1
|
Nasif D, Laurito S, Real S, Branham MT. Exploring the epigenetic profile of ID4 in breast cancer: bioinformatic insights into methylation patterns and chromatin accessibility dynamics. Breast Cancer Res Treat 2024; 207:91-101. [PMID: 38702584 DOI: 10.1007/s10549-024-07343-5] [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: 01/11/2024] [Accepted: 04/10/2024] [Indexed: 05/06/2024]
Abstract
PURPOSE Inhibitor of differentiation 4 (ID4) is a dominant-negative regulator of basic helix-loop-helix (bHLH) transcription factors. The expression of ID4 is dysregulated in various breast cancer subtypes, indicating a potential role for ID4 in subtype-specific breast cancer development. This study aims to elucidate the epigenetic regulation of ID4 within breast cancer subtypes, with a particular focus on DNA methylation and chromatin accessibility. METHODS Bioinformatic analyses were conducted to assess DNA methylation and chromatin accessibility in ID4 regulatory regions across breast cancer subtypes. Gene Set Enrichment Analysis (GSEA) was conducted to identify related gene sets. Transcription factor binding within ID4 enhancer and promoter regions was explored. In vitro experiments involved ER+ breast cancer cell lines treated with estradiol (E2) and Tamoxifen. RESULTS Distinct epigenetic profiles of ID4 were observed, revealing increased methylation and reduced chromatin accessibility in luminal subtypes compared to the basal subtype. Gene Set Enrichment Analysis (GSEA) implicated estrogen-related pathways, suggesting a potential link between estrogen signaling and the regulation of ID4 expression. Transcription factor analysis identified ER and FOXA1 as regulators of ID4 enhancer regions. In vitro experiments confirmed the role of ER, demonstrating reduced ID4 expression and increased methylation with estradiol treatment. Conversely, Tamoxifen treatment increased ID4 expression, indicating the potential involvement of ER signaling through ERα in the epigenetic regulation of ID4 in breast cancer cells. CONCLUSION This study shows the intricate epigenetic regulation of ID4 in breast cancer, highlighting subtype-specific differences in DNA methylation and chromatin accessibility.
Collapse
Affiliation(s)
- Daniela Nasif
- Institute of Histology and Embryology, National Council of Scientific and Technological Research (CONICET), Parque General San Martin, 5500, Mendoza, Argentina
| | - Sergio Laurito
- Institute of Histology and Embryology, National Council of Scientific and Technological Research (CONICET), Parque General San Martin, 5500, Mendoza, Argentina
- Faculty of Exact and Natural Sciences, National University of Cuyo, Parque General San Martin, 5500, Mendoza, Argentina
| | - Sebastian Real
- Institute of Histology and Embryology, National Council of Scientific and Technological Research (CONICET), Parque General San Martin, 5500, Mendoza, Argentina
- Faculty of Medical Science, National University of Cuyo, Parque General San Martin, 5500, Mendoza, Argentina
| | - María Teresita Branham
- Institute of Histology and Embryology, National Council of Scientific and Technological Research (CONICET), Parque General San Martin, 5500, Mendoza, Argentina.
- Faculty of Medical Science, University of Mendoza, Boulogne Sur Mer 683, 5500, Mendoza, Argentina.
| |
Collapse
|
2
|
Deng Z, Xu M, Ding Z, Kong J, Liu J, Zhang Z, Cao P. ID2 promotes tumor progression and metastasis in thyroid cancer. Endocrine 2024; 84:1051-1063. [PMID: 38195969 PMCID: PMC11208273 DOI: 10.1007/s12020-023-03674-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/20/2023] [Indexed: 01/11/2024]
Abstract
BACKGROUND Inhibitor of DNA Binding 2 (ID2) plays a crucial role in tumor cell proliferation, invasion, metastasis, and stemness. Aberrant ID2 expression is associated with poor prognosis in various cancers. However, the specific function of ID2 in thyroid cancer remain unclear. METHOD The TCGA database were utilized to explore the clinical relevance of ID2 in cancer. GO, KEGG, and TIMER were employed to predict the potential roles of ID2 in cancer. Functional analysis, including CCK-8, colony formation, transwell, wound healing, and sphere formation experiments, were conducted to determine the biological functions of ID2 in human cancers. Western blot (WB), RT-qPCR, and immunohistochemical (IHC) analyses were used to investigate the relationship between ID2 and downstream targets. RESULTS Our study revealed significant overexpression of ID2 in various malignant tumor cells. Knocking ID2 significantly inhibited cancer cell proliferation and invasion, while overexpressing ID2 enhanced these capabilities. Additionally, ID2 mediates resistance of cancer cells to protein kinase B (or Akt) inhibitions. Further WB and IHC experiments indicated that ID2 promotes the phosphorylation activation of phosphatidylinositol 3-kinase (PI3K)/Akt signaling pathway, thereby upregulating the expression of downstream proliferation, epithelial-mesenchymal transition (EMT), and stemness-related markers. CONCLUSION We found that ID2 significantly promotes thyroid cancer cell proliferation, migration, EMT, and stemness through the PI3K/Akt pathway. Moreover, ID2 plays a crucial role in regulating cancer immune responses. It may serve as a potential biomarker for enhancing the efficacy of chemotherapy, targeted therapy, and immunotherapy against cancer.
Collapse
Affiliation(s)
- Zhongming Deng
- Department of General Surgery, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, 441000, China
| | - Min Xu
- Department of Anesthesiology, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, 441000, China
| | - Zhenghua Ding
- Department of General Surgery, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, 441000, China
| | - Jianqiao Kong
- Department of General Surgery, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, 441000, China
| | - Juanjuan Liu
- Department of Anesthesiology, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, 441000, China
| | - Zelin Zhang
- Department of Oncology Department, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, 441000, China.
| | - Ping Cao
- Department of Oncology Department, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, 441000, China.
| |
Collapse
|
3
|
Verdura S, Encinar JA, Gratchev A, Llop-Hernández À, López J, Serrano-Hervás E, Teixidor E, López-Bonet E, Martin-Castillo B, Micol V, Bosch-Barrera J, Cuyàs E, Menendez JA. Silibinin is a suppressor of the metastasis-promoting transcription factor ID3. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 128:155493. [PMID: 38484626 DOI: 10.1016/j.phymed.2024.155493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/31/2024] [Accepted: 02/26/2024] [Indexed: 05/01/2024]
Abstract
BACKGROUND ID3 (inhibitor of DNA binding/differentiation-3) is a transcription factor that enables metastasis by promoting stem cell-like properties in endothelial and tumor cells. The milk thistle flavonolignan silibinin is a phytochemical with anti-metastatic potential through largely unknown mechanisms. HYPOTHESIS/PURPOSE We have mechanistically investigated the ability of silibinin to inhibit the aberrant activation of ID3 in brain endothelium and non-small cell lung cancer (NSCLC) models. METHODS Bioinformatic analyses were performed to investigate the co-expression correlation between ID3 and bone morphogenic protein (BMP) ligands/BMP receptors (BMPRs) genes in NSCLC patient datasets. ID3 expression was assessed by immunoblotting and qRT-PCR. Luciferase reporter assays were used to evaluate the gene sequences targeted by silibinin to regulate ID3 transcription. In silico computational modeling and LanthaScreen TR-FRET kinase assays were used to characterize and validate the BMPR inhibitory activity of silibinin. Tumor tissues from NSCLC xenograft models treated with oral silibinin were used to evaluate the in vivo anti-ID3 effects of silibinin. RESULTS Analysis of lung cancer patient datasets revealed a top-ranked positive association of ID3 with the BMP9 endothelial receptor ACVRL1/ALK1 and the BMP ligand BMP6. Silibinin treatment blocked the BMP9-induced activation of the ALK1-phospho-SMAD1/5-ID3 axis in brain endothelial cells. Constitutive, acquired, and adaptive expression of ID3 in NSCLC cells were all significantly downregulated in response to silibinin. Silibinin blocked ID3 transcription via BMP-responsive elements in ID3 gene enhancers. Silibinin inhibited the kinase activities of BMPRs in the micromolar range, with the lower IC50 values occurring against ACVRL1/ALK1 and BMPR2. In an in vivo NSCLC xenograft model, tumoral overexpression of ID3 was completely suppressed by systematically achievable oral doses of silibinin. CONCLUSIONS ID3 is a largely undruggable metastasis-promoting transcription factor. Silibinin is a novel suppressor of ID3 that may be explored as a novel therapeutic approach to interfere with the metastatic dissemination capacity of NSCLC.
Collapse
Affiliation(s)
- Sara Verdura
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology, Girona, 17007, Spain; Metabolism and Cancer Group, Girona Biomedical Research Institute (IDIBGI), Girona 17190, Spain
| | - José Antonio Encinar
- Institute of Research, Development and Innovation in Health Biotechnology of Elche (IDiBE), Universitas Miguel Hernández (UMH), Elche 03202, Spain
| | - Alexei Gratchev
- Laboratory for Tumor Stromal Cell Biology, Institute of Carcinogenesis, Nikolaj Nikolajevich (N.N.) Blokhin National Medical Research Center of Oncology, Moscow 115478, Russia
| | - Àngela Llop-Hernández
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology, Girona, 17007, Spain; Metabolism and Cancer Group, Girona Biomedical Research Institute (IDIBGI), Girona 17190, Spain
| | - Júlia López
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology, Girona, 17007, Spain; Metabolism and Cancer Group, Girona Biomedical Research Institute (IDIBGI), Girona 17190, Spain
| | - Eila Serrano-Hervás
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology, Girona, 17007, Spain; Metabolism and Cancer Group, Girona Biomedical Research Institute (IDIBGI), Girona 17190, Spain
| | - Eduard Teixidor
- Precision Oncology Group (OncoGir-Pro), Girona Biomedical Research Institute (IDIBGI), Girona 17190, Spain; Medical Oncology, Catalan Institute of Oncology, Girona, 17007, Spain
| | - Eugeni López-Bonet
- Metabolism and Cancer Group, Girona Biomedical Research Institute (IDIBGI), Girona 17190, Spain; Department of Anatomical Pathology, Dr. Josep Trueta Hospital of Girona, Girona 17007, Spain
| | - Begoña Martin-Castillo
- Metabolism and Cancer Group, Girona Biomedical Research Institute (IDIBGI), Girona 17190, Spain; Unit of Clinical Research, Catalan Institute of Oncology, Girona, 17007, Spain
| | - Vicente Micol
- Institute of Research, Development and Innovation in Health Biotechnology of Elche (IDiBE), Universitas Miguel Hernández (UMH), Elche 03202, Spain; CIBER Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III (ISCIII), Madrid, 28029, Spain
| | - Joaquim Bosch-Barrera
- Precision Oncology Group (OncoGir-Pro), Girona Biomedical Research Institute (IDIBGI), Girona 17190, Spain; Medical Oncology, Catalan Institute of Oncology, Girona, 17007, Spain; Department of Medical Sciences, Medical School, University of Girona, Girona, Spain
| | - Elisabet Cuyàs
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology, Girona, 17007, Spain; Metabolism and Cancer Group, Girona Biomedical Research Institute (IDIBGI), Girona 17190, Spain
| | - Javier A Menendez
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology, Girona, 17007, Spain; Metabolism and Cancer Group, Girona Biomedical Research Institute (IDIBGI), Girona 17190, Spain.
| |
Collapse
|
4
|
Luo W, Egger M, Cruz-Ochoa N, Tse A, Maloveczky G, Tamás B, Lukacsovich D, Seng C, Amrein I, Lukacsovich T, Wolfer D, Földy C. Activation of feedforward wiring in adult hippocampal neurons by the basic-helix-loop-helix transcription factor Ascl4. PNAS NEXUS 2024; 3:pgae174. [PMID: 38711810 PMCID: PMC11071515 DOI: 10.1093/pnasnexus/pgae174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/17/2024] [Indexed: 05/08/2024]
Abstract
Although evidence indicates that the adult brain retains a considerable capacity for circuit formation, adult wiring has not been broadly considered and remains poorly understood. In this study, we investigate wiring activation in adult neurons. We show that the basic-helix-loop-helix transcription factor Ascl4 can induce wiring in different types of hippocampal neurons of adult mice. The new axons are mainly feedforward and reconfigure synaptic weights in the circuit. Mice with the Ascl4-induced circuits do not display signs of pathology and solve spatial problems equally well as controls. Our results demonstrate reprogrammed connectivity by a single transcriptional factor and provide insights into the regulation of brain wiring in adults.
Collapse
Affiliation(s)
- Wenshu Luo
- Laboratory of Neural Connectivity, Brain Research Institute, Faculties of Medicine and Science, University of Zürich, Zürich 8057, Switzerland
| | - Matteo Egger
- Laboratory of Neural Connectivity, Brain Research Institute, Faculties of Medicine and Science, University of Zürich, Zürich 8057, Switzerland
- Adaptive Brain Circuits in Development and Learning (AdaBD), University Research Priority Program (URPP), University of Zürich, Zürich 8057, Switzerland
| | - Natalia Cruz-Ochoa
- Laboratory of Neural Connectivity, Brain Research Institute, Faculties of Medicine and Science, University of Zürich, Zürich 8057, Switzerland
- Adaptive Brain Circuits in Development and Learning (AdaBD), University Research Priority Program (URPP), University of Zürich, Zürich 8057, Switzerland
| | - Alice Tse
- Laboratory of Neural Connectivity, Brain Research Institute, Faculties of Medicine and Science, University of Zürich, Zürich 8057, Switzerland
| | - Gyula Maloveczky
- Laboratory of Neural Connectivity, Brain Research Institute, Faculties of Medicine and Science, University of Zürich, Zürich 8057, Switzerland
| | - Bálint Tamás
- Laboratory of Neural Connectivity, Brain Research Institute, Faculties of Medicine and Science, University of Zürich, Zürich 8057, Switzerland
| | - David Lukacsovich
- Laboratory of Neural Connectivity, Brain Research Institute, Faculties of Medicine and Science, University of Zürich, Zürich 8057, Switzerland
| | - Charlotte Seng
- Laboratory of Neural Connectivity, Brain Research Institute, Faculties of Medicine and Science, University of Zürich, Zürich 8057, Switzerland
| | - Irmgard Amrein
- Institute of Anatomy, Faculty of Medicine, University of Zürich, Zürich 8057, Switzerland
| | - Tamás Lukacsovich
- Laboratory of Neural Connectivity, Brain Research Institute, Faculties of Medicine and Science, University of Zürich, Zürich 8057, Switzerland
| | - David Wolfer
- Institute of Anatomy, Faculty of Medicine, University of Zürich, Zürich 8057, Switzerland
- Institute of Human Movement Sciences and Sport, D-HEST, ETH Zürich, Zürich 8057, Switzerland
| | - Csaba Földy
- Laboratory of Neural Connectivity, Brain Research Institute, Faculties of Medicine and Science, University of Zürich, Zürich 8057, Switzerland
- Adaptive Brain Circuits in Development and Learning (AdaBD), University Research Priority Program (URPP), University of Zürich, Zürich 8057, Switzerland
| |
Collapse
|
5
|
Tresenrider A, Hooper M, Todd L, Kierney F, Blasdel N, Trapnell C, Reh TA. A multiplexed, single-cell sequencing screen identifies compounds that increase neurogenic reprogramming of murine Muller glia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.26.559569. [PMID: 37808650 PMCID: PMC10557658 DOI: 10.1101/2023.09.26.559569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Retinal degeneration in mammals causes permanent loss of vision, due to an inability to regenerate naturally. Some non-mammalian vertebrates show robust regeneration, via Muller glia (MG). We have recently made significant progress in stimulating adult mouse MG to regenerate functional neurons by transgenic expression of the proneural transcription factor Ascl1. While these results showed that MG can serve as an endogenous source of neuronal replacement, the efficacy of this process is limited. With the goal of improving this in mammals, we designed a small molecule screen using sci-Plex, a method to multiplex up to thousands of single nucleus RNA-seq conditions into a single experiment. We used this technology to screen a library of 92 compounds, identified, and validated two that promote neurogenesis in vivo. Our results demonstrate that high-throughput single-cell molecular profiling can substantially improve the discovery process for molecules and pathways that can stimulate neural regeneration and further demonstrate the potential for this approach to restore vision in patients with retinal disease.
Collapse
Affiliation(s)
- Amy Tresenrider
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Marcus Hooper
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Levi Todd
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Faith Kierney
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Nicolai Blasdel
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Brotman-Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98195, USA
| | - Thomas A. Reh
- Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
6
|
González-Álvarez H, Ensan D, Xin T, Wong JF, Zepeda-Velázquez CA, Cros J, Sweeney MN, Hoffer L, Kiyota T, Wilson BJ, Aman A, Roberts O, Isaac MB, Bullock AN, Smil D, Al-awar R. Discovery of Conformationally Constrained ALK2 Inhibitors. J Med Chem 2024; 67:4707-4725. [PMID: 38498998 PMCID: PMC10983009 DOI: 10.1021/acs.jmedchem.3c02308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 03/20/2024]
Abstract
Despite decades of research on new diffuse intrinsic pontine glioma (DIPG) treatments, little or no progress has been made on improving patient outcomes. In this work, we explored novel scaffold modifications of M4K2009, a 3,5-diphenylpyridine ALK2 inhibitor previously reported by our group. Here we disclose the design, synthesis, and evaluation of a first-in-class set of 5- to 7-membered ether-linked and 7-membered amine-linked constrained inhibitors of ALK2. This rigidification strategy led us to the discovery of the ether-linked inhibitors M4K2308 and M4K2281 and the amine-linked inhibitors M4K2304 and M4K2306, each with superior potency against ALK2. Notably, M4K2304 and M4K2306 exhibit exceptional selectivity for ALK2 over ALK5, surpassing the reference compound. Preliminary studies on their in vivo pharmacokinetics, including blood-brain barrier penetration, revealed that these constrained scaffolds have favorable exposure and do open a novel chemical space for further optimization and future evaluation in orthotopic models of DIPG.
Collapse
Affiliation(s)
- Héctor González-Álvarez
- Drug
Discovery Program, Ontario Institute for
Cancer Research, 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada
- Department
of Pharmacology and Toxicology, University
of Toronto, Medical Sciences Building, Room 4207, 1 King’s College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Deeba Ensan
- Drug
Discovery Program, Ontario Institute for
Cancer Research, 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada
- Department
of Pharmacology and Toxicology, University
of Toronto, Medical Sciences Building, Room 4207, 1 King’s College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Tao Xin
- Drug
Discovery Program, Ontario Institute for
Cancer Research, 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada
| | - Jong Fu Wong
- Structural
Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, U.K.
| | - Carlos A. Zepeda-Velázquez
- Drug
Discovery Program, Ontario Institute for
Cancer Research, 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada
| | - Julien Cros
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Melissa N. Sweeney
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Laurent Hoffer
- Drug
Discovery Program, Ontario Institute for
Cancer Research, 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada
| | - Taira Kiyota
- Drug
Discovery Program, Ontario Institute for
Cancer Research, 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada
| | - Brian J. Wilson
- Drug
Discovery Program, Ontario Institute for
Cancer Research, 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada
| | - Ahmed Aman
- Drug
Discovery Program, Ontario Institute for
Cancer Research, 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada
- Leslie
Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Owen Roberts
- M4K Pharma, 101 College Street, MaRS Centre,
South Tower, Toronto, Ontario M5G 1L7, Canada
| | - Methvin B. Isaac
- Drug
Discovery Program, Ontario Institute for
Cancer Research, 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada
| | - Alex N. Bullock
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - David Smil
- Drug
Discovery Program, Ontario Institute for
Cancer Research, 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada
| | - Rima Al-awar
- Drug
Discovery Program, Ontario Institute for
Cancer Research, 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada
- Department
of Pharmacology and Toxicology, University
of Toronto, Medical Sciences Building, Room 4207, 1 King’s College Circle, Toronto, Ontario M5S 1A8, Canada
- Department
of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| |
Collapse
|
7
|
Lyu P, Jiang H. Chromatin profiling reveals TFAP4 as a critical transcriptional regulator of bovine satellite cell differentiation. BMC Genomics 2024; 25:272. [PMID: 38475725 DOI: 10.1186/s12864-024-10189-2] [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: 01/23/2024] [Accepted: 03/05/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Satellite cells are myogenic precursor cells in adult skeletal muscle and play a crucial role in skeletal muscle regeneration, maintenance, and growth. Like embryonic myoblasts, satellite cells have the ability to proliferate, differentiate, and fuse to form multinucleated myofibers. In this study, we aimed to identify additional transcription factors that control gene expression during bovine satellite cell proliferation and differentiation. RESULTS Using chromatin immunoprecipitation followed by sequencing, we identified 56,973 and 54,470 genomic regions marked with both the histone modifications H3K4me1 and H3K27ac, which were considered active enhancers, and 50,956 and 59,174 genomic regions marked with H3K27me3, which were considered repressed enhancers, in proliferating and differentiating bovine satellite cells, respectively. In addition, we identified 1,216 and 1,171 super-enhancers in proliferating and differentiating bovine satellite cells, respectively. Analyzing these enhancers showed that in proliferating bovine satellite cells, active enhancers were associated with genes stimulating cell proliferation or inhibiting myoblast differentiation whereas repressed enhancers were associated with genes essential for myoblast differentiation, and that in differentiating satellite cells, active enhancers were associated with genes essential for myoblast differentiation or muscle contraction whereas repressed enhancers were associated with genes stimulating cell proliferation or inhibiting myoblast differentiation. Active enhancers in proliferating bovine satellite cells were enriched with binding sites for many transcription factors such as MYF5 and the AP-1 family transcription factors; active enhancers in differentiating bovine satellite cells were enriched with binding sites for many transcription factors such as MYOG and TFAP4; and repressed enhancers in both proliferating and differentiating bovine satellite cells were enriched with binding sites for NF-kB, ZEB-1, and several other transcription factors. The role of TFAP4 in satellite cell or myoblast differentiation was previously unknown, and through gene knockdown and overexpression, we experimentally validated a critical role for TFAP4 in the differentiation and fusion of bovine satellite cells into myofibers. CONCLUSIONS Satellite cell proliferation and differentiation are controlled by many transcription factors such as AP-1, TFAP4, NF-kB, and ZEB-1 whose roles in these processes were previously unknown in addition to those transcription factors such as MYF5 and MYOG whose roles in these processes are widely known.
Collapse
Affiliation(s)
- Pengcheng Lyu
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Honglin Jiang
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
| |
Collapse
|
8
|
Song P, Zhao J, Zhang W, Li X, Ji B, Zhao J. Vitamin a potentiates sheep myoblasts myogenic differentiation through BHLHE40-modulated ID3 expression. BMC Genomics 2024; 25:244. [PMID: 38443816 PMCID: PMC10913236 DOI: 10.1186/s12864-024-10161-0] [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: 12/15/2023] [Accepted: 02/25/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Vitamin A and retinoic acid (RA, a metabolite of vitamin A), are inextricably involved to the development of skeletal muscle in animals. However, the mechanisms regulating skeletal muscle development by vitamin A remain poorly reported. The current study designed to investigate the underlying mechanism of vitamin A affecting myogenic differentiation of lamb myoblasts through transcriptome sequencing (RNA-Seq) and gene function validation experiments. It provides a theoretical basis for elucidating the regulation of vitamin A on skeletal muscle development as well as for improving the economic benefits of the mutton sheep industry. RESULTS Newborn lambs were injected with 7,500 IU vitamin A, and longissimus dorsi (LD) muscle tissue was surgically sampled for RNA-Seq analysis and primary myoblasts isolation at 3 weeks of age. The results showed that a total of 14 down-regulated and 3 up-regulated genes, were identified between control and vitamin A groups. Among them, BHLHE40 expression was upregulated in vitamin A group lambs. Furthermore, BHLHE40 expression is significantly increased after initiation of differentiation in myoblasts, and RA addition during differentiation greatly promoted BHLHE40 mRNA expression. In vitro, RA inhibited myoblasts proliferation and promoted myoblasts myogenic differentiation through BHLHE40. Moreover, BHLHE40 was proved to inhibit the expression of the DNA binding inhibitor 3 (ID3), and meanwhile, ID3 could effectively promote myoblasts proliferation and inhibit myoblasts myogenic differentiation. CONCLUSIONS Taken together, our results suggested that vitamin A inhibited myoblasts proliferation and promoted myoblasts myogenic differentiation by inhibiting ID3 expression through BHLHE40.
Collapse
Affiliation(s)
- Pengkang Song
- College of Animal Science, Shanxi Agricultural University, 030801, Taigu, Shanxi, P. R. China
- Shanxi Key Laboratory of Animal Genetics Resource Utilization and Breeding, Taigu, P. R. China
| | - Jiamin Zhao
- College of Animal Science, Shanxi Agricultural University, 030801, Taigu, Shanxi, P. R. China
- Shanxi Key Laboratory of Animal Genetics Resource Utilization and Breeding, Taigu, P. R. China
| | - Weipeng Zhang
- College of Animal Science, Shanxi Agricultural University, 030801, Taigu, Shanxi, P. R. China
| | - Xuying Li
- College of Animal Science, Shanxi Agricultural University, 030801, Taigu, Shanxi, P. R. China
| | - Bingzhen Ji
- College of Animal Science, Shanxi Agricultural University, 030801, Taigu, Shanxi, P. R. China
| | - Junxing Zhao
- College of Animal Science, Shanxi Agricultural University, 030801, Taigu, Shanxi, P. R. China.
- Shanxi Key Laboratory of Animal Genetics Resource Utilization and Breeding, Taigu, P. R. China.
| |
Collapse
|
9
|
Kazanietz MG, Cooke M. Protein kinase C signaling "in" and "to" the nucleus: Master kinases in transcriptional regulation. J Biol Chem 2024; 300:105692. [PMID: 38301892 PMCID: PMC10907189 DOI: 10.1016/j.jbc.2024.105692] [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: 10/23/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 02/03/2024] Open
Abstract
PKC is a multifunctional family of Ser-Thr kinases widely implicated in the regulation of fundamental cellular functions, including proliferation, polarity, motility, and differentiation. Notwithstanding their primary cytoplasmic localization and stringent activation by cell surface receptors, PKC isozymes impel prominent nuclear signaling ultimately impacting gene expression. While transcriptional regulation may be wielded by nuclear PKCs, it most often relies on cytoplasmic phosphorylation events that result in nuclear shuttling of PKC downstream effectors, including transcription factors. As expected from the unique coupling of PKC isozymes to signaling effector pathways, glaring disparities in gene activation/repression are observed upon targeting individual PKC family members. Notably, specific PKCs control the expression and activation of transcription factors implicated in cell cycle/mitogenesis, epithelial-to-mesenchymal transition and immune function. Additionally, PKCs isozymes tightly regulate transcription factors involved in stepwise differentiation of pluripotent stem cells toward specific epithelial, mesenchymal, and hematopoietic cell lineages. Aberrant PKC expression and/or activation in pathological conditions, such as in cancer, leads to profound alterations in gene expression, leading to an extensive rewiring of transcriptional networks associated with mitogenesis, invasiveness, stemness, and tumor microenvironment dysregulation. In this review, we outline the current understanding of PKC signaling "in" and "to" the nucleus, with significant focus on established paradigms of PKC-mediated transcriptional control. Dissecting these complexities would allow the identification of relevant molecular targets implicated in a wide spectrum of diseases.
Collapse
Affiliation(s)
- Marcelo G Kazanietz
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
| | - Mariana Cooke
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
| |
Collapse
|
10
|
Rezaie N, Rebboah E, Williams BA, Liang HY, Reese F, Balderrama-Gutierrez G, Dionne LA, Reinholdt L, Trout D, Wold BJ, Mortazavi A. Identification of robust cellular programs using reproducible LDA that impact sex-specific disease progression in different genotypes of a mouse model of AD. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.26.582178. [PMID: 38464087 PMCID: PMC10925135 DOI: 10.1101/2024.02.26.582178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The gene expression profiles of distinct cell types reflect complex genomic interactions among multiple simultaneous biological processes within each cell that can be altered by disease progression as well as genetic background. The identification of these active cellular programs is an open challenge in the analysis of single-cell RNA-seq data. Latent Dirichlet Allocation (LDA) is a generative method used to identify recurring patterns in counts data, commonly referred to as topics that can be used to interpret the state of each cell. However, LDA's interpretability is hindered by several key factors including the hyperparameter selection of the number of topics as well as the variability in topic definitions due to random initialization. We developed Topyfic, a Reproducible LDA (rLDA) package, to accurately infer the identity and activity of cellular programs in single-cell data, providing insights into the relative contributions of each program in individual cells. We apply Topyfic to brain single-cell and single-nucleus datasets of two 5xFAD mouse models of Alzheimer's disease crossed with C57BL6/J or CAST/EiJ mice to identify distinct cell types and states in different cell types such as microglia. We find that 8-month 5xFAD/Cast F1 males show higher level of microglial activation than matching 5xFAD/BL6 F1 males, whereas female mice show similar levels of microglial activation. We show that regulatory genes such as TFs, microRNA host genes, and chromatin regulatory genes alone capture cell types and cell states. Our study highlights how topic modeling with a limited vocabulary of regulatory genes can identify gene expression programs in single-cell data in order to quantify similar and divergent cell states in distinct genotypes.
Collapse
Affiliation(s)
- Narges Rezaie
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Elisabeth Rebboah
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Brian A Williams
- Division of Biology, California Institute of Technology, Pasadena, CA, USA
| | - Heidi Yahan Liang
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Fairlie Reese
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Gabriela Balderrama-Gutierrez
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | | | | | - Diane Trout
- Division of Biology, California Institute of Technology, Pasadena, CA, USA
| | - Barbara J Wold
- Division of Biology, California Institute of Technology, Pasadena, CA, USA
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| |
Collapse
|
11
|
Zheng LL, Wang LT, Pang YW, Sun LP, Shi L. Recent advances in the development of deubiquitinases inhibitors as antitumor agents. Eur J Med Chem 2024; 266:116161. [PMID: 38262120 DOI: 10.1016/j.ejmech.2024.116161] [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: 11/01/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/25/2024]
Abstract
Ubiquitination is a type of post-translational modification that covalently links ubiquitin to a target protein, which plays a critical role in modulating protein activity, stability, and localization. In contrast, this process is reversed by deubiquitinases (DUBs), which remove ubiquitin from ubiquitinated substrates. Dysregulation of DUBs is associated with several human diseases, such as cancer, inflammation, neurodegenerative disorders, and autoimmune diseases. Thus, DUBs have become promising targets for drug development. Although the physiological and pathological effects of DUBs are increasingly well understood, the clinical drug discovery of selective DUB inhibitors has been challenging. Herein, we summarize the structures and functions of main classes of DUBs and discuss the recent progress in developing selective small-molecule DUB inhibitors as antitumor agents.
Collapse
Affiliation(s)
- Li-Li Zheng
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Li-Ting Wang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Ye-Wei Pang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Li-Ping Sun
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| | - Lei Shi
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| |
Collapse
|
12
|
Zhang B, He P, Lawrence JEG, Wang S, Tuck E, Williams BA, Roberts K, Kleshchevnikov V, Mamanova L, Bolt L, Polanski K, Li T, Elmentaite R, Fasouli ES, Prete M, He X, Yayon N, Fu Y, Yang H, Liang C, Zhang H, Blain R, Chedotal A, FitzPatrick DR, Firth H, Dean A, Bayraktar OA, Marioni JC, Barker RA, Storer MA, Wold BJ, Zhang H, Teichmann SA. A human embryonic limb cell atlas resolved in space and time. Nature 2023:10.1038/s41586-023-06806-x. [PMID: 38057666 DOI: 10.1038/s41586-023-06806-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 10/31/2023] [Indexed: 12/08/2023]
Abstract
Human limbs emerge during the fourth post-conception week as mesenchymal buds, which develop into fully formed limbs over the subsequent months1. This process is orchestrated by numerous temporally and spatially restricted gene expression programmes, making congenital alterations in phenotype common2. Decades of work with model organisms have defined the fundamental mechanisms underlying vertebrate limb development, but an in-depth characterization of this process in humans has yet to be performed. Here we detail human embryonic limb development across space and time using single-cell and spatial transcriptomics. We demonstrate extensive diversification of cells from a few multipotent progenitors to myriad differentiated cell states, including several novel cell populations. We uncover two waves of human muscle development, each characterized by different cell states regulated by separate gene expression programmes, and identify musculin (MSC) as a key transcriptional repressor maintaining muscle stem cell identity. Through assembly of multiple anatomically continuous spatial transcriptomic samples using VisiumStitcher, we map cells across a sagittal section of a whole fetal hindlimb. We reveal a clear anatomical segregation between genes linked to brachydactyly and polysyndactyly, and uncover transcriptionally and spatially distinct populations of the mesenchyme in the autopod. Finally, we perform single-cell RNA sequencing on mouse embryonic limbs to facilitate cross-species developmental comparison, finding substantial homology between the two species.
Collapse
Affiliation(s)
- Bao Zhang
- The Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Peng He
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - John E G Lawrence
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Department of Trauma and Orthopaedics, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, UK
| | - Shuaiyu Wang
- The Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Obstetrics, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Elizabeth Tuck
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Brian A Williams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Kenny Roberts
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Enhanc3D Genomics Ltd, Cambridge, UK
| | - Liam Bolt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Genomics England, London, UK
| | | | - Tong Li
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Rasa Elmentaite
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Eirini S Fasouli
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Basic Research Center, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Martin Prete
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Xiaoling He
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Nadav Yayon
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Yixi Fu
- The Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Hao Yang
- The Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Chen Liang
- The Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Hui Zhang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Raphael Blain
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Alain Chedotal
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
- Institut de pathologie, groupe hospitalier Est, hospices civils de Lyon, Lyon, France
- University Claude Bernard Lyon 1, MeLiS, CNRS UMR5284, INSERM U1314, Lyon, France
| | | | - Helen Firth
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Andrew Dean
- Department of Clinical Neurosciences, Cambridge University Hospitals NHS Foundation, Cambridge, UK
| | | | - John C Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Roger A Barker
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Mekayla A Storer
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Barbara J Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Hongbo Zhang
- The Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
- Advanced Medical Technology Center, the First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
- Theory of Condensed Matter Group, Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK.
| |
Collapse
|
13
|
Krzysiek-Maczka G, Brzozowski T, Ptak-Belowska A. Helicobacter pylori-activated fibroblasts as a silent partner in gastric cancer development. Cancer Metastasis Rev 2023; 42:1219-1256. [PMID: 37460910 PMCID: PMC10713772 DOI: 10.1007/s10555-023-10122-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/20/2023] [Indexed: 12/18/2023]
Abstract
The discovery of Helicobacter pylori (Hp) infection of gastric mucosa leading to active chronic gastritis, gastroduodenal ulcers, and MALT lymphoma laid the groundwork for understanding of the general relationship between chronic infection, inflammation, and cancer. Nevertheless, this sequence of events is still far from full understanding with new players and mediators being constantly identified. Originally, the Hp virulence factors affecting mainly gastric epithelium were proposed to contribute considerably to gastric inflammation, ulceration, and cancer. Furthermore, it has been shown that Hp possesses the ability to penetrate the mucus layer and directly interact with stroma components including fibroblasts and myofibroblasts. These cells, which are the source of biophysical and biochemical signals providing the proper balance between cell proliferation and differentiation within gastric epithelial stem cell compartment, when exposed to Hp, can convert into cancer-associated fibroblast (CAF) phenotype. The crosstalk between fibroblasts and myofibroblasts with gastric epithelial cells including stem/progenitor cell niche involves several pathways mediated by non-coding RNAs, Wnt, BMP, TGF-β, and Notch signaling ligands. The current review concentrates on the consequences of Hp-induced increase in gastric fibroblast and myofibroblast number, and their activation towards CAFs with the emphasis to the altered communication between mesenchymal and epithelial cell compartment, which may lead to inflammation, epithelial stem cell overproliferation, disturbed differentiation, and gradual gastric cancer development. Thus, Hp-activated fibroblasts may constitute the target for anti-cancer treatment and, importantly, for the pharmacotherapies diminishing their activation particularly at the early stages of Hp infection.
Collapse
Affiliation(s)
- Gracjana Krzysiek-Maczka
- Department of Physiology, the Faculty of Medicine, Jagiellonian University Medical College, 16 Grzegorzecka Street, 31-531, Kraków, Poland.
| | - Tomasz Brzozowski
- Department of Physiology, the Faculty of Medicine, Jagiellonian University Medical College, 16 Grzegorzecka Street, 31-531, Kraków, Poland.
| | - Agata Ptak-Belowska
- Department of Physiology, the Faculty of Medicine, Jagiellonian University Medical College, 16 Grzegorzecka Street, 31-531, Kraków, Poland
| |
Collapse
|
14
|
Albrecht M, Sticht C, Wagner T, Hettler SA, De La Torre C, Qiu J, Gretz N, Albrecht T, Yard B, Sleeman JP, Garvalov BK. The crosstalk between glomerular endothelial cells and podocytes controls their responses to metabolic stimuli in diabetic nephropathy. Sci Rep 2023; 13:17985. [PMID: 37863933 PMCID: PMC10589299 DOI: 10.1038/s41598-023-45139-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 10/16/2023] [Indexed: 10/22/2023] Open
Abstract
In diabetic nephropathy (DN), glomerular endothelial cells (GECs) and podocytes undergo pathological alterations, which are influenced by metabolic changes characteristic of diabetes, including hyperglycaemia (HG) and elevated methylglyoxal (MGO) levels. However, it remains insufficiently understood what effects these metabolic factors have on GEC and podocytes and to what extent the interactions between the two cell types can modulate these effects. To address these questions, we established a co-culture system in which GECs and podocytes were grown together in close proximity, and assessed transcriptional changes in each cell type after exposure to HG and MGO. We found that HG and MGO had distinct effects on gene expression and that the effect of each treatment was markedly different between GECs and podocytes. HG treatment led to upregulation of "immediate early response" genes, particularly those of the EGR family, as well as genes involved in inflammatory responses (in GECs) or DNA replication/cell cycle (in podocytes). Interestingly, both HG and MGO led to downregulation of genes related to extracellular matrix organisation in podocytes. Crucially, the transcriptional responses of GECs and podocytes were dependent on their interaction with each other, as many of the prominently regulated genes in co-culture of the two cell types were not significantly changed when monocultures of the cells were exposed to the same stimuli. Finally, the changes in the expression of selected genes were validated in BTBR ob/ob mice, an established model of DN. This work highlights the molecular alterations in GECs and podocytes in response to the key diabetic metabolic triggers HG and MGO, as well as the central role of GEC-podocyte crosstalk in governing these responses.
Collapse
Affiliation(s)
- Michael Albrecht
- European Center for Angioscience (ECAS), Medical Faculty Mannheim of the University of Heidelberg, Ludolf-Krehl-Strasse 13-17, 68167, Mannheim, Germany
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim of the University of Heidelberg, Ludolf-Krehl-Strasse 13-17, 68167, Mannheim, Germany
| | - Carsten Sticht
- Center of Medical Research, Bioinformatics and Statistics, Medical Faculty Mannheim of the University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
- NGS Core Facility, Medical Faculty Mannheim of the University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - Tabea Wagner
- European Center for Angioscience (ECAS), Medical Faculty Mannheim of the University of Heidelberg, Ludolf-Krehl-Strasse 13-17, 68167, Mannheim, Germany
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim of the University of Heidelberg, Ludolf-Krehl-Strasse 13-17, 68167, Mannheim, Germany
| | - Steffen A Hettler
- Department of Nephrology, Hypertensiology, Endocrinology, Diabetology, Rheumatology and Pneumology, Fifth Department of Medicine, Medical Faculty Mannheim of the University of Heidelberg, Mannheim, Germany
| | - Carolina De La Torre
- Center of Medical Research, Bioinformatics and Statistics, Medical Faculty Mannheim of the University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
- NGS Core Facility, Medical Faculty Mannheim of the University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - Jiedong Qiu
- Department of Nephrology, Hypertensiology, Endocrinology, Diabetology, Rheumatology and Pneumology, Fifth Department of Medicine, Medical Faculty Mannheim of the University of Heidelberg, Mannheim, Germany
| | - Norbert Gretz
- Center of Medical Research, Bioinformatics and Statistics, Medical Faculty Mannheim of the University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - Thomas Albrecht
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, Heidelberg, Germany
| | - Benito Yard
- Department of Nephrology, Hypertensiology, Endocrinology, Diabetology, Rheumatology and Pneumology, Fifth Department of Medicine, Medical Faculty Mannheim of the University of Heidelberg, Mannheim, Germany
| | - Jonathan P Sleeman
- European Center for Angioscience (ECAS), Medical Faculty Mannheim of the University of Heidelberg, Ludolf-Krehl-Strasse 13-17, 68167, Mannheim, Germany.
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim of the University of Heidelberg, Ludolf-Krehl-Strasse 13-17, 68167, Mannheim, Germany.
- Institute of Biological and Chemical Systems - Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology Campus North, Building 319, Hermann-Von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.
| | - Boyan K Garvalov
- European Center for Angioscience (ECAS), Medical Faculty Mannheim of the University of Heidelberg, Ludolf-Krehl-Strasse 13-17, 68167, Mannheim, Germany.
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim of the University of Heidelberg, Ludolf-Krehl-Strasse 13-17, 68167, Mannheim, Germany.
| |
Collapse
|
15
|
Oswald J, Constantine M, Adegbuyi A, Omorogbe E, Dellomo AJ, Ehrlich ES. E3 Ubiquitin Ligases in Gammaherpesviruses and HIV: A Review of Virus Adaptation and Exploitation. Viruses 2023; 15:1935. [PMID: 37766341 PMCID: PMC10535929 DOI: 10.3390/v15091935] [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: 08/21/2023] [Revised: 09/10/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
For productive infection and replication to occur, viruses must control cellular machinery and counteract restriction factors and antiviral proteins. Viruses can accomplish this, in part, via the regulation of cellular gene expression and post-transcriptional and post-translational control. Many viruses co-opt and counteract cellular processes via modulation of the host post-translational modification machinery and encoding or hijacking kinases, SUMO ligases, deubiquitinases, and ubiquitin ligases, in addition to other modifiers. In this review, we focus on three oncoviruses, Epstein-Barr virus (EBV), Kaposi's sarcoma herpesvirus (KSHV), and human immunodeficiency virus (HIV) and their interactions with the ubiquitin-proteasome system via viral-encoded or cellular E3 ubiquitin ligase activity.
Collapse
Affiliation(s)
| | | | | | | | | | - Elana S. Ehrlich
- Department of Biological Sciences, Towson University, Towson, MD 21252, USA
| |
Collapse
|
16
|
Arnosti DN. Soft repression and chromatin modification by conserved transcriptional corepressors. Enzymes 2023; 53:69-96. [PMID: 37748837 DOI: 10.1016/bs.enz.2023.08.001] [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] [Indexed: 09/27/2023]
Abstract
Transcriptional regulation in eukaryotic cells involves the activity of multifarious DNA-binding transcription factors and recruited corepressor complexes. Together, these complexes interact with the core transcriptional machinery, chromatin, and nuclear environment to effect complex patterns of gene regulation. Much focus has been paid to the action of master regulatory switches that are key to developmental and environmental responses, as these genetic elements have important phenotypic effects. The regulation of widely-expressed metabolic control genes has been less well studied, particularly in cases in which physically-interacting repressors and corepressors have subtle influences on steady-state expression. This latter phenomenon, termed "soft repression" is a topic of increasing interest as genomic approaches provide ever more powerful tools to uncover the significance of this level of control. This review provides an oversight of classic and current approaches to the study of transcriptional repression in eukaryotic systems, with a specific focus on opportunities and challenges that lie ahead in the study of soft repression.
Collapse
Affiliation(s)
- David N Arnosti
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States.
| |
Collapse
|
17
|
Riege D, Herschel S, Heintze L, Fenkl T, Wesseler F, Sievers S, Peifer C, Schade D. Identification of Maleimide-Fused Carbazoles as Novel Noncanonical Bone Morphogenetic Protein Synergizers. ACS Pharmacol Transl Sci 2023; 6:1207-1220. [PMID: 37588754 PMCID: PMC10426274 DOI: 10.1021/acsptsci.3c00103] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Indexed: 08/18/2023]
Abstract
Morphogenic signaling pathways govern embryonic development and tissue homeostasis on the cellular level. Precise control of such signaling events paves the way for innovative therapeutic approaches in the field of regenerative medicine. In line with these notions, bone morphogenic protein (BMP) is a major osteogenic driver and pharmacological stimulation of BMP signaling holds supreme potential for diseases and defects of the skeleton. Efforts to identify small-molecule modalities that activate or potentiate the BMP pathway have primarily been focused on the canonical signaling cascade. Here, we describe the phenotypic identification and development of specific carbazolomaleimides 2 as novel noncanonical BMP synergizers with submicromolar osteogenic cellular potency. The devised chemical tools are characterized to specifically regulate Id gene expression in a SMAD-independent, yet highly BMP-dependent fashion. Mechanistic studies revealed that GSK3 inhibition and increased β-catenin levels are partly responsible for this activity. The utility of the new BMP synergizer profile was further exemplified by showing how the synergistic action of canonical and noncanonical BMP enhancers additively amplifies BMP-dependent osteogenic outputs. Carbazolomaleimide 2b serves as a new and unique pharmacological tool for the modulation and study of the BMP pathway.
Collapse
Affiliation(s)
- Daniel Riege
- Department of Pharmaceutical &
Medicinal Chemistry, Christian-Albrechts-University of
Kiel, Gutenbergstrasse 76, 24118 Kiel,
Germany
| | - Sven Herschel
- Department of Pharmaceutical &
Medicinal Chemistry, Christian-Albrechts-University of
Kiel, Gutenbergstrasse 76, 24118 Kiel,
Germany
| | - Linda Heintze
- Department of Pharmaceutical &
Medicinal Chemistry, Christian-Albrechts-University of
Kiel, Gutenbergstrasse 76, 24118 Kiel,
Germany
| | - Teresa Fenkl
- Department of Pharmaceutical &
Medicinal Chemistry, Christian-Albrechts-University of
Kiel, Gutenbergstrasse 76, 24118 Kiel,
Germany
| | - Fabian Wesseler
- Department of Pharmaceutical &
Medicinal Chemistry, Christian-Albrechts-University of
Kiel, Gutenbergstrasse 76, 24118 Kiel,
Germany
- Compound Management and
Screening Center, Otto-Hahn-Strasse 11, 44227
Dortmund, Germany
| | - Sonja Sievers
- Compound Management and
Screening Center, Otto-Hahn-Strasse 11, 44227
Dortmund, Germany
| | - Christian Peifer
- Department of Pharmaceutical &
Medicinal Chemistry, Christian-Albrechts-University of
Kiel, Gutenbergstrasse 76, 24118 Kiel,
Germany
| | - Dennis Schade
- Department of Pharmaceutical &
Medicinal Chemistry, Christian-Albrechts-University of
Kiel, Gutenbergstrasse 76, 24118 Kiel,
Germany
- Partner Site Kiel, DZHK,
German Center for Cardiovascular Research, 24105
Kiel, Germany
| |
Collapse
|
18
|
Perbal B, Perbal M, Perbal A. Cooperation is the key: the CCN biological system as a gate to high complex protein superfamilies' signaling. J Cell Commun Signal 2023:10.1007/s12079-023-00749-8. [PMID: 37166690 DOI: 10.1007/s12079-023-00749-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
Cellular signaling is generally understood as the support of communication between contiguous cells belonging to the same tissue or cells being far apart of each other, at a molecular scale, when the message emitted by the transmitters is traveling in liquid or solid matter to reach recipient targets. Subcellular signaling is also important to ensure the proper cell constitution and functioning. However cell signaling is mostly used in the first understanding, to describe how the message sent from one point to another one, will reach a target where it will be interpreted. The Cellular Communication Network (CCN) factors (Perbal et al. 2018) constitute a family of biological regulators thought to be responsible for signaling pathways coordination (Perbal 2018). Indeed, these proteins interact with a diverse group of cell receptors, such as integrins, low density lipoprotein receptors, heparan sulfate proteoglycan receptors (HSPG), and the immunoglobulin superfamily expressed exclusively in the nervous system, or with soluble factors such as bone morphogenetic proteins (BMPS) and other growth factors such as vascular endothelial growth factor, fibroblastic growth factor, and transforming growth factor (TGFbeta). Starting from the recapitulation of basic concepts in enzymology and protein-ligands interactions, we consider, in this manuscript, interpretations of the mechanistic interactions that have been put forward to explain the diversity of CCN proteins biological activities. We suggest that the cross-talks between superfamilies of proteins under the control of CCNs might play a central role in the coordination of developmental signaling pathways.
Collapse
Affiliation(s)
| | - Matthieu Perbal
- M2 Probabilités et Modèles Aléatoires, Sorbonne Université, Paris, France
| | | |
Collapse
|
19
|
Ravirala S, Sura MB, Murugesan P, Tangutur AD, Ponnapalli MG. Click linker: efficient and high yielding synthesis of a new family of kojic acid congeners as cytotoxic agents. Nat Prod Res 2023; 37:1161-1167. [PMID: 34720015 DOI: 10.1080/14786419.2021.1998897] [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: 10/20/2022]
Abstract
Highly efficient methodology was developed for the construction of functionalized Kojic acid involving Click linker via 1,3-dipolar cycloaddition and their cytotoxicity against MCF-7, MIAPaCa-2 and DU145 mammalian cell lines were evaluated. Preliminary studies on structure-activity-relationship (SAR) revealed that substitution at C-2 of kojic acid as well as C-5 of 1,2,3-triazole motif played a major role in the activity profile. Kojic acid 1,2,3-triazole analogue 3 b containing an alkyl chain (n = 6) exhibited two fold potent activity than the parent compound, kojic acid against MCF-7 and MIA PaCa-2 cell lines. It induced apoptosis in these cell lines via ID1/PARP1 mediated pathway. The structures of the new analogues of kojic acid 1,2,3-triazole were confirmed by the detailed spectroscopic data analysis.
Collapse
Affiliation(s)
- Saidulu Ravirala
- Centre for Natural Products and Traditional Knowledge, Indian Institute of Chemical Technology, Hyderabad, India
| | - Madhu Babu Sura
- Centre for Natural Products and Traditional Knowledge, Indian Institute of Chemical Technology, Hyderabad, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Periyasamy Murugesan
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.,Applied biology Department, Indian Institute of Chemical Technology, Hyderabad, India
| | - Anjana Devi Tangutur
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.,Applied biology Department, Indian Institute of Chemical Technology, Hyderabad, India
| | - Mangala Gowri Ponnapalli
- Centre for Natural Products and Traditional Knowledge, Indian Institute of Chemical Technology, Hyderabad, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| |
Collapse
|
20
|
Role of Genetic and Epigenetic Modifications in the Progression of Hepatocellular Carcinoma in Chronic HCV Patients. LIVERS 2023. [DOI: 10.3390/livers3010008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/22/2023] Open
Abstract
Globally, hepatocellular carcinoma (HCC) is a significant cause of mortality and morbidity among chronically infected HCV patients. It is established that HCV is a primary risk factor for HCC progression. The treatment of HCV infection has been transformed by the introduction of DAAs with high rates of virological clearance. The reduction in cirrhosis-related consequences, particularly HCC, is the long-term objective of DAAs therapy for HCV. Although the risk of developing HCC is decreased in HCV patients who achieve a disease-sustaining virological response, these patients are nevertheless at risk, especially those with severe fibrosis and cirrhosis. Previous studies have shown that HCV induce several mechanisms of hepatocarcinogenesis in the host’s hepatic micro- and macro-environment, which leads to HCC progression. In an HCV-altered environment, compensatory liver regeneration favors chromosomal instability and irreversible alterations, which encourage hepatocyte neoplastic transformation and the development of malignant clones. These mechanisms involve a series of genetic and epigenetic modifications including host genetic factors, dysregulation of several signaling pathways, histone, and DNA modifications including methylation and acetylation. This review highlights the genetic and epigenetic factors that lead to the development of HCC in chronic HCV-infected individuals and can be targeted for earlier HCC diagnosis and prevention.
Collapse
|
21
|
Murugesan P, Begum H, Tangutur AD. Inhibitor of DNA binding/differentiation proteins as IDs for pancreatic cancer: Role in pancreatic cancer initiation, development and prognosis. Gene 2023; 853:147092. [PMID: 36464175 DOI: 10.1016/j.gene.2022.147092] [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: 08/01/2022] [Revised: 11/11/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
A family of inhibitors of cell differentiation or DNA-binding proteins, known as ID proteins (ID1-4), function as mighty transcription factors in various cellular processes, such as inhibiting differentiation, promoting cell-cycle progression, senescence, angiogenesis, tumorigenesis, and metastasis in cancer. Pancreatic cancer represents the deadliest cancer with the lowest survival rate of 10% due to the diagnosis at an advanced fatal stage and therapeutic resistance. Modestly, the only curative option for this lethal cancer is surgery but is done in less than 15-20% of patients because of the locally aggressive and early metastatic nature. Finding the earliest biomarkers and targeting the various hallmarks of pancreatic cancer can improve the treatment and survival of pancreatic cancer patients. Therefore, herein in this review, we explore in depth the potential roles of ID proteins function in hallmarks of pancreatic cancer, signaling pathways, and its oncogenic and tumor-suppressive effects. Hence, understanding the roles of dysregulated ID proteins would provide new insights into its function in pancreatic cancer tumorigenesis.
Collapse
Affiliation(s)
- Periyasamy Murugesan
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India; Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh 201002, India
| | - Habeebunnisa Begum
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India; Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh 201002, India
| | - Anjana Devi Tangutur
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India; Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh 201002, India.
| |
Collapse
|
22
|
Yiou W, Zhihong W, Shibai Z, Shanni L, Wenwei Q. MiR-326 regulates cell proliferation and apoptosis in fibroblast-like synoviocytes in rheumatoid arthritis. Hum Cell 2023; 36:987-996. [PMID: 36749538 DOI: 10.1007/s13577-023-00873-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 01/28/2023] [Indexed: 02/08/2023]
Abstract
The dysregulation of microRNAs plays a critical role in the development of rheumatoid arthritis (RA). This study aims to explore the functional significance of miR-326 in RA. The RT-qPCR results showed that miR-326 was downregulated in synovial tissues of RA patients and RA fibroblast-like synoviocytes (RA-FLS). We found that miR-326 could target and reduce the expression of inhibitor of DNA binding 1 (Id1). MTT assay and flow cytometry were conducted to explore the biological function of miR-326. Our data revealed that the upregulation of miR-326 suppressed cell proliferation and induced apoptosis in RA-FLS. In collagen-induced arthritis mice, intraarticular injection of lentivirus carrying miR-326 overexpression vectors could reduce the arthritis score and attenuate synovial inflammation and cartilage destruction. We also found that long non-coding RNA-Ewing sarcoma-associated transcript 1 (lncRNA-EWSAT1) was significantly increased in RA synovial tissues and RA-FLS. The RNA immunoprecipitation and RNA pull-down assay indicated that lncRNA-EWSAT1 directly bound and negatively regulated the expression of miR-326. Knockdown of lncRNA-EWSAT1 could upregulate miR-326 expression and attenuate its proliferation inhibition and apoptosis induction effect in RA-FLS. In conclusion, the lncRNA-EWSAT1/miR-326 axis might provide a novel therapeutic target in the treatment of RA.
Collapse
Affiliation(s)
- Wang Yiou
- Department of Plastic and Reconstructive Surgery, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100144, China
| | - Wang Zhihong
- Department of Orthopedic Surgery, The Third Hospital of Hebei Medical University, Shijiazhuang, 050051, Hebei Province, China
| | - Zhu Shibai
- Department of Orthopedic Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, 100176, China
| | - Li Shanni
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Qian Wenwei
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| |
Collapse
|
23
|
Sokolowski DJ, Ahn J, Erdman L, Hou H, Ellis K, Wang L, Goldenberg A, Wilson M. Differential Expression Enrichment Tool (DEET): an interactive atlas of human differential gene expression. NAR Genom Bioinform 2023; 5:lqad003. [PMID: 36694664 PMCID: PMC9869326 DOI: 10.1093/nargab/lqad003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 12/14/2022] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
Differential gene expression analysis using RNA sequencing (RNA-seq) data is a standard approach for making biological discoveries. Ongoing large-scale efforts to process and normalize publicly available gene expression data enable rapid and systematic reanalysis. While several powerful tools systematically process RNA-seq data, enabling their reanalysis, few resources systematically recompute differentially expressed genes (DEGs) generated from individual studies. We developed a robust differential expression analysis pipeline to recompute 3162 human DEG lists from The Cancer Genome Atlas, Genotype-Tissue Expression Consortium, and 142 studies within the Sequence Read Archive. After measuring the accuracy of the recomputed DEG lists, we built the Differential Expression Enrichment Tool (DEET), which enables users to interact with the recomputed DEG lists. DEET, available through CRAN and RShiny, systematically queries which of the recomputed DEG lists share similar genes, pathways, and TF targets to their own gene lists. DEET identifies relevant studies based on shared results with the user's gene lists, aiding in hypothesis generation and data-driven literature review.
Collapse
Affiliation(s)
| | - Jedid Ahn
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada,Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Lauren Erdman
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada,Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Huayun Hou
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada
| | - Kai Ellis
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Liangxi Wang
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Anna Goldenberg
- Genetics and Genome Biology, SickKids Research Institute, Toronto, ON, Canada,Department of Computer Science, University of Toronto, Toronto, ON, Canada,Vector Institute, Toronto, ON, Canada,CIFAR, Toronto, ON, Canada
| | - Michael D Wilson
- To whom correspondence should be addressed. Tel: +1 416 813 7654 (Ext 328699); Fax: +1 416 813 4931;
| |
Collapse
|
24
|
Sun H, Wang H, Zhang W, Mao H, Li B. Single-cell RNA sequencing reveals resident progenitor and vascularization-associated cell subpopulations in rat annulus fibrosus. J Orthop Translat 2022; 38:256-267. [PMID: 36568849 PMCID: PMC9758498 DOI: 10.1016/j.jot.2022.11.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/08/2022] [Accepted: 11/15/2022] [Indexed: 12/14/2022] Open
Abstract
Background One of the main causes of low back pain is intervertebral disc degeneration (IDD). Annulus fibrosus (AF) is important for the integrity and functions of the intervertebral disc (IVD). However, the resident functional cell components such as progenitors and vascularization-associated cells in AF are yet to be fully identified. Purpose Identification of functional AF cell subpopulations including resident progenitors and vascularization-associated cells. Methods In this study, the single-cell RNA sequencing data of rat IVDs from a public database were analyzed using Seurat for cell clustering, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) for functional analysis, StemID for stem cell identification, Monocle and RNA velocity for pseudotime differentiation trajectory validation, single-cell regulatory network inference and clustering (SCENIC) for gene regulatory network (GRN) analysis, and CellChat for cell-cell interaction analysis. Immunostaining on normal and degenerated rat IVDs, as well as human AF, was used for validations. Results From the data analysis, seven AF cell clusters were identified, including two newly discovered functional clusters, the Grem1 + subpopulation and the Lum + subpopulation. The Grem1 + subpopulation had progenitor characteristics, while the Lum + subpopulation was associated with vascularization during IDD. The GRN analysis showed that Sox9 and Id1 were among the key regulators in the Grem1 + subpopulation, and Nr2f2 and Creb5 could be responsible for the vascularization function in the Lum + subpopulation. Cell-cell interaction analysis revealed highly regulated cellular communications between these cells, and multiple signaling networks including PDGF and MIF signaling pathways were involved in the interactions. Conclusions Our results revealed two new functional AF cell subpopulations, with stemness and vascularization induction potential, respectively. The Translational potential of this article These findings complement our knowledge about IVDs, especially the AF, and in return provide potential cell source and regulation targets for IDD treatment and tissue repair. The existence of the cell subpopulations was also validated in human AF, which strengthen the clinical relevance of the findings.
Collapse
Affiliation(s)
- Heng Sun
- Department of Orthopaedic Surgery, Orthopedic Institute, The First Affiliated Hospital, Suzhou Medical College, Soochow University, Suzhou, Jiangsu, China
| | - Huan Wang
- Department of Orthopaedic Surgery, Orthopedic Institute, The First Affiliated Hospital, Suzhou Medical College, Soochow University, Suzhou, Jiangsu, China
| | - Weidong Zhang
- Department of Orthopaedic Surgery, Orthopedic Institute, The First Affiliated Hospital, Suzhou Medical College, Soochow University, Suzhou, Jiangsu, China
| | - Haijiao Mao
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, Zhejiang, China,Corresponding author.
| | - Bin Li
- Department of Orthopaedic Surgery, Orthopedic Institute, The First Affiliated Hospital, Suzhou Medical College, Soochow University, Suzhou, Jiangsu, China,Collaborative Innovation Center of Hematology, Soochow University, Suzhou, Jiangsu, China,Corresponding author. 178 Ganjiang Rd, Rm 201 Bldg 18, Soochow University (North Campus), Suzhou, Jiangsu, 215007, China.
| |
Collapse
|
25
|
Zhao Q, Wang Y, Yu D, Leng JY, Zhao Y, Chu M, Xu Z, Ding H, Zhou J, Zhang T. Comprehensive analysis of ID genes reveals the clinical and prognostic value of ID3 expression in acute myeloid leukemia using bioinformatics identification and experimental validation. BMC Cancer 2022; 22:1229. [PMID: 36443709 PMCID: PMC9707109 DOI: 10.1186/s12885-022-10352-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/22/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Dysregulation of inhibitor of differentiation/DNA binding (ID) genes is linked to cancer growth, angiogenesis, invasiveness, metastasis and patient survival. Nevertheless, few investigations have systematically determined the expression and prognostic value of ID genes in acute myeloid leukemia (AML). METHODS The expression and clinical prognostic value of ID genes in AML were first identified by public databases and further validated by our research cohort. RESULTS Using public data, the expression of ID1/ID3 was markedly downregulated in AML, and the expression of ID2 was greatly upregulated in AML, whereas ID4 showed no significant difference. Among the ID genes, only ID3 expression may be the most valuable prognostic biomarker in both total AML and cytogenetically normal AML (CN-AML) and especially in CN-AML. Clinically, reduced ID3 expression was greatly associated with higher white blood cell counts, peripheral blood/bone marrow blasts, normal karyotypes and intermediate cytogenetic risk. In addition, low ID3 expression was markedly related to FLT3 and NPM1 mutations as well as wild-type TP53. Despite these associations, multivariate Cox regression analysis revealed that ID3 expression was an independent risk factor affecting overall survival (OS) and disease free survival (DFS) in CN-AML patients. Biologically, a total of 839 mRNAs/lncRNAs and 72 microRNAs were found to be associated with ID3 expression in AML. Importantly, the expression of ID3 with discriminative value in AML was further confirmed in our research cohort. CONCLUSION The bioinformatics analysis and experimental verification demonstrate that low ID3 expression independently affects OS and DFS in patients with CN-AML, which might be seen as a potential prognostic indicator in CN-AML.
Collapse
Affiliation(s)
- Qi Zhao
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd, 212002, Zhenjiang, Jiangsu, P. R. China.,Zhenjiang Clinical Research Center of Hematology, 212002, Zhenjiang, Jiangsu, P. R. China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Jiangsu, 212002, Zhenjiang, P. R. China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, 212002, Zhenjiang, Jiangsu, P. R. China.,Department of Respiratory Disease, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd, 212002, Zhenjiang, Jiangsu, P. R. China
| | - Yun Wang
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd, 212002, Zhenjiang, Jiangsu, P. R. China.,Zhenjiang Clinical Research Center of Hematology, 212002, Zhenjiang, Jiangsu, P. R. China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Jiangsu, 212002, Zhenjiang, P. R. China
| | - Di Yu
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd, 212002, Zhenjiang, Jiangsu, P. R. China.,Zhenjiang Clinical Research Center of Hematology, 212002, Zhenjiang, Jiangsu, P. R. China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Jiangsu, 212002, Zhenjiang, P. R. China
| | - Jia-Yan Leng
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd, 212002, Zhenjiang, Jiangsu, P. R. China.,Zhenjiang Clinical Research Center of Hematology, 212002, Zhenjiang, Jiangsu, P. R. China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Jiangsu, 212002, Zhenjiang, P. R. China
| | - Yangjing Zhao
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, 212013, Zhenjiang, Jiangsu, P. R. China
| | - Mingqiang Chu
- Zhenjiang Clinical Research Center of Hematology, 212002, Zhenjiang, Jiangsu, P. R. China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Jiangsu, 212002, Zhenjiang, P. R. China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, 212002, Zhenjiang, Jiangsu, P. R. China.,Department of Respiratory Disease, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd, 212002, Zhenjiang, Jiangsu, P. R. China
| | - Zijun Xu
- Zhenjiang Clinical Research Center of Hematology, 212002, Zhenjiang, Jiangsu, P. R. China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Jiangsu, 212002, Zhenjiang, P. R. China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, 212002, Zhenjiang, Jiangsu, P. R. China
| | - Hao Ding
- Department of Respiratory Disease, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd, 212002, Zhenjiang, Jiangsu, P. R. China.
| | - Jingdong Zhou
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd, 212002, Zhenjiang, Jiangsu, P. R. China. .,Zhenjiang Clinical Research Center of Hematology, 212002, Zhenjiang, Jiangsu, P. R. China. .,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Jiangsu, 212002, Zhenjiang, P. R. China.
| | - Tingjuan Zhang
- Zhenjiang Clinical Research Center of Hematology, 212002, Zhenjiang, Jiangsu, P. R. China. .,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Jiangsu, 212002, Zhenjiang, P. R. China. .,Department of Oncology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd, 212002, Zhenjiang, Jiangsu, P. R. China.
| |
Collapse
|
26
|
Neary B, Lin S, Qiu P. Methylation of CpG Sites as Biomarkers Predictive of Drug-Specific
Patient Survival in Cancer. Cancer Inform 2022; 21:11769351221131124. [PMID: 36340286 PMCID: PMC9634212 DOI: 10.1177/11769351221131124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 09/18/2022] [Indexed: 11/06/2022] Open
Abstract
Background: Though the development of targeted cancer drugs continues to accelerate,
doctors still lack reliable methods for predicting patient response to
standard-of-care therapies for most cancers. DNA methylation has been
implicated in tumor drug response and is a promising source of predictive
biomarkers of drug efficacy, yet the relationship between drug efficacy and
DNA methylation remains largely unexplored. Method: In this analysis, we performed log-rank survival analyses on patients grouped
by cancer and drug exposure to find CpG sites where binary methylation
status is associated with differential survival in patients treated with a
specific drug but not in patients with the same cancer who were not exposed
to that drug. We also clustered these drug-specific CpG sites based on
co-methylation among patients to identify broader methylation patterns that
may be related to drug efficacy, which we investigated for transcription
factor binding site enrichment using gene set enrichment analysis. Results: We identified CpG sites that were drug-specific predictors of survival in 38
cancer-drug patient groups across 15 cancers and 20 drugs. These included 11
CpG sites with similar drug-specific survival effects in multiple cancers.
We also identified 76 clusters of CpG sites with stronger associations with
patient drug response, many of which contained CpG sites in gene promoters
containing transcription factor binding sites. Conclusion: These findings are promising biomarkers of drug response for a variety of
drugs and contribute to our understanding of drug-methylation interactions
in cancer. Investigation and validation of these results could lead to the
development of targeted co-therapies aimed at manipulating methylation in
order to improve efficacy of commonly used therapies and could improve
patient survival and quality of life by furthering the effort toward drug
response prediction.
Collapse
Affiliation(s)
- Bridget Neary
- School of Biological Sciences, Georgia
Institute of Technology, Atlanta, GA, USA
| | - Shuting Lin
- School of Biological Sciences, Georgia
Institute of Technology, Atlanta, GA, USA
| | - Peng Qiu
- Department of Biomedical Engineering,
Georgia Institute of Technology and Emory University, Atlanta, GA, USA,Peng Qiu, Department of Biomedical
Engineering, Georgia Institute of Technology and Emory University, 950 Atlantic
Dr. NW, Atlanta, GA 30332 USA.
| |
Collapse
|
27
|
Cooke M, Zhang X, Zhang S, Eruslanov E, Lal P, Daniel RE, Feldman MD, Abba MC, Kazanietz MG. PROTEIN KINASE C ALPHA IS A CENTRAL NODE FOR TUMORIGENIC TRANSCRIPTIONAL NETWORKS IN HUMAN PROSTATE CANCER. CANCER RESEARCH COMMUNICATIONS 2022; 2:1372-1387. [PMID: 36818489 PMCID: PMC9933888 DOI: 10.1158/2767-9764.crc-22-0170] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 08/12/2022] [Accepted: 09/26/2022] [Indexed: 06/18/2023]
Abstract
Aberrant expression of protein kinase C (PKC) isozymes is a hallmark of cancer. The different members of the PKC family control cellular events associated with cancer development and progression. Whereas the classical/conventional PKCα isozyme has been linked to tumor suppression in most cancer types, here we demonstrate that this kinase is required for the mitogenic activity of aggressive human prostate cancer cells displaying aberrantly high PKCα expression. Immunohistochemical analysis showed abnormal up-regulation of PKCα in human primary prostate tumors. Interestingly, silencing PKCα expression from aggressive prostate cancer cells impairs cell cycle progression, proliferation and invasion, as well as their tumorigenic activity in a mouse xenograft model. Mechanistic analysis revealed that PKCα exerts a profound control of gene expression, particularly over genes and transcriptional networks associated with cell cycle progression and E2F transcription factors. PKCα RNAi depletion from PC3 prostate cancer cells led to a reduction in the expression of pro-inflammatory cytokine and epithelial-to-mesenchymal transition (EMT) genes, as well as a prominent down-regulation of the immune checkpoint ligand PD-L1. This PKCα-dependent gene expression profile was corroborated in silico using human prostate cancer databases. Our studies established PKCα as a multifunctional kinase that plays pleiotropic roles in prostate cancer, particularly by controlling genetic networks associated with tumor growth and progression. The identification of PKCα as a pro-tumorigenic kinase in human prostate cancer provides strong rationale for the development of therapeutic approaches towards targeting PKCα or its effectors.
Collapse
Affiliation(s)
- Mariana Cooke
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Medicine, Einstein Medical Center Philadelphia, Philadelphia, Pennsylvania
| | - Xuyao Zhang
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Suli Zhang
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Evgeniy Eruslanov
- Division of Thoracic Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Priti Lal
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Reba E. Daniel
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Michael D. Feldman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Martin C. Abba
- Centro de Investigaciones Inmunológicas Básicas y Aplicadas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Marcelo G. Kazanietz
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| |
Collapse
|
28
|
Nuclear Proteomics of Induced Leukemia Cell Differentiation. Cells 2022; 11:cells11203221. [PMID: 36291090 PMCID: PMC9600443 DOI: 10.3390/cells11203221] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/06/2022] [Accepted: 10/11/2022] [Indexed: 11/16/2022] Open
Abstract
Studies of induced granulocytic differentiation help to reveal molecular mechanisms of cell maturation. The nuclear proteome represents a rich source of regulatory molecules, including transcription factors (TFs). It is important to have an understanding of molecular perturbations at the early stages of the differentiation processes. By applying the proteomic quantitative profiling using isobaric labeling, we found that the contents of 214, 319, 376, 426, and 391 proteins were altered at 3, 6, 9, 12, and 72 h, respectively, compared to 0 h in the HL-60 cell nuclear fraction under all-trans-retinoid acid (ATRA) treatment. From 1860 identified nuclear proteins, 231 proteins were annotated as proteins with transcription factor (TF) activity. Six TFs (RREB1, SRCAP, CCDC124, TRIM24, BRD7, and BUD31) were downregulated and three TFs EWSR1, ENO1, and FUS were upregulated at early time points (3–12 h) after ATRA treatment. Bioinformatic annotation indicates involvement of the HL-60 nuclear proteome in DNA damage recognition in the RUNX1-triggered pathway, and in the p53-regulation pathway. By applying scheduled multiple reaction monitoring using stable isotopically labeled peptide standards (MRM/SIS), we found a persistent increase in the content of the following proteins: PRAM1, CEPBP, RBPJ, and HIC1 in the HL-60 cell nuclear fraction during ATRA-induced granulocytic differentiation. In the case of STAT1, CASP3, PARP1, and PRKDC proteins, a transient increase in their content was observed at early time points (3–12 h) after the ATRA treatment. Obtained data on nuclear proteome composition and dynamics during granulocytic differentiation could be beneficial for the development of new treatment approaches for leukemias with the mutated p53 gene.
Collapse
|
29
|
Kim M, Singh M, Lee BK, Hibbs M, Richardson K, Ellies L, Wintle L, Stuart LM, Wang JY, Voon DC, Blancafort P, Wang J, Kim J, Leedman PJ, Woo AJ. A MYC-ZNF148-ID1/3 regulatory axis modulating cancer stem cell traits in aggressive breast cancer. Oncogenesis 2022; 11:60. [PMID: 36207293 PMCID: PMC9546828 DOI: 10.1038/s41389-022-00435-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 09/17/2022] [Accepted: 09/22/2022] [Indexed: 11/13/2022] Open
Abstract
The MYC proto-oncogene (MYC) is one of the most frequently overexpressed genes in breast cancer that drives cancer stem cell-like traits, resulting in aggressive disease progression and poor prognosis. In this study, we identified zinc finger transcription factor 148 (ZNF148, also called Zfp148 and ZBP-89) as a direct target of MYC. ZNF148 suppressed cell proliferation and migration and was transcriptionally repressed by MYC in breast cancer. Depletion of ZNF148 by short hairpin RNA (shRNA) and CRISPR/Cas9 increased triple-negative breast cancer (TNBC) cell proliferation and migration. Global transcriptome and chromatin occupancy analyses of ZNF148 revealed a central role in inhibiting cancer cell de-differentiation and migration. Mechanistically, we identified the Inhibitor of DNA binding 1 and 3 (ID1, ID3), drivers of cancer stemness and plasticity, as previously uncharacterized targets of transcriptional repression by ZNF148. Silencing of ZNF148 increased the stemness and tumorigenicity in TNBC cells. These findings uncover a previously unknown tumor suppressor role for ZNF148, and a transcriptional regulatory circuitry encompassing MYC, ZNF148, and ID1/3 in driving cancer stem cell traits in aggressive breast cancer.
Collapse
Affiliation(s)
- Mijeong Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Manjot Singh
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Perth, WA, 6000, Australia
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, 6027, Australia
| | - Bum-Kyu Lee
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, State University of New York, Rensselaer, NY, 12144, USA
| | - Moira Hibbs
- RPH Research Centre, Royal Perth Hospital, Perth, WA, 6000, Australia
| | - Kirsty Richardson
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Perth, WA, 6000, Australia
| | - Lesley Ellies
- Division of Pharmacology and Toxicology, School of Biomedical Sciences, The University of Western Australia, Perth, WA, 6000, Australia
| | - Larissa Wintle
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Perth, WA, 6000, Australia
| | - Lisa M Stuart
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Perth, WA, 6000, Australia
| | - Jenny Y Wang
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, 2006, Australia
| | - Dominic C Voon
- Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, 920-1192, Japan
- Cancer Research Institute, Kanazawa University, Kanazawa, 920-1192, Japan
| | - Pilar Blancafort
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Perth, WA, 6000, Australia
- School of Human Sciences, The University of Western Australia, Perth, WA, 6000, Australia
- The Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Jianlong Wang
- Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Peter J Leedman
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Perth, WA, 6000, Australia.
| | - Andrew J Woo
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands and Centre for Medical Research, The University of Western Australia, Perth, WA, 6000, Australia.
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, 6027, Australia.
- School of Medical and Health Sciences, Edith Cowan University, Perth, WA, 6000, Australia.
| |
Collapse
|
30
|
Gupta S, Fink MK, Kempuraj D, Sinha NR, Martin LM, Keele LM, Sinha PR, Giuliano EA, Hesemann NP, Raikwar SP, Chaurasia SS, Mohan RR. Corneal fibrosis abrogation by a localized AAV-mediated inhibitor of differentiation 3 (Id3) gene therapy in rabbit eyes in vivo. Mol Ther 2022; 30:3257-3269. [PMID: 35780298 PMCID: PMC9552811 DOI: 10.1016/j.ymthe.2022.06.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/18/2022] [Accepted: 06/29/2022] [Indexed: 11/28/2022] Open
Abstract
Previously we found that inhibitor of differentiation 3 (Id3) gene, a transcriptional repressor, efficiently inhibits corneal keratocyte differentiation to myofibroblasts in vitro. This study evaluated the potential of adeno-associated virus 5 (AAV5)-mediated Id3 gene therapy to treat corneal scarring using an established rabbit in vivo disease model. Corneal scarring/fibrosis in rabbit eyes was induced by alkali trauma, and 24 h thereafter corneas were administered with either balanced salt solution AAV5-naked vector, or AAV5-Id3 vector (n = 6/group) via an optimized reported method. Therapeutic effects of AAV5-Id3 gene therapy on corneal pathology and ocular health were evaluated with clinical, histological, and molecular techniques. Localized AAV5-Id3 gene therapy significantly inhibited corneal fibrosis/haze clinically from 2.7 to 0.7 on the Fantes scale in live animals (AAV5-naked versus AAV5-Id3; p < 0.001). Furthermore, AAV5-Id3 treatment significantly reduced profibrotic gene mRNA levels: α-smooth muscle actin (α-SMA) (2.8-fold; p < 0.001), fibronectin (3.2-fold; p < 0.001), collagen I (0.8-fold; p < 0.001), and collagen III (1.4-fold; p < 0.001), as well as protein levels of α-SMA (23.8%; p < 0.001) and collagens (1.8-fold; p < 0.001). The anti-fibrotic activity of AAV5-Id3 is attributed to reduced myofibroblast formation by disrupting the binding of E-box proteins to the promoter of α-SMA, a transforming growth factor-β signaling downstream target gene. In conclusion, these results indicate that localized AAV5-Id3 delivery in stroma caused no clinically relevant ocular symptoms or corneal cellular toxicity in the rabbit eyes.
Collapse
Affiliation(s)
- Suneel Gupta
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO 65201, USA; Departments of Veterinary Medicine & Surgery and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, 1600 East Rollins Street, Columbia, MO 65211, USA
| | - Michael K Fink
- Department of Pathology, School of Medicine, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Duraisamy Kempuraj
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO 65201, USA; Departments of Veterinary Medicine & Surgery and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, 1600 East Rollins Street, Columbia, MO 65211, USA
| | - Nishant R Sinha
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO 65201, USA; Departments of Veterinary Medicine & Surgery and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, 1600 East Rollins Street, Columbia, MO 65211, USA
| | - Lynn M Martin
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO 65201, USA; Departments of Veterinary Medicine & Surgery and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, 1600 East Rollins Street, Columbia, MO 65211, USA
| | - Landon M Keele
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO 65201, USA; Departments of Veterinary Medicine & Surgery and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, 1600 East Rollins Street, Columbia, MO 65211, USA
| | - Prashant R Sinha
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO 65201, USA; Departments of Veterinary Medicine & Surgery and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, 1600 East Rollins Street, Columbia, MO 65211, USA
| | - Elizabeth A Giuliano
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO 65201, USA; Departments of Veterinary Medicine & Surgery and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, 1600 East Rollins Street, Columbia, MO 65211, USA
| | - Nathan P Hesemann
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO 65201, USA; Department of Pathology, School of Medicine, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sudhanshu P Raikwar
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO 65201, USA; Departments of Veterinary Medicine & Surgery and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, 1600 East Rollins Street, Columbia, MO 65211, USA
| | - Shyam S Chaurasia
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO 65201, USA; Departments of Veterinary Medicine & Surgery and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, 1600 East Rollins Street, Columbia, MO 65211, USA; Department of Ophthalmology & Visual Sciences, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Rajiv R Mohan
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO 65201, USA; Departments of Veterinary Medicine & Surgery and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, 1600 East Rollins Street, Columbia, MO 65211, USA; Mason Eye Institute, School of Medicine, University of Missouri, 1600 East Rollins Street, Columbia, MO 65212, USA.
| |
Collapse
|
31
|
Luo D, Shi F, Wang S, Yang J, Zhou R. Tongue squamous cell carcinoma resists hyperthermia treatment by promoting Id-1 expression mediated EMT. Bull Cancer 2022; 109:886-894. [DOI: 10.1016/j.bulcan.2022.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 04/22/2022] [Accepted: 05/02/2022] [Indexed: 11/29/2022]
|
32
|
Singh S, Sarkar T, Jakubison B, Gadomski S, Spradlin A, Gudmundsson KO, Keller JR. Inhibitor of DNA binding proteins revealed as orchestrators of steady state, stress and malignant hematopoiesis. Front Immunol 2022; 13:934624. [PMID: 35990659 PMCID: PMC9389078 DOI: 10.3389/fimmu.2022.934624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/12/2022] [Indexed: 11/24/2022] Open
Abstract
Adult mammalian hematopoiesis is a dynamic cellular process that provides a continuous supply of myeloid, lymphoid, erythroid/megakaryocyte cells for host survival. This process is sustained by regulating hematopoietic stem cells (HSCs) quiescence, proliferation and activation under homeostasis and stress, and regulating the proliferation and differentiation of downstream multipotent progenitor (MPP) and more committed progenitor cells. Inhibitor of DNA binding (ID) proteins are small helix-loop-helix (HLH) proteins that lack a basic (b) DNA binding domain present in other family members, and function as dominant-negative regulators of other bHLH proteins (E proteins) by inhibiting their transcriptional activity. ID proteins are required for normal T cell, B cell, NK and innate lymphoid cells, dendritic cell, and myeloid cell differentiation and development. However, recent evidence suggests that ID proteins are important regulators of normal and leukemic hematopoietic stem and progenitor cells (HSPCs). This chapter will review our current understanding of the function of ID proteins in HSPC development and highlight future areas of scientific investigation.
Collapse
Affiliation(s)
- Shweta Singh
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute (NCI)- Frederick, Frederick, MD, United States
| | - Tanmoy Sarkar
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute (NCI)- Frederick, Frederick, MD, United States
| | - Brad Jakubison
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute (NCI)- Frederick, Frederick, MD, United States
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Stephen Gadomski
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute (NCI)- Frederick, Frederick, MD, United States
| | - Andrew Spradlin
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute (NCI)- Frederick, Frederick, MD, United States
| | - Kristbjorn O. Gudmundsson
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute (NCI)- Frederick, Frederick, MD, United States
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Jonathan R. Keller
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute (NCI)- Frederick, Frederick, MD, United States
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
- *Correspondence: Jonathan R. Keller,
| |
Collapse
|
33
|
Hwang SM, Im SH, Rudra D. Signaling networks controlling ID and E protein activity in T cell differentiation and function. Front Immunol 2022; 13:964581. [PMID: 35983065 PMCID: PMC9379924 DOI: 10.3389/fimmu.2022.964581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/18/2022] [Indexed: 11/24/2022] Open
Abstract
E and inhibitor of DNA binding (ID) proteins are involved in various cellular developmental processes and effector activities in T cells. Recent findings indicate that E and ID proteins are not only responsible for regulating thymic T cell development but also modulate the differentiation, function, and fate of peripheral T cells in multiple immune compartments. Based on the well-established E and ID protein axis (E-ID axis), it has been recognized that ID proteins interfere with the dimerization of E proteins, thus restricting their transcriptional activities. Given this close molecular relationship, the extent of expression or stability of these two protein families can dynamically affect the expression of specific target genes involved in multiple aspects of T cell biology. Therefore, it is essential to understand the endogenous proteins or extrinsic signaling pathways that can influence the dynamics of the E-ID axis in a cell-specific and context-dependent manner. Here, we provide an overview of E and ID proteins and the functional outcomes of the E-ID axis in the activation and function of multiple peripheral T cell subsets, including effector and memory T cell populations. Further, we review the mechanisms by which endogenous proteins and signaling pathways alter the E-ID axis in various T cell subsets influencing T cell function and fate at steady-state and in pathological settings. A comprehensive understanding of the functions of E and ID proteins in T cell biology can be instrumental in T cell-specific targeting of the E-ID axis to develop novel therapeutic modalities in the context of autoimmunity and cancer.
Collapse
Affiliation(s)
- Sung-Min Hwang
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, United States
| | - Sin-Hyeog Im
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, South Korea
- Institute for Convergence Research and Education, Yonsei University, Seoul, South Korea
- ImmunoBiome Inc., Bio Open Innovation Center, Pohang, South Korea
- *Correspondence: Sin-Hyeog Im, ; Dipayan Rudra,
| | - Dipayan Rudra
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- *Correspondence: Sin-Hyeog Im, ; Dipayan Rudra,
| |
Collapse
|
34
|
Chen PY, Wang CY, Tsao EC, Chen YT, Wu MJ, Ho CT, Yen JH. 5-Demethylnobiletin Inhibits Cell Proliferation, Downregulates ID1 Expression, Modulates the NF-κB/TNF-α Pathway and Exerts Antileukemic Effects in AML Cells. Int J Mol Sci 2022; 23:ijms23137392. [PMID: 35806401 PMCID: PMC9266321 DOI: 10.3390/ijms23137392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 02/06/2023] Open
Abstract
Acute myeloid leukemia (AML) is characterized by the dysregulation of hematopoietic cell proliferation, resulting in the accumulation of immature myeloid cells in bone marrow. 5-Demethylnobiletin (5-demethyl NOB), a citrus 5-hydroxylated polymethoxyflavone, has been reported to exhibit various bioactivities, such as antioxidant, anti-inflammatory and anticancer properties. In this study, we investigated the antileukemic effects of 5-demethyl NOB and its underlying molecular mechanisms in human AML cells. We found that 5-demethyl NOB (20−80 μM) significantly reduced human leukemia cell viability, and the following trend of effectiveness was observed: THP-1 ≈ U-937 > HEL > HL-60 > K562 cells. 5-Demethyl NOB (20 and 40 μM) modulated the cell cycle through the regulation of p21, cyclin E1 and cyclin A1 expression and induced S phase arrest. 5-Demethyl NOB also promoted leukemia cell apoptosis and differentiation. Microarray-based transcriptome, Gene Ontology (GO) and Gene Set Enrichment Analysis (GSEA) of differentially expressed genes (DEGs) analysis showed that the expression of inhibitor of differentiation/DNA binding 1 (ID1), a gene associated with the GO biological process (BP) cell population proliferation (GO: 0008283), was most strongly suppressed by 5-demethyl NOB (40 μM) in THP-1 cells. We further demonstrated that 5-demethyl NOB-induced ID1 reduction was associated with the inhibition of leukemia cell growth. Moreover, DEGs involved in the hallmark gene set NF-κB/TNF-α signaling pathway were markedly enriched and downregulated by 5-demethyl NOB. Finally, we demonstrated that 5-demethyl NOB (20 and 40 μM), combined with cytarabine, synergistically reduced THP-1 and U-937 cell viability. Our current findings support that 5-demethyl NOB dramatically suppresses leukemia cell proliferation and may serve as a potential phytochemical for human AML chemotherapy.
Collapse
Affiliation(s)
- Pei-Yi Chen
- Center of Medical Genetics, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien 97004, Taiwan;
- Department of Molecular Biology and Human Genetics, Tzu Chi University, Hualien 97004, Taiwan; (E.-C.T.); (Y.-T.C.)
| | - Chih-Yang Wang
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, Taipei Medical University, Taipei 11031, Taiwan;
- Graduate Institute of Cancer Biology and Drug Discovery, Taipei Medical University, Taipei 11031, Taiwan
| | - En-Ci Tsao
- Department of Molecular Biology and Human Genetics, Tzu Chi University, Hualien 97004, Taiwan; (E.-C.T.); (Y.-T.C.)
| | - Yu-Ting Chen
- Department of Molecular Biology and Human Genetics, Tzu Chi University, Hualien 97004, Taiwan; (E.-C.T.); (Y.-T.C.)
| | - Ming-Jiuan Wu
- Department of Biotechnology, Chia Nan University of Pharmacy and Science, Tainan 71710, Taiwan;
| | - Chi-Tang Ho
- Department of Food Science, Rutgers University, New Brunswick, NJ 08901, USA;
| | - Jui-Hung Yen
- Department of Molecular Biology and Human Genetics, Tzu Chi University, Hualien 97004, Taiwan; (E.-C.T.); (Y.-T.C.)
- Institute of Medical Sciences, Tzu Chi University, Hualien 970, Taiwan
- Correspondence: ; Tel.: +886-3-856-5301 (ext. 2683)
| |
Collapse
|
35
|
Jakubison BL, Sarkar T, Gudmundsson KO, Singh S, Sun L, Morris HM, Klarmann KD, Keller JR. ID2 and HIF-1α collaborate to protect quiescent hematopoietic stem cells from activation, differentiation, and exhaustion. J Clin Invest 2022; 132:152599. [PMID: 35775482 PMCID: PMC9246389 DOI: 10.1172/jci152599] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 04/26/2022] [Indexed: 11/17/2022] Open
Abstract
Defining mechanism(s) that maintain tissue stem quiescence is important for improving tissue regeneration, cell therapies, aging, and cancer. We report here that genetic ablation of Id2 in adult hematopoietic stem cells (HSCs) promotes increased HSC activation and differentiation, which results in HSC exhaustion and bone marrow failure over time. Id2Δ/Δ HSCs showed increased cycling, ROS production, mitochondrial activation, ATP production, and DNA damage compared with Id2+/+ HSCs, supporting the conclusion that Id2Δ/Δ HSCs are less quiescent. Mechanistically, HIF-1α expression was decreased in Id2Δ/Δ HSCs, and stabilization of HIF-1α in Id2Δ/Δ HSCs restored HSC quiescence and rescued HSC exhaustion. Inhibitor of DNA binding 2 (ID2) promoted HIF-1α expression by binding to the von Hippel-Lindau (VHL) protein and interfering with proteasomal degradation of HIF-1α. HIF-1α promoted Id2 expression and enforced a positive feedback loop between ID2 and HIF-1α to maintain HSC quiescence. Thus, sustained ID2 expression could protect HSCs during stress and improve HSC expansion for gene editing and cell therapies.
Collapse
Affiliation(s)
- Brad L Jakubison
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA.,Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute (NCI) - Frederick, NIH, Frederick, Maryland, USA
| | - Tanmoy Sarkar
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute (NCI) - Frederick, NIH, Frederick, Maryland, USA
| | - Kristbjorn O Gudmundsson
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA.,Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute (NCI) - Frederick, NIH, Frederick, Maryland, USA
| | - Shweta Singh
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute (NCI) - Frederick, NIH, Frederick, Maryland, USA
| | - Lei Sun
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute (NCI) - Frederick, NIH, Frederick, Maryland, USA
| | - Holly M Morris
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute (NCI) - Frederick, NIH, Frederick, Maryland, USA
| | - Kimberly D Klarmann
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Jonathan R Keller
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA.,Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute (NCI) - Frederick, NIH, Frederick, Maryland, USA
| |
Collapse
|
36
|
Combs LR, Spires LM, Alonso JD, Papp B, Toth Z. KSHV RTA Induces Degradation of the Host Transcription Repressor ID2 To Promote the Viral Lytic Cycle. J Virol 2022; 96:e0010122. [PMID: 35604218 PMCID: PMC9215225 DOI: 10.1128/jvi.00101-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/05/2022] [Indexed: 11/20/2022] Open
Abstract
The immediate early viral protein replication and transcription activator (RTA) of Kaposi's sarcoma-associated herpesvirus (KSHV) is essential for activating the lytic cycle of KSHV. RTA induces the KSHV lytic cycle by several mechanisms, acting as a viral transcription factor that directly induces viral and host genes and acting as a viral E3 ubiquitin ligase by degrading host proteins that block viral lytic replication. Recently, we have characterized the global gene expression changes in primary effusion lymphoma (PEL) upon lytic reactivation of KSHV, which also led to the identification of rapidly downregulated genes such as ID2, an inhibitor of basic helix-loop-helix transcription factors. Here, we demonstrate that ID2 overexpression in PEL ablates KSHV lytic reactivation, indicating that ID2 inhibits the KSHV lytic cycle. Furthermore, we show that while ID2 is highly expressed during latency, its protein level is rapidly reduced by 4 h postinduction during lytic reactivation. Our results indicate that RTA binds to ID2 and induces its degradation during the KSHV lytic cycle by N-terminal ubiquitination through the ubiquitin-proteasome pathway. Importantly, we found that not only KSHV RTA but also its Epstein-Barr virus (EBV) and murine gammaherpesvirus 68 (MHV68) homologs interact with ID2, and they can induce the degradation of all four members of the ID protein family, suggesting an evolutionarily conserved interplay between gammaherpesvirus RTAs and ID proteins. Taken together, we propose that ID2 acts as a repressor of the KSHV lytic cycle, which is counteracted by its RTA-mediated degradation. We also predict that ID proteins may act as restriction factors of the lytic phase of the other gammaherpesviruses as well. IMPORTANCE In addition to its transcription regulatory role, RTA is also known to have an E3 ubiquitin ligase activity, which RTA utilizes for inducing protein degradation. However, it is still largely unknown what host factors are downregulated during KSHV lytic reactivation by RTA-mediated protein degradation and what the biological significance of the degradation of these host factors is. In this study, we discovered that RTA employs N-terminal ubiquitination to induce degradation of ID2, a potent transcription repressor of host genes, via the ubiquitin-proteasome pathway to promote KSHV lytic reactivation in PEL cells. Furthermore, we found that not only KSHV RTA but also RTA of EBV and MHV68 gammaherpesviruses can induce the degradation of all four human ID proteins, indicating that the interplay between gammaherpesvirus RTAs and ID proteins is evolutionarily conserved.
Collapse
Affiliation(s)
- Lauren R. Combs
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, USA
| | - Lauren McKenzie Spires
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, USA
| | - Juan D. Alonso
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, USA
| | - Bernadett Papp
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, USA
- University of Florida Genetics Institute, Gainesville, Florida, USA
- University of Florida Health Cancer Center, Gainesville, Florida, USA
- University of Florida Center for Orphaned Autoimmune Disorders, Gainesville, Florida, USA
- University of Florida Informatics Institute, Gainesville, Florida, USA
| | - Zsolt Toth
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, USA
- University of Florida Genetics Institute, Gainesville, Florida, USA
- University of Florida Health Cancer Center, Gainesville, Florida, USA
| |
Collapse
|
37
|
Heo J, Lee J, Nam YJ, Kim Y, Yun H, Lee S, Ju H, Ryu CM, Jeong SM, Lee J, Lim J, Cho YM, Jeong EM, Hong B, Son J, Shin DM. The CDK1/TFCP2L1/ID2 cascade offers a novel combination therapy strategy in a preclinical model of bladder cancer. Exp Mol Med 2022; 54:801-811. [PMID: 35729325 PMCID: PMC9256744 DOI: 10.1038/s12276-022-00786-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/14/2022] [Accepted: 04/06/2022] [Indexed: 01/03/2023] Open
Abstract
Aberrant activation of embryogenesis-related molecular programs in urothelial bladder cancer (BC) is associated with stemness features related to oncogenic dedifferentiation and tumor metastasis. Recently, we reported that overexpression of transcription factor CP2-like protein-1 (TFCP2L1) and its phosphorylation at Thr177 by cyclin-dependent kinase-1 (CDK1) play key roles in regulating bladder carcinogenesis. However, the clinical relevance and therapeutic potential of this novel CDK1-TFCP2L1 molecular network remain elusive. Here, we demonstrated that inhibitor of DNA binding-2 (ID2) functions as a crucial mediator by acting as a direct repressive target of TFCP2L1 to modulate the stemness features and survival of BC cells. Low ID2 and high CDK1 expression were significantly associated with unfavorable clinical characteristics. TFCP2L1 downregulated ID2 by directly binding to its promoter region. Consistent with these findings, ectopic expression of ID2 or treatment with apigenin, a chemical activator of ID2, triggered apoptosis and impaired the proliferation, suppressed the stemness features, and reduced the invasive capacity of BC cells. Combination treatment with the specific CDK1 inhibitor RO-3306 and apigenin significantly suppressed tumor growth in an orthotopic BC xenograft animal model. This study demonstrates the biological role and clinical utility of ID2 as a direct target of the CDK1-TFCP2L1 pathway for modulating the stemness features of BC cells. Combination therapy with apigenin, a powerful antioxidant found in plants such as parsley and camomile, and a drug that inhibits the cell cycle protein CDK1 shows promise for developing therapies for bladder cancer (BC). Switching on genes usually activated in stem cells can cause cancer, including BC. Although CDK1 was known to activate one of these genes in BC cells, no way to suppress the activation had been identified. Jinbeom Heo at University of Ulsan College of Medicine, South Korea, and coworkers investigated CDK1’s role in BC. They found that the transcription factor activated by CDK1 suppressed a protein, ID2, that suppressed stem cell-like characteristics. Simultaneously suppressing CDK1 and boosting ID2 with apigenin strongly repressed tumor growth in a mouse model. These results help point the way to developing new treatment options for BC patients.
Collapse
Affiliation(s)
- Jinbeom Heo
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.,Department of Physiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jinyoung Lee
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Yun Ji Nam
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.,Department of Physiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - YongHwan Kim
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.,Department of Physiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - HongDuck Yun
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.,Department of Physiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Seungun Lee
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.,Department of Physiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hyein Ju
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.,Department of Physiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Chae-Min Ryu
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.,Department of Urology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.,Center for Cell Therapy, Asan Medical Center, Seoul, Korea
| | - Seon Min Jeong
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.,Department of Physiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jinwon Lee
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.,Department of Physiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jisun Lim
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.,Department of Physiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Yong Mee Cho
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Eui Man Jeong
- Department of Pharmacy, College of Pharmacy, Jeju National University, Jeju, Korea.,Interdisciplinary Graduate Program in Advanced Convergence Technology and Science, Bio-Health Materials Core-Facility Center and Practical Translational Research Center, Jeju National University, Jeju, Korea
| | - Bumsik Hong
- Department of Urology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
| | - Jaekyoung Son
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
| | - Dong-Myung Shin
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea. .,Department of Physiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea. .,Center for Cell Therapy, Asan Medical Center, Seoul, Korea.
| |
Collapse
|
38
|
Characterization of Chicken α2A-Adrenoceptor: Molecular Cloning, Functional Analysis, and Its Involvement in Ovarian Follicular Development. Genes (Basel) 2022; 13:genes13071113. [PMID: 35885896 PMCID: PMC9315859 DOI: 10.3390/genes13071113] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 06/17/2022] [Accepted: 06/17/2022] [Indexed: 01/21/2023] Open
Abstract
Adrenoceptors are suggested to mediate the functions of norepinephrine (NE) and epinephrine (EPI) in the central nervous system (CNS) and peripheral tissues in vertebrates. Compared to mammals, the functionality and expression of adrenoceptors have not been well characterized in birds. Here, we reported the structure, expression, and functionality of chicken functional α2A-adrenoceptor, named ADRA2A. The cloned chicken ADRA2A cDNA is 1335 bp in length, encoding the receptor with 444 amino acids (a.a.), which shows high amino acid sequence identity (63.4%) with its corresponding ortholog in humans. Using cell-based luciferase reporter assays and Western blot, we demonstrated that the ADRA2A could be activated by both NE and EPI through multiple signaling pathways, including MAPK/ERK signaling cascade. In addition, the mRNA expression of ADRA2A is found to be expressed abundantly in adult chicken tissues including thyroid, lung, ovary and adipose from the reported RNA-Seq data sets. Moreover, the mRNA expression of ADRA2A is also found to be highly expressed in the granulosa cells of 6–8 mm and F5 chicken ovarian follicles, which thus supports that ADRA2A signaling may play a role in ovarian follicular growth and differentiation. Taken together, our data provide the first proof that the α2A-adrenoceptor is functional in birds involving avian ovarian follicular development.
Collapse
|
39
|
Seng C, Luo W, Földy C. Circuit formation in the adult brain. Eur J Neurosci 2022; 56:4187-4213. [PMID: 35724981 PMCID: PMC9546018 DOI: 10.1111/ejn.15742] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/30/2022]
Abstract
Neurons in the mammalian central nervous system display an enormous capacity for circuit formation during development but not later in life. In principle, new circuits could be also formed in adult brain, but the absence of the developmental milieu and the presence of growth inhibition and hundreds of working circuits are generally viewed as unsupportive for such a process. Here, we bring together evidence from different areas of neuroscience—such as neurological disorders, adult‐brain neurogenesis, innate behaviours, cell grafting, and in vivo cell reprogramming—which demonstrates robust circuit formation in adult brain. In some cases, adult‐brain rewiring is ongoing and required for certain types of behaviour and memory, while other cases show significant promise for brain repair in disease models. Together, these examples highlight that the adult brain has higher capacity for structural plasticity than previously recognized. Understanding the underlying mechanisms behind this retained plasticity has the potential to advance basic knowledge regarding the molecular organization of synaptic circuits and could herald a new era of neural circuit engineering for therapeutic repair.
Collapse
Affiliation(s)
- Charlotte Seng
- Laboratory of Neural Connectivity, Brain Research Institute, Faculties of Medicine and Science, University of Zurich, Zürich, Switzerland
| | - Wenshu Luo
- Laboratory of Neural Connectivity, Brain Research Institute, Faculties of Medicine and Science, University of Zurich, Zürich, Switzerland
| | - Csaba Földy
- Laboratory of Neural Connectivity, Brain Research Institute, Faculties of Medicine and Science, University of Zurich, Zürich, Switzerland
| |
Collapse
|
40
|
Jiang H, Du M, Li Y, Zhou T, Lei J, Liang H, Zhong Z, Al-Lamki RS, Jiang M, Yang J. ID proteins promote the survival and primed-to-naive transition of human embryonic stem cells through TCF3-mediated transcription. Cell Death Dis 2022; 13:549. [PMID: 35701409 PMCID: PMC9198052 DOI: 10.1038/s41419-022-04958-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 05/05/2022] [Accepted: 05/16/2022] [Indexed: 01/21/2023]
Abstract
Inhibition of DNA binding proteins 1 and 3 (ID1 and ID3) are important downstream targets of BMP signalling that are necessary for embryonic development. However, their specific roles in regulating the pluripotency of human embryonic stem cells (hESCs) remain unclear. Here, we examined the roles of ID1 and ID3 in primed and naive-like hESCs and showed that ID1 and ID3 knockout lines (IDs KO) exhibited decreased survival in both primed and naive-like state. IDs KO lines in the primed state also tended to undergo pluripotent dissolution and ectodermal differentiation. IDs KO impeded the primed-to-naive transition (PNT) of hESCs, and overexpression of ID1 in primed hESCs promoted PNT. Furthermore, single-cell RNA sequencing demonstrated that ID1 and ID3 regulated the survival and pluripotency of hESCs through the AKT signalling pathway. Finally, we showed that TCF3 mediated transcriptional inhibition of MCL1 promotes AKT phosphorylation, which was confirmed by TCF3 knockdown in KO lines. Our study suggests that IDs/TCF3 acts through AKT signalling to promote survival and maintain pluripotency of both primed and naive-like hESCs.
Collapse
Affiliation(s)
- Haibin Jiang
- grid.506261.60000 0001 0706 7839Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China ,grid.13402.340000 0004 1759 700XDepartment of Physiology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Mingxia Du
- grid.506261.60000 0001 0706 7839Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Yaning Li
- grid.13402.340000 0004 1759 700XDepartment of Physiology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Tengfei Zhou
- grid.414906.e0000 0004 1808 0918Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang China
| | - Jia Lei
- grid.13402.340000 0004 1759 700XDepartment of Physiology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Hongqing Liang
- grid.13402.340000 0004 1759 700XDivision of Human Reproduction and Developmental Genetics, Women’s Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang China
| | - Zhen Zhong
- grid.13402.340000 0004 1759 700XDepartment of human anatomy and histoembryology, Zhejiang University School of Medicine, Hangzhou, Zhejiang China
| | - Rafia S. Al-Lamki
- grid.5335.00000000121885934Department of Medicine, National Institute of Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Ming Jiang
- grid.13402.340000 0004 1759 700XDepartment of Gastroenterology of The Children’s Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang China
| | - Jun Yang
- grid.13402.340000 0004 1759 700XDepartment of Physiology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| |
Collapse
|
41
|
Wu Z, Fang L, Yang S, Gao Y, Wang Z, Meng Q, Dang X, Sun YP, Cheng JC. GDF-11 promotes human trophoblast cell invasion by increasing ID2-mediated MMP2 expression. Cell Commun Signal 2022; 20:89. [PMID: 35705978 PMCID: PMC9202197 DOI: 10.1186/s12964-022-00899-z] [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: 01/24/2022] [Accepted: 05/15/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Growth differentiation factor-11 (GDF-11), also known as bone morphogenetic protein-11, belongs to the transforming growth factor-beta superfamily. GDF-11 was first identified as an important regulator during embryonic development. Increasing evidence has demonstrated that GDF-11 regulates the development of various organs and its aberrant expressions are associated with the risk of cardiovascular diseases and cancers. Extravillous trophoblast (EVT) cells invasion is a critical event for placenta development and needs to be finely regulated. However, to date, the biological function of GDF-11 in the human EVT cells remains unknown. METHODS HTR-8/SVneo, a human EVT cell line, and primary cultures of human EVT cells were used to examine the effect of GDF-11 on matrix metalloproteinase 2 (MMP2) expression. Matrigel-coated transwell invasion assay was used to examine cell invasiveness. A series of in vitro experiments were applied to explore the underlying mechanisms that mediate the effect of GDF-11 on MMP2 expression and cell invasion. RESULTS Treatment with GDF-11 stimulates MMP2 expression, in the HTR-8/SVneo and primary human EVT cells. Using a pharmacological inhibitor and siRNA-mediated knockdown approaches, our results demonstrated that the stimulatory effect of GDF-11 on MMP2 expression was mediated by the ALK4/5-SMAD2/3 signaling pathways. In addition, the expression of inhibitor of DNA-binding protein 2 (ID2) was upregulated by GDF-11 and that was required for the GDF-11-stimulated MMP2 expression and EVT cell invasion. CONCLUSIONS These findings discover a new biological function and underlying molecular mechanisms of GDF-11 in the regulation of human EVT cell invasion. Video Abstract.
Collapse
Affiliation(s)
- Ze Wu
- Henan Key Laboratory of Reproduction and Genetics, Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, Zhengzhou, 450052, Henan, China
| | - Lanlan Fang
- Henan Key Laboratory of Reproduction and Genetics, Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, Zhengzhou, 450052, Henan, China
| | - Sizhu Yang
- Henan Key Laboratory of Reproduction and Genetics, Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, Zhengzhou, 450052, Henan, China
| | - Yibo Gao
- Henan Key Laboratory of Reproduction and Genetics, Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, Zhengzhou, 450052, Henan, China
| | - Zhen Wang
- Henan Key Laboratory of Reproduction and Genetics, Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, Zhengzhou, 450052, Henan, China
| | - Qingxue Meng
- Henan Key Laboratory of Reproduction and Genetics, Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, Zhengzhou, 450052, Henan, China
| | - Xuan Dang
- Henan Key Laboratory of Reproduction and Genetics, Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, Zhengzhou, 450052, Henan, China
| | - Ying-Pu Sun
- Henan Key Laboratory of Reproduction and Genetics, Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, Zhengzhou, 450052, Henan, China
| | - Jung-Chien Cheng
- Henan Key Laboratory of Reproduction and Genetics, Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, 40 Daxue Road, Zhengzhou, 450052, Henan, China.
| |
Collapse
|
42
|
BMP4 Exerts Anti-Neurogenic Effect via Inducing Id3 during Aging. Biomedicines 2022; 10:biomedicines10051147. [PMID: 35625884 PMCID: PMC9138880 DOI: 10.3390/biomedicines10051147] [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: 03/24/2022] [Revised: 04/29/2022] [Accepted: 05/07/2022] [Indexed: 02/04/2023] Open
Abstract
Bone morphogenetic protein (BMP) signaling has been shown to be intimately associated with adult neurogenesis in the subventricular zone (SVZ) and subgranular zone (SGZ). Adult neurogenesis declines in aging rodents and primates. However, the role of BMP signaling in the age-related neurogenesis decline remains elusive and the effect of BMP4 on adult SVZ neurogenesis remains controversial. Here, the expression of BMP4 and its canonical effector phosphorylated-Smad1/5/8 (p-Smad1/5/8) in the murine SVZ and SGZ were found to be increased markedly with age. We identified Id3 as a major target of BMP4 in neuronal stem cells (NSCs) of both neurogenic regions, which exhibited a similar increase during aging. Intracerebroventricular infusion of BMP4 activated Smad1/5/8 phosphorylation and upregulated Id3 expression, which further restrained NeuroD1, leading to attenuated neurogenesis in both neurogenic regions and defective differentiation in the SGZ. Conversely, noggin, a potent inhibitor of BMP4, demonstrated opposing effects. In support of this, BMP4 treatment or lentiviral overexpression of Id3 resulted in decreased NeuroD1 protein levels in NSCs of both neurogenic regions and significantly inhibited neurogenesis. Thus, our findings revealed that the increased BMP4 signaling with age inhibited adult neurogenesis in both SVZ and SGZ, which may be attributed at least in part, to the changes in the Id3-NeuroD1 axis.
Collapse
|
43
|
Li L, Liu Y, Zhao Y, Feng R, Li Y, Yu X, Liu Z, Wang L. Deubiquitinase USP8 increases ID1 stability and promotes esophageal squamous cell carcinoma tumorigenesis. Cancer Lett 2022; 542:215760. [DOI: 10.1016/j.canlet.2022.215760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/23/2022] [Accepted: 05/23/2022] [Indexed: 11/02/2022]
|
44
|
Liu F, Chen S, Yu Y, Huang C, Chen H, Wang L, Zhang W, Wu J, Ye Y. Inhibitor of DNA binding 2 knockdown inhibits the growth and liver metastasis of colorectal cancer. Gene 2022; 819:146240. [PMID: 35114275 DOI: 10.1016/j.gene.2022.146240] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 12/22/2021] [Accepted: 01/18/2022] [Indexed: 12/17/2022]
Abstract
BACKGROUND Liver metastasis of colorectal cancer (CRC) remains high mortality and the mechanism is still unknown. Here we investigated the effects of inhibitor of DNA binding 2 (Id2) on growth and liver metastasis of CRC. METHODS qPCR and western blotting were used to demonstrate mRNA and protein expressions in Id2-knockdown HCT116 cells. Cell growth was observed by cell proliferation assay, colony formation assay and flow cytometry. Cell migration and invasion were observed with wound healing assay and transwell migration and invasion assay. The effects of Id2 knockdown on tumor growth and liver metastasis in vivo were evaluated respectively with subcutaneous tumor model and colorectal liver metastasis model by injecting HCT116 cells into the mesentery triangle of cecum in mice. RESULTS Id2 overexpression was found in CRC cell lines. Id2 knockdown resulted in a reduction in the proliferation, colony formation, migration and invasion of HCT116 cells. The suppression of cell proliferation was accompanied by the cell cycle arrest in the G0/G1 phase with down-regulation of Cyclin D1, Cyclin E, p-Cdk2/3, Cdk6, p-p27 and up-regulation of p21 and p27. Id2 knockdown reversed epithelial-mesenchymal transition (EMT) through increasing E-Cadherin and inhibiting N-Cadherin, Vimentin, β-catenin, Snail and Slug. Id2 was also found to inhibit CRC metastasis via MMP2, MMP9 and TIMP-1. Furthermore, Id2 knockdown suppressed CRC liver metastasis in vivo. CONCLUSION Id2 promotes CRC growth through activation of the PI3K/AKT signaling pathway, and triggers EMT to enhance CRC migration and invasion.
Collapse
Affiliation(s)
- Fang Liu
- Laboratory of Immuno-Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou 350014, China; The School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China; Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou 350014, China
| | - Shuping Chen
- Laboratory of Immuno-Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou 350014, China; Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou 350014, China
| | - Yue Yu
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China
| | - Chuanzhong Huang
- Laboratory of Immuno-Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou 350014, China; Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou 350014, China
| | - Huijing Chen
- Laboratory of Immuno-Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou 350014, China; Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou 350014, China
| | - Ling Wang
- Laboratory of Immuno-Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou 350014, China; Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou 350014, China
| | - Wanping Zhang
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China
| | - Junxin Wu
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou 350014, China; Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou 350014, China.
| | - Yunbin Ye
- Laboratory of Immuno-Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou 350014, China; The School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China; Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou 350014, China.
| |
Collapse
|
45
|
Inhibitor of DNA binding 2 (ID2) regulates the expression of developmental genes and tumorigenesis in ewing sarcoma. Oncogene 2022; 41:2873-2884. [PMID: 35422476 PMCID: PMC9107507 DOI: 10.1038/s41388-022-02310-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 11/24/2022]
Abstract
Sarcomas are difficult to treat and the therapy, even when effective, is associated with long-term and life-threatening side effects. In addition, the treatment regimens for many sarcomas, including Ewing sarcoma, rhabdomyosarcoma, and osteosarcoma, are relatively unchanged over the past two decades, indicating a critical lack of progress. Although differentiation-based therapies are used for the treatment of some cancers, the application of this approach to sarcomas has proven challenging. Here, using a CRISPR-mediated gene knockout approach, we show that Inhibitor of DNA Binding 2 (ID2) is a critical regulator of developmental-related genes and tumor growth in vitro and in vivo in Ewing sarcoma tumors. We also identified that homoharringtonine, which is an inhibitor of protein translation and FDA-approved for the treatment of leukemia, decreases the level of the ID2 protein and significantly reduces tumor growth and prolongs mouse survival in an Ewing sarcoma xenograft model. Furthermore, in addition to targeting ID2, homoharringtonine also reduces the protein levels of ID1 and ID3, which are additional members of the ID family of proteins with well-described roles in tumorigenesis, in multiple types of cancer. Overall, these results provide insight into developmental regulation in Ewing sarcoma tumors and identify a novel, therapeutic approach to target the ID family of proteins using an FDA-approved drug.
Collapse
|
46
|
Tazawa H, Shigeyasu K, Noma K, Kagawa S, Sakurai F, Mizuguchi H, Kobayashi H, Imamura T, Fujiwara T. Tumor‐targeted fluorescence labeling systems for cancer diagnosis and treatment. Cancer Sci 2022; 113:1919-1929. [PMID: 35398956 PMCID: PMC9207361 DOI: 10.1111/cas.15369] [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: 09/23/2021] [Revised: 03/25/2022] [Accepted: 04/02/2022] [Indexed: 11/28/2022] Open
Abstract
Conventional imaging techniques are available for clinical identification of tumor sites. However, detecting metastatic tumor cells that are spreading from primary tumor sites using conventional imaging techniques remains difficult. In contrast, fluorescence‐based labeling systems are useful tools for detecting tumor cells at the single‐cell level in cancer research. The ability to detect fluorescent‐labeled tumor cells enables investigations of the biodistribution of tumor cells for the diagnosis and treatment of cancer. For example, the presence of fluorescent tumor cells in the peripheral blood of cancer patients is a predictive biomarker for early diagnosis of distant metastasis. The elimination of fluorescent tumor cells without damaging normal tissues is ideal for minimally invasive treatment of cancer. To capture fluorescent tumor cells within normal tissues, however, tumor‐specific activated target molecules are needed. This review focuses on recent advances in tumor‐targeted fluorescence labeling systems, in which indirect reporter labeling using tumor‐specific promoters is applied to fluorescence labeling of tumor cells for the diagnosis and treatment of cancer. Telomerase promoter‐dependent fluorescence labeling using replication‐competent viral vectors produces fluorescent proteins that can be used to detect and eliminate telomerase‐positive tumor cells. Tissue‐specific promoter‐dependent fluorescence labeling enables identification of specific tumor cells. Vimentin promoter‐dependent fluorescence labeling is a useful tool for identifying tumor cells that undergo epithelial–mesenchymal transition (EMT). The evaluation of tumor cells undergoing EMT is important for accurately assessing metastatic potential. Thus, tumor‐targeted fluorescence labeling systems represent novel platforms that enable the capture of tumor cells for the diagnosis and treatment of cancer.
Collapse
Affiliation(s)
- Hiroshi Tazawa
- Department of Gastroenterological Surgery Okayama University Graduate School of Medicine Dentistry and Pharmaceutical Sciences Okayama Japan
- Center for Innovative Clinical Medicine Okayama University Hospital Okayama Japan
| | - Kunitoshi Shigeyasu
- Department of Gastroenterological Surgery Okayama University Graduate School of Medicine Dentistry and Pharmaceutical Sciences Okayama Japan
| | - Kazuhiro Noma
- Department of Gastroenterological Surgery Okayama University Graduate School of Medicine Dentistry and Pharmaceutical Sciences Okayama Japan
| | - Shunsuke Kagawa
- Department of Gastroenterological Surgery Okayama University Graduate School of Medicine Dentistry and Pharmaceutical Sciences Okayama Japan
- Minimally Invasive Therapy Center Okayama University Hospital Okayama Japan
| | - Fuminori Sakurai
- Laboratory of Biochemistry and Molecular Biology Graduate School of Pharmaceutical Sciences Osaka University Osaka Japan
| | - Hiroyuki Mizuguchi
- Laboratory of Biochemistry and Molecular Biology Graduate School of Pharmaceutical Sciences Osaka University Osaka Japan
| | - Hisataka Kobayashi
- Molecular Imaging Branch Center for Cancer Research National Cancer Institute National Institutes of Health Bethesda MD USA
| | - Takeshi Imamura
- Department of Molecular Medicine for Pathogenesis Ehime University Graduate School of Medicine Ehime Japan
| | - Toshiyoshi Fujiwara
- Department of Gastroenterological Surgery Okayama University Graduate School of Medicine Dentistry and Pharmaceutical Sciences Okayama Japan
| |
Collapse
|
47
|
Kozlov AP. Mammalian tumor-like organs. 2. Mammalian adipose has many tumor features and obesity is a tumor-like process. Infect Agent Cancer 2022; 17:15. [PMID: 35395810 PMCID: PMC8994355 DOI: 10.1186/s13027-022-00423-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/03/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND In previous publications, the author developed the theory of carcino-evo-devo, which predicts that evolutionarily novel organs should recapitulate some features of tumors in their development. MAIN TEXT Mammalian adipose is currently recognized as a multi-depot metabolic and endocrine organ consisting of several adipose tissues. Although lipid-storing cells and proteins are ancient, the adipose organ as a whole is evolutionarily novel to mammals. The adipose expansion has remarkable similarities with the growth of solid tumors. These similarities are the following: (1) The capability to unlimited expansion; (2) Reversible plasticity; (3) Induction of angiogenesis; (4) Chronic inflammation; (5) Remodeling and disfunction; (6) Systemic influence on the organism; (7) Hormone production; (8) Production of miRNAs that influence other tissues; (9) Immunosuppression; (10) DNA damage and resistance to apoptosis; (11) Destructive infiltration in other organs and tissues. These similarities include the majority of "hallmarks of cancer". In addition, lipomas are the most frequent soft tissue tumors, and similar drugs may be used for the treatment of obesity and cancer by preventing infiltration. This raises the possibility that obesity, at least in part, may represent an oncological problem. The existing similarities between adipose and tumors suggest the possible evolutionary origin of mammalian adipose from some ancestral benign mesenchymal hereditary tumors. Indeed, using a transgenic inducible zebrafish tumor model, we described many genes, which originated in fish and were expressed in fish tumors. Their human orthologs LEP, NOTCH1, SPRY1, PPARG, ID2, and CIDEA acquired functions connected with the adipose organ. They are also involved in tumor development in humans. CONCLUSION If the hypothesis of the evolutionary origin of the adipose organ from the ancestral hereditary tumor is correct, it may open new opportunities to resolve the oncological problem and the problem of the obesity epidemic. New interventions targeting LEP, NOTCH1, SPRY1, PPARG, ID2, and CIDEA gene network, in addition to what already is going on, can be designed for treatment and prevention of both obesity and tumors.
Collapse
Affiliation(s)
- A P Kozlov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 3, Gubkina Street, Moscow, Russia, 117971.
- Peter the Great St. Petersburg Polytechnic University, 29, Polytekhnicheskaya Street, St. Petersburg, Russia, 195251.
- The Biomedical Center, 8, Viborgskaya Street, St. Petersburg, Russia, 194044.
| |
Collapse
|
48
|
Tompkins VS, Rouse WB, O’Leary CA, Andrews RJ, Moss WN. Analyses of human cancer driver genes uncovers evolutionarily conserved RNA structural elements involved in posttranscriptional control. PLoS One 2022; 17:e0264025. [PMID: 35213597 PMCID: PMC8880891 DOI: 10.1371/journal.pone.0264025] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/01/2022] [Indexed: 12/02/2022] Open
Abstract
Experimental breakthroughs have provided unprecedented insights into the genes involved in cancer. The identification of such cancer driver genes is a major step in gaining a fuller understanding of oncogenesis and provides novel lists of potential therapeutic targets. A key area that requires additional study is the posttranscriptional control mechanisms at work in cancer driver genes. This is important not only for basic insights into the biology of cancer, but also to advance new therapeutic modalities that target RNA—an emerging field with great promise toward the treatment of various cancers. In the current study we performed an in silico analysis on the transcripts associated with 800 cancer driver genes (10,390 unique transcripts) that identified 179,190 secondary structural motifs with evidence of evolutionarily ordered structures with unusual thermodynamic stability. Narrowing to one transcript per gene, 35,426 predicted structures were subjected to phylogenetic comparisons of sequence and structural conservation. This identified 7,001 RNA secondary structures embedded in transcripts with evidence of covariation between paired sites, supporting structure models and suggesting functional significance. A select set of seven structures were tested in vitro for their ability to regulate gene expression; all were found to have significant effects. These results indicate potentially widespread roles for RNA structure in posttranscriptional control of human cancer driver genes.
Collapse
Affiliation(s)
- Van S. Tompkins
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, United States of America
| | - Warren B. Rouse
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, United States of America
| | - Collin A. O’Leary
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, United States of America
| | - Ryan J. Andrews
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, United States of America
| | - Walter N. Moss
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, United States of America
- * E-mail:
| |
Collapse
|
49
|
Pattarabanjird T, Marshall M, Upadhye A, Srikakulapu P, Garmey J, Haider A, Taylor AM, Lutgens E, McNamara CA. B-1b Cells Possess Unique bHLH-Driven P62-Dependent Self-Renewal and Atheroprotection. Circ Res 2022; 130:981-993. [PMID: 35209718 PMCID: PMC9075598 DOI: 10.1161/circresaha.121.320436] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND B1a and B1b lymphocytes produce IgM that inactivates oxidation-specific epitopes (IgMOSE) on LDL (low-density lipoprotein) and protects against atherosclerosis. Loss of ID3 (inhibitor of differentiation 3) in B cells selectively promotes B1b but not B1a cell numbers, leading to higher IgMOSE production and reduction in atherosclerotic plaque formation. Yet, the mechanism underlying this regulation remains unexplored. METHODS Bulk RNA sequencing was utilized to identify differentially expressed genes in B1a and B1b cells from Id3KO and Id3WT mice. CRISPR/Cas9 and lentiviral genome editing coupled with adoptive transfer were used to identify key Id3-dependent signaling pathways regulating B1b cell proliferation and the impact on atherosclerosis. Biospecimens from humans with advanced coronary artery disease imaging were analyzed to translate murine findings to human subjects with coronary artery disease. RESULTS Through RNA sequencing, P62 was found to be enriched in Id3KO B1b cells. Further in vitro characterization reveals a novel role for P62 in mediating BAFF (B-cell activating factor)-induced B1b cell proliferation through interacting with TRAF6 and activating NF-κB (nuclear factor kappa B), leading to subsequent C-MYC upregulation. Promoter-reporter assays reveal that Id3 inhibits the E2A protein from activating the P62 promoter. Mice adoptively transferred with B1 cells overexpressing P62 exhibited an increase in B1b cell number and IgMOSE levels and were protected against atherosclerosis. Consistent with murine mechanistic findings, P62 expression in human B1 cells was significantly higher in subjects harboring a function-impairing SNP (rs11574) in the ID3 gene and directly correlated with plasma IgMOSE levels. CONCLUSIONS This study unveils a novel role for P62 in driving BAFF-induced B1b cell proliferation and IgMOSE production to attenuate diet-induced atherosclerosis. Results identify a direct role for Id3 in antagonizing E2A from activating the p62 promoter. Moreover, analysis of putative human B1 cells also implicates these pathways in coronary artery disease subjects, suggesting P62 as a new immunomodulatory target for treating atherosclerosis.
Collapse
Affiliation(s)
- Tanyaporn Pattarabanjird
- Carter Immunology Center, University of Virginia, Charlottesville, Virginia, United States
- Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, United States
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States
| | - Melissa Marshall
- Carter Immunology Center, University of Virginia, Charlottesville, Virginia, United States
- Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, United States
| | - Aditi Upadhye
- Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, United States
| | - Prasad Srikakulapu
- Carter Immunology Center, University of Virginia, Charlottesville, Virginia, United States
- Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, United States
| | - James Garmey
- Carter Immunology Center, University of Virginia, Charlottesville, Virginia, United States
- Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, United States
| | - Antony Haider
- Carter Immunology Center, University of Virginia, Charlottesville, Virginia, United States
- Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, United States
| | - Angela M. Taylor
- Division of Cardiovascular Medicine, Department of Medicine, University of Virginia, Charlottesville, Virginia, United States
| | - Esther Lutgens
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität, Munich, Germany; and German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany
| | - Coleen A. McNamara
- Carter Immunology Center, University of Virginia, Charlottesville, Virginia, United States
- Cardiovascular Research Center, University of Virginia, Charlottesville, Virginia, United States
- Division of Cardiovascular Medicine, Department of Medicine, University of Virginia, Charlottesville, Virginia, United States
- Correspondence: Corresponding Author, , Phone: 434-243-5854, Address: 345 Crispell Dr. Charlottesville, VA 22908
| |
Collapse
|
50
|
Milk-Derived Proteins and Peptides in Head and Neck Carcinoma Treatment. Biomolecules 2022; 12:biom12020290. [PMID: 35204791 PMCID: PMC8961572 DOI: 10.3390/biom12020290] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 12/24/2022] Open
Abstract
Research investigating milk-derived proteins has brought to light the potential for their use as novel anticancer agents. This paper aims to systematically review studies examining the effectiveness of milk-derived proteins in the treatment of head and neck cancer. A systematic literature search of Medline, Evidence-Based Medicine, and Web of Science databases including papers published from all dates was completed. Inter-rater reliability was high during the title, abstract, and full-text screening phases. Inclusion criteria, exclusion criteria, and data extraction were based on the PICOS tool and research questions. Reporting followed the Preferred Reporting Items for Systematic Review and Meta-Analysis criteria. Eligible in vitro and in vivo studies (n = 8/658) evaluated lactoferrin, α-lactalbumin, and its complexes, such as HAMLET, BAMLET and lactalbumin-oleic acid complexes, as well as lactoperoxidase, whey, and casein. Their effectiveness in the treatment of head and neck cancer cells lines found that these compounds can inhibit tumour growth modulate cancer gene expression, and have cytotoxic effects on cancer cells. However, the exact mechanisms by which these effects are achieved are not well understood. Systematically designed, large, optimally controlled, collaborative studies, both in vitro and in vivo, will be required to gain a better understanding of their potential role in the treatment of head and neck cancer.
Collapse
|