early multicellular development of flatworms.
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Affiliation(s)
- Stephanie Wood
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA; (S.W.); (K.I.); (J.R.H.)
| | - Kenji Ishida
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA; (S.W.); (K.I.); (J.R.H.)
| | - James R. Hagerty
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA; (S.W.); (K.I.); (J.R.H.)
| | - Anida Karahodza
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA; (S.W.); (K.I.); (J.R.H.)
| | - Janay N. Dennis
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA; (S.W.); (K.I.); (J.R.H.)
| | - Emmitt R. Jolly
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA; (S.W.); (K.I.); (J.R.H.)
- Center for Global Health and Disease, Case Western Reserve University, Cleveland, OH 44106, USA
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25
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Li T, Conroy KL, Kim AM, Halmai J, Gao K, Moreno E, Wang A, Passerini AG, Nolta JA, Zhou P. Role of MEF2C in the Endothelial Cells Derived from Human Induced Pluripotent Stem Cells. Stem Cells 2023; 41:341-353. [PMID: 36639926 PMCID: PMC10128960 DOI: 10.1093/stmcls/sxad005] [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: 08/27/2021] [Accepted: 01/08/2023] [Indexed: 01/15/2023]
Abstract
Human induced pluripotent stem cells (hiPSCs) not only provide an abundant source of vascular cells for potential therapeutic applications in vascular disease but also constitute an excellent model for understanding the mechanisms that regulate the differentiation and the functionality of vascular cells. Here, we reported that myocyte enhancer factor 2C (MEF2C) transcription factor, but not any other members of the MEF2 family, was robustly upregulated during the differentiation of vascular progenitors and endothelial cells (ECs) from hiPSCs. Vascular endothelial growth factors (VEGF) strongly induced MEF2C expression in endothelial lineage cells. The specific upregulation of MEF2C during the commitment of endothelial lineage was dependent on the extracellular signal regulated kinase (ERK). Moreover, knockdown of MEF2C with shRNA in hiPSCs did not affect the differentiation of ECs from these hiPSCs, but greatly reduced the migration and tube formation capacity of the hiPSC-derived ECs. Through a chromatin immunoprecipitation-sequencing, genome-wide RNA-sequencing, quantitative RT-PCR, and immunostaining analyses of the hiPSC-derived endothelial lineage cells with MEF2C inhibition or knockdown compared to control hiPSC-derived ECs, we identified TNF-related apoptosis inducing ligand (TRAIL) and transmembrane protein 100 (TMEM100) as novel targets of MEF2C. This study demonstrates an important role for MEF2C in regulating human EC functions and highlights MEF2C and its downstream effectors as potential targets to treat vascular malfunction-associated diseases.
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Affiliation(s)
- Tao Li
- School of Medicine, Hunan Normal University, Changsha, Hunan, People’s Republic of China
- Stem Cell Program and Department of Internal Medicine, University of California Davis Medical Center, Sacramento, CA, USA
| | - Kelsey L Conroy
- Stem Cell Program and Department of Internal Medicine, University of California Davis Medical Center, Sacramento, CA, USA
| | - Amy M Kim
- Stem Cell Program and Department of Internal Medicine, University of California Davis Medical Center, Sacramento, CA, USA
| | - Julian Halmai
- Stem Cell Program and Department of Internal Medicine, University of California Davis Medical Center, Sacramento, CA, USA
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA, USA
- University of California Davis Gene Therapy Center, Sacramento, CA, USA
| | - Kewa Gao
- Department of Surgery, University of California Davis, Sacramento, CA, USA
| | - Emily Moreno
- Department of Biomedical Engineering, University of California Davis, Davis, CA, USA
| | - Aijun Wang
- Department of Surgery, University of California Davis, Sacramento, CA, USA
- Department of Biomedical Engineering, University of California Davis, Davis, CA, USA
| | - Anthony G Passerini
- Department of Biomedical Engineering, University of California Davis, Davis, CA, USA
| | - Jan A Nolta
- Stem Cell Program and Department of Internal Medicine, University of California Davis Medical Center, Sacramento, CA, USA
- University of California Davis Gene Therapy Center, Sacramento, CA, USA
| | - Ping Zhou
- Stem Cell Program and Department of Internal Medicine, University of California Davis Medical Center, Sacramento, CA, USA
- University of California Davis Gene Therapy Center, Sacramento, CA, USA
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Gene Structure, Expression and Function Analysis of MEF2 in the Pacific White Shrimp Litopenaeus vannamei. Int J Mol Sci 2023; 24:ijms24065832. [PMID: 36982906 PMCID: PMC10051702 DOI: 10.3390/ijms24065832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/08/2023] [Accepted: 03/15/2023] [Indexed: 03/22/2023] Open
Abstract
The Pacific white shrimp Litopenaeus vannamei is the most economically important crustacean in the world. The growth and development of shrimp muscle has always been the focus of attention. Myocyte Enhancer Factor 2 (MEF2), a member of MADS transcription factor, has an essential influence on various growth and development programs, including myogenesis. In this study, based on the genome and transcriptome data of L. vannamei, the gene structure and expression profiles of MEF2 were characterized. We found that the LvMEF2 was widely expressed in various tissues, mainly in the Oka organ, brain, intestine, heart, and muscle. Moreover, LvMEF2 has a large number of splice variants, and the main forms are the mutually exclusive exon and alternative 5′ splice site. The expression profiles of the LvMEF2 splice variants varied under different conditions. Interestingly, some splice variants have tissue or developmental expression specificity. After RNA interference into LvMEF2, the increment in the body length and weight decreased significantly and even caused death, suggesting that LvMEF2 can affect the growth and survival of L. vannamei. Transcriptome analysis showed that after LvMEF2 was knocked down, the protein synthesis and immune-related pathways were affected, and the associated muscle protein synthesis decreased, indicating that LvMEF2 affected muscle formation and the immune system. The results provide an important basis for future studies of the MEF2 gene and the mechanism of muscle growth and development in shrimp.
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Rubalcava-Gracia D, García-Villegas R, Larsson NG. No role for nuclear transcription regulators in mammalian mitochondria? Mol Cell 2023; 83:832-842. [PMID: 36182692 DOI: 10.1016/j.molcel.2022.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/17/2022] [Accepted: 09/08/2022] [Indexed: 10/14/2022]
Abstract
Although the mammalian mtDNA transcription machinery is simple and resembles bacteriophage systems, there are many reports that nuclear transcription regulators, as exemplified by MEF2D, MOF, PGC-1α, and hormone receptors, are imported into mammalian mitochondria and directly interact with the mtDNA transcription machinery. However, the supporting experimental evidence for this concept is open to alternate interpretations, and a main issue is the difficulty in distinguishing indirect regulation of mtDNA transcription, caused by altered nuclear gene expression, from direct intramitochondrial effects. We provide a critical discussion and experimental guidelines to stringently assess roles of intramitochondrial factors implicated in direct regulation of mammalian mtDNA transcription.
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Affiliation(s)
- Diana Rubalcava-Gracia
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Rodolfo García-Villegas
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Nils-Göran Larsson
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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28
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Bai YM, Yang F, Luo P, Xie LL, Chen JH, Guan YD, Zhou HC, Xu TF, Hao HW, Chen B, Zhao JH, Liang CL, Dai LY, Geng QS, Wang JG. Single-cell transcriptomic dissection of the cellular and molecular events underlying the triclosan-induced liver fibrosis in mice. Mil Med Res 2023; 10:7. [PMID: 36814339 PMCID: PMC9945401 DOI: 10.1186/s40779-023-00441-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 01/16/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Triclosan [5-chloro-2-(2,4-dichlorophenoxy) phenol, TCS], a common antimicrobial additive in many personal care and health care products, is frequently detected in human blood and urine. Therefore, it has been considered an emerging and potentially toxic pollutant in recent years. Long-term exposure to TCS has been suggested to exert endocrine disruption effects, and promote liver fibrogenesis and tumorigenesis. This study was aimed at clarifying the underlying cellular and molecular mechanisms of hepatotoxicity effect of TCS at the initiation stage. METHODS C57BL/6 mice were exposed to different dosages of TCS for 2 weeks and the organ toxicity was evaluated by various measurements including complete blood count, histological analysis and TCS quantification. Single cell RNA sequencing (scRNA-seq) was then carried out on TCS- or mock-treated mouse livers to delineate the TCS-induced hepatotoxicity. The acquired single-cell transcriptomic data were analyzed from different aspects including differential gene expression, transcription factor (TF) regulatory network, pseudotime trajectory, and cellular communication, to systematically dissect the molecular and cellular events after TCS exposure. To verify the TCS-induced liver fibrosis, the expression levels of key fibrogenic proteins were examined by Western blotting, immunofluorescence, Masson's trichrome and Sirius red staining. In addition, normal hepatocyte cell MIHA and hepatic stellate cell LX-2 were used as in vitro cell models to experimentally validate the effects of TCS by immunological, proteomic and metabolomic technologies. RESULTS We established a relatively short term TCS exposure murine model and found the TCS mainly accumulated in the liver. The scRNA-seq performed on the livers of the TCS-treated and control group profiled the gene expressions of > 76,000 cells belonging to 13 major cell types. Among these types, hepatocytes and hepatic stellate cells (HSCs) were significantly increased in TCS-treated group. We found that TCS promoted fibrosis-associated proliferation of hepatocytes, in which Gata2 and Mef2c are the key driving TFs. Our data also suggested that TCS induced the proliferation and activation of HSCs, which was experimentally verified in both liver tissue and cell model. In addition, other changes including the dysfunction and capillarization of endothelial cells, an increase of fibrotic characteristics in B plasma cells, and M2 phenotype-skewing of macrophage cells, were also deduced from the scRNA-seq analysis, and these changes are likely to contribute to the progression of liver fibrosis. Lastly, the key differential ligand-receptor pairs involved in cellular communications were identified and we confirmed the role of GAS6_AXL interaction-mediated cellular communication in promoting liver fibrosis. CONCLUSIONS TCS modulates the cellular activities and fates of several specific cell types (including hepatocytes, HSCs, endothelial cells, B cells, Kupffer cells and liver capsular macrophages) in the liver, and regulates the ligand-receptor interactions between these cells, thereby promoting the proliferation and activation of HSCs, leading to liver fibrosis. Overall, we provide the first comprehensive single-cell atlas of mouse livers in response to TCS and delineate the key cellular and molecular processes involved in TCS-induced hepatotoxicity and fibrosis.
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Affiliation(s)
- Yun-Meng Bai
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, the First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, China
| | - Fan Yang
- Department of Urology, Shenzhen People's Hospital, the First Affiliated Hospital, Southern University Science and Technology, the Second Clinical Medical College, Jinan University, Shenzhen, 518020, China.,Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, 510632, China
| | - Piao Luo
- Department of Urology, Shenzhen People's Hospital, the First Affiliated Hospital, Southern University Science and Technology, the Second Clinical Medical College, Jinan University, Shenzhen, 518020, China
| | - Lu-Lin Xie
- Department of Urology, Shenzhen People's Hospital, the First Affiliated Hospital, Southern University Science and Technology, the Second Clinical Medical College, Jinan University, Shenzhen, 518020, China
| | - Jun-Hui Chen
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, the First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, China
| | - Yu-Dong Guan
- Department of Urology, Shenzhen People's Hospital, the First Affiliated Hospital, Southern University Science and Technology, the Second Clinical Medical College, Jinan University, Shenzhen, 518020, China
| | - Hong-Chao Zhou
- Department of Urology, Shenzhen People's Hospital, the First Affiliated Hospital, Southern University Science and Technology, the Second Clinical Medical College, Jinan University, Shenzhen, 518020, China
| | - Teng-Fei Xu
- Department of Urology, Shenzhen People's Hospital, the First Affiliated Hospital, Southern University Science and Technology, the Second Clinical Medical College, Jinan University, Shenzhen, 518020, China
| | - Hui-Wen Hao
- Department of Urology, Shenzhen People's Hospital, the First Affiliated Hospital, Southern University Science and Technology, the Second Clinical Medical College, Jinan University, Shenzhen, 518020, China
| | - Bing Chen
- Department of Urology, Shenzhen People's Hospital, the First Affiliated Hospital, Southern University Science and Technology, the Second Clinical Medical College, Jinan University, Shenzhen, 518020, China.,Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, 510632, China
| | - Jia-Hui Zhao
- Department of Urology, Shenzhen People's Hospital, the First Affiliated Hospital, Southern University Science and Technology, the Second Clinical Medical College, Jinan University, Shenzhen, 518020, China.,Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, 510632, China
| | - Cai-Ling Liang
- Department of Urology, Shenzhen People's Hospital, the First Affiliated Hospital, Southern University Science and Technology, the Second Clinical Medical College, Jinan University, Shenzhen, 518020, China
| | - Ling-Yun Dai
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, the First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, China. .,Department of Urology, Shenzhen People's Hospital, the First Affiliated Hospital, Southern University Science and Technology, the Second Clinical Medical College, Jinan University, Shenzhen, 518020, China.
| | - Qing-Shan Geng
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, the First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, China. .,Department of Urology, Shenzhen People's Hospital, the First Affiliated Hospital, Southern University Science and Technology, the Second Clinical Medical College, Jinan University, Shenzhen, 518020, China.
| | - Ji-Gang Wang
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, and Shenzhen Clinical Research Centre for Geriatrics, Shenzhen People's Hospital, the First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, 518020, China. .,Department of Urology, Shenzhen People's Hospital, the First Affiliated Hospital, Southern University Science and Technology, the Second Clinical Medical College, Jinan University, Shenzhen, 518020, China. .,Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China. .,Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China. .,Center for Reproductive Medicine, Dongguan Maternal and Child Health Care Hospital, Southern Medical University, Dongguan, 523125, Guangdong, China.
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Samak M, Kues A, Kaltenborn D, Klösener L, Mietsch M, Germena G, Hinkel R. Dysregulation of Krüppel-like Factor 2 and Myocyte Enhancer Factor 2D Drive Cardiac Microvascular Inflammation and Dysfunction in Diabetes. Int J Mol Sci 2023; 24:2482. [PMID: 36768805 PMCID: PMC9916909 DOI: 10.3390/ijms24032482] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/24/2023] [Accepted: 01/25/2023] [Indexed: 02/03/2023] Open
Abstract
Cardiovascular complications are the main cause of morbidity and mortality from diabetes. Herein, vascular inflammation is a major pathological manifestation. We previously characterized the cardiac microvascular inflammatory phenotype in diabetic patients and highlighted micro-RNA 92a (miR-92a) as a driver of endothelial dysfunction. In this article, we further dissect the molecular underlying of these findings by addressing anti-inflammatory Krüppel-like factors 2 and 4 (KLF2 and KLF4). We show that KLF2 dysregulation in diabetes correlates with greater monocyte adhesion as well as migratory defects in cardiac microvascular endothelial cells. We also describe, for the first time, a role for myocyte enhancer factor 2D (MEF2D) in cardiac microvascular dysfunction in diabetes. We show that both KLFs 2 and 4, as well as MEF2D, are dysregulated in human and porcine models of diabetes. Furthermore, we prove a direct interaction between miR-92a and all three targets. Altogether, our data strongly qualify miR-92a as a potential therapeutic target for diabetes-associated cardiovascular disease.
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Affiliation(s)
- Mostafa Samak
- Laboratory Animal Science Unit, Leibniz-Institut für Primatenforschung, Deutsches Primatenzentrum GmbH, Kellnerweg 4, 37077 Göttingen, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Göttingen, 37075 Göttingen, Germany
| | - Andreas Kues
- Laboratory Animal Science Unit, Leibniz-Institut für Primatenforschung, Deutsches Primatenzentrum GmbH, Kellnerweg 4, 37077 Göttingen, Germany
| | - Diana Kaltenborn
- Laboratory Animal Science Unit, Leibniz-Institut für Primatenforschung, Deutsches Primatenzentrum GmbH, Kellnerweg 4, 37077 Göttingen, Germany
| | - Lina Klösener
- Laboratory Animal Science Unit, Leibniz-Institut für Primatenforschung, Deutsches Primatenzentrum GmbH, Kellnerweg 4, 37077 Göttingen, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Göttingen, 37075 Göttingen, Germany
- Institute for Animal Hygiene, Animal Welfare and Farm Animal Behaviour, University of Veterinary Medicine, 30173 Hannover, Germany
| | - Matthias Mietsch
- Laboratory Animal Science Unit, Leibniz-Institut für Primatenforschung, Deutsches Primatenzentrum GmbH, Kellnerweg 4, 37077 Göttingen, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Göttingen, 37075 Göttingen, Germany
| | - Giulia Germena
- Laboratory Animal Science Unit, Leibniz-Institut für Primatenforschung, Deutsches Primatenzentrum GmbH, Kellnerweg 4, 37077 Göttingen, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Göttingen, 37075 Göttingen, Germany
| | - Rabea Hinkel
- Laboratory Animal Science Unit, Leibniz-Institut für Primatenforschung, Deutsches Primatenzentrum GmbH, Kellnerweg 4, 37077 Göttingen, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Göttingen, 37075 Göttingen, Germany
- Institute for Animal Hygiene, Animal Welfare and Farm Animal Behaviour, University of Veterinary Medicine, 30173 Hannover, Germany
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30
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Muacevic A, Adler JR, Arora M, Ali MS, Pandey AK, Benjamin M, Palanichamy JK, Bakhshi S, Qamar I, Chopra A. Copy Number Alterations in CDKN2A/2B and MTAP Genes Are Associated With Low MEF2C Expression in T-cell Acute Lymphoblastic Leukemia. Cureus 2022; 14:e32151. [PMID: 36601176 PMCID: PMC9806946 DOI: 10.7759/cureus.32151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2022] [Indexed: 12/07/2022] Open
Abstract
The molecular heterogeneity of T-cell acute lymphoblastic leukemia (T-ALL) makes this disease complex. Early T-cell precursor ALL (ETP-ALL) is a recognized subtype of T-ALL associated with a high probability of induction failure with conventional therapy. Higher expression of myocyte enhancer factor 2C (MEF2C) and the absence of a biallelic deletion (ABD) are the designated markers for the ETP-ALL. Co-deletion of the contiguous genes cyclin-dependent kinase inhibitor 2A/2B (CDKN2A/2B) and the methylthioadenosine phosphorylase (MTAP) cluster, located at 9p21.3, is another common alteration in T-ALL and confers poor response to treatment. We used real-time polymerase chain reaction (PCR) analysis to assess MEF2C mRNA expression and ABD status. Copy number alterations (CNAs) in key genes previously reported to be altered in T-ALL were assessed using multiple ligation probe amplification (MLPA). We observed that CNAs in this co-deletion cluster of CDKN2A/B and MTAP genes exhibited low MEF2C expression while ABD was associated with CNA in the Abelson murine leukemia 1 (ABL1) gene. Assessment of MEF2C expression based on immunophenotype revealed that its association with CDKN2A/2B alteration is present in non-immature immunophenotype. Additionally, ABD was associated with copy number alterations of T-cell acute lymphocytic leukemia protein 1 (TAL1), myeloblastosis (MYB), and LIM domain only 2 (LMO2) genes in immature immunophenotypes. Further, STIL::TAL1 fusion was associated with low expression of MEF2C. These associations may help explain the difficulties in assessing disease heterogeneity and the prognostic importance of 9p21.3 alterations in T-ALL.
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31
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Pingul BY, Huang H, Chen Q, Alikarami F, Zhang Z, Qi J, Bernt KM, Berger SL, Cao Z, Shi J. Dissection of the MEF2D-IRF8 transcriptional circuit dependency in acute myeloid leukemia. iScience 2022; 25:105139. [PMID: 36193052 PMCID: PMC9526175 DOI: 10.1016/j.isci.2022.105139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 08/05/2022] [Accepted: 09/10/2022] [Indexed: 11/26/2022] Open
Abstract
Transcriptional dysregulation is a prominent feature in leukemia. Here, we systematically surveyed transcription factor (TF) vulnerabilities in leukemia and uncovered TF clusters that exhibit context-specific vulnerabilities within and between different subtypes of leukemia. Among these TF clusters, we demonstrated that acute myeloid leukemia (AML) with high IRF8 expression was addicted to MEF2D. MEF2D and IRF8 form an autoregulatory loop via direct binding to mutual enhancer elements. One important function of this circuit in AML is to sustain PU.1/MEIS1 co-regulated transcriptional outputs via stabilizing PU.1’s chromatin occupancy. We illustrated that AML could acquire dependency on this circuit through various oncogenic mechanisms that results in the activation of their enhancers. In addition to forming a circuit, MEF2D and IRF8 can also separately regulate gene expression, and dual perturbation of these two TFs leads to a more robust inhibition of AML proliferation. Collectively, our results revealed a TF circuit essential for AML survival. MEF2D is a context-specific vulnerability in IRF8hi AML MEF2D and IRF8 form a transcriptional circuit via binding to each other’s enhancers MEF2D-IRF8 circuit supports PU.1’s chromatin occupancy and transcriptional output MEF2D and IRF8 can regulate separate gene expression programs alongside the circuit
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32
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Coradduzza D, Garroni G, Congiargiu A, Balzano F, Cruciani S, Sedda S, Nivoli A, Maioli M. MicroRNAs, Stem Cells in Bipolar Disorder, and Lithium Therapeutic Approach. Int J Mol Sci 2022; 23:ijms231810489. [PMID: 36142403 PMCID: PMC9502703 DOI: 10.3390/ijms231810489] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 11/22/2022] Open
Abstract
Bipolar disorder (BD) is a severe, chronic, and disabling neuropsychiatric disorder characterized by recurrent mood disturbances (mania/hypomania and depression, with or without mixed features) and a constellation of cognitive, psychomotor, autonomic, and endocrine abnormalities. The etiology of BD is multifactorial, including both biological and epigenetic factors. Recently, microRNAs (miRNAs), a class of epigenetic regulators of gene expression playing a central role in brain development and plasticity, have been related to several neuropsychiatric disorders, including BD. Moreover, an alteration in the number/distribution and differentiation potential of neural stem cells has also been described, significantly affecting brain homeostasis and neuroplasticity. This review aimed to evaluate the most reliable scientific evidence on miRNAs as biomarkers for the diagnosis of BD and assess their implications in response to mood stabilizers, such as lithium. Neural stem cell distribution, regulation, and dysfunction in the etiology of BD are also dissected.
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Affiliation(s)
| | - Giuseppe Garroni
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | | | - Francesca Balzano
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Sara Cruciani
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Stefania Sedda
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Alessandra Nivoli
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, 07100 Sassari, Italy
- Correspondence: (A.N.); (M.M.); Tel.: +39-079-228-277 (A.N.); +39-079-255-406-228350 (M.M.)
| | - Margherita Maioli
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Center for Developmental Biology and Reprogramming (CEDEBIOR), Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy
- Correspondence: (A.N.); (M.M.); Tel.: +39-079-228-277 (A.N.); +39-079-255-406-228350 (M.M.)
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33
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Rysenkova KD, Troyanovskiy KE, Klimovich PS, Bulyakova TR, Shelomentseva EM, Shmakova AA, Tanygina DY, Ivashkina OI, Anokhin KV, Karagyaur MN, Zvereva MI, Rubina KA, Tkachuk VA, Semina EV. Identification of a Novel Small RNA Encoded in the Mouse Urokinase Receptor uPAR Gene ( Plaur) and Its Molecular Target Mef2d. Front Mol Neurosci 2022; 15:865858. [PMID: 35875662 PMCID: PMC9298986 DOI: 10.3389/fnmol.2022.865858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 05/16/2022] [Indexed: 12/24/2022] Open
Abstract
Urokinase receptor (uPAR) is a glycosylphosphatidylinositol (GPI)-anchored receptor of urokinase (uPA), which is involved in brain development, nerve regeneration, wound healing and tissue remodeling. We have recently shown that Plaur, which encodes uPAR, is an early response gene in murine brain. Assumingly, diverse functions of Plaur might be attributed to hypothetical, unidentified microRNAs encoded within introns of the Plaur gene. Using a bioinformatic approach we identified novel small RNAs within the Plaur gene and named them Plaur-miR1-3p and Plaur-miR1-5p. We confirmed Plaur-dependent expression of Plaur-miR1-3p and Plaur-miR1-5p in the mouse brain and mouse neuroblastoma Neuro2a cells. Utilizing an in silico MR-microT algorithm in DianaTools we selected two target genes – Mef2d and Emx2 with the highest binding scores to small RNAs selected from identified Plaur-Pre-miR1. Furthermore, sequencing of mouse brain samples for Plaur-miR1-5p target genes revealed two more genes—Nrip3 and Snrnp200. The expression of Emx2, Mef2d, and Snrnp200 in the mouse brain and Mef2d and Snrnp200 in Neuro2a cells correlated with expression of Plaur and small RNAs—Plaur-miR1-3p and Plaur-miR1-5p. Finally, we demonstrated elevated MEF2D protein expression in the mouse brain after Plaur induction and displayed activating effects of Plaur-miR1-5p on Mef2d expression in Neuro2a cells using Luciferase reporter assay. In conclusion, we have identified Plaur-miR1-3p and Plaur-miR1-5p as novel small RNAs encoded in the Plaur gene. This finding expands the current understanding of Plaur function in brain development and functioning.
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Affiliation(s)
- Karina D Rysenkova
- Institute of Experimental Cardiology, National Medical Research Centre of Cardiology named after academician E.I. Chazov, Moscow, Russia.,Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | | | - Polina S Klimovich
- Institute of Experimental Cardiology, National Medical Research Centre of Cardiology named after academician E.I. Chazov, Moscow, Russia.,Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | | | | | - Anna A Shmakova
- Institute of Experimental Cardiology, National Medical Research Centre of Cardiology named after academician E.I. Chazov, Moscow, Russia.,Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Daria Yu Tanygina
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Olga I Ivashkina
- Institute for Advanced Brain Studies, Lomonosov Moscow State University, Moscow, Russia.,Laboratory of Neurobiology of Memory, P.K. Anokhin Research Institute of Normal Physiology, Moscow, Russia.,Laboratory of Neuroscience, National Research Center "Kurchatov Institute", Moscow, Russia
| | - Konstantin V Anokhin
- Institute for Advanced Brain Studies, Lomonosov Moscow State University, Moscow, Russia.,Laboratory of Neurobiology of Memory, P.K. Anokhin Research Institute of Normal Physiology, Moscow, Russia
| | - Maxim N Karagyaur
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Maria I Zvereva
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Kseniya A Rubina
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Vsevolod A Tkachuk
- Institute of Experimental Cardiology, National Medical Research Centre of Cardiology named after academician E.I. Chazov, Moscow, Russia.,Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Ekaterina V Semina
- Institute of Experimental Cardiology, National Medical Research Centre of Cardiology named after academician E.I. Chazov, Moscow, Russia.,Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
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34
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Lu Z, Mao W, Yang H, Santiago-O'Farrill JM, Rask PJ, Mondal J, Chen H, Ivan C, Liu X, Liu CG, Xi Y, Masuda K, Carrami EM, Chen M, Tang Y, Pang L, Lakomy DS, Calin GA, Liang H, Ahmed AA, Vankayalapati H, Bast RC. SIK2 inhibition enhances PARP inhibitor activity synergistically in ovarian and triple-negative breast cancers. J Clin Invest 2022; 132:146471. [PMID: 35642638 PMCID: PMC9151707 DOI: 10.1172/jci146471] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/19/2022] [Indexed: 12/21/2022] Open
Abstract
Poly(ADP-ribose) polymerase inhibitors (PARP inhibitors) have had an increasing role in the treatment of ovarian and breast cancers. PARP inhibitors are selectively active in cells with homologous recombination DNA repair deficiency caused by mutations in BRCA1/2 and other DNA repair pathway genes. Cancers with homologous recombination DNA repair proficiency respond poorly to PARP inhibitors. Cancers that initially respond to PARP inhibitors eventually develop drug resistance. We have identified salt-inducible kinase 2 (SIK2) inhibitors, ARN3236 and ARN3261, which decreased DNA double-strand break (DSB) repair functions and produced synthetic lethality with multiple PARP inhibitors in both homologous recombination DNA repair deficiency and proficiency cancer cells. SIK2 is required for centrosome splitting and PI3K activation and regulates cancer cell proliferation, metastasis, and sensitivity to chemotherapy. Here, we showed that SIK2 inhibitors sensitized ovarian and triple-negative breast cancer (TNBC) cells and xenografts to PARP inhibitors. SIK2 inhibitors decreased PARP enzyme activity and phosphorylation of class-IIa histone deacetylases (HDAC4/5/7). Furthermore, SIK2 inhibitors abolished class-IIa HDAC4/5/7-associated transcriptional activity of myocyte enhancer factor-2D (MEF2D), decreasing MEF2D binding to regulatory regions with high chromatin accessibility in FANCD2, EXO1, and XRCC4 genes, resulting in repression of their functions in the DNA DSB repair pathway. The combination of PARP inhibitors and SIK2 inhibitors provides a therapeutic strategy to enhance PARP inhibitor sensitivity for ovarian cancer and TNBC.
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Affiliation(s)
- Zhen Lu
- Department of Experimental Therapeutics
| | | | | | | | | | | | - Hu Chen
- Department of Bioinformatics & Computational Biology, and
| | - Cristina Ivan
- Department of Experimental Therapeutics.,Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | | | - Yuanxin Xi
- Department of Bioinformatics & Computational Biology, and
| | - Kenta Masuda
- The University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA.,Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford, United Kingdom
| | - Eli M Carrami
- The University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA.,Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford, United Kingdom
| | - Meng Chen
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yitao Tang
- Department of Bioinformatics & Computational Biology, and.,The University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Lan Pang
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - George A Calin
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Han Liang
- Department of Bioinformatics & Computational Biology, and.,Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ahmed A Ahmed
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Headington, Oxford, United Kingdom.,Nuffield Department of Women's & Reproductive Health, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford, United Kingdom.,Oxford NIHR Biomedical Research Centre, Oxford, United Kingdom
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35
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Obata-Ninomiya K, de Jesus Carrion S, Hu A, Ziegler SF. Emerging role for thymic stromal lymphopoietin-responsive regulatory T cells in colorectal cancer progression in humans and mice. Sci Transl Med 2022; 14:eabl6960. [PMID: 35584230 DOI: 10.1126/scitranslmed.abl6960] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recruitment of regulatory T cells (Tregs) to tumors is a hallmark of cancer progression. Tumor-derived factors, such as the cytokine thymic stromal lymphopoietin (TSLP), can influence Treg function in tumors. In our study, we identified a subset of Tregs expressing the receptor for TSLP (TSLPR+ Tregs) that were increased in colorectal tumors in humans and mice and largely absent in adjacent normal colon. This Treg subset was also found in the peripheral blood of patients with colon cancer but not in the peripheral blood of healthy control subjects. Mechanistically, we found that this Treg subset coexpressed the interleukin-33 (IL-33) receptor [suppressor of tumorigenicity 2 (ST2)] and had high programmed cell death 1 (PD-1) and cytotoxic lymphocyte-associated antigen 4 (CTLA-4) expression, regulated in part by the transcription factor Mef2c. Treg-specific deletion of TSLPR, but not ST2, was associated with a reduction in tumor number and size with concomitant increase in TH1 cells in tumors in chemically induced mouse models of colorectal cancer. Therapeutic blockade of TSLP using TSLP-specific monoclonal antibodies effectively inhibited the progression of colorectal tumors in this mouse model. Collectively, these data suggest that TSLP controls the progression of colorectal cancer through regulation of tumor-specific Treg function and represents a potential therapeutic target that requires further investigation.
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Affiliation(s)
| | | | - Alex Hu
- Center for Systems Immunology, Benaroya Research Institute, Seattle, WA 98101, USA
| | - Steven F Ziegler
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA 98101, USA
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36
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Ruskovska T, Morand C, Bonetti CI, Gebara KS, Cardozo Junior EL, Milenkovic D. Multigenomic modifications in human circulating immune cells in response to consumption of polyphenol rich extract of yerba mate ( Ilex paraguariensis A. St.-Hil.) are suggestive of cardiometabolic protective effects. Br J Nutr 2022; 129:1-60. [PMID: 35373729 DOI: 10.1017/s0007114522001027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Mate is a traditional drink obtained from the leaves of yerba mate and rich in a diversity of plant bioactive compounds including polyphenols, particularly chlorogenic acids. Studies, even though limited, suggest that consumption of mate is associated with health effects, including prevention of cardiometabolic disorders. Molecular mechanisms underlying the potential health properties are still largely unknown, especially in humans. The aim of this study was to investigate nutrigenomic effects of mate consumption and identify regulatory networks potentially mediating cardiometabolic health benefits. Healthy middle-aged men at risk for cardiovascular disease consumed a standardized mate extract or placebo for 4 weeks. Global gene expression, including protein coding and non-coding RNAs profiles were determined using microarrays. Biological function analyses were performed using integrated bioinformatic tools. Comparison of global gene expression profiles showed significant change following mate consumption with 2635 significantly differentially expressed genes, among which 6 are miRNAs and 244 are lncRNAs. Functional analyses showed that these genes are involved in regulation of cell interactions and motility, inflammation or cell signaling. Transcription factors, such as MEF2A, MYB or HNF1A, could have their activity modulated by mate consumption either by direct interaction with polyphenol metabolites or by interactions of metabolites with cell signaling proteins, like p38 or ERK1/2, that could modulate transcription factor activity and regulate expression of genes observed. Correlation analysis suggests that expression profile is inversely associated with gene expression profiles of patients with cardiometabolic disorders. Therefore, mate consumption may exert cardiometabolic protective effects by modulating gene expression towards a protective profile.
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Affiliation(s)
- Tatjana Ruskovska
- Faculty of Medical Sciences, Goce Delcev University, 2000 Stip, North Macedonia
| | - Christine Morand
- Human Nutrition Unit, Université Clermont Auvergne, INRAE, F-63003 Clermont-Ferrand, France
| | - Carla Indianara Bonetti
- Institute of Biological, Medical and Health Sciences, Universidade Paranaense, Av. Parigot de Souza, 3636 J. Prada, Toledo 85903-170, PR, Brazil
| | - Karimi Sater Gebara
- Grande Dourados University Center, UNIGRAN, R. Balbina de Matos, 2121 - J. Universitario, Dourados 79824-900, MS, Brazil
| | - Euclides Lara Cardozo Junior
- Institute of Biological, Medical and Health Sciences, Universidade Paranaense, Av. Parigot de Souza, 3636 J. Prada, Toledo 85903-170, PR, Brazil
| | - Dragan Milenkovic
- Human Nutrition Unit, Université Clermont Auvergne, INRAE, F-63003 Clermont-Ferrand, France
- Department of Nutrition, University of California, Davis, Davis, CA, USA
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37
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Minisini M, Di Giorgio E, Kerschbamer E, Dalla E, Faggiani M, Franforte E, Meyer-Almes FJ, Ragno R, Antonini L, Mai A, Fiorentino F, Rotili D, Chinellato M, Perin S, Cendron L, Weichenberger CX, Angelini A, Brancolini C. Transcriptomic and genomic studies classify NKL54 as a histone deacetylase inhibitor with indirect influence on MEF2-dependent transcription. Nucleic Acids Res 2022; 50:2566-2586. [PMID: 35150567 PMCID: PMC8934631 DOI: 10.1093/nar/gkac081] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 01/25/2022] [Indexed: 12/23/2022] Open
Abstract
In leiomyosarcoma class IIa HDACs (histone deacetylases) bind MEF2 and convert these transcription factors into repressors to sustain proliferation. Disruption of this complex with small molecules should antagonize cancer growth. NKL54, a PAOA (pimeloylanilide o-aminoanilide) derivative, binds a hydrophobic groove of MEF2, which is used as a docking site by class IIa HDACs. However, NKL54 could also act as HDAC inhibitor (HDACI). Therefore, it is unclear which activity is predominant. Here, we show that NKL54 and similar derivatives are unable to release MEF2 from binding to class IIa HDACs. Comparative transcriptomic analysis classifies these molecules as HDACIs strongly related to SAHA/vorinostat. Low expressed genes are upregulated by HDACIs, while abundant genes are repressed. This transcriptional resetting correlates with a reorganization of H3K27 acetylation around the transcription start site (TSS). Among the upregulated genes there are several BH3-only family members, thus explaining the induction of apoptosis. Moreover, NKL54 triggers the upregulation of MEF2 and the downregulation of class IIa HDACs. NKL54 also increases the binding of MEF2D to promoters of genes that are upregulated after treatment. In summary, although NKL54 cannot outcompete MEF2 from binding to class IIa HDACs, it supports MEF2-dependent transcription through several actions, including potentiation of chromatin binding.
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Affiliation(s)
- Martina Minisini
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine Italy
| | - Eros Di Giorgio
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine Italy
| | - Emanuela Kerschbamer
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck. Via Galvani 31, 39100 Bolzano, Italy
| | - Emiliano Dalla
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine Italy
| | - Massimo Faggiani
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine Italy
| | - Elisa Franforte
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine Italy
| | - Franz-Josef Meyer-Almes
- Department of Chemical Engineering and Biotechnology, University of Applied Science, Haardtring 100, 64295 Darmstadt, Germany
| | - Rino Ragno
- Rome Center for Molecular Design, Department of Chemistry and Technology of Drugs, "Sapienza" University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Lorenzo Antonini
- Rome Center for Molecular Design, Department of Chemistry and Technology of Drugs, "Sapienza" University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Antonello Mai
- Department of Chemistry and Technology of Drugs, "Sapienza" University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Francesco Fiorentino
- Department of Chemistry and Technology of Drugs, "Sapienza" University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Dante Rotili
- Department of Chemistry and Technology of Drugs, "Sapienza" University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Monica Chinellato
- Department of Biology, University of Padova, Via U. Bassi, 58/B, 35121 Padova, Italy
| | - Stefano Perin
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Mestre, Italy.,European Centre for Living Technology (ECLT), Dorsoduro 3911, Calle Crosera, 30123 Venice, Italy
| | - Laura Cendron
- Department of Biology, University of Padova, Via U. Bassi, 58/B, 35121 Padova, Italy
| | - Christian X Weichenberger
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck. Via Galvani 31, 39100 Bolzano, Italy
| | - Alessandro Angelini
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Mestre, Italy.,European Centre for Living Technology (ECLT), Dorsoduro 3911, Calle Crosera, 30123 Venice, Italy
| | - Claudio Brancolini
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine Italy
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38
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Erber L, Liu S, Gong Y, Tran P, Chen Y. Quantitative Proteome and Transcriptome Dynamics Analysis Reveals Iron Deficiency Response Networks and Signature in Neuronal Cells. Molecules 2022; 27:484. [PMID: 35056799 PMCID: PMC8779535 DOI: 10.3390/molecules27020484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 01/17/2023] Open
Abstract
Iron and oxygen deficiencies are common features in pathophysiological conditions, such as ischemia, neurological diseases, and cancer. Cellular adaptive responses to such deficiencies include repression of mitochondrial respiration, promotion of angiogenesis, and cell cycle control. We applied a systematic proteomics analysis to determine the global proteomic changes caused by acute hypoxia and chronic and acute iron deficiency (ID) in hippocampal neuronal cells. Our analysis identified over 8600 proteins, revealing similar and differential effects of each treatment on activation and inhibition of pathways regulating neuronal development. In addition, comparative analysis of ID-induced proteomics changes in cultured cells and transcriptomic changes in the rat hippocampus identified common altered pathways, indicating specific neuronal effects. Transcription factor enrichment and correlation analysis identified key transcription factors that were activated in both cultured cells and tissue by iron deficiency, including those implicated in iron regulation, such as HIF1, NFY, and NRF1. We further identified MEF2 as a novel transcription factor whose activity was induced by ID in both HT22 proteome and rat hippocampal transcriptome, thus linking iron deficiency to MEF2-dependent cellular signaling pathways in neuronal development. Taken together, our study results identified diverse signaling networks that were differentially regulated by hypoxia and ID in neuronal cells.
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Affiliation(s)
- Luke Erber
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA; (L.E.); (Y.G.)
| | - Shirelle Liu
- Department of Pediatrics, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA;
| | - Yao Gong
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA; (L.E.); (Y.G.)
| | - Phu Tran
- Department of Pediatrics, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA;
| | - Yue Chen
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota at Twin Cities, Minneapolis, MN 55455, USA; (L.E.); (Y.G.)
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39
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Nair VD, Vasoya M, Nair V, Smith GR, Pincas H, Ge Y, Douglas CM, Esser KA, Sealfon SC. Differential analysis of chromatin accessibility and gene expression profiles identifies cis-regulatory elements in rat adipose and muscle. Genomics 2021; 113:3827-3841. [PMID: 34547403 DOI: 10.1016/j.ygeno.2021.09.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 09/08/2021] [Accepted: 09/15/2021] [Indexed: 01/04/2023]
Abstract
Chromatin accessibility is a key factor influencing gene expression. We optimized the Omni-ATAC-seq protocol and used it together with RNA-seq to investigate cis-regulatory elements in rat white adipose and skeletal muscle, two tissues with contrasting metabolic functions. While promoter accessibility correlated with RNA expression, integration of the two datasets identified tissue-specific differentially accessible regions (DARs) that predominantly localized in intergenic and intron regions. DARs were mapped to differentially expressed (DE) genes enriched in distinct biological processes in each tissue. Randomly selected DE genes were validated by qPCR. Top enriched motifs in DARs predicted binding sites for transcription factors (TFs) showing tissue-specific up-regulation. The correlation between differential chromatin accessibility at a given TF binding motif and differential expression of target genes further supported the functional relevance of that motif. Our study identified cis-regulatory regions that likely play a major role in the regulation of tissue-specific gene expression in adipose and muscle.
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Affiliation(s)
- Venugopalan D Nair
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Mital Vasoya
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Vishnu Nair
- Department of Computer Sciences, Columbia University, New York, NY 10027, USA
| | - Gregory R Smith
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hanna Pincas
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yongchao Ge
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Collin M Douglas
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, FL 32610, USA
| | - Karyn A Esser
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, FL 32610, USA
| | - Stuart C Sealfon
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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40
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Otmani K, Lewalle P. Tumor Suppressor miRNA in Cancer Cells and the Tumor Microenvironment: Mechanism of Deregulation and Clinical Implications. Front Oncol 2021; 11:708765. [PMID: 34722255 PMCID: PMC8554338 DOI: 10.3389/fonc.2021.708765] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/27/2021] [Indexed: 01/07/2023] Open
Abstract
MicroRNAs (miRNAs) are noncoding RNAs that have been identified as important posttranscriptional regulators of gene expression. miRNAs production is controlled at multiple levels, including transcriptional and posttranscriptional regulation. Extensive profiling studies have shown that the regulation of mature miRNAs expression plays a causal role in cancer development and progression. miRNAs have been identified to act as tumor suppressors (TS) or as oncogenes based on their modulating effect on the expression of their target genes. Upregulation of oncogenic miRNAs blocks TS genes and leads to tumor formation. In contrast, downregulation of miRNAs with TS function increases the translation of oncogenes. Several miRNAs exhibiting TS properties have been studied. In this review we focus on recent studies on the role of TS miRNAs in cancer cells and the tumor microenvironment (TME). Furthermore, we discuss how TS miRNA impacts the aggressiveness of cancer cells, with focus of the mechanism that regulate its expression. The study of the mechanisms of miRNA regulation in cancer cells and the TME may paved the way to understand its critical role in the development and progression of cancer and is likely to have important clinical implications in a near future. Finally, the potential roles of miRNAs as specific biomarkers for the diagnosis and the prognosis of cancer and the replacement of tumor suppressive miRNAs using miRNA mimics could be promising approaches for cancer therapy.
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Affiliation(s)
- Khalid Otmani
- Experimental Hematology Laboratory, Jules Bordet Institute, Université libre de Bruxelles, Brussels, Belgium
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41
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Peaslee C, Esteva-Font C, Su T, Munoz-Howell A, Duwaerts CC, Liu Z, Rao S, Liu K, Medina M, Sneddon JB, Maher JJ, Mattis AN. Doxycycline Significantly Enhances Induction of Induced Pluripotent Stem Cells to Endoderm by Enhancing Survival Through Protein Kinase B Phosphorylation. Hepatology 2021; 74:2102-2117. [PMID: 33982322 PMCID: PMC8544023 DOI: 10.1002/hep.31898] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 03/15/2021] [Accepted: 04/22/2021] [Indexed: 01/10/2023]
Abstract
BACKGROUND AND AIMS Induced pluripotent stem cells (iPSCs) provide an important tool for the generation of patient-derived cells, including hepatocyte-like cells, by developmental cues through an endoderm intermediate. However, most iPSC lines fail to differentiate into endoderm, with induction resulting in apoptosis. APPROACH AND RESULTS To address this issue, we built upon published methods to develop an improved protocol. We discovered that doxycycline dramatically enhances the efficiency of iPSCs to endoderm differentiation by inhibiting apoptosis and promoting proliferation through the protein kinase B pathway. We tested this protocol in >70 iPSC lines, 90% of which consistently formed complete sheets of endoderm. Endoderm generated by our method achieves similar transcriptomic profiles, expression of endoderm protein markers, and the ability to be further differentiated to downstream lineages. CONCLUSIONS Furthermore, this method achieves a 4-fold increase in endoderm cell number and will accelerate studies of human diseases in vitro and facilitate the expansion of iPSC-derived cells for transplantation studies.
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Affiliation(s)
- Caitlin Peaslee
- Department of Pathology, University of California San Francisco, San Francisco, CA
| | - Cristina Esteva-Font
- Department of Pathology, University of California San Francisco, San Francisco, CA
| | - Tao Su
- Department of Pathology, University of California San Francisco, San Francisco, CA
| | - Antonio Munoz-Howell
- Children’s Hospital Oakland Research Institute, University of California San Francisco, San Francisco, CA
| | - Caroline C. Duwaerts
- Department of Medicine, University of California San Francisco, San Francisco, CA
- Liver Center, University of California San Francisco, San Francisco, CA
| | - Zhe Liu
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA
- Diabetes Center, University of California San Francisco, San Francisco, CA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA
| | - Sneha Rao
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA
- Diabetes Center, University of California San Francisco, San Francisco, CA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA
| | - Ke Liu
- Children’s Hospital Oakland Research Institute, University of California San Francisco, San Francisco, CA
| | - Marisa Medina
- Children’s Hospital Oakland Research Institute, University of California San Francisco, San Francisco, CA
- Liver Center, University of California San Francisco, San Francisco, CA
| | - Julie B. Sneddon
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA
- Diabetes Center, University of California San Francisco, San Francisco, CA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA
- Department of Anatomy, University of California San Francisco, San Francisco, CA
| | - Jacquelyn J. Maher
- Department of Medicine, University of California San Francisco, San Francisco, CA
- Liver Center, University of California San Francisco, San Francisco, CA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA
| | - Aras N. Mattis
- Department of Pathology, University of California San Francisco, San Francisco, CA
- Liver Center, University of California San Francisco, San Francisco, CA
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42
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Oliveira RADC, Imparato DO, Fernandes VGS, Cavalcante JVF, Albanus RD, Dalmolin RJS. Reverse Engineering of the Pediatric Sepsis Regulatory Network and Identification of Master Regulators. Biomedicines 2021; 9:biomedicines9101297. [PMID: 34680414 PMCID: PMC8533457 DOI: 10.3390/biomedicines9101297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 01/04/2023] Open
Abstract
Sepsis remains a leading cause of death in ICUs all over the world, with pediatric sepsis accounting for a high percentage of mortality in pediatric ICUs. Its complexity makes it difficult to establish a consensus on genetic biomarkers and therapeutic targets. A promising strategy is to investigate the regulatory mechanisms involved in sepsis progression, but there are few studies regarding gene regulation in sepsis. This work aimed to reconstruct the sepsis regulatory network and identify transcription factors (TFs) driving transcriptional states, which we refer to here as master regulators. We used public gene expression datasets to infer the co-expression network associated with sepsis in a retrospective study. We identified a set of 15 TFs as potential master regulators of pediatric sepsis, which were divided into two main clusters. The first cluster corresponded to TFs with decreased activity in pediatric sepsis, and GATA3 and RORA, as well as other TFs previously implicated in the context of inflammatory response. The second cluster corresponded to TFs with increased activity in pediatric sepsis and was composed of TRIM25, RFX2, and MEF2A, genes not previously described as acting in a coordinated way in pediatric sepsis. Altogether, these results show how a subset of master regulators TF can drive pathological transcriptional states, with implications for sepsis biology and treatment.
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Affiliation(s)
- Raffael Azevedo de Carvalho Oliveira
- Bioinformatics Multidisciplinary Environment–BioME, Instituto Metrópole Digital, Universidade Federal do Rio Grande do Norte, Natal 59078-400, Brazil; (R.A.d.C.O.); (D.O.I.); (V.G.S.F.); (J.V.F.C.)
| | - Danilo Oliveira Imparato
- Bioinformatics Multidisciplinary Environment–BioME, Instituto Metrópole Digital, Universidade Federal do Rio Grande do Norte, Natal 59078-400, Brazil; (R.A.d.C.O.); (D.O.I.); (V.G.S.F.); (J.V.F.C.)
| | - Vítor Gabriel Saldanha Fernandes
- Bioinformatics Multidisciplinary Environment–BioME, Instituto Metrópole Digital, Universidade Federal do Rio Grande do Norte, Natal 59078-400, Brazil; (R.A.d.C.O.); (D.O.I.); (V.G.S.F.); (J.V.F.C.)
| | - João Vitor Ferreira Cavalcante
- Bioinformatics Multidisciplinary Environment–BioME, Instituto Metrópole Digital, Universidade Federal do Rio Grande do Norte, Natal 59078-400, Brazil; (R.A.d.C.O.); (D.O.I.); (V.G.S.F.); (J.V.F.C.)
| | - Ricardo D’Oliveira Albanus
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Rodrigo Juliani Siqueira Dalmolin
- Bioinformatics Multidisciplinary Environment–BioME, Instituto Metrópole Digital, Universidade Federal do Rio Grande do Norte, Natal 59078-400, Brazil; (R.A.d.C.O.); (D.O.I.); (V.G.S.F.); (J.V.F.C.)
- Department of Biochemistry–DBQ–CB, Federal University of Rio Grande do Norte, Natal 59064-741, Brazil
- Correspondence:
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43
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Alexandre PA, Naval-Sánchez M, Menzies M, Nguyen LT, Porto-Neto LR, Fortes MRS, Reverter A. Chromatin accessibility and regulatory vocabulary across indicine cattle tissues. Genome Biol 2021; 22:273. [PMID: 34548076 PMCID: PMC8454054 DOI: 10.1186/s13059-021-02489-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 09/08/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Spatiotemporal changes in the chromatin accessibility landscape are essential to cell differentiation, development, health, and disease. The quest of identifying regulatory elements in open chromatin regions across different tissues and developmental stages is led by large international collaborative efforts mostly focusing on model organisms, such as ENCODE. Recently, the Functional Annotation of Animal Genomes (FAANG) has been established to unravel the regulatory elements in non-model organisms, including cattle. Now, we can transition from prediction to validation by experimentally identifying the regulatory elements in tropical indicine cattle. The identification of regulatory elements, their annotation and comparison with the taurine counterpart, holds high promise to link regulatory regions to adaptability traits and improve animal productivity and welfare. RESULTS We generate open chromatin profiles for liver, muscle, and hypothalamus of indicine cattle through ATAC-seq. Using robust methods for motif discovery, motif enrichment and transcription factor binding sites, we identify potential master regulators of the epigenomic profile in these three tissues, namely HNF4, MEF2, and SOX factors, respectively. Integration with transcriptomic data allows us to confirm some of their target genes. Finally, by comparing our results with Bos taurus data we identify potential indicine-specific open chromatin regions and overlaps with indicine selective sweeps. CONCLUSIONS Our findings provide insights into the identification and analysis of regulatory elements in non-model organisms, the evolution of regulatory elements within two cattle subspecies as well as having an immediate impact on the animal genetics community in particular for a relevant productive species such as tropical cattle.
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Affiliation(s)
- Pâmela A Alexandre
- CSIRO Agriculture & Food, 306 Carmody Rd., QLD, 4067, Brisbane, Australia.
| | - Marina Naval-Sánchez
- CSIRO Agriculture & Food, 306 Carmody Rd., QLD, 4067, Brisbane, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Moira Menzies
- CSIRO Agriculture & Food, 306 Carmody Rd., QLD, 4067, Brisbane, Australia
| | - Loan T Nguyen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | | | - Marina R S Fortes
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Antonio Reverter
- CSIRO Agriculture & Food, 306 Carmody Rd., QLD, 4067, Brisbane, Australia
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44
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Xu TT, Zeng XW, Wang XH, Yang LX, Luo G, Yu T. Cystatin-B Negatively Regulates the Malignant Characteristics of Oral Squamous Cell Carcinoma Possibly Via the Epithelium Proliferation/Differentiation Program. Front Oncol 2021; 11:707066. [PMID: 34504787 PMCID: PMC8421684 DOI: 10.3389/fonc.2021.707066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 07/30/2021] [Indexed: 12/24/2022] Open
Abstract
Disturbance in the proteolytic process is one of the malignant signs of tumors. Proteolysis is highly orchestrated by cysteine cathepsin and its inhibitors. Cystatin-B (CSTB) is a general cysteine cathepsin inhibitor that prevents cysteine cathepsin from leaking from lysosomes and causing inappropriate proteolysis. Our study found that CSTB was downregulated in both oral squamous cell carcinoma (OSCC) tissues and cells compared with normal controls. Immunohistochemical analysis showed that CSTB was mainly distributed in the epithelial structure of OSCC tissues, and its expression intensity was related to the grade classification. A correlation analysis between CSTB and clinical prognosis was performed using gene expression data and clinical information acquired from The Cancer Genome Atlas (TCGA) database. Patients with lower expression levels of CSTB had shorter disease-free survival times and poorer clinicopathological features (e.g., lymph node metastases, perineural invasion, low degree of differentiation, and advanced tumor stage). OSCC cell models overexpressing CSTB were constructed to assess the effects of CSTB on malignant biological behaviors and upregulation of CSTB inhibited cell proliferation, migration, and invasion in vitro. Weighted gene correlation network analysis (WGCNA) and gene set enrichment analysis (GSEA) were performed based on the TCGA data to explore potential mechanisms, and CSTB appeared to correlate with squamous epithelial proliferation-differentiation processes, such as epidermal cell differentiation and keratinization. Moreover, in WGCNA, the gene module most associated with CSTB expression (i.e., the brown module) was also the one most associated with grade classification. Upregulation of CSTB promoted the expression levels of markers (LOR, IVL, KRT5/14, and KRT1/10), reflecting a tendency for differentiation and keratinization in vitro. Gene expression profile data of the overexpressed CSTB cell line were obtained by RNA sequencing (RNA-seq) technology. By comparing the GSEA enrichment results of RNA-seq data (from the OSCC models overexpressing CSTB) and existing public database data, three gene sets (i.e., apical junction, G2/M checkpoint, etc.) and six pathways (e.g., NOTCH signaling pathway, glycosaminoglycan degradation, mismatch repair, etc.) were enriched in the data from both sources. Overall, our study shows that CSTB is downregulated in OSCC and might regulate the malignant characteristics of OSCC via the epithelial proliferation/differentiation program.
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Affiliation(s)
- Tian-Tian Xu
- Department of Periodontics, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China
| | - Xiao-Wen Zeng
- Department of Periodontics, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China
| | - Xin-Hong Wang
- Department of Oral Pathology and Medicine, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China
| | - Lu-Xi Yang
- Department of Periodontics, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China
| | - Gang Luo
- Department of Periodontics, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China
| | - Ting Yu
- Department of Periodontics, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Guangzhou, China
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Seo MH, Yeo S. Srpk3 Decrease Associated with Alpha-Synuclein Increase in Muscles of MPTP-Induced Parkinson's Disease Mice. Int J Mol Sci 2021; 22:9375. [PMID: 34502283 PMCID: PMC8430752 DOI: 10.3390/ijms22179375] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/17/2021] [Accepted: 08/26/2021] [Indexed: 11/17/2022] Open
Abstract
Parkinson's disease (PD) is characterized by a loss of dopaminergic cells in the substantia nigra, and its histopathological features include the presence of fibrillar aggregates of α-synuclein (α-syn), which are called Lewy bodies and Lewy neurites. Lewy pathology has been identified not only in the brain but also in various tissues, including muscles. This study aimed to investigate the link between serine/arginine-rich protein specific kinase 3 (srpk3) and α-syn in muscles in PD. We conducted experiments on the quadriceps femoris of a 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced PD mouse model and the C2C12 cell line after treatment with 1-methyl-4-phenylpyridinium (MPP+) and srpk3 short interfering RNA (siRNA). Compared to the control group, the MPTP group showed significantly reduced expression of srpk3, but increased expression of α-syn. In MPP+-treated C2C12 cells, srpk3 expression gradually decreased and α-syn expression increased with the increasing MPP+ concentration. Moreover, experiments in C2C12 cells using srpk3 siRNA showed increased expressions of α-syn and phosphorylated α-syn. Our results showed that srpk3 expression could be altered by MPTP intoxication in muscles, and this change may be related to changes in α-syn expression. Furthermore, this study could contribute to advancement of research on the mechanism by which srpk3 plays a role in PD.
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Affiliation(s)
- Min Hyung Seo
- Department of Meridian and Acupoint, College of Korean Medicine, Sang Ji University, Wonju 26339, Korea;
| | - Sujung Yeo
- Department of Meridian and Acupoint, College of Korean Medicine, Sang Ji University, Wonju 26339, Korea;
- Research Institute of Korean Medicine, Sang Ji University, Wonju 26339, Korea
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Zia A, Rashid S. Systematic transition modeling analysis in the MEF2B-DNA binding interface due to Y69H and K4E variants. J Mol Graph Model 2021; 108:108009. [PMID: 34418874 DOI: 10.1016/j.jmgm.2021.108009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 10/20/2022]
Abstract
Transcriptional coactivator myocyte enhancer factor 2B (MEF2B) mutations are the most common cause of germinal center-derived B-cell non-Hodgkin lymphoma. Despite well-established contributions in lymphomagenesis, the structure-function paradigms of these mutations are largely unknown. Here through in silico approaches, we present structural evaluation of two reported missense variants (K4E and Y69H) in MEF2B to investigate their impact on DNA-binding through molecular dynamics simulation assays. Notably, MEF2B-specific MADs box domain (Lys23, Arg24 and Lys31) and N-terminal loop residues (Gly2, Arg3, Lys4, Lys5, Ile6 and Asn13) contribute in DNA binding, while in MEF2BK4E, DNA binding is facilitated by Gly2, Arg3 and Arg91 (α3) residues. Conversely, in MEF2BY69H, Arg3, Lys5, Ser78, Arg79 and Asn81 residues mediate DNA binding. DNA binding induces pronounced conformational readjustments in MEF2BWT-specific α1-N-terminal loop region, while MEF2BY69H and MEF2BK4E exhibit fluctuations in both α1 and α3. Hydrogen (H)-bond occupancy analysis reveals a similar DNA binding behavior for MEF2WT and MEF2BY69H, compared to MEF2BK4E structure. The Anisotropic Network Model analysis depicts α1 and α3 as more fluctuant regions in MEF2BK4E as compared to other systems. MEF2BWT and MEF2BK4E, Tyr69 residue is involved in p300 binding thus possible influence of Y69H variation in the functions other than DNA binding, such as p300 co-activator recruitment may explain the reduced transcriptional activation of MEF2BY69H. Thus, present study may provide a structural basis of DNA recognition by pinpointing the underlying conformational changes in the dynamics of MEF2BK4E, MEF2BY69H, and MEF2BWT structures that may contribute in the identification of novel therapeutic strategies for lymphomagenesis.
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Affiliation(s)
- Ayisha Zia
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan.
| | - Sajid Rashid
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan.
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Sunderaraman P, Cosentino S, Schupf N, Manly J, Gu Y, Barral S. MEF2C Common Genetic Variation Is Associated With Different Aspects of Cognition in Non-Hispanic White and Caribbean Hispanic Non-demented Older Adults. Front Genet 2021; 12:642327. [PMID: 34386032 PMCID: PMC8353395 DOI: 10.3389/fgene.2021.642327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/21/2021] [Indexed: 02/01/2023] Open
Abstract
OBJECTIVES Myocyte Enhancer Factor 2C (MEF2C) is identified as a candidate gene contributing to the risk of developing Alzheimer's disease. However, little is known about whether MEF2C plays a role in specific aspects of cognition among older adults. The current study investigated the association of common variants in the MEF2C gene with four cognitive domains including memory, visuospatial functioning, processing speed and language among non-demented individuals. METHOD Participants from two ethnic groups, Non-Hispanic White (NHW; n = 537) and Caribbean Hispanic (CH; n = 1,197) from the Washington Heights-Inwood Community Aging Project (WHICAP) study, were included. Genetic association analyses using WHICAP imputed genome-wide data (GWAS) were conducted for the various cognition domains. RESULTS Single nucleotide polymorphisms (SNP) variants in the MEF2C gene showed nominally significant associations in all cognitive domains but for different SNPs across both the ethnic groups. In NHW participants, the strongest associations were present for memory (rs302484), language (rs619584), processing speed (rs13159808), and visuospatial functioning (several SNPs). In CH, strongest associations were observed for memory (rs34822815), processing speed (rs304141), visuospatial functioning (rs10066711 and rs10038371), and language (rs304153). DISCUSSION MEF2C variant-cognitive associations shed light on an apparent role for MEF2C in both memory and non-memory aspects of cognition in individuals from NHW and CH ancestries. However, the little overlap in the specific SNP-cognition associations in CH versus NHW highlights the differences in genetic architectural variations among those from different ancestries that should be considered while studying the MEF2C gene.
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Affiliation(s)
- Preeti Sunderaraman
- Cognitive Neuroscience Division of the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, G.H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, United States
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Wang S, Cao Q, Cui X, Jing J, Li F, Shi H, Xue B, Shi H. Dnmt3b Deficiency in Myf5 +-Brown Fat Precursor Cells Promotes Obesity in Female Mice. Biomolecules 2021; 11:1087. [PMID: 34439754 PMCID: PMC8393658 DOI: 10.3390/biom11081087] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 11/17/2022] Open
Abstract
Increasing energy expenditure through activation of brown fat thermogenesis is a promising therapeutic strategy for the treatment of obesity. Epigenetic regulation has emerged as a key player in regulating brown fat development and thermogenic program. Here, we aimed to study the role of DNA methyltransferase 3b (Dnmt3b), a DNA methyltransferase involved in de novo DNA methylation, in the regulation of brown fat function and energy homeostasis. We generated a genetic model with Dnmt3b deletion in brown fat-skeletal lineage precursor cells (3bKO mice) by crossing Dnmt3b-floxed (fl/fl) mice with Myf5-Cre mice. Female 3bKO mice are prone to diet-induced obesity, which is associated with decreased energy expenditure. Dnmt3b deficiency also impairs cold-induced thermogenic program in brown fat. Surprisingly, further RNA-seq analysis reveals a profound up-regulation of myogenic markers in brown fat of 3bKO mice, suggesting a myocyte-like remodeling in brown fat. Further motif enrichment and pyrosequencing analysis suggests myocyte enhancer factor 2C (Mef2c) as a mediator for the myogenic alteration in Dnmt3b-deficient brown fat, as indicated by decreased methylation at its promoter. Our data demonstrate that brown fat Dnmt3b is a key regulator of brown fat development, energy metabolism and obesity in female mice.
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Affiliation(s)
- Shirong Wang
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA; (S.W.); (Q.C.); (X.C.); (J.J.); (F.L.)
| | - Qiang Cao
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA; (S.W.); (Q.C.); (X.C.); (J.J.); (F.L.)
| | - Xin Cui
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA; (S.W.); (Q.C.); (X.C.); (J.J.); (F.L.)
| | - Jia Jing
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA; (S.W.); (Q.C.); (X.C.); (J.J.); (F.L.)
| | - Fenfen Li
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA; (S.W.); (Q.C.); (X.C.); (J.J.); (F.L.)
| | - Huidong Shi
- Georgia Cancer Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA;
| | - Bingzhong Xue
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA; (S.W.); (Q.C.); (X.C.); (J.J.); (F.L.)
| | - Hang Shi
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA; (S.W.); (Q.C.); (X.C.); (J.J.); (F.L.)
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Sharma T, Robinson DCL, Witwicka H, Dilworth FJ, Imbalzano AN. The Bromodomains of the mammalian SWI/SNF (mSWI/SNF) ATPases Brahma (BRM) and Brahma Related Gene 1 (BRG1) promote chromatin interaction and are critical for skeletal muscle differentiation. Nucleic Acids Res 2021; 49:8060-8077. [PMID: 34289068 PMCID: PMC8373147 DOI: 10.1093/nar/gkab617] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 06/17/2021] [Accepted: 07/08/2021] [Indexed: 12/12/2022] Open
Abstract
Skeletal muscle regeneration is mediated by myoblasts that undergo epigenomic changes to establish the gene expression program of differentiated myofibers. mSWI/SNF chromatin remodeling enzymes coordinate with lineage-determining transcription factors to establish the epigenome of differentiated myofibers. Bromodomains bind to acetylated lysines on histone N-terminal tails and other proteins. The mutually exclusive ATPases of mSWI/SNF complexes, BRG1 and BRM, contain bromodomains with undefined functional importance in skeletal muscle differentiation. Pharmacological inhibition of mSWI/SNF bromodomain function using the small molecule PFI-3 reduced differentiation in cell culture and in vivo through decreased myogenic gene expression, while increasing cell cycle-related gene expression and the number of cells remaining in the cell cycle. Comparative gene expression analysis with data from myoblasts depleted of BRG1 or BRM showed that bromodomain function was required for a subset of BRG1- and BRM-dependent gene expression. Reduced binding of BRG1 and BRM after PFI-3 treatment showed that the bromodomain is required for stable chromatin binding at target gene promoters to alter gene expression. Our findings demonstrate that mSWI/SNF ATPase bromodomains permit stable binding of the mSWI/SNF ATPases to promoters required for cell cycle exit and establishment of muscle-specific gene expression.
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Affiliation(s)
- Tapan Sharma
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Daniel C L Robinson
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, University of Ottawa, Ottawa, ON K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Hanna Witwicka
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - F Jeffrey Dilworth
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, University of Ottawa, Ottawa, ON K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Anthony N Imbalzano
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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Katopodis P, Kerslake R, Zikopoulos A, Beri N, Anikin V. p38β - MAPK11 and its role in female cancers. J Ovarian Res 2021; 14:84. [PMID: 34174910 PMCID: PMC8236201 DOI: 10.1186/s13048-021-00834-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 06/07/2021] [Indexed: 12/24/2022] Open
Abstract
Background The p38MAPK family of Mitogen Activated Protein Kinases are a group of signalling molecules involved in cell growth, survival, proliferation and differentiation. The widely studied p38α isoform is ubiquitously expressed and is implicated in a number of cancer pathologies, as are p38γ and p38δ. However, the mechanistic role of the isoform, p38β, remains fairly elusive. Recent studies suggest a possible role of p38β in both breast and endometrial cancer with research suggesting involvement in bone metastasis and cancer cell survival. Female tissue specific cancers such as breast, endometrial, uterine and ovary account for over 3,000,000 cancer related incidents annually; advancements in therapeutics and treatment however require a deeper understanding of the molecular aetiology associated with these diseases. This study provides an overview of the MAPK signalling molecule p38β (MAPK11) in female cancers using an in-silico approach. Methods A detailed gene expression and methylation analysis was performed using datasets from cBioportal, CanSar and MEXPRESS. Breast, Uterine Endometrial, Cervical, Ovarian and Uterine Carcinosarcoma TCGA cancer datasets were used and analysed. Results Data using cBioportal and CanSAR suggest that expression of p38β is lower in cancers: BRCA, UCEC, UCS, CESC and OV compared to normal tissue. Methylation data from SMART and MEXPRESS indicate significant probe level variation of CpG island methylation status of the gene MAPK11. Analysis of the genes’ two CpG islands shows that the gene was hypermethylated in the CpG1 with increased methylation seen in BRCA, CESC and UCEC cancer data sets with a slight increase of expression recorded in cancer samples. CpG2 exhibited hypomethylation with no significant difference between samples and high levels of expression. Further analysis from MEXPRESS revealed no significance between probe methylation and altered levels of expression. In addition, no difference in the expression of BRCA oestrogen/progesterone/HER2 status was seen. Conclusion This data provides an overview of the expression of p38β in female tissue specific cancers, showing a decrease in expression of the gene in BRCA, UCEC, CESC, UCS and OV, increasing the understanding of p38β MAPK expression and offering insight for future in-vitro investigation and therapeutic application. Supplementary Information The online version contains supplementary material available at 10.1186/s13048-021-00834-9.
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Affiliation(s)
- Periklis Katopodis
- Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UK. .,Division of Thoracic Surgery, The Royal Brompton & Harefield NHS Foundation Trust, Harefield Hospital, London, UB9 6JH, UK.
| | - Rachel Kerslake
- Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UK
| | - Athanasios Zikopoulos
- Obstetrics and Gynaecology Department, Royal Cornwall Hospitals NHS Foundation Trust, Royal Cornwall Hospital, Truro, TR1 3LJ, UK
| | - Nefeli Beri
- Department of Medicine, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Vladimir Anikin
- Division of Thoracic Surgery, The Royal Brompton & Harefield NHS Foundation Trust, Harefield Hospital, London, UB9 6JH, UK.,Department of Oncology and Reconstructive Surgery, Sechenov First Moscow State Medical University, Moscow, Russian Federation, 119146
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