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Schaefer Z, Iradukunda J, Lumngwena E, Basso K, Blackburn J, Parker I. Multi-Level Proteomics Reveals Epigenetic Signatures in BCG-mediated Macrophage Activation. Mol Cell Proteomics 2024:100851. [PMID: 39366656 DOI: 10.1016/j.mcpro.2024.100851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 09/17/2024] [Accepted: 09/30/2024] [Indexed: 10/06/2024] Open
Abstract
The bacillus Calmette-Guérin BCG vaccine (Mycobacterium bovis) is primarily used to prevent tuberculosis (TB) infections but has wide-ranging immunogenic effects. One of its most notable properties is its ability to induce trained immunity, a memory-like response in innate immune cells such as macrophages. Through targeted analyses of well-established histone marks, prior research has shown that these changes are generated through epigenetic modification. Mass spectrometry-based proteomic approaches provide a way to globally profile various aspects of the proteome, providing data to further identify unexplored mechanisms of BCG-mediated immunomodulation. Here we use multi-level proteomics (total, histone, and phospho to identify networks and potential mechanisms that mediate BCG induced immunomodulation in macrophages. Histone-focused proteomics and total proteomics were performed at the University of Cape Town (data available via ProteomeXchange with identifier PXD051187), while phosphoproteomics data was retrieved from the ProteomeXchange Repository (identifier PXD013171). We identify several epigenetic mechanisms that may drive BCG-induced training phenotypes. Evidence across the proteomics and histone-focused proteomics data sets pair 6 epigenetic effectors (NuA4, NuRD, NSL, Sin3A, SIRT2, SIRT6) and their substrates.
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Affiliation(s)
- Zoe Schaefer
- Department of Biomedical Engineering, University of Florida, Gainesville, FL, USA
| | - John Iradukunda
- Division of Chemical & Systems Biology, University of Cape Town, Cape Town, South Africa
| | - Evelyn Lumngwena
- School of Clinical Medicine, University of The Witwatersrand, Johannesburg, South Africa; Center for the Study of Emerging and Re-emerging Infections (CREMER), Institute for Medical Research and Medicinal Plant Studies (IMPM), Ministry of Scientific Research and Innovation, Cameroon
| | - Kari Basso
- Mass Spectrometry Research and Education Center, Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Jonathan Blackburn
- Division of Chemical & Systems Biology, University of Cape Town, Cape Town, South Africa
| | - Ivana Parker
- Department of Biomedical Engineering, University of Florida, Gainesville, FL, USA
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2
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Attaran N, Coates PJ, Zborayova K, Sgaramella N, Nylander K, Gu X. Upregulation of Apoptosis Related Genes in Clinically Normal Tongue Contralateral to Squamous Cell Carcinoma of the Oral Tongue, an Effort to Maintain Tissue Homeostasis. Head Neck Pathol 2024; 18:89. [PMID: 39348078 PMCID: PMC11442960 DOI: 10.1007/s12105-024-01695-6] [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: 08/02/2024] [Accepted: 08/27/2024] [Indexed: 10/01/2024]
Abstract
PURPOSE The field cancerization concept indicates the presence of pre-cancerous changes in clinically normal tissue surrounding the tumor. In squamous cell carcinoma of the oral tongue (SCCOT) which is infrequently linked to human papillomavirus infection, we have previously reported that clinically normal tongue contralateral to tumor (NTCT) is molecularly abnormal. Here, combining our transcriptomic and genomic data, we aimed to investigate the contribution of molecular changes in NTCT to cancer development. METHODS Microarray gene expression data of 14 healthy controls, 23 NTCT and 29 SCCOT samples were investigated to characterize transcriptional profiles in NTCT. Whole exome sequencing and RNA-sequencing data of paired NTCT and tumor samples from 15 SCCOT patients were used to study correlation between copy number variation and differential gene expression. RESULTS Using supervised multivariate partial least squares discriminant analysis, a total of 61 mRNAs that distinguish NTCT from healthy tongue were selected. Functional enrichment analysis of the 22 upregulated genes showed increased "positive regulation of nitrogen compound metabolic process" in NTCT. All 12 genes involved in this process have roles in apoptosis (anti- and/or pro-apoptotic). Compared to healthy controls, Zinc Finger Protein 395 (ZNF395), a pro-apoptotic tumor suppressor located on chromosome 8p, was the only gene showing increased mRNA level in NTCT whereas decreased in SCCOT. Given the frequent loss of chromosome 8p in SCCOT, the impact of ZNF395 copy number variation on gene expression was further examined, revealing a positive correlation between copy number and mRNA level (correlation coefficient = 0.572, p < 0.001). CONCLUSION NTCT is susceptible to malignant transformation, where tissue homeostasis is maintained at least partly through regulation of apoptosis. Loss of the pro-apoptotic gene ZNF395 could thus initiate cancer development.
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Affiliation(s)
- Nima Attaran
- Department of Medical Biosciences/Pathology, Umeå University, Building 6M, 2nd floor, Analysvägen 9, Umeå, 90187, Sweden
- Department of Clinical Sciences, Umeå University, Umeå, 90187, Sweden
| | - Philip J Coates
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, Brno, 65653, Czech Republic
| | | | - Nicola Sgaramella
- Department of Medical Biosciences/Pathology, Umeå University, Building 6M, 2nd floor, Analysvägen 9, Umeå, 90187, Sweden
- Department of Oral and Maxillo-Facial Surgery, Mater Dei Hospital, 70125, Bari, Italy
| | - Karin Nylander
- Department of Medical Biosciences/Pathology, Umeå University, Building 6M, 2nd floor, Analysvägen 9, Umeå, 90187, Sweden
| | - Xiaolian Gu
- Department of Medical Biosciences/Pathology, Umeå University, Building 6M, 2nd floor, Analysvägen 9, Umeå, 90187, Sweden.
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3
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Tatnell HR, Novakovic S, Boag PR, Davis GM. EYA-1 is required for genomic integrity independent of H2AX signalling in Caenorhabditis elegans. Mol Biol Rep 2024; 51:1009. [PMID: 39316168 PMCID: PMC11422256 DOI: 10.1007/s11033-024-09933-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 09/10/2024] [Indexed: 09/25/2024]
Abstract
BACKGROUND Resolving genomic insults is essential for the survival of any species. In the case of eukaryotes, several pathways comprise the DNA damage repair network, and many components have high evolutionary conservation. These pathways ensure that DNA damage is resolved which prevents disease associated mutations from occurring in a de novo manner. In this study, we investigated the role of the Eyes Absent (EYA) homologue in Caenorhabditis elegans and its role in DNA damage repair. Current understanding of mammalian EYA1 suggests that EYA1 is recruited in response to H2AX signalling to dsDNA breaks. C. elegans do not possess a H2AX homologue, although they do possess homologues of the core DNA damage repair proteins. Due to this, we aimed to determine if eya-1 contributes to DNA damage repair independent of H2AX. METHODS AND RESULTS We used a putative null mutant for eya-1 in C. elegans and observed that absence of eya-1 results in abnormal chromosome morphology in anaphase embryos, including chromosomal bridges, missegregated chromosomes, and embryos with abnormal nuclei. Additionally, inducing different types of genomic insults, we show that eya-1 mutants are highly sensitive to induction of DNA damage, yet show little change to induced DNA replication stress and display a mortal germline resulting in sterility over successive generations. CONCLUSIONS Collectively, this study suggests that the EYA family of proteins may have a greater involvement in maintaining genomic integrity than previously thought and unveils novel roles of EYA associated DNA damage repair.
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Affiliation(s)
- Hannah R Tatnell
- Institute of Innovation, Science and Sustainability, Federation University, Churchill, VIC, Australia
| | - Stevan Novakovic
- Department of Biochemistry and Molecular Biology, Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC, Australia
| | - Peter R Boag
- Department of Biochemistry and Molecular Biology, Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, VIC, Australia
| | - Gregory M Davis
- Institute of Innovation, Science and Sustainability, Federation University, Churchill, VIC, Australia.
- Department of Health Sciences and Biostatistics, Swinburne University of Technology, Hawthorn, Australia.
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4
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Reshi HA, Medishetti R, Ahuja A, Balasubramanian D, Babu K, Jaiswal M, Chatti K, Maddika S. EYA protein complex is required for Wntless retrograde trafficking from endosomes to Golgi. Dev Cell 2024; 59:2443-2459.e7. [PMID: 38870942 DOI: 10.1016/j.devcel.2024.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 12/01/2023] [Accepted: 05/17/2024] [Indexed: 06/15/2024]
Abstract
Retrograde transport of WLS (Wntless) from endosomes to trans-Golgi network (TGN) is required for efficient Wnt secretion during development. However, the molecular players connecting endosomes to TGN during WLS trafficking are limited. Here, we identified a role for Eyes Absent (EYA) proteins during retrograde trafficking of WLS to TGN in human cell lines. By using worm, fly, and zebrafish models, we found that the EYA-secretory carrier-associated membrane protein 3 (SCAMP3) axis is evolved in vertebrates. EYAs form a complex and interact with retromer on early endosomes. Retromer-bound EYA complex recruits SCAMP3 to endosomes, which is necessary for the fusion of WLS-containing endosomes to TGN. Loss of EYA complex or SCAMP3 leads to defective transport of WLS to TGN and failed Wnt secretion. EYA mutations found in patients with hearing loss form a dysfunctional EYA-retromer complex that fails to activate Wnt signaling. These findings identify the EYA complex as a component of retrograde trafficking of WLS from the endosome to TGN.
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Affiliation(s)
- Hilal Ahmad Reshi
- Laboratory of Cell Death & Cell Survival, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad 500039, India; Graduate Studies, Regional Centre for Biotechnology, Faridabad 121001, India
| | - Raghavender Medishetti
- Dr. Reddy's Institute of Life Sciences (DRILS), University of Hyderabad Campus, Hyderabad 500046, India
| | - Aishwarya Ahuja
- Centre for Neuroscience, Indian Institute of Science (IISc), Bangalore 560012, India
| | | | - Kavita Babu
- Centre for Neuroscience, Indian Institute of Science (IISc), Bangalore 560012, India
| | - Manish Jaiswal
- Tata Institute of Fundamental Research, Hyderabad 500046, India
| | - Kiranam Chatti
- Dr. Reddy's Institute of Life Sciences (DRILS), University of Hyderabad Campus, Hyderabad 500046, India
| | - Subbareddy Maddika
- Laboratory of Cell Death & Cell Survival, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad 500039, India.
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Nelson CB, Wells JK, Pickett HA. The Eyes Absent family: At the intersection of DNA repair, mitosis, and replication. DNA Repair (Amst) 2024; 141:103729. [PMID: 39089192 DOI: 10.1016/j.dnarep.2024.103729] [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: 05/04/2024] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 08/03/2024]
Abstract
The Eyes Absent family (EYA1-4) are a group of dual function proteins that act as both tyrosine phosphatases and transcriptional co-activators. EYA proteins play a vital role in development, but are also aberrantly overexpressed in cancers, where they often confer an oncogenic effect. Precisely how the EYAs impact cell biology is of growing interest, fuelled by the therapeutic potential of an expanding repertoire of EYA inhibitors. Recent functional studies suggest that the EYAs are important players in the regulation of genome maintenance pathways including DNA repair, mitosis, and DNA replication. While the characterized molecular mechanisms have predominantly been ascribed to EYA phosphatase activities, EYA co-transcriptional activity has also been found to impact the expression of genes that support these pathways. This indicates functional convergence of EYA phosphatase and co-transcriptional activities, highlighting the emerging importance of the EYA protein family at the intersection of genome maintenance mechanisms. In this review, we discuss recent progress in defining EYA protein substrates and transcriptional effects, specifically in the context of genome maintenance. We then outline future directions relevant to the field and discuss the clinical utility of EYA inhibitors.
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Affiliation(s)
- Christopher B Nelson
- Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, Australia
| | - Jadon K Wells
- Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, Australia
| | - Hilda A Pickett
- Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW, Australia.
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Rosenbaum SR, Hughes CJ, Fields KM, Purdy SC, Gustafson A, Wolin A, Hampton D, Turner N, Ebmeier C, Costello JC, Ford HL. An EYA3/NF-κB/CCL2 signaling axis suppresses cytotoxic NK cells in the pre-metastatic niche to promote triple negative breast cancer metastasis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.31.606072. [PMID: 39211066 PMCID: PMC11360953 DOI: 10.1101/2024.07.31.606072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Patients with Triple Negative Breast Cancer (TNBC) exhibit high rates of metastases and poor prognoses. The Eyes absent (EYA) family of proteins are developmental transcriptional cofactors/phosphatases that are re-expressed and/or upregulated in numerous cancers. Herein, we demonstrate that EYA3 correlates with decreased survival in breast cancer, and that it strongly, and specifically, regulates metastasis via a novel mechanism that involves NF-kB signaling and an altered innate immune profile at the pre-metastatic niche (PMN). Remarkably, restoration of NF-kB signaling downstream of Eya3 knockdown (KD) restores metastasis without restoring primary tumor growth, isolating EYA3/NF-kB effects to the metastatic site. We show that secreted CCL2, regulated downstream of EYA3/NF-kB, specifically decreases cytotoxic NK cells in the PMN and that re-expression of Ccl2 in Eya3 -KD cells is sufficient to rescue activation/levels of cytotoxic NK cells in vitro and at the PMN, where EYA3-mediated decreases in cytotoxic NK cells are required for metastatic outgrowth. Importantly, analysis of public breast cancer datasets uncovers a significant correlation of EYA3 with NF-kB/CCL2, underscoring the relevance of EYA3/NF-kB/CCL2 to human disease. Our findings suggest that inhibition of EYA3 could be a powerful means to re-activate the innate immune response at the PMN, inhibiting TNBC metastasis. Significance EYA3 promotes metastasis of TNBC cells by promoting NF-kB-mediated CCL2 expression and inhibiting cytotoxic NK cells at the pre-metastatic niche, highlighting a potential therapeutic target in this subset of breast cancer.
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Heng W, Wang T, Wei F, Yang F, Chen C, Yu Z, Du M, Qian J, Zhou C. EYA4 reduces chemosensitivity of osteosarcoma to doxorubicin through DNA damage repair. Biochem Pharmacol 2024; 226:116366. [PMID: 38876260 DOI: 10.1016/j.bcp.2024.116366] [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: 03/15/2024] [Revised: 05/23/2024] [Accepted: 06/11/2024] [Indexed: 06/16/2024]
Abstract
Previous studies have demonstrated that Eyes Absent 4 (EYA4) influences the proliferation and migration of tumor cells. Notably, studies have established that EYA4 can also limit tumor sensitivity to chemotherapeutic agents. The objective of this study was to investigate the effect of EYA4 in conferring drug resistance in osteosarcoma (OS). Bioinformatics, histological, and cellular analyses revealed that the expression level of EYA4 was higher in OS tissues than in healthy tissues/cells and in resistant tissues/cells compared with sensitive tissues/cells. In vitro and in vivo experiments demonstrated that EYA4 knockdown increased the sensitivity of OS to doxorubicin (DOX). Conversely, overexpression of EYA4 decreased the sensitivity of OS to DOX. Exploration of the resistance mechanism exposed that EYA4 facilitates DNA double-strand break (DSB) repair, a typical mode of DNA damage repair (DDR). Subsequently, our findings indicated that EYA4 could directly interact with histone H2AX to activate the DDR pathway. Taken together, our observations indicated that EYA4 may serve as a target molecule for reversing drug resistance in OS patients.
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Affiliation(s)
- Wei Heng
- Department of Orthopedics, Tangdu Hospital, Air Force Military Medical University, Xi'an 710038, China
| | - Tianfu Wang
- Department of Orthopedics, Tangdu Hospital, Air Force Military Medical University, Xi'an 710038, China
| | - Feilong Wei
- Department of Orthopedics, Tangdu Hospital, Air Force Military Medical University, Xi'an 710038, China
| | - Fan Yang
- Department of Orthopedics, Tangdu Hospital, Air Force Military Medical University, Xi'an 710038, China
| | - Chaobo Chen
- Department of Orthopedics, Tangdu Hospital, Air Force Military Medical University, Xi'an 710038, China
| | - Zhe Yu
- Department of Orthopedics, Tangdu Hospital, Air Force Military Medical University, Xi'an 710038, China
| | - Mingrui Du
- Department of Orthopedics, Tangdu Hospital, Air Force Military Medical University, Xi'an 710038, China; Western Theater Command Air Force Hospital, Chengdu 610065, China.
| | - Jixian Qian
- Department of Orthopedics, Tangdu Hospital, Air Force Military Medical University, Xi'an 710038, China.
| | - Chengpei Zhou
- Department of Orthopedics, Tangdu Hospital, Air Force Military Medical University, Xi'an 710038, China.
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Chouhan S, Sridaran D, Weimholt C, Luo J, Li T, Hodgson MC, Santos LN, Le Sommer S, Fang B, Koomen JM, Seeliger M, Qu CK, Yart A, Kontaridis MI, Mahajan K, Mahajan NP. SHP2 as a primordial epigenetic enzyme expunges histone H3 pTyr-54 to amend androgen receptor homeostasis. Nat Commun 2024; 15:5629. [PMID: 38965223 PMCID: PMC11224269 DOI: 10.1038/s41467-024-49978-4] [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: 04/05/2023] [Accepted: 06/27/2024] [Indexed: 07/06/2024] Open
Abstract
Mutations that decrease or increase the activity of the tyrosine phosphatase, SHP2 (encoded by PTPN11), promotes developmental disorders and several malignancies by varying phosphatase activity. We uncovered that SHP2 is a distinct class of an epigenetic enzyme; upon phosphorylation by the kinase ACK1/TNK2, pSHP2 was escorted by androgen receptor (AR) to chromatin, erasing hitherto unidentified pY54-H3 (phosphorylation of histones H3 at Tyr54) epigenetic marks to trigger a transcriptional program of AR. Noonan Syndrome with Multiple Lentigines (NSML) patients, SHP2 knock-in mice, and ACK1 knockout mice presented dramatic increase in pY54-H3, leading to loss of AR transcriptome. In contrast, prostate tumors with high pSHP2 and pACK1 activity exhibited progressive downregulation of pY54-H3 levels and higher AR expression that correlated with disease severity. Overall, pSHP2/pY54-H3 signaling acts as a sentinel of AR homeostasis, explaining not only growth retardation, genital abnormalities and infertility among NSML patients, but also significant AR upregulation in prostate cancer patients.
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Affiliation(s)
- Surbhi Chouhan
- Department of Surgery, Washington University in St Louis, St Louis, MO, 63110, USA
- 6601, Cancer Research Building, Washington University in St Louis, St Louis, MO, 63110, USA
| | - Dhivya Sridaran
- Department of Surgery, Washington University in St Louis, St Louis, MO, 63110, USA
- 6601, Cancer Research Building, Washington University in St Louis, St Louis, MO, 63110, USA
| | - Cody Weimholt
- Department of Pathology and Immunology, Washington University in St Louis, St Louis, MO, 63110, USA
| | - Jingqin Luo
- Division of Public Health Sciences, Washington University in St Louis, St Louis, MO, 63110, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, 63110, USA
| | - Tiandao Li
- Bioinformatics Research Core, Center of Regenerative Medicine, Washington University in St Louis, St Louis, MO, 63110, USA
| | - Myles C Hodgson
- Department of Biomedical Research and Translational Medicine, Masonic Medical Research Institute, 2150 Bleecker St, Utica, NY, 13501, USA
| | - Luana N Santos
- Department of Biomedical Research and Translational Medicine, Masonic Medical Research Institute, 2150 Bleecker St, Utica, NY, 13501, USA
| | - Samantha Le Sommer
- Department of Biomedical Research and Translational Medicine, Masonic Medical Research Institute, 2150 Bleecker St, Utica, NY, 13501, USA
| | - Bin Fang
- Moffitt Cancer Center, SRB3, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - John M Koomen
- Moffitt Cancer Center, SRB3, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Markus Seeliger
- Department of Pharmacological Sciences, Stony Brook University Medical School, BST 7-120, Stony Brook, NY, 11794-8651, USA
| | - Cheng-Kui Qu
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Winship Cancer Institute, Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Armelle Yart
- UMR 1301-Inserm 5070-CNRS EFS Univ. P. Sabatier, 4bis Ave Hubert Curien, 31100, Toulouse, France
| | - Maria I Kontaridis
- Department of Biomedical Research and Translational Medicine, Masonic Medical Research Institute, 2150 Bleecker St, Utica, NY, 13501, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Division of Cardiology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Kiran Mahajan
- Department of Surgery, Washington University in St Louis, St Louis, MO, 63110, USA
- 6601, Cancer Research Building, Washington University in St Louis, St Louis, MO, 63110, USA
| | - Nupam P Mahajan
- Department of Surgery, Washington University in St Louis, St Louis, MO, 63110, USA.
- 6601, Cancer Research Building, Washington University in St Louis, St Louis, MO, 63110, USA.
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, 63110, USA.
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Hu Y, Mostert D, Orgler C, Andler O, Zischka H, Kazmaier U, Vollmar AM, Braig S, Sieber SA, Zahler S. Thermal Proteome Profiling Reveals Insight to Antiproliferative and Pro-Apoptotic Effects of Lagunamide A in the Modulation of DNA Damage Repair. Chembiochem 2024; 25:e202400024. [PMID: 38716781 DOI: 10.1002/cbic.202400024] [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: 01/09/2024] [Revised: 05/06/2024] [Indexed: 06/18/2024]
Abstract
Lagunamide A is a biologically active natural product with a yet unidentified molecular mode of action. Cellular studies revealed that lagunamide A is a potent inhibitor of cancer cell proliferation, promotes apoptosis and causes mitochondrial dysfunction. To decipher the cellular mechanism responsible for these effects, we utilized thermal protein profiling (TPP) and identified EYA3 as a stabilized protein in cells upon lagunamide A treatment. EYA3, involved in the DNA damage repair process, was functionally investigated via siRNA based knockdown studies and corresponding effects of lagunamide A on DNA repair were confirmed. Furthermore, we showed that lagunamide A sensitized tumor cells to treatment with the drug doxorubicin highlighting a putative therapeutic strategy.
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Affiliation(s)
- Yudong Hu
- Department of Pharmacy, Ludwig-Maximilians-University, Butenandtstr. 5, 81377, Munich, Germany
| | - Dietrich Mostert
- Center for Functional Protein Assemblies (CPA), Department of Chemistry, Chair of Organic Chemistry II, Technical University of Munich, 85748, Garching, Germany
| | - Christina Orgler
- Department of Pharmacy, Ludwig-Maximilians-University, Butenandtstr. 5, 81377, Munich, Germany
| | - Oliver Andler
- Organic Chemistry, Saarland University, 66123, Saarbrücken, Germany
| | - Hans Zischka
- Institute of Molecular Toxicology and Pharmacology, Helmholtz Center Munich, German Research Center for Environmental Health Neuherberg, Germany
- Institute of Toxicology and Environmental Hygiene, Technical University of Munich, Munich, Germany
| | - Uli Kazmaier
- Organic Chemistry, Saarland University, 66123, Saarbrücken, Germany
| | - Angelika M Vollmar
- Department of Pharmacy, Ludwig-Maximilians-University, Butenandtstr. 5, 81377, Munich, Germany
| | - Simone Braig
- Department of Pharmacy, Ludwig-Maximilians-University, Butenandtstr. 5, 81377, Munich, Germany
| | - Stephan A Sieber
- Center for Functional Protein Assemblies (CPA), Department of Chemistry, Chair of Organic Chemistry II, Technical University of Munich, 85748, Garching, Germany
| | - Stefan Zahler
- Department of Pharmacy, Ludwig-Maximilians-University, Butenandtstr. 5, 81377, Munich, Germany
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10
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Alderman C, Anderson R, Zhang L, Hughes CJ, Li X, Ebmeier C, Wagley ME, Ahn NG, Ford HL, Zhao R. Biochemical characterization of the Eya and PP2A-B55α interaction. J Biol Chem 2024; 300:107408. [PMID: 38796066 PMCID: PMC11328874 DOI: 10.1016/j.jbc.2024.107408] [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] [Revised: 04/22/2024] [Accepted: 05/09/2024] [Indexed: 05/28/2024] Open
Abstract
The eyes absent (Eya) proteins were first identified as co-activators of the six homeobox family of transcription factors and are critical in embryonic development. These proteins are also re-expressed in cancers after development is complete, where they drive tumor progression. We have previously shown that the Eya3 N-terminal domain (NTD) contains Ser/Thr phosphatase activity through an interaction with the protein phosphatase 2A (PP2A)-B55α holoenzyme and that this interaction increases the half-life of Myc through pT58 dephosphorylation. Here, we showed that Eya3 directly interacted with the NTD of Myc, recruiting PP2A-B55α to Myc. We also showed that Eya3 increased the Ser/Thr phosphatase activity of PP2A-B55α but not PP2A-B56α. Furthermore, we demonstrated that the NTD (∼250 amino acids) of Eya3 was completely disordered, and it used a 38-residue segment to interact with B55α. In addition, knockdown and phosphoproteomic analyses demonstrated that Eya3 and B55α affected highly similar phosphosite motifs with a preference for Ser/Thr followed by Pro, consistent with Eya3's apparent Ser/Thr phosphatase activity being mediated through its interaction with PP2A-B55α. Intriguingly, mutating this Pro to other amino acids in a Myc peptide dramatically increased dephosphorylation by PP2A. Not surprisingly, MycP59A, a naturally occurring mutation hotspot in several cancers, enhanced Eya3-PP2A-B55α-mediated dephosphorylation of pT58 on Myc, leading to increased Myc stability and cell proliferation, underscoring the critical role of this phosphosite in regulating Myc stability.
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Affiliation(s)
- Christopher Alderman
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA; Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA; Molecular Biology Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Ryan Anderson
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Lingdi Zhang
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Connor J Hughes
- Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA; Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Xueni Li
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Chris Ebmeier
- Department of Biochemistry, University of Colorado-Boulder, Boulder, Colorado, USA
| | - Marisa E Wagley
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Natalie G Ahn
- Department of Biochemistry, University of Colorado-Boulder, Boulder, Colorado, USA
| | - Heide L Ford
- Molecular Biology Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA; Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA; Molecular Biology Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.
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Wei F, Li D, Chen X, Li Y, Zeng Y, Cai Y, Zeng Y, Chen Y, Ma X, Zeng J. Therapeutic effects of epigallocatechin-3-gallate for inflammatory bowel disease: A preclinical meta-analysis. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 128:155408. [PMID: 38503153 DOI: 10.1016/j.phymed.2024.155408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/23/2024] [Accepted: 02/01/2024] [Indexed: 03/21/2024]
Abstract
BACKGROUND Epigallocatechin-3-gallate (EGCG), the primary active compound in green tea, is recognized for its significant anti-inflammatory properties and potential pharmacological effects on inflammatory bowel disease (IBD). However, comprehensive preclinical evidence supporting the use of EGCG in treating IBD is currently insufficient. PURPOSE To evaluate the efficacy of EGCG in animal models of IBD and explore potential underlying mechanisms, serving as a groundwork for future clinical investigations. METHODS A systematic review of pertinent preclinical studies published until September 1, 2023, in databases such as PubMed, Embase, Web of Science, and Cochrane Library was conducted, adhering to stringent quality criteria. The potential mechanisms via which EGCG may address IBD were summarized. STATA v16.0 was used to perform a meta-analysis to assess IBD pathology, inflammation, and indicators of oxidative stress. Additionally, dose-response analysis and machine learning models were utilized to evaluate the dose-effect relationship and determine the optimal dosage of EGCG for IBD treatment. RESULTS The analysis included 19 studies involving 309 animals. The findings suggest that EGCG can ameliorate IBD-related pathology in animals, with a reduction in inflammatory and oxidative stress indicators. These effects were observed through significant changes in histological scores, Disease Activity Index, Colitis Macroscopic Damage Index and colon length; a decrease in markers such as interleukin (IL)-1β, IL-6 and interferon-γ; and alterations in malondialdehyde, superoxide dismutase, glutathione, and catalase levels. Subgroup analysis indicated that the oral administration route of EGCG exhibited superior efficacy over other administration routes. Dose-response analysis and machine learning outcomes highlighted an optimal EGCG dosage range of 32-62 mg/kg/day, with an intervention duration of 4.8-13.6 days. CONCLUSIONS EGCG exhibits positive effects on IBD, particularly when administered at the dose range of 32 - 62 mg/kg/day, primarily attributed to its ability to regulate inflammation and oxidative stress levels.
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Affiliation(s)
- Feng Wei
- Department of Oncology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, China; School of Clinical Medicine, Chengdu University of Chinese Medicine, Chengdu 610075, China
| | - Delin Li
- School of Clinical Medicine, Chengdu University of Chinese Medicine, Chengdu 610075, China
| | - Xiaodong Chen
- Department of Gastric Surgery, Sichuan Clinical Research Centre for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Centre Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, Sichuan 610041, China
| | - Yubing Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yuting Zeng
- Department of Gastroenterology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, China; TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, China
| | - Yilin Cai
- Department of Oncology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, China; School of Clinical Medicine, Chengdu University of Chinese Medicine, Chengdu 610075, China
| | - Youtao Zeng
- Department of Gastroenterology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, China
| | - Yu Chen
- Department of Oncology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, China
| | - Xiao Ma
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jinhao Zeng
- Department of Gastroenterology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, China; TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, China.
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12
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Kelliher JL, Folkerts ML, Shen KV, Song W, Tengler K, Stiefel CM, Lee SO, Dray E, Zhao W, Koss B, Pannunzio NR, Leung JW. Evolved histone tail regulates 53BP1 recruitment at damaged chromatin. Nat Commun 2024; 15:4634. [PMID: 38821984 PMCID: PMC11143218 DOI: 10.1038/s41467-024-49071-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 05/22/2024] [Indexed: 06/02/2024] Open
Abstract
The master DNA damage repair histone protein, H2AX, is essential for orchestrating the recruitment of downstream mediator and effector proteins at damaged chromatin. The phosphorylation of H2AX at S139, γH2AX, is well-studied for its DNA repair function. However, the extended C-terminal tail is not characterized. Here, we define the minimal motif on H2AX for the canonical function in activating the MDC1-RNF8-RNF168 phosphorylation-ubiquitination pathway that is important for recruiting repair proteins, such as 53BP1 and BRCA1. Interestingly, H2AX recruits 53BP1 independently from the MDC1-RNF8-RNF168 pathway through its evolved C-terminal linker region with S139 phosphorylation. Mechanistically, 53BP1 recruitment to damaged chromatin is mediated by the interaction between the H2AX C-terminal tail and the 53BP1 Oligomerization-Tudor domains. Moreover, γH2AX-linker mediated 53BP1 recruitment leads to camptothecin resistance in H2AX knockout cells. Overall, our study uncovers an evolved mechanism within the H2AX C-terminal tail for regulating DNA repair proteins at damaged chromatin.
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Affiliation(s)
- Jessica L Kelliher
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Melissa L Folkerts
- Department of Medicine, Division of Hematology/Oncology, University of California, Irvine, Irvine, CA, 92697, USA
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92626, USA
| | - Kaiyuan V Shen
- Department of Medicine, Division of Hematology/Oncology, University of California, Irvine, Irvine, CA, 92697, USA
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92626, USA
| | - Wan Song
- Department of Radiation Oncology, University of Texas Health and Science Center, San Antonio, TX, 78229, USA
| | - Kyle Tengler
- Department of Radiation Oncology, University of Texas Health and Science Center, San Antonio, TX, 78229, USA
| | - Clara M Stiefel
- Department of Radiation Oncology, University of Texas Health and Science Center, San Antonio, TX, 78229, USA
| | - Seong-Ok Lee
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Eloise Dray
- Department of Biochemistry and Structural Biology, University of Texas Health and Science Center, San Antonio, TX, 78229, USA
| | - Weixing Zhao
- Department of Biochemistry and Structural Biology, University of Texas Health and Science Center, San Antonio, TX, 78229, USA
| | - Brian Koss
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Nicholas R Pannunzio
- Department of Medicine, Division of Hematology/Oncology, University of California, Irvine, Irvine, CA, 92697, USA.
| | - Justin W Leung
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA.
- Department of Radiation Oncology, University of Texas Health and Science Center, San Antonio, TX, 78229, USA.
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13
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Runnebohm AM, Wijeratne HRS, Justice SAP, Wijeratne AB, Roy G, Singh N, Hergenrother P, Boothman DA, Motea EA, Mosley AL. IB-DNQ and Rucaparib dual treatment alters cell cycle regulation and DNA repair in triple negative breast cancer cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.15.594427. [PMID: 38798459 PMCID: PMC11118307 DOI: 10.1101/2024.05.15.594427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Background Triple negative breast cancer (TNBC), characterized by the lack of three canonical receptors, is unresponsive to commonly used hormonal therapies. One potential TNBC-specific therapeutic target is NQO1, as it is highly expressed in many TNBC patients and lowly expressed in non-cancer tissues. DNA damage induced by NQO1 bioactivatable drugs in combination with Rucaparib-mediated inhibition of PARP1-dependent DNA repair synergistically induces cell death. Methods To gain a better understanding of the mechanisms behind this synergistic effect, we used global proteomics, phosphoproteomics, and thermal proteome profiling to analyze changes in protein abundance, phosphorylation and protein thermal stability. Results Very few protein abundance changes resulted from single or dual agent treatment; however, protein phosphorylation and thermal stability were impacted. Histone H2AX was among several proteins identified to have increased phosphorylation when cells were treated with the combination of IB-DNQ and Rucaparib, validating that the drugs induced persistent DNA damage. Thermal proteome profiling revealed destabilization of H2AX following combination treatment, potentially a result of the increase in phosphorylation. Kinase substrate enrichment analysis predicted altered activity for kinases involved in DNA repair and cell cycle following dual agent treatment. Further biophysical analysis of these two processes revealed alterations in SWI/SNF complex association and tubulin / p53 interactions. Conclusions Our findings that the drugs target DNA repair and cell cycle regulation, canonical cancer treatment targets, in a way that is dependent on increased expression of a protein selectively found to be upregulated in cancers without impacting protein abundance illustrate that multi-omics methodologies are important to gain a deeper understanding of the mechanisms behind treatment induced cancer cell death.
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Affiliation(s)
- Avery M Runnebohm
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN
| | - H R Sagara Wijeratne
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN
| | - Sarah A Peck Justice
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN
- Department of Biology, Marian University, Indianapolis, IN
| | - Aruna B Wijeratne
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN
- IU Simon Comprehensive Cancer Center, Indianapolis, IN
| | - Gitanjali Roy
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN
| | | | - Paul Hergenrother
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL
| | - David A Boothman
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN
- IU Simon Comprehensive Cancer Center, Indianapolis, IN
| | - Edward A Motea
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN
- IU Simon Comprehensive Cancer Center, Indianapolis, IN
| | - Amber L Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN
- IU Simon Comprehensive Cancer Center, Indianapolis, IN
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN
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14
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Tyagi S, Singh A, Sharma N, Chaturvedi R, Kushwaha HR. Insights into existing and futuristic treatment approach for chronic myeloid leukaemia. Indian J Med Res 2024; 159:455-467. [PMID: 39382408 PMCID: PMC11463244 DOI: 10.25259/ijmr_1716_22] [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: 03/09/2024] [Indexed: 10/10/2024] Open
Abstract
Oncogenes play a crucial part in human cancer development, and when particular drugs obstruct the proteins produced by these oncogenes, the tumoural process can be ceased. For instance, in chronic myeloid leukaemia (CML), all pathological traits are associated with a single oncogene, BCR-ABL1. CML is a triphasic cancerous disorder of haematopoietic stem cells, marked by a balanced translocation between chromosomes 9 and 22, leading to the genesis of a Philadelphia chromosome encompassing the BCR-ABL1 fusion gene. This fusion oncogene further produces a constitutive active tyrosine kinase protein, enhancing the downstream signalling pathways and constitutes cancer. The treatment for CML has been entirely altered from chemotherapy and immunotherapy to targeted therapy with the emergence of tyrosine kinase inhibitors (TKIs) which inhibit BCR-ABL1 kinase activity. However, the inhibitory mechanism of TKIs is constrained by BCR-ABL1 dependent and independent resistance mechanisms, prompting the exploration of novel therapeutics through extensive clinical trials to develop next-generation drugs with enhanced potency. The persistent challenges posed by CML have motivated researchers to seek innovative strategies for its eradication, such as the application of the genome editing tool CRISPR/Cas9. This review provides insights into existing CML diagnoses, treatment modalities, resistance mechanisms, drugs under trial phases and new potential therapeutic drugs. Furthermore, the review looks ahead to a visionary perspective wherein the CRISPR/Cas9 approach holds the potential to evolve into a prospective curative measure for CML.
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MESH Headings
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/antagonists & inhibitors
- Protein Kinase Inhibitors/therapeutic use
- Gene Editing
- Drug Resistance, Neoplasm/genetics
- CRISPR-Cas Systems/genetics
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Affiliation(s)
- Sourabh Tyagi
- Special Centre for Systems Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Anu Singh
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Naveen Sharma
- Biomedical Informatics Division, Indian Council of Medical Research, New Delhi, India
| | - Rupesh Chaturvedi
- Special Centre for Systems Medicine, Jawaharlal Nehru University, New Delhi, India
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Hemant Ritturaj Kushwaha
- Special Centre for Systems Medicine, Jawaharlal Nehru University, New Delhi, India
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
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15
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Hughes CJ, Alderman C, Wolin AR, Fields KM, Zhao R, Ford HL. All eyes on Eya: A unique transcriptional co-activator and phosphatase in cancer. Biochim Biophys Acta Rev Cancer 2024; 1879:189098. [PMID: 38555001 PMCID: PMC11111358 DOI: 10.1016/j.bbcan.2024.189098] [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] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/02/2024]
Abstract
The Eya family of proteins (consisting of Eyas1-4 in mammals) play vital roles in embryogenesis by regulating processes such as proliferation, migration/invasion, cellular survival and pluripotency/plasticity of epithelial and mesenchymal states. Eya proteins carry out such diverse functions through a unique combination of transcriptional co-factor, Tyr phosphatase, and PP2A/B55α-mediated Ser/Thr phosphatase activities. Since their initial discovery, re-expression of Eyas has been observed in numerous tumor types, where they are known to promote tumor progression through a combination of their transcriptional and enzymatic activities. Eya proteins thus reinstate developmental processes during malignancy and represent a compelling class of therapeutic targets for inhibiting tumor progression.
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Affiliation(s)
- Connor J Hughes
- Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States of America; Department of Pharmacology, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045, United States of America
| | - Christopher Alderman
- Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States of America; Molecular Biology Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States of America; Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States of America
| | - Arthur R Wolin
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045, United States of America; Molecular Biology Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States of America
| | - Kaiah M Fields
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045, United States of America; Molecular Biology Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States of America
| | - Rui Zhao
- Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States of America; Molecular Biology Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States of America; Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States of America.
| | - Heide L Ford
- Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States of America; Department of Pharmacology, University of Colorado Anschutz Medical Campus, 12800 East 19th Avenue, Aurora, CO 80045, United States of America; Molecular Biology Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States of America.
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16
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Guo B, Huo X, Xie X, Zhang X, Lian J, Zhang X, Gong Y, Dou H, Fan Y, Mao Y, Wang J, Hu H. Dynamic role of CUL4B in radiation-induced intestinal injury-regeneration. Sci Rep 2024; 14:9906. [PMID: 38689033 PMCID: PMC11061312 DOI: 10.1038/s41598-024-60704-4] [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: 01/18/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024] Open
Abstract
CUL4B, a crucial scaffolding protein in the largest E3 ubiquitin ligase complex CRL4B, is involved in a broad range of physiological and pathological processes. While previous research has shown that CUL4B participates in maintaining intestinal homeostasis and function, its involvement in facilitating intestinal recovery following ionizing radiation (IR) damage has not been fully elucidated. Here, we utilized in vivo and in vitro models to decipher the role of CUL4B in intestinal repair after IR-injury. Our findings demonstrated that prior to radiation exposure, CUL4B inhibited the ubiquitination modification of PSME3, which led to the accumulation of PSME3 and subsequent negative regulation of p53-mediated apoptosis. In contrast, after radiation, CUL4B dissociated from PSME3 and translocated into the nucleus at phosphorylated histones H2A (γH2AX) foci, thereby impeding DNA damage repair and augmenting p53-mediated apoptosis through inhibition of BRCA1 phosphorylation and RAD51. Our study elucidated the dynamic role of CUL4B in the repair of radiation-induced intestinal damage and uncovered novel molecular mechanisms underlying the repair process, suggesting a potential therapeutic strategy of intestinal damage after radiation therapy for cancers.
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Affiliation(s)
- Beibei Guo
- The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Systems Biomedicine and Research, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, 250012, China
| | - Xiaohan Huo
- The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Systems Biomedicine and Research, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, 250012, China
- The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Molecular Medicine and Genetics, School of Basic Medical Sciences, Shandong University Cheeloo Medical College, Jinan, 250012, China
| | - Xueyong Xie
- The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Molecular Medicine and Genetics, School of Basic Medical Sciences, Shandong University Cheeloo Medical College, Jinan, 250012, China
| | - Xiaohui Zhang
- The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Systems Biomedicine and Research, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, 250012, China
| | - Jiabei Lian
- The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Systems Biomedicine and Research, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, 250012, China
| | - Xiyu Zhang
- The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Molecular Medicine and Genetics, School of Basic Medical Sciences, Shandong University Cheeloo Medical College, Jinan, 250012, China
| | - Yaoqin Gong
- The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Molecular Medicine and Genetics, School of Basic Medical Sciences, Shandong University Cheeloo Medical College, Jinan, 250012, China
| | - Hao Dou
- The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Molecular Medicine and Genetics, School of Basic Medical Sciences, Shandong University Cheeloo Medical College, Jinan, 250012, China
| | - Yujia Fan
- The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Systems Biomedicine and Research, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, 250012, China
| | - Yunuo Mao
- The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Systems Biomedicine and Research, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, 250012, China
| | - Jinshen Wang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China.
| | - Huili Hu
- The Key Laboratory of Experimental Teratology, Ministry of Education and Department of Systems Biomedicine and Research, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, 250012, China.
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17
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Holguin-Cruz JA, Bui JM, Jha A, Na D, Gsponer J. Widespread alteration of protein autoinhibition in human cancers. Cell Syst 2024; 15:246-263.e7. [PMID: 38366601 DOI: 10.1016/j.cels.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 06/20/2023] [Accepted: 01/26/2024] [Indexed: 02/18/2024]
Abstract
Autoinhibition is a prevalent allosteric regulatory mechanism in signaling proteins. Reduced autoinhibition underlies the tumorigenic effect of some known cancer drivers, but whether autoinhibition is altered generally in cancer remains elusive. Here, we demonstrate that cancer-associated missense mutations, in-frame insertions/deletions, and fusion breakpoints are enriched within inhibitory allosteric switches (IASs) across all cancer types. Selection for IASs that are recurrently mutated in cancers identifies established and unknown cancer drivers. Recurrent missense mutations in IASs of these drivers are associated with distinct, cancer-specific changes in molecular signaling. For the specific case of PPP3CA, the catalytic subunit of calcineurin, we provide insights into the molecular mechanisms of altered autoinhibition by cancer mutations using biomolecular simulations, and demonstrate that such mutations are associated with transcriptome changes consistent with increased calcineurin signaling. Our integrative study shows that autoinhibition-modulating genetic alterations are positively selected for by cancer cells.
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Affiliation(s)
- Jorge A Holguin-Cruz
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jennifer M Bui
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Ashwani Jha
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Dokyun Na
- School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 156-756, Republic of Korea
| | - Jörg Gsponer
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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18
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Hwang GH, Pazyra-Murphy MF, Seo HS, Dhe-Paganon S, Stopka SA, DiPiazza M, Sutter N, Gero TW, Volkert A, Ombelets L, Dittemore G, Rees MG, Ronan MM, Roth JA, Agar NYR, Scott DA, Segal RA. A Benzarone Derivative Inhibits EYA to Suppress Tumor Growth in SHH Medulloblastoma. Cancer Res 2024; 84:872-886. [PMID: 38486486 PMCID: PMC10948029 DOI: 10.1158/0008-5472.can-22-3784] [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: 12/02/2022] [Revised: 04/07/2023] [Accepted: 01/10/2024] [Indexed: 03/19/2024]
Abstract
Medulloblastoma is one of the most common malignant brain tumors of children, and 30% of medulloblastomas are driven by gain-of-function genetic lesions in the Sonic Hedgehog (SHH) signaling pathway. EYA1, a haloacid dehalogenase phosphatase and transcription factor, is critical for tumorigenesis and proliferation of SHH medulloblastoma (SHH-MB). Benzarone and benzbromarone have been identified as allosteric inhibitors of EYA proteins. Using benzarone as a point of departure, we developed a panel of 35 derivatives and tested them in SHH-MB. Among these compounds, DS-1-38 functioned as an EYA antagonist and opposed SHH signaling. DS-1-38 inhibited SHH-MB growth in vitro and in vivo, showed excellent brain penetrance, and increased the lifespan of genetically engineered mice predisposed to fatal SHH-MB. These data suggest that EYA inhibitors represent promising therapies for pediatric SHH-MB. SIGNIFICANCE Development of a benzarone derivative that inhibits EYA1 and impedes the growth of SHH medulloblastoma provides an avenue for improving treatment of this malignant pediatric brain cancer.
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Affiliation(s)
- Grace H. Hwang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Maria F. Pazyra-Murphy
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Sylwia A. Stopka
- Department of Neurosurgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Marina DiPiazza
- Department of Neurosurgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Nizhoni Sutter
- Department of Neurosurgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Brigham Young University-Hawaii, Kulanui St, HI, USA
| | - Thomas W. Gero
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alison Volkert
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Lincoln Ombelets
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Georgia Dittemore
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | | | - Nathalie Y. R. Agar
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Neurosurgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Radiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - David A. Scott
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Rosalind A. Segal
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
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19
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Lai PM, Chan KM. Roles of Histone H2A Variants in Cancer Development, Prognosis, and Treatment. Int J Mol Sci 2024; 25:3144. [PMID: 38542118 PMCID: PMC10969971 DOI: 10.3390/ijms25063144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/09/2024] [Accepted: 02/09/2024] [Indexed: 07/16/2024] Open
Abstract
Histones are nuclear proteins essential for packaging genomic DNA and epigenetic gene regulation. Paralogs that can substitute core histones (H2A, H2B, H3, and H4), named histone variants, are constitutively expressed in a replication-independent manner throughout the cell cycle. With specific chaperones, they can be incorporated to chromatin to modify nucleosome stability by modulating interactions with nucleosomal DNA. This allows the regulation of essential fundamental cellular processes for instance, DNA damage repair, chromosomal segregation, and transcriptional regulation. Among all the histone families, histone H2A family has the largest number of histone variants reported to date. Each H2A variant has multiple functions apart from their primary role and some, even be further specialized to perform additional tasks in distinct lineages, such as testis specific shortH2A (sH2A). In the past decades, the discoveries of genetic alterations and mutations in genes encoding H2A variants in cancer had revealed variants' potentiality in driving carcinogenesis. In addition, there is growing evidence that H2A variants may act as novel prognostic indicators or biomarkers for both early cancer detection and therapeutic treatments. Nevertheless, no studies have ever concluded all identified variants in a single report. Here, in this review, we summarize the respective functions for all the 19 mammalian H2A variants and their roles in cancer biology whilst potentiality being used in clinical setting.
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Affiliation(s)
| | - Kui Ming Chan
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China;
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20
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Pyndiah S. [A new mechanism by which cancers can circumvent cisplatin resistance: The E2F1/BIN1 axis]. Med Sci (Paris) 2024; 40:241-244. [PMID: 38520097 DOI: 10.1051/medsci/2024009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024] Open
Affiliation(s)
- Slovénie Pyndiah
- Université Paris-Est Créteil, Faculté de médecine, Inserm U955, Institut Mondor de recherche biomédicale, Créteil, France
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21
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Zhigulev A, Norberg Z, Cordier J, Spalinskas R, Bassereh H, Björn N, Pradhananga S, Gréen H, Sahlén P. Enhancer mutations modulate the severity of chemotherapy-induced myelosuppression. Life Sci Alliance 2024; 7:e202302244. [PMID: 38228368 PMCID: PMC10796589 DOI: 10.26508/lsa.202302244] [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: 06/30/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/18/2024] Open
Abstract
Non-small cell lung cancer is often diagnosed at advanced stages, and many patients are still treated with classical chemotherapy. The unselective nature of chemotherapy often results in severe myelosuppression. Previous studies showed that protein-coding mutations could not fully explain the predisposition to myelosuppression. Here, we investigate the possible role of enhancer mutations in myelosuppression susceptibility. We produced transcriptome and promoter-interaction maps (using HiCap) of three blood stem-like cell lines treated with carboplatin or gemcitabine. Taking advantage of publicly available enhancer datasets, we validated HiCap results in silico and in living cells using epigenetic CRISPR technology. We also developed a network approach for interactome analysis and detection of differentially interacting genes. Differential interaction analysis provided additional information on relevant genes and pathways for myelosuppression compared with differential gene expression analysis at the bulk level. Moreover, we showed that enhancers of differentially interacting genes are highly enriched for variants associated with differing levels of myelosuppression. Altogether, our work represents a prominent example of integrative transcriptome and gene regulatory datasets analysis for the functional annotation of noncoding mutations.
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Affiliation(s)
- Artemy Zhigulev
- https://ror.org/026vcq606 Royal Institute of Technology - KTH, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
| | - Zandra Norberg
- https://ror.org/026vcq606 Royal Institute of Technology - KTH, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
| | - Julie Cordier
- https://ror.org/026vcq606 Royal Institute of Technology - KTH, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
| | - Rapolas Spalinskas
- https://ror.org/026vcq606 Royal Institute of Technology - KTH, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
| | - Hassan Bassereh
- https://ror.org/026vcq606 Royal Institute of Technology - KTH, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
| | - Niclas Björn
- Division of Clinical Chemistry and Pharmacology, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Sailendra Pradhananga
- https://ror.org/026vcq606 Royal Institute of Technology - KTH, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
| | - Henrik Gréen
- Division of Clinical Chemistry and Pharmacology, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
| | - Pelin Sahlén
- https://ror.org/026vcq606 Royal Institute of Technology - KTH, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
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22
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de la Peña Avalos B, Paquet N, Tropée R, Coulombe Y, Palacios H, Leung J, Masson JY, Duijf PG, Dray E. The protein phosphatase EYA4 promotes homologous recombination (HR) through dephosphorylation of tyrosine 315 on RAD51. Nucleic Acids Res 2024; 52:1173-1187. [PMID: 38084915 PMCID: PMC10853800 DOI: 10.1093/nar/gkad1177] [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: 04/15/2023] [Revised: 11/20/2023] [Accepted: 11/27/2023] [Indexed: 01/07/2024] Open
Abstract
Efficient DNA repair and limitation of genome rearrangements rely on crosstalk between different DNA double-strand break (DSB) repair pathways, and their synchronization with the cell cycle. The selection, timing and efficacy of DSB repair pathways are influenced by post-translational modifications of histones and DNA damage repair (DDR) proteins, such as phosphorylation. While the importance of kinases and serine/threonine phosphatases in DDR have been extensively studied, the role of tyrosine phosphatases in DNA repair remains poorly understood. In this study, we have identified EYA4 as the protein phosphatase that dephosphorylates RAD51 on residue Tyr315. Through its Tyr phosphatase activity, EYA4 regulates RAD51 localization, presynaptic filament formation, foci formation, and activity. Thus, it is essential for homologous recombination (HR) at DSBs. DNA binding stimulates EYA4 phosphatase activity. Depletion of EYA4 decreases single-stranded DNA accumulation following DNA damage and impairs HR, while overexpression of EYA4 in cells promotes dephosphorylation and stabilization of RAD51, and thereby nucleoprotein filament formation. Our data have implications for a pathological version of RAD51 in EYA4-overexpressing cancers.
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Affiliation(s)
- Bárbara de la Peña Avalos
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
- Mays Cancer Center at UT Health San Antonio MD Anderson, San Antonio, TX, USA
| | - Nicolas Paquet
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Romain Tropée
- Queensland University of Technology, Translational Research Institute, Brisbane, QLD, Australia
| | - Yan Coulombe
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Québec City, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC, Canada
| | - Hannah Palacios
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Justin W Leung
- Department of Radiation Oncology, University of Texas Health and Science Center, San Antonio, TX 78229, USA
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Québec City, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC, Canada
| | - Pascal H G Duijf
- Centre for Cancer Biology, Clinical and Health Sciences, University of South Australia & SA Pathology, Adelaide SA, Australia
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Eloïse Dray
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
- Mays Cancer Center at UT Health San Antonio MD Anderson, San Antonio, TX, USA
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
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23
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Sabet Sarvestani F, Afshari A, Azarpira N. The role of non-protein-coding RNAs in ischemic acute kidney injury. Front Immunol 2024; 15:1230742. [PMID: 38390339 PMCID: PMC10881863 DOI: 10.3389/fimmu.2024.1230742] [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: 05/29/2023] [Accepted: 01/26/2024] [Indexed: 02/24/2024] Open
Abstract
Acute kidney injury (AKI) is a condition characterized by a rapid decline in kidney function within a span of 48 hours. It is influenced by various factors including inflammation, oxidative stress, excessive calcium levels within cells, activation of the renin-angiotensin system, and dysfunction in microcirculation. Ischemia-reperfusion injury (IRI) is recognized as a major cause of AKI; however, the precise mechanisms behind this process are not yet fully understood and effective treatments are still needed. To enhance the accuracy of diagnosing AKI during its early stages, the utilization of innovative markers is crucial. Numerous studies suggest that certain noncoding RNAs (ncRNAs), such as long noncoding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs), play a central role in regulating gene expression and protein synthesis. These ncRNAs are closely associated with the development and recovery of AKI and have been detected in both kidney tissue and bodily fluids. Furthermore, specific ncRNAs may serve as diagnostic markers and potential targets for therapeutic interventions in AKI. This review aims to summarize the functional roles and changes observed in noncoding RNAs during ischemic AKI, as well as explore their therapeutic potential.
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Affiliation(s)
| | - Afsoon Afshari
- Shiraz Nephro-Urology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Negar Azarpira
- Shiraz Transplant Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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24
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Singh S, Parthasarathi KTS, Bhat MY, Gopal C, Sharma J, Pandey A. Profiling Kinase Activities for Precision Oncology in Diffuse Gastric Cancer. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024; 28:76-89. [PMID: 38271566 DOI: 10.1089/omi.2023.0173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Gastric cancer (GC) remains a leading cause of cancer-related mortality globally. This is due to the fact that majority of the cases of GC are diagnosed at an advanced stage when the treatment options are limited and prognosis is poor. The diffuse subtype of gastric cancer (DGC) under Lauren's classification is more aggressive and usually occurs in younger patients than the intestinal subtype. The concept of personalized medicine is leading to the identification of multiple biomarkers in a large variety of cancers using different combinations of omics technologies. Proteomic changes including post-translational modifications are crucial in oncogenesis. We analyzed the phosphoproteome of DGC by using paired fresh frozen tumor and adjacent normal tissue from five patients diagnosed with DGC. We found proteins involved in the epithelial-to-mesenchymal transition (EMT), c-MYC pathway, and semaphorin pathways to be differentially phosphorylated in DGC tissues. We identified three kinases, namely, bromodomain adjacent to the zinc finger domain 1B (BAZ1B), WNK lysine-deficient protein kinase 1 (WNK1), and myosin light-chain kinase (MLCK) to be hyperphosphorylated, and one kinase, AP2-associated protein kinase 1 (AAK1), to be hypophosphorylated. LMNA hyperphosphorylation at serine 392 (S392) was demonstrated in DGC using immunohistochemistry. Importantly, we have detected heparin-binding growth factor (HDGF), heat shock protein 90 (HSP90), and FTH1 as potential therapeutic targets in DGC, as drugs targeting these proteins are currently under investigation in clinical trials. Although these new findings need to be replicated in larger study samples, they advance our understanding of signaling alterations in DGC, which could lead to potentially novel actionable targets in GC.
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Affiliation(s)
- Smrita Singh
- Manipal Academy of Higher Education (MAHE), Manipal, India
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Center for Molecular Medicine, National Institute of Mental Health and Neuro-Sciences (NIMHANS), Bangalore, India
| | - K T Shreya Parthasarathi
- Manipal Academy of Higher Education (MAHE), Manipal, India
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Mohd Younis Bhat
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Amrita School of Biotechnology, Amrita Vishwapeetham University, Kollam, India
| | - Champaka Gopal
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore, India
| | - Jyoti Sharma
- Manipal Academy of Higher Education (MAHE), Manipal, India
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Akhilesh Pandey
- Manipal Academy of Higher Education (MAHE), Manipal, India
- Center for Molecular Medicine, National Institute of Mental Health and Neuro-Sciences (NIMHANS), Bangalore, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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25
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Tian W, Zhong W, Yang Z, Chen L, Lin S, Li Y, Wang Y, Yang P, Long X. Synthesis, characterization and discovery of multiple anticancer mechanisms of dibutyltin complexes based on salen-like ligands. J Inorg Biochem 2024; 251:112434. [PMID: 38029537 DOI: 10.1016/j.jinorgbio.2023.112434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/15/2023] [Accepted: 11/19/2023] [Indexed: 12/01/2023]
Abstract
A series of novel dibutyltin complexes based on salen-like ligands (S01-S03) were synthesized and characterized using ultraviolet-visible spectra,infrared spectra, 1H, 13C, and 119Sn nuclear magnetic resonance, high-resolution mass spectrometry, X-ray crystallography, and thermogravimetric analysis. Complex S03 had excellent anticancer activity in vitro (IC50 = 1.5 ± 0.2 μM in CAL-27 cell lines), which highly activated ROS expression levels and induced apoptosis and cell cycle arrest at the G2/M phase. Interestingly, complex S03 induced cancer cell death through multiple mechanisms (mitochondrial pathway, ER-stress pathway, and DNA damage pathway). This study reveals new mechanisms of organotin complexes and provides new insights into the development of organotin metal complexes as anticancer drugs in the future, and compounds with multiple anticancer mechanisms may be a new strategy for delaying or overcoming drug resistance to chemotherapy and target therapy.
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Affiliation(s)
- Wei Tian
- Guangxi International Zhuang Medicine Hospital, Nanning 530201, China; Guangxi International Zhuang Medicine Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning 530201, China; Guangxi Institute of Ethnic Medicine, Nanning 530201, China.
| | - Wen Zhong
- Guangxi International Zhuang Medicine Hospital, Nanning 530201, China; Guangxi International Zhuang Medicine Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning 530201, China; Guangxi Institute of Ethnic Medicine, Nanning 530201, China
| | - Zengyan Yang
- Guangxi International Zhuang Medicine Hospital, Nanning 530201, China; Guangxi International Zhuang Medicine Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning 530201, China; Guangxi Institute of Ethnic Medicine, Nanning 530201, China
| | - Ling Chen
- Guangxi International Zhuang Medicine Hospital, Nanning 530201, China; Guangxi International Zhuang Medicine Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning 530201, China; Guangxi Institute of Ethnic Medicine, Nanning 530201, China
| | - Shijie Lin
- Guangxi International Zhuang Medicine Hospital, Nanning 530201, China; Guangxi International Zhuang Medicine Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning 530201, China; Guangxi Institute of Ethnic Medicine, Nanning 530201, China
| | - Yanping Li
- Guangxi International Zhuang Medicine Hospital, Nanning 530201, China; Guangxi International Zhuang Medicine Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning 530201, China; Guangxi Institute of Ethnic Medicine, Nanning 530201, China
| | - Yuxing Wang
- Guangxi International Zhuang Medicine Hospital, Nanning 530201, China; Guangxi International Zhuang Medicine Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning 530201, China; Guangxi Institute of Ethnic Medicine, Nanning 530201, China
| | - Peilin Yang
- Guangxi Key Laboratory of Special Biomedicine, School of Medicine, Guangxi University, Nanning 530004, China
| | - Xing Long
- Guangxi International Zhuang Medicine Hospital, Nanning 530201, China; Guangxi International Zhuang Medicine Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning 530201, China; Guangxi Institute of Ethnic Medicine, Nanning 530201, China
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26
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Alderman C, Krueger A, Rossi J, Ford HL, Zhao R. In Vitro Phosphatase Assays for the Eya2 Tyrosine Phosphatase. Methods Mol Biol 2024; 2743:285-300. [PMID: 38147222 DOI: 10.1007/978-1-0716-3569-8_18] [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] [Indexed: 12/27/2023]
Abstract
Protein tyrosine phosphatases (PTP), such as the Eyes Absent (Eya) family of proteins, play important roles in diverse biological processes. In vitro phosphatase assays are essential tools for characterizing the enzymatic activity as well as discovering inhibitors and regulators of these phosphatases. Two common types of in vitro phosphatase assays use either a small molecule substrate that produces a fluorescent or colored product, or a peptide substrate that produces a colorimetric product in a malachite green assay. In this chapter, we describe detailed protocols of a phosphatase assay using small molecule 3-O-methylfluorescein phosphate (OMFP) as a substrate and a malachite green assay using the pH2AX peptide as a substrate to evaluate the phosphatase activity of EYA2 and the effect of small molecule inhibitors of EYA2. These protocols can be easily adapted to study other protein tyrosine phosphatases.
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Affiliation(s)
- Christopher Alderman
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Aaron Krueger
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- KBI Biopharma, Inc., Boulder, CO, USA
| | - John Rossi
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Heide L Ford
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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27
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Wolin AR, Vincent MY, Hotz T, Purdy SC, Rosenbaum SR, Hughes CJ, Hsu JY, Oliphant MUJ, Armstrong B, Wessells V, Varella-Garcia M, Galbraith MD, Pierce A, Wang D, Venkataraman S, Danis E, Veo B, Serkova N, Espinosa JM, Gustafson DL, Vibhakar R, Ford HL. EYA2 tyrosine phosphatase inhibition reduces MYC and prevents medulloblastoma progression. Neuro Oncol 2023; 25:2287-2301. [PMID: 37486991 PMCID: PMC10708924 DOI: 10.1093/neuonc/noad128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND Medulloblastoma is the most common pediatric brain malignancy. Patients with the Group 3 subtype of medulloblastoma (MB) often exhibit MYC amplification and/or overexpression and have the poorest prognosis. While Group 3 MB is known to be highly dependent on MYC, direct targeting of MYC remains elusive. METHODS Patient gene expression data were used to identify highly expressed EYA2 in Group 3 MB samples, assess the correlation between EYA2 and MYC, and examine patient survival. Genetic and pharmacological studies were performed on EYA2 in Group 3 derived MB cell models to assess MYC regulation and viability in vitro and in vivo. RESULTS EYA2 is more highly expressed in Group 3 MB than other MB subgroups and is essential for Group 3 MB growth in vitro and in vivo. EYA2 regulates MYC expression and protein stability in Group 3 MB, resulting in global alterations of MYC transcription. Inhibition of EYA2 tyrosine phosphatase activity, using a novel small molecule inhibitor (NCGC00249987, or 9987), significantly decreases Group 3 MB MYC expression in both flank and intracranial growth in vivo. Human MB RNA-seq data show that EYA2 and MYC are significantly positively correlated, high EYA2 expression is significantly associated with a MYC transcriptional signature, and patients with high EYA2 and MYC expression have worse prognoses than those that do not express both genes at high levels. CONCLUSIONS Our data demonstrate that EYA2 is a critical regulator of MYC in Group 3 MB and suggest a novel therapeutic avenue to target this highly lethal disease.
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Affiliation(s)
- Arthur R Wolin
- Department of Pharmacology, University of Colorado Anschutz Medical Campus (AMC), Aurora, Colorado, USA
- Molecular Biology Graduate Program, University of Colorado AMC, Aurora, Colorado, USA
| | - Melanie Y Vincent
- Department of Pharmacology, University of Colorado Anschutz Medical Campus (AMC), Aurora, Colorado, USA
| | - Taylor Hotz
- Department of Pharmacology, University of Colorado Anschutz Medical Campus (AMC), Aurora, Colorado, USA
| | - Stephen C Purdy
- Department of Pharmacology, University of Colorado Anschutz Medical Campus (AMC), Aurora, Colorado, USA
- Cancer Biology Graduate Program, University of Colorado AMC, Aurora, Colorado, USA
| | - Sheera R Rosenbaum
- Department of Pharmacology, University of Colorado Anschutz Medical Campus (AMC), Aurora, Colorado, USA
| | - Connor J Hughes
- Department of Pharmacology, University of Colorado Anschutz Medical Campus (AMC), Aurora, Colorado, USA
- Pharmacology Graduate Program, University of Colorado AMC, Aurora, Colorado, USA
- Medical Scientist Training Program, University of Colorado AMC, Aurora, Colorado, USA
| | - Jessica Y Hsu
- Department of Pharmacology, University of Colorado Anschutz Medical Campus (AMC), Aurora, Colorado, USA
- Pharmacology Graduate Program, University of Colorado AMC, Aurora, Colorado, USA
| | - Michael U J Oliphant
- Department of Pharmacology, University of Colorado Anschutz Medical Campus (AMC), Aurora, Colorado, USA
- Integrated Physiology Graduate Program, University of Colorado AMC, Aurora, Colorado, USA
| | - Brock Armstrong
- Department of Pharmacology, University of Colorado Anschutz Medical Campus (AMC), Aurora, Colorado, USA
| | - Veronica Wessells
- Department of Medicine, Division of Medical Oncology, University of Colorado AMC, Aurora, Colorado, USA
| | - Marileila Varella-Garcia
- Department of Medicine, Division of Medical Oncology, University of Colorado AMC, Aurora, Colorado, USA
| | - Matthew D Galbraith
- Department of Pharmacology, University of Colorado Anschutz Medical Campus (AMC), Aurora, Colorado, USA
- Linda Crnic Institute for Down Syndrome, University of Colorado AMC, Aurora, Colorado, USA
| | - Angela Pierce
- Department of Pediatrics, Division of Hematology and Oncology, University of Colorado AMC, Aurora, Colorado, USA
| | - Dong Wang
- Department of Pediatrics, Division of Hematology and Oncology, University of Colorado AMC, Aurora, Colorado, USA
| | - Sujatha Venkataraman
- Department of Pediatrics, Division of Hematology and Oncology, University of Colorado AMC, Aurora, Colorado, USA
| | - Etienne Danis
- Department of Pharmacology, University of Colorado Anschutz Medical Campus (AMC), Aurora, Colorado, USA
| | - Bethany Veo
- Department of Pediatrics, Division of Hematology and Oncology, University of Colorado AMC, Aurora, Colorado, USA
| | - Natalie Serkova
- Department of Radiology, University of Colorado AMC, Aurora, Colorado, USA
| | - Joaquin M Espinosa
- Department of Pharmacology, University of Colorado Anschutz Medical Campus (AMC), Aurora, Colorado, USA
- Linda Crnic Institute for Down Syndrome, University of Colorado AMC, Aurora, Colorado, USA
| | - Daniel L Gustafson
- Clinical Sciences Department, Colorado State University, Fort Collins, Colorado, USA
| | - Rajeev Vibhakar
- Department of Pediatrics, Division of Hematology and Oncology, University of Colorado AMC, Aurora, Colorado, USA
| | - Heide L Ford
- Department of Pharmacology, University of Colorado Anschutz Medical Campus (AMC), Aurora, Colorado, USA
- Molecular Biology Graduate Program, University of Colorado AMC, Aurora, Colorado, USA
- Cancer Biology Graduate Program, University of Colorado AMC, Aurora, Colorado, USA
- Pharmacology Graduate Program, University of Colorado AMC, Aurora, Colorado, USA
- Medical Scientist Training Program, University of Colorado AMC, Aurora, Colorado, USA
- Integrated Physiology Graduate Program, University of Colorado AMC, Aurora, Colorado, USA
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28
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Vcelkova T, Reiter W, Zylka M, Hollenstein D, Schuckert S, Hartl M, Seiser C. GSE1 links the HDAC1/CoREST co-repressor complex to DNA damage. Nucleic Acids Res 2023; 51:11748-11769. [PMID: 37878419 PMCID: PMC10681733 DOI: 10.1093/nar/gkad911] [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: 03/16/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 10/27/2023] Open
Abstract
Post-translational modifications of histones are important regulators of the DNA damage response (DDR). By using affinity purification mass spectrometry (AP-MS) we discovered that genetic suppressor element 1 (GSE1) forms a complex with the HDAC1/CoREST deacetylase/demethylase co-repressor complex. In-depth phosphorylome analysis revealed that loss of GSE1 results in impaired DDR, ATR signalling and γH2AX formation upon DNA damage induction. Altered profiles of ATR target serine-glutamine motifs (SQ) on DDR-related hallmark proteins point to a defect in DNA damage sensing. In addition, GSE1 knock-out cells show hampered DNA damage-induced phosphorylation on SQ motifs of regulators of histone post-translational modifications, suggesting altered histone modification. While loss of GSE1 does not affect the histone deacetylation activity of CoREST, GSE1 appears to be essential for binding of the deubiquitinase USP22 to CoREST and for the deubiquitination of H2B K120 in response to DNA damage. The combination of deacetylase, demethylase, and deubiquitinase activity makes the USP22-GSE1-CoREST subcomplex a multi-enzymatic eraser that seems to play an important role during DDR. Since GSE1 has been previously associated with cancer progression and survival our findings are potentially of high medical relevance.
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Affiliation(s)
- Terezia Vcelkova
- Center for Anatomy and Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Wolfgang Reiter
- Mass Spectrometry Facility, Max Perutz Labs, Vienna BioCenter, 1030 Vienna, Austria
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Martha Zylka
- Center for Anatomy and Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - David M Hollenstein
- Mass Spectrometry Facility, Max Perutz Labs, Vienna BioCenter, 1030 Vienna, Austria
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Stefan Schuckert
- Center for Anatomy and Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Markus Hartl
- Mass Spectrometry Facility, Max Perutz Labs, Vienna BioCenter, 1030 Vienna, Austria
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Christian Seiser
- Center for Anatomy and Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
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Auschwitz E, Almeda J, Andl CD. Mechanisms of E-Cigarette Vape-Induced Epithelial Cell Damage. Cells 2023; 12:2552. [PMID: 37947630 PMCID: PMC10650279 DOI: 10.3390/cells12212552] [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: 07/25/2023] [Revised: 10/24/2023] [Accepted: 10/28/2023] [Indexed: 11/12/2023] Open
Abstract
E-cigarette use has been reported to affect cell viability, induce DNA damage, and modulate an inflammatory response resulting in negative health consequences. Most studies focus on oral and lung disease associated with e-cigarette use. However, tissue damage can be found in the cardio-vascular system and even the bladder. While the levels of carcinogenic compounds found in e-cigarette aerosols are lower than those in conventional cigarette smoke, the toxicants generated by the heat of the vaping device may include probable human carcinogens. Furthermore, nicotine, although not a carcinogen, can be metabolized to nitrosamines. Nitrosamines are known carcinogens and have been shown to be present in the saliva of e-cig users, demonstrating the health risk of e-cigarette vaping. E-cig vape can induce DNA adducts, promoting oxidative stress and DNA damage and NF-kB-driven inflammation. Together, these processes increase the transcription of pro-inflammatory cytokines. This creates a microenvironment thought to play a key role in tumorigenesis, although it is too early to know the long-term effects of vaping. This review considers different aspects of e-cigarette-induced cellular changes, including the generation of reactive oxygen species, DNA damage, DNA repair, inflammation, and the possible tumorigenic effects.
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Affiliation(s)
| | | | - Claudia D. Andl
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32816, USA
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Aptecar L, Puech C, Lopez-Crapez E, Peter M, Coopman P, D’Hondt V, Freiss G. PTPN13 Participates in the Regulation of Epithelial-Mesenchymal Transition and Platinum Sensitivity in High-Grade Serous Ovarian Carcinoma Cells. Int J Mol Sci 2023; 24:15413. [PMID: 37895093 PMCID: PMC10607604 DOI: 10.3390/ijms242015413] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
Epithelial ovarian cancer (EOC) is the leading cause of death from gynecological cancers in Western countries. High-Grade Serous Ovarian Carcinoma (HGSOC) accounts for 60-70% of EOC and is the most aggressive subtype. Reduced PTPN13 expression levels have been previously correlated with worse prognosis in HGSOC. However, PTPN13's exact role and mechanism of action in these tumors remained to be investigated. To elucidate PTPN13's role in HGSOC aggressiveness, we used isogenic PTPN13-overexpressing clones of the OVCAR-8 cell line, which poorly expresses PTPN13, and also PTPN13 CRISPR/Cas9-mediated knockout/knockdown clones of the KURAMOCHI cell line, which strongly expresses PTPN13. We investigated their migratory and invasive capacity using a wound healing assay, their mesenchymal-epithelial transition (EMT) status using microscopy and RT-qPCR, and their sensitivity to chemotherapeutic drugs used for HGSOC. We found that (i) PTPN13 knockout/knockdown increased migration and invasion in KURAMOCHI cells that also displayed a more mesenchymal phenotype and increased expression of the SLUG, SNAIL, ZEB-1, and ZEB-2 EMT master genes; and (ii) PTPN13 expression increased the platinum sensitivity of HGSOC cells. These results suggest that PTPN13 might be a predictive marker of response to platinum salts in HGSOC.
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Affiliation(s)
- Leticia Aptecar
- IRCM (Institut de Recherche en Cancérologie de Montpellier), University of Montpellier, Inserm, ICM (Institut du Cancer de Montpellier), F-34000 Montpellier, France (E.L.-C.)
| | - Carole Puech
- IRCM (Institut de Recherche en Cancérologie de Montpellier), University of Montpellier, Inserm, ICM (Institut du Cancer de Montpellier), F-34000 Montpellier, France (E.L.-C.)
| | - Evelyne Lopez-Crapez
- IRCM (Institut de Recherche en Cancérologie de Montpellier), University of Montpellier, Inserm, ICM (Institut du Cancer de Montpellier), F-34000 Montpellier, France (E.L.-C.)
| | - Marion Peter
- IRCM (Institut de Recherche en Cancérologie de Montpellier), University of Montpellier, Inserm, ICM (Institut du Cancer de Montpellier), F-34000 Montpellier, France (E.L.-C.)
- CNRS—Centre National de la Recherche Scientifique, 1919 Route de Mende, F-34293 Montpellier, France; (M.P.); (P.C.)
| | - Peter Coopman
- IRCM (Institut de Recherche en Cancérologie de Montpellier), University of Montpellier, Inserm, ICM (Institut du Cancer de Montpellier), F-34000 Montpellier, France (E.L.-C.)
- CNRS—Centre National de la Recherche Scientifique, 1919 Route de Mende, F-34293 Montpellier, France; (M.P.); (P.C.)
| | - Véronique D’Hondt
- IRCM (Institut de Recherche en Cancérologie de Montpellier), University of Montpellier, Inserm, ICM (Institut du Cancer de Montpellier), F-34000 Montpellier, France (E.L.-C.)
| | - Gilles Freiss
- IRCM (Institut de Recherche en Cancérologie de Montpellier), University of Montpellier, Inserm, ICM (Institut du Cancer de Montpellier), F-34000 Montpellier, France (E.L.-C.)
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de la Peña Avalos B, Tropée R, Duijf PHG, Dray E. EYA4 promotes breast cancer progression and metastasis through its role in replication stress avoidance. Mol Cancer 2023; 22:158. [PMID: 37777742 PMCID: PMC10543271 DOI: 10.1186/s12943-023-01861-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 09/13/2023] [Indexed: 10/02/2023] Open
Abstract
The Eyes Absent (EYA) family of proteins is an atypical group of four dual-functioning protein phosphatases (PP), which have been linked to many vital cellular processes and organogenesis pathways. The four family members of this PP family possess transcriptional activation and phosphatase functions, with serine/threonine and tyrosine phosphatase domains. EYA4 has been associated with several human cancers, with tumor-suppressing and tumor-promoting roles. However, EYA4 is the least well-characterized member of this unique family of PP, with its biological functions and molecular mechanisms in cancer progression, particularly in breast cancer, still largely unknown. In the present study, we found that the over-expression of EYA4 in breast tissue leads to an aggressive and invasive breast cancer phenotype, while the inhibition of EYA4 reduced tumorigenic properties of breast cancer cells in vitro and in vivo. Cellular changes downstream of EYA4, including cell proliferation and migration, may explain the increased metastatic power of breast cancer cells over-expressing EYA4. Mechanistically, EYA4 prevents genome instability by inhibiting the accumulation of replication-associated DNA damage. Its depletion results in polyploidy as a consequence of endoreplication, a phenomenon that can occur in response to stress. The absence of EYA4 leads to spontaneous replication stress characterized by the activation of the ATR pathway, sensitivity to hydroxyurea, and accumulation of endogenous DNA damage as indicated by increased γH2AX levels. In addition, we show that EYA4, specifically its serine/threonine phosphatase domain, plays an important and so far, unexpected role in replication fork progression. This phosphatase activity is essential for breast cancer progression and metastasis. Taken together, our data indicate that EYA4 is a novel potential breast cancer oncogene that supports primary tumor growth and metastasis. Developing therapeutics aimed at the serine/threonine phosphatase activity of EYA4 represents a robust strategy for killing breast cancer cells, to limit metastasis and overcome chemotherapy resistance caused by endoreplication and genomic rearrangements.
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Affiliation(s)
- Bárbara de la Peña Avalos
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
- Mays Cancer Center at UT Health San Antonio MD Anderson, San Antonio, TX, USA
| | - Romain Tropée
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
- Present Address: Southern RNA, Springfield Central, QLD, 4300, Australia
| | - Pascal H G Duijf
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
- Centre for Cancer Biology, Clinical and Health Sciences, & SA Pathology, University of South Australia, Adelaide, SA, Australia
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Eloïse Dray
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia.
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
- Mays Cancer Center at UT Health San Antonio MD Anderson, San Antonio, TX, USA.
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Zhang CT, Qin DL, Cao XY, Kan JS, Huang XX, Gao DS, Gao J. Dephosphorylation of Six2Y129 protects tyrosine hydroxylase-positive cells in SNpc by regulating TEA domain 1 expression. iScience 2023; 26:107049. [PMID: 37534182 PMCID: PMC10391717 DOI: 10.1016/j.isci.2023.107049] [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: 12/25/2022] [Revised: 04/03/2023] [Accepted: 06/01/2023] [Indexed: 08/04/2023] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disease characterized by selective loss of dopaminergic (DA) neurons in the substantia nigra pars compacta (SNpc). We recently reported that Six2 could reverse the degeneration of DA neurons in a dephosphorylation state. Here we further identified that Eya1 was the phosphatase of Six2 that could dephosphorylate the tyrosine 129 (Y129) site by forming a complex with Six2 in damaged DA cells. Dephosphorylated Six2 then translocates from the cytoplasm to the nucleus. Using ChIP-qPCR and dual luciferase assay, we found that dephosphorylated Six2 down-regulates TEA domain1 (Tead1) expression, thus inhibiting 6-hydroxydopamine (6-OHDA)-induced apoptosis in DA cells. Furthermore, we showed Six2Y129F/Tead1 signaling could protect against the loss of SNpc tyrosine hydroxylase-positive (TH+) cells and improve motor function in PD model rats. Our results demonstrate a dephosphorylation-dependent mechanism of Six2 that restores the degeneration of DA neurons, which could represent a potential therapeutic target for PD.
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Affiliation(s)
- Can-tang Zhang
- Department of Respiratory and Critical Care, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Deng-li Qin
- Department of Neurobiology and Cell Biology, Xuzhou Key Laboratory of Neurobiology, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Xia-yin Cao
- Department of Neurobiology and Cell Biology, Xuzhou Key Laboratory of Neurobiology, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Jia-shuo Kan
- Department of Neurobiology and Cell Biology, Xuzhou Key Laboratory of Neurobiology, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Xin-xing Huang
- Department of Neurobiology and Cell Biology, Xuzhou Key Laboratory of Neurobiology, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Dian-shuai Gao
- Department of Neurobiology and Cell Biology, Xuzhou Key Laboratory of Neurobiology, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Jin Gao
- Department of Neurobiology and Cell Biology, Xuzhou Key Laboratory of Neurobiology, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
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33
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Qin S, Kitty I, Hao Y, Zhao F, Kim W. Maintaining Genome Integrity: Protein Kinases and Phosphatases Orchestrate the Balancing Act of DNA Double-Strand Breaks Repair in Cancer. Int J Mol Sci 2023; 24:10212. [PMID: 37373360 DOI: 10.3390/ijms241210212] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
DNA double-strand breaks (DSBs) are the most lethal DNA damages which lead to severe genome instability. Phosphorylation is one of the most important protein post-translation modifications involved in DSBs repair regulation. Kinases and phosphatases play coordinating roles in DSB repair by phosphorylating and dephosphorylating various proteins. Recent research has shed light on the importance of maintaining a balance between kinase and phosphatase activities in DSB repair. The interplay between kinases and phosphatases plays an important role in regulating DNA-repair processes, and alterations in their activity can lead to genomic instability and disease. Therefore, study on the function of kinases and phosphatases in DSBs repair is essential for understanding their roles in cancer development and therapeutics. In this review, we summarize the current knowledge of kinases and phosphatases in DSBs repair regulation and highlight the advancements in the development of cancer therapies targeting kinases or phosphatases in DSBs repair pathways. In conclusion, understanding the balance of kinase and phosphatase activities in DSBs repair provides opportunities for the development of novel cancer therapeutics.
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Affiliation(s)
- Sisi Qin
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Ichiwa Kitty
- Department of Integrated Biomedical Science, Soonchunhyang Institute of Medi-Bio Science (SIMS), Soonchunhyang University, Cheonan 31151, Chungcheongnam-do, Republic of Korea
| | - Yalan Hao
- Analytical Instrumentation Center, Hunan University, Changsha 410082, China
| | - Fei Zhao
- College of Biology, Hunan University, Changsha 410082, China
| | - Wootae Kim
- Department of Integrated Biomedical Science, Soonchunhyang Institute of Medi-Bio Science (SIMS), Soonchunhyang University, Cheonan 31151, Chungcheongnam-do, Republic of Korea
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34
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Bassal MA. The Interplay between Dysregulated Metabolism and Epigenetics in Cancer. Biomolecules 2023; 13:944. [PMID: 37371524 DOI: 10.3390/biom13060944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/21/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Cellular metabolism (or energetics) and epigenetics are tightly coupled cellular processes. It is arguable that of all the described cancer hallmarks, dysregulated cellular energetics and epigenetics are the most tightly coregulated. Cellular metabolic states regulate and drive epigenetic changes while also being capable of influencing, if not driving, epigenetic reprogramming. Conversely, epigenetic changes can drive altered and compensatory metabolic states. Cancer cells meticulously modify and control each of these two linked cellular processes in order to maintain their tumorigenic potential and capacity. This review aims to explore the interplay between these two processes and discuss how each affects the other, driving and enhancing tumorigenic states in certain contexts.
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Affiliation(s)
- Mahmoud Adel Bassal
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
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35
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Vigašová K, Durdík M, Jakl L, Dolinská Z, Pobijaková M, Fekete M, Závacká I, Belyaev I, Marková E. Chemotherapy and cryopreservation affects DNA repair foci in lymphocytes of breast cancer patients. Int J Radiat Biol 2023; 99:1660-1668. [PMID: 37145321 DOI: 10.1080/09553002.2023.2211140] [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: 02/28/2022] [Accepted: 04/20/2023] [Indexed: 05/06/2023]
Abstract
PURPOSE Although breast cancer (BC) patients benefit from radiotherapy (RT), some radiosensitive (RS) patients suffer from side effects caused by ionizing radiation in healthy tissues. It is thought that RS is underlaid by a deficiency in the repair of DNA double-strand breaks (DSB). DNA repair proteins such as p53-binding protein 1 (53BP1) and phosphorylated histone H2AX (γH2AX), form DNA repair foci at the DSB locations and thus serve as DSB biomarkers. Peripheral blood lymphocytes (PBL) are commonly believed to be an appropriate cell system for RS assessment using DNA repair foci. The amount of DSB may also be influenced by chemotherapy (CHT), which is often chosen as the first treatment modality before RT. As it is not always possible to analyze blood samples immediately after collection, there is a need for cryopreservation of PBL in liquid nitrogen. However, cryopreservation may potentially affect the number of DNA repair foci. In this work, we studied the effect of cryopreservation and CHT on the amount of DNA repair foci in PBL of BC patients undergoing radiotherapy. MATERIALS AND METHODS The effect of cryopreservation was studied by immunofluorescence analysis of 53BP1 and γH2AX proteins at different time intervals after in vitro irradiation. The effect of chemotherapy was analyzed by fluorescent labelling of 53BP1 and γH2AX proteins in PBL collected before, during, and after RT. RESULTS Higher number of primary 53BP1/γH2AX foci was observed in frozen cells indicating that cryopreservation affects the formation of DNA repair foci in PBL of BC patients. In CHT-treated patients, a higher number of foci were found before RT, but no differences were observed during and after the RT. CONCLUSIONS Cryopreservation is the method of choice for analyzing DNA repair residual foci, but only similarly treated and preserved cells should be used for comparison of primary foci. CHT induces DNA repair foci in PBL of BC patients, but this effect disappears during radiotherapy.
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Affiliation(s)
- Katarína Vigašová
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Matúš Durdík
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Lukáš Jakl
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Zuzana Dolinská
- Department of Radiation Oncology, Radiological Centrum, National Cancer Institute, Bratislava, Slovakia
| | - Margita Pobijaková
- Department of Radiation Oncology, Radiological Centrum, National Cancer Institute, Bratislava, Slovakia
| | - Marta Fekete
- Department of Radiation Oncology, Radiological Centrum, National Cancer Institute, Bratislava, Slovakia
| | - Ingrid Závacká
- Department of Radiation Oncology, Radiological Centrum, National Cancer Institute, Bratislava, Slovakia
| | - Igor Belyaev
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Eva Marková
- Department of Radiobiology, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
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36
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Nesovic Ostojic J, Zivotic M, Kovacevic S, Ivanov M, Brkic P, Mihailovic-Stanojevic N, Karanovic D, Vajic UJ, Miloradovic Z, Jovovic D, Radojevic Skodric S. Immunohistochemical Pattern of Histone H2A Variant Expression in an Experimental Model of Ischemia-Reperfusion-Induced Acute Kidney Injury. Int J Mol Sci 2023; 24:ijms24098085. [PMID: 37175793 PMCID: PMC10179385 DOI: 10.3390/ijms24098085] [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: 03/25/2023] [Revised: 04/20/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Ischemia-reperfusion injury (IRI) is a frequent cause of AKI, resulting in vasoconstriction, cellular dysfunction, inflammation and the induction of oxidative stress. DNA damage, including physical DNA strand breaks, is also a potential consequence of renal IRI. The histone H2A variants, primary H2AX and H2AZ participate in DNA damage response pathways to promote genome stability. The aim of this study was to evaluate the immunohistochemical pattern of histone H2A variants' (H2AX, γH2AX(S139), H2AXY142ph and H2AZ) expression in an experimental model of ischemia-reperfusion-induced acute kidney injury in spontaneously hypertensive rats. Comparing the immunohistochemical nuclear expression of γH2AX(S139) and H2AXY142ph in AKI, we observed that there is an inverse ratio of these two histone H2AX variants. If we follow different regions from the subcapsular structures to the medulla, there is an increasing extent gradient in the nuclear expression of H2AXY142ph, accompanied by a decreasing nuclear expression of γH2AX. In addition, we observed that different structures dominated when γH2AX and H2AXY142ph expression levels were compared. γH2AX was expressed only in the proximal tubule, with the exception of when they were dilated. In the medulla, H2AXY142ph is predominantly expressed in the loop of Henle and the collecting ducts. Our results show moderate sporadic nuclear H2AZ expression mainly in the cells of the distal tubules and the collecting ducts that were surrounded by dilated tubules with PAS (periodic acid-Schiff stain)-positive casts. These findings may indicate the degree of DNA damage, followed by postischemic AKI, with potential clinical and prognostic implications regarding this condition.
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Affiliation(s)
- Jelena Nesovic Ostojic
- Department of Pathological Physiology, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | - Maja Zivotic
- Institute of Pathology, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | - Sanjin Kovacevic
- Department of Pathological Physiology, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | - Milan Ivanov
- Institute for Medical Research, Department of Cardiovascular Physiology, National Institute of Republic of Serbia, University of Belgrade, 11000 Belgrade, Serbia
| | - Predrag Brkic
- Department of Medical Physiology, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | - Nevena Mihailovic-Stanojevic
- Institute for Medical Research, Department of Cardiovascular Physiology, National Institute of Republic of Serbia, University of Belgrade, 11000 Belgrade, Serbia
| | - Danijela Karanovic
- Institute for Medical Research, Department of Cardiovascular Physiology, National Institute of Republic of Serbia, University of Belgrade, 11000 Belgrade, Serbia
| | - Una Jovana Vajic
- Institute for Medical Research, Department of Cardiovascular Physiology, National Institute of Republic of Serbia, University of Belgrade, 11000 Belgrade, Serbia
| | - Zoran Miloradovic
- Institute for Medical Research, Department of Cardiovascular Physiology, National Institute of Republic of Serbia, University of Belgrade, 11000 Belgrade, Serbia
| | - Djurdjica Jovovic
- Institute for Medical Research, Department of Cardiovascular Physiology, National Institute of Republic of Serbia, University of Belgrade, 11000 Belgrade, Serbia
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Kropivsek K, Kachel P, Goetze S, Wegmann R, Festl Y, Severin Y, Hale BD, Mena J, van Drogen A, Dietliker N, Tchinda J, Wollscheid B, Manz MG, Snijder B. Ex vivo drug response heterogeneity reveals personalized therapeutic strategies for patients with multiple myeloma. NATURE CANCER 2023; 4:734-753. [PMID: 37081258 DOI: 10.1038/s43018-023-00544-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 03/17/2023] [Indexed: 04/22/2023]
Abstract
Multiple myeloma (MM) is a plasma cell malignancy defined by complex genetics and extensive patient heterogeneity. Despite a growing arsenal of approved therapies, MM remains incurable and in need of guidelines to identify effective personalized treatments. Here, we survey the ex vivo drug and immunotherapy sensitivities across 101 bone marrow samples from 70 patients with MM using multiplexed immunofluorescence, automated microscopy and deep-learning-based single-cell phenotyping. Combined with sample-matched genetics, proteotyping and cytokine profiling, we map the molecular regulatory network of drug sensitivity, implicating the DNA repair pathway and EYA3 expression in proteasome inhibitor sensitivity and major histocompatibility complex class II expression in the response to elotuzumab. Globally, ex vivo drug sensitivity associated with bone marrow microenvironmental signatures reflecting treatment stage, clonality and inflammation. Furthermore, ex vivo drug sensitivity significantly stratified clinical treatment responses, including to immunotherapy. Taken together, our study provides molecular and actionable insights into diverse treatment strategies for patients with MM.
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Affiliation(s)
- Klara Kropivsek
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Paul Kachel
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Sandra Goetze
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Swiss Multi-Omics Center, PHRT-CPAC, ETH Zurich, Zurich, Switzerland
| | - Rebekka Wegmann
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Yasmin Festl
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Yannik Severin
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Benjamin D Hale
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Julien Mena
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Audrey van Drogen
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Swiss Multi-Omics Center, PHRT-CPAC, ETH Zurich, Zurich, Switzerland
| | - Nadja Dietliker
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Joëlle Tchinda
- Pediatric Oncology, Children's Research Centre, University Children's Hospital Zurich, Zurich, Switzerland
| | - Bernd Wollscheid
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Swiss Multi-Omics Center, PHRT-CPAC, ETH Zurich, Zurich, Switzerland
| | - Markus G Manz
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
- Comprehensive Cancer Center Zurich (CCCZ), Zurich, Switzerland
| | - Berend Snijder
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Comprehensive Cancer Center Zurich (CCCZ), Zurich, Switzerland.
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38
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Stillger MN, Chen CY, Lai ZW, Li M, Schäfer A, Pagenstecher A, Nimsky C, Bartsch JW, Schilling O. Changes in calpain-2 expression during glioblastoma progression predisposes tumor cells to temozolomide resistance by minimizing DNA damage and p53-dependent apoptosis. Cancer Cell Int 2023; 23:49. [PMID: 36932402 PMCID: PMC10022304 DOI: 10.1186/s12935-023-02889-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/04/2023] [Indexed: 03/19/2023] Open
Abstract
BACKGROUND Glioblastoma multiforme (GBM) is characterized by an unfavorable prognosis for patients affected. During standard-of-care chemotherapy using temozolomide (TMZ), tumors acquire resistance thereby causing tumor recurrence. Thus, deciphering essential molecular pathways causing TMZ resistance are of high therapeutic relevance. METHODS Mass spectrometry based proteomics were used to study the GBM proteome. Immunohistochemistry staining of human GBM tissue for either calpain-1 or -2 was performed to locate expression of proteases. In vitro cell based assays were used to measure cell viability and survival of primary patient-derived GBM cells and established GBM cell lines after TMZ ± calpain inhibitor administration. shRNA expression knockdowns of either calpain-1 or calpain-2 were generated to study TMZ sensitivity of the specific subunits. The Comet assay and ɣH2AX signal measurements were performed in order to assess the DNA damage amount and recognition. Finally, quantitative real-time PCR of target proteins was applied to differentiate between transcriptional and post-translational regulation. RESULTS Calcium-dependent calpain proteases, in particular calpain-2, are more abundant in glioblastoma compared to normal brain and increased in patient-matched initial and recurrent glioblastomas. On the cellular level, pharmacological calpain inhibition increased the sensitivities of primary glioblastoma cells towards TMZ. A genetic knockdown of calpain-2 in U251 cells led to increased caspase-3 cleavage and sensitivity to neocarzinostatin, which rapidly induces DNA strand breakage. We hypothesize that calpain-2 causes desensitization of tumor cells against TMZ by preventing strong DNA damage and subsequent apoptosis via post-translational TP53 inhibition. Indeed, proteomic comparison of U251 control vs. U251 calpain-2 knockdown cells highlights perturbed levels of numerous proteins involved in DNA damage response and downstream pathways affecting TP53 and NF-κB signaling. TP53 showed increased protein abundance, but no transcriptional regulation. CONCLUSION TMZ-induced cell death in the presence of calpain-2 expression appears to favor DNA repair and promote cell survival. We conclude from our experiments that calpain-2 expression represents a proteomic mode that is associated with higher resistance via "priming" GBM cells to TMZ chemotherapy. Thus, calpain-2 could serve as a prognostic factor for GBM outcome.
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Affiliation(s)
- Maren Nicole Stillger
- Institute for Surgical Pathology, Faculty of Medicine, Medical Center - University of Freiburg, University of Freiburg, Freiburg, Germany.,Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Chia-Yi Chen
- Institute for Surgical Pathology, Faculty of Medicine, Medical Center - University of Freiburg, University of Freiburg, Freiburg, Germany
| | - Zon Weng Lai
- Internal Medicine Research Unit, Pfizer Inc, Cambridge, MA, USA
| | - Mujia Li
- Institute for Surgical Pathology, Faculty of Medicine, Medical Center - University of Freiburg, University of Freiburg, Freiburg, Germany.,Department of Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg, Germany
| | - Agnes Schäfer
- Department of Neurosurgery, Philipps-University Marburg, Marburg, Germany
| | - Axel Pagenstecher
- Institute of Neuropathology, Philipps-University, Marburg, Germany.,Center for Mind, Brain and Behavior, CMBB, Marburg University, Hans-Meerwein-Strasse 6, 35032, Marburg, Germany
| | - Christopher Nimsky
- Department of Neurosurgery, Philipps-University Marburg, Marburg, Germany.,Center for Mind, Brain and Behavior, CMBB, Marburg University, Hans-Meerwein-Strasse 6, 35032, Marburg, Germany
| | - Jörg Walter Bartsch
- Department of Neurosurgery, Philipps-University Marburg, Marburg, Germany. .,Center for Mind, Brain and Behavior, CMBB, Marburg University, Hans-Meerwein-Strasse 6, 35032, Marburg, Germany. .,Philipps-University Marburg, Laboratory, Department of Neurosurgery, University Hospital Marburg, Baldingerstr., 35033, Marburg, Germany.
| | - Oliver Schilling
- Institute for Surgical Pathology, Faculty of Medicine, Medical Center - University of Freiburg, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
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Oberdoerffer P, Miller KM. Histone H2A variants: Diversifying chromatin to ensure genome integrity. Semin Cell Dev Biol 2023; 135:59-72. [PMID: 35331626 PMCID: PMC9489817 DOI: 10.1016/j.semcdb.2022.03.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 12/12/2022]
Abstract
Histone variants represent chromatin components that diversify the structure and function of the genome. The variants of H2A, primarily H2A.X, H2A.Z and macroH2A, are well-established participants in DNA damage response (DDR) pathways, which function to protect the integrity of the genome. Through their deposition, post-translational modifications and unique protein interaction networks, these variants guard DNA from endogenous threats including replication stress and genome fragility as well as from DNA lesions inflicted by exogenous sources. A growing body of work is now providing a clearer picture on the involvement and mechanistic basis of H2A variant contribution to genome integrity. Beyond their well-documented role in gene regulation, we review here how histone H2A variants promote genome stability and how alterations in these pathways contribute to human diseases including cancer.
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Affiliation(s)
- Philipp Oberdoerffer
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA.
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA.
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40
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Joseph FM, Young NL. Histone variant-specific post-translational modifications. Semin Cell Dev Biol 2023; 135:73-84. [PMID: 35277331 PMCID: PMC9458767 DOI: 10.1016/j.semcdb.2022.02.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/11/2022] [Accepted: 02/12/2022] [Indexed: 01/12/2023]
Abstract
Post-translational modifications (PTMs) of histones play a key role in DNA-based processes and contribute to cell differentiation and gene function by adding an extra layer of regulation. Variations in histone sequences within each family of histones expands the chromatin repertoire and provide further mechanisms for regulation and signaling. While variants are known to be present in certain genomic loci and carry out important functions, much remains unknown about variant-specific PTMs and their role in regulating chromatin. This ambiguity is in part due to the limited technologies and appropriate reagents to identify and quantitate variant-specific PTMs. Nonetheless, histone variants are an integral portion of the chromatin system and the understanding of their modifications and resolving how PTMs function differently on specific variants is paramount to the advancement of the field. Here we review the current knowledge on post-translational modifications specific to histone variants, with an emphasis on well-characterized PTMs of known function. While not every possible PTM is addressed, we present key variant-specific PTMs and what is known about their function and mechanisms in convenient reference tables.
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Affiliation(s)
- Faith M Joseph
- Translational Biology and Molecular Medicine Graduate Program, USA
| | - Nicolas L Young
- Translational Biology and Molecular Medicine Graduate Program, USA; Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA.
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41
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Zhu S, Li W, Zhang H, Yan Y, Mei Q, Wu K. Retinal determination gene networks: from biological functions to therapeutic strategies. Biomark Res 2023; 11:18. [PMID: 36750914 PMCID: PMC9906957 DOI: 10.1186/s40364-023-00459-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/28/2023] [Indexed: 02/09/2023] Open
Abstract
The retinal determinant gene network (RDGN), originally discovered as a critical determinator in Drosophila eye specification, has become an important regulatory network in tumorigenesis and progression, as well as organogenesis. This network is not only associated with malignant biological behaviors of tumors, such as proliferation, and invasion, but also regulates the development of multiple mammalian organs. Three members of this conservative network have been extensively investigated, including DACH, SIX, and EYA. Dysregulated RDGN signaling is associated with the initiation and progression of tumors. In recent years, it has been found that the members of this network can be used as prognostic markers for cancer patients. Moreover, they are considered to be potential therapeutic targets for cancer. Here, we summarize the research progress of RDGN members from biological functions to signaling transduction, especially emphasizing their effects on tumors. Additionally, we discuss the roles of RDGN members in the development of organs and tissue as well as their correlations with the pathogenesis of chronic kidney disease and coronary heart disease. By summarizing the roles of RDGN members in human diseases, we hope to promote future investigations into RDGN and provide potential therapeutic strategies for patients.
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Affiliation(s)
- Shuangli Zhu
- grid.412793.a0000 0004 1799 5032Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China
| | - Wanling Li
- grid.412793.a0000 0004 1799 5032Department of Geriatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China ,grid.470966.aCancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, 030032 China
| | - Hao Zhang
- grid.412793.a0000 0004 1799 5032Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China
| | - Yuheng Yan
- grid.412793.a0000 0004 1799 5032Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China
| | - Qi Mei
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China. .,Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, 030032, China.
| | - Kongming Wu
- Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Science, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, 030032, China. .,Cancer Center, Tongji hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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Yu L, Davis IJ, Liu P. Regulation of EWSR1-FLI1 Function by Post-Transcriptional and Post-Translational Modifications. Cancers (Basel) 2023; 15:382. [PMID: 36672331 PMCID: PMC9857208 DOI: 10.3390/cancers15020382] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Ewing sarcoma is the second most common bone tumor in childhood and adolescence. Currently, first-line therapy includes multidrug chemotherapy with surgery and/or radiation. Although most patients initially respond to chemotherapy, recurrent tumors become treatment refractory. Pathologically, Ewing sarcoma consists of small round basophilic cells with prominent nuclei marked by expression of surface protein CD99. Genetically, Ewing sarcoma is driven by a fusion oncoprotein that results from one of a small number of chromosomal translocations composed of a FET gene and a gene encoding an ETS family transcription factor, with ~85% of tumors expressing the EWSR1::FLI1 fusion. EWSR1::FLI1 regulates transcription, splicing, genome instability and other cellular functions. Although a tumor-specific target, EWSR1::FLI1-targeted therapy has yet to be developed, largely due to insufficient understanding of EWSR1::FLI1 upstream and downstream signaling, and the challenges in targeting transcription factors with small molecules. In this review, we summarize the contemporary molecular understanding of Ewing sarcoma, and the post-transcriptional and post-translational regulatory mechanisms that control EWSR1::FLI1 function.
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Affiliation(s)
- Le Yu
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ian J. Davis
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pediatrics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Pengda Liu
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Mechanisms of DNA methylation and histone modifications. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 197:51-92. [PMID: 37019597 DOI: 10.1016/bs.pmbts.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The field of genetics has expanded a lot in the past few decades due to the accessibility of human genome sequences, but still, the regulation of transcription cannot be explicated exclusively by the sequence of DNA of an individual. The coordination and crosstalk between chromatin factors which are conserved is indispensable for all living creatures. The regulation of gene expression has been dependent on the methylation of DNA, post-translational modifications of histones, effector proteins, chromatin remodeler enzymes that affect the chromatin structure and function, and other cellular activities such as DNA replication, DNA repair, proliferation and growth. The mutation and deletion of these factors can lead to human diseases. Various studies are being performed to identify and understand the gene regulatory mechanisms in the diseased state. The information from these high throughput screening studies is able to aid the treatment developments based on the epigenetics regulatory mechanisms. This book chapter will discourse on various modifications and their mechanisms that take place on histones and DNA that regulate the transcription of genes.
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Antitumor Effect of Cycloastragenol in Colon Cancer Cells via p53 Activation. Int J Mol Sci 2022; 23:ijms232315213. [PMID: 36499536 PMCID: PMC9737126 DOI: 10.3390/ijms232315213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer cell (CRC) is the fourth most common cancer in the world. There are several chemotherapy drugs available for its treatment, though they have side effects. Cycloastragenol (CY) is a compound from Astragalus membranaceus (Fisch.) Bge known to be effective in aging, anti-inflammatory, anticancer, and anti-heart failure treatments. Although many studies have demonstrated the functions of CY in cancer cells, no studies have shown the effects of p53 in colon cancer cells. In this study, we found that CY reduces the viability of colon cancer cells in p53 wild-type cells compared to p53 null cells and HT29. Furthermore, CY induces apoptosis by p53 activation in a dose- and time-dependent manner. And it was confirmed that it affects the L5 gene related to p53. Additionally, CY enhanced p53 expression compared to when either doxorubicin or 5-FU was used alone. Altogether, our findings suggest that CY induces apoptosis via p53 activation and inhibits the proliferation of colon cancer cells. In addition, apoptosis occurs in colon cancer cells due to other factors. Moreover, CY is expected to have a combined effect when used together with existing treatments for colon cancer in the future.
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45
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Bölük A, Yavuz M, Demircan T. Axolotl: A resourceful vertebrate model for regeneration and beyond. Dev Dyn 2022; 251:1914-1933. [PMID: 35906989 DOI: 10.1002/dvdy.520] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/04/2022] [Accepted: 07/21/2022] [Indexed: 01/30/2023] Open
Abstract
The regenerative capacity varies significantly among the animal kingdom. Successful regeneration program in some animals results in the functional restoration of tissues and lost structures. Among the highly regenerative animals, axolotl provides multiple experimental advantages with its many extraordinary characteristics. It has been positioned as a regeneration model organism due to its exceptional renewal capacity, including the internal organs, central nervous system, and appendages, in a scar-free manner. In addition to this unique regeneration ability, the observed low cancer incidence, its resistance to carcinogens, and the reversing effect of its cell extract on neoplasms strongly suggest its usability in cancer research. Axolotl's longevity and efficient utilization of several anti-aging mechanisms underline its potential to be employed in aging studies.
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Affiliation(s)
- Aydın Bölük
- School of Medicine, Muğla Sıtkı Koçman University, Muğla, Turkey
| | - Mervenur Yavuz
- Institute of Health Sciences, Muğla Sıtkı Koçman University, Muğla, Turkey
| | - Turan Demircan
- Department of Medical Biology, School of Medicine, Muğla Sıtkı Koçman University, Muğla, Turkey
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46
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Kuthala N, Shanmugam M, Yao CL, Chiang CS, Hwang KC. One step synthesis of 10B-enriched 10BPO4 nanoparticles for effective boron neutron capture therapeutic treatment of recurrent head-and-neck tumor. Biomaterials 2022; 290:121861. [DOI: 10.1016/j.biomaterials.2022.121861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 10/08/2022] [Accepted: 10/13/2022] [Indexed: 11/15/2022]
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Clark LN, Gao Y, Wang GT, Hernandez N, Ashley-Koch A, Jankovic J, Ottman R, Leal SM, Rodriguez SMB, Louis ED. Whole genome sequencing identifies candidate genes for familial essential tremor and reveals biological pathways implicated in essential tremor aetiology. EBioMedicine 2022; 85:104290. [PMID: 36183486 PMCID: PMC9525816 DOI: 10.1016/j.ebiom.2022.104290] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 08/25/2022] [Accepted: 09/13/2022] [Indexed: 12/13/2022] Open
Abstract
Background Essential tremor (ET), one of the most common neurological disorders, has a phenotypically heterogeneous presentation characterized by bilateral kinetic tremor of the arms and, in some patients, tremor involving other body regions (e.g., head, voice). Genetic studies suggest that ET is genetically heterogeneous. Methods We analyzed whole genome sequence data (WGS) generated on 104 multi-generational white families with European ancestry affected by ET. Genome-wide parametric linkage and association scans were analyzed using adjusted logistic regression models through the application of the Pseudomarker software. To investigate the additional contribution of rare variants in familial ET, we also performed an aggregate variant non-parametric linkage (NPL) analysis using the collapsed haplotype method implemented in CHP-NPL software. Findings Parametric linkage analysis of common variants identified several loci with significant evidence of linkage (HLOD ≥3.6). Among the gene regions within the strongest ET linkage peaks were BTC (4q13.3, HLOD=4.53), N6AMT1 (21q21.3, HLOD=4.31), PCDH9 (13q21.32, HLOD=4.21), EYA1 (8q13.3, HLOD=4.04), RBFOX1 (16p13.3, HLOD=4.02), MAPT (17q21.31, HLOD=3.99) and SCARB2 (4q21.1, HLOD=3.65). CHP-NPL analysis identified fifteen additional genes with evidence of significant linkage (LOD ≥3.8). These genes include TUBB2A, VPS33B, STEAP1B, SPINK5, ZRANB1, TBC1D3C, PDPR, NPY4R, ETS2, ZNF736, SPATA21, ARL17A, PZP, BLK and CCDC94. In one ET family contributing to the linkage peak on chromosome 16p13.3, we identified a likely pathogenic heterozygous canonical splice acceptor variant in exon 2 of RBFOX1 (ENST00000547372; c.4-2A>G), that co-segregated with the ET phenotype in the family. Interpretation Linkage and association analyses of WGS identified several novel ET candidate genes, which are implicated in four major pathways that include 1) the epidermal growth factor receptor-phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha-AKT serine/threonine kinase 1 (EGFR-PI3K-AKT) and Mitogen-activated protein Kinase 1 (ERK) pathways, 2) Reactive oxygen species (ROS) and DNA repair, 3) gamma-aminobutyric acid-ergic (GABAergic) system and 4) RNA binding and regulation of RNA processes. Our study provides evidence for a possible overlap in the genetic architecture of ET, neurological disease, cancer and aging. The genes and pathways identified can be prioritized in future genetic and functional studies. Funding National Institutes of Health, NINDS, NS073872 (USA) and NIA AG058131(USA).
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Affiliation(s)
- Lorraine N Clark
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA; The Taub Institute for Research on Alzheimer's Disease and The Aging Brain, Columbia University Irving Medical Center, New York, NY, USA.
| | - Yizhe Gao
- The G.H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA; Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA; The Center for Statistical Genetics, Columbia University Irving Medical Center, New York, NY, USA
| | - Gao T Wang
- The G.H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA; Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA; The Center for Statistical Genetics, Columbia University Irving Medical Center, New York, NY, USA
| | - Nora Hernandez
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas TX, USA
| | - Allison Ashley-Koch
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Joseph Jankovic
- Parkinson's Disease Center and Movement Disorders Clinic, Department of Neurology, Baylor College of Medicine, Houston TX, USA
| | - Ruth Ottman
- The G.H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA; Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA; Department of Epidemiology, Mailman School of Public Health, Columbia University Irving Medical Center, New York, NY, USA; Division of Translational Epidemiology, New York State Psychiatric Institute, New York, NY, USA
| | - Suzanne M Leal
- The Taub Institute for Research on Alzheimer's Disease and The Aging Brain, Columbia University Irving Medical Center, New York, NY, USA; The G.H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA; Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA; The Center for Statistical Genetics, Columbia University Irving Medical Center, New York, NY, USA
| | - Sandra M Barral Rodriguez
- The Taub Institute for Research on Alzheimer's Disease and The Aging Brain, Columbia University Irving Medical Center, New York, NY, USA; The G.H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA; Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA.
| | - Elan D Louis
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas TX, USA.
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Min S, Ji JH, Heo Y, Cho H. Transcriptional regulation and chromatin dynamics at DNA double-strand breaks. Exp Mol Med 2022; 54:1705-1712. [PMID: 36229590 PMCID: PMC9636152 DOI: 10.1038/s12276-022-00862-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/27/2022] [Accepted: 08/01/2022] [Indexed: 12/29/2022] Open
Abstract
In eukaryotic cells, DNA damage can occur at any time and at any chromatin locus, including loci at which active transcription is taking place. DNA double-strand breaks affect chromatin integrity and elicit a DNA damage response to facilitate repair of the DNA lesion. Actively transcribed genes near DNA lesions are transiently suppressed by crosstalk between DNA damage response factors and polycomb repressive complexes. Epigenetic modulation of the chromatin environment also contributes to efficient DNA damage response signaling and transcriptional repression. On the other hand, RNA transcripts produced in the G1 phase, as well as the active chromatin context of the lesion, appear to drive homologous recombination repair. Here, we discuss how the ISWI family of chromatin remodeling factors coordinates the DNA damage response and transcriptional repression, especially in transcriptionally active regions, highlighting the direct modulation of the epigenetic environment.
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Affiliation(s)
- Sunwoo Min
- grid.251916.80000 0004 0532 3933Department of Biochemistry, Ajou University School of Medicine, Suwon, 16499 Korea ,grid.251916.80000 0004 0532 3933Genomic Instability Research Center, Ajou University School of Medicine, Suwon, 16499 Korea
| | - Jae-Hoon Ji
- grid.267309.90000 0001 0629 5880Department of Biochemistry and Structural Biology, The University of Texas Health San Antonio, Texas, 78229-3000 USA
| | - Yungyeong Heo
- grid.251916.80000 0004 0532 3933Department of Biochemistry, Ajou University School of Medicine, Suwon, 16499 Korea ,grid.251916.80000 0004 0532 3933Genomic Instability Research Center, Ajou University School of Medicine, Suwon, 16499 Korea
| | - Hyeseong Cho
- grid.251916.80000 0004 0532 3933Department of Biochemistry, Ajou University School of Medicine, Suwon, 16499 Korea ,grid.251916.80000 0004 0532 3933Genomic Instability Research Center, Ajou University School of Medicine, Suwon, 16499 Korea
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Li J, Cheng C, Xu J, Zhang T, Tokat B, Dolios G, Ramakrishnan A, Shen L, Wang R, Xu PX. The transcriptional coactivator Eya1 exerts transcriptional repressive activity by interacting with REST corepressors and REST-binding sequences to maintain nephron progenitor identity. Nucleic Acids Res 2022; 50:10343-10359. [PMID: 36130284 PMCID: PMC9561260 DOI: 10.1093/nar/gkac760] [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: 05/19/2022] [Revised: 08/18/2022] [Accepted: 08/27/2022] [Indexed: 11/15/2022] Open
Abstract
Eya1 is critical for establishing and maintaining nephron progenitor cells (NPCs). It belongs to a family of proteins called phosphatase-transcriptional activators but without intrinsic DNA-binding activity. However, the spectrum of the Eya1-centered networks is underexplored. Here, we combined transcriptomic, genomic and proteomic approaches to characterize gene regulation by Eya1 in the NPCs. We identified Eya1 target genes, associated cis-regulatory elements and partner proteins. Eya1 preferentially occupies promoter sequences and interacts with general transcription factors (TFs), RNA polymerases, different types of TFs, chromatin-remodeling factors with ATPase or helicase activity, and DNA replication/repair proteins. Intriguingly, we identified REST-binding motifs in 76% of Eya1-occupied sites without H3K27ac-deposition, which were present in many Eya1 target genes upregulated in Eya1-deficient NPCs. Eya1 copurified REST-interacting chromatin-remodeling factors, histone deacetylase/lysine demethylase, and corepressors. Coimmunoprecipitation validated physical interaction between Eya1 and Rest/Hdac1/Cdyl/Hltf in the kidneys. Collectively, our results suggest that through interactions with chromatin-remodeling factors and specialized DNA-binding proteins, Eya1 may modify chromatin structure to facilitate the assembly of regulatory complexes that regulate transcription positively or negatively. These findings provide a mechanistic basis for how Eya1 exerts its activity by forming unique multiprotein complexes in various biological processes to maintain the cellular state of NPCs.
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Affiliation(s)
- Jun Li
- Department of Genetics and Genomic Sciences, New York, NY 10029, USA
| | - Chunming Cheng
- Department of Genetics and Genomic Sciences, New York, NY 10029, USA
| | - Jinshu Xu
- Department of Genetics and Genomic Sciences, New York, NY 10029, USA
| | - Ting Zhang
- Department of Genetics and Genomic Sciences, New York, NY 10029, USA
| | - Bengu Tokat
- Department of Genetics and Genomic Sciences, New York, NY 10029, USA
| | - Georgia Dolios
- Department of Genetics and Genomic Sciences, New York, NY 10029, USA
| | | | - Li Shen
- Department of Neurosciences, New York, NY 10029, USA
| | - Rong Wang
- Department of Genetics and Genomic Sciences, New York, NY 10029, USA
| | - Pin-Xian Xu
- Department of Genetics and Genomic Sciences, New York, NY 10029, USA.,Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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Chen BR, Sleckman BP. The regulation of DNA end resection by chromatin response to DNA double strand breaks. Front Cell Dev Biol 2022; 10:932633. [PMID: 35912102 PMCID: PMC9335370 DOI: 10.3389/fcell.2022.932633] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/29/2022] [Indexed: 11/18/2022] Open
Abstract
DNA double-strand breaks (DSBs) constantly arise upon exposure to genotoxic agents and during physiological processes. The timely repair of DSBs is important for not only the completion of the cellular functions involving DSBs as intermediates, but also the maintenance of genome stability. There are two major pathways dedicated to DSB repair: homologous recombination (HR) and non-homologous end joining (NHEJ). The decision of deploying HR or NHEJ to repair DSBs largely depends on the structures of broken DNA ends. DNA ends resected to generate extensive single-strand DNA (ssDNA) overhangs are repaired by HR, while those remaining blunt or minimally processed can be repaired by NHEJ. As the generation and repair of DSB occurs within the context of chromatin, the resection of broken DNA ends is also profoundly affected by the state of chromatin flanking DSBs. Here we review how DNA end resection can be regulated by histone modifications, chromatin remodeling, and the presence of ssDNA structure through altering the accessibility to chromatin and the activity of pro- and anti-resection proteins.
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Affiliation(s)
- Bo-Ruei Chen
- Division of Hematology and Oncology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States
- *Correspondence: Bo-Ruei Chen,
| | - Barry P. Sleckman
- Division of Hematology and Oncology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States
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