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Jurkowska RZ. Role of epigenetic mechanisms in the pathogenesis of chronic respiratory diseases and response to inhaled exposures: From basic concepts to clinical applications. Pharmacol Ther 2024:108732. [PMID: 39426605 DOI: 10.1016/j.pharmthera.2024.108732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 08/15/2024] [Accepted: 10/11/2024] [Indexed: 10/21/2024]
Abstract
Epigenetic modifications are chemical groups in our DNA (and chromatin) that determine which genes are active and which are shut off. Importantly, they integrate environmental signals to direct cellular function. Upon chronic environmental exposures, the epigenetic signature of lung cells gets altered, triggering aberrant gene expression programs that can lead to the development of chronic lung diseases. In addition to driving disease, epigenetic marks can serve as attractive lung disease biomarkers, due to early onset, disease specificity, and stability, warranting the need for more epigenetic research in the lung field. Despite substantial progress in mapping epigenetic alterations (mostly DNA methylation) in chronic lung diseases, the molecular mechanisms leading to their establishment are largely unknown. This review is meant as a guide for clinicians and lung researchers interested in epigenetic regulation with a focus on DNA methylation. It provides a short introduction to the main epigenetic mechanisms (DNA methylation, histone modifications and non-coding RNA) and the machinery responsible for their establishment and removal. It presents examples of epigenetic dysregulation across a spectrum of chronic lung diseases and discusses the current state of epigenetic therapies. Finally, it introduces the concept of epigenetic editing, an exciting novel approach to dissecting the functional role of epigenetic modifications. The promise of this emerging technology for the functional study of epigenetic mechanisms in cells and its potential future use in the clinic is further discussed.
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Affiliation(s)
- Renata Z Jurkowska
- Division of Biomedicine, School of Biosciences, Cardiff University, Cardiff, UK.
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2
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Bomsztyk K, Mar D, Denisenko O, Powell S, Vishnoi M, Yin Z, Delegard J, Hadley C, Tandon N, Patel A, Patel A, Ellenbogen RG, Ramakrishna R, Rostomily R. Analysis of gliomas DNA methylation: Assessment of pre-analytical variables. J Transl Med 2024:102160. [PMID: 39426568 DOI: 10.1016/j.labinv.2024.102160] [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: 04/08/2024] [Revised: 10/01/2024] [Accepted: 10/09/2024] [Indexed: 10/21/2024] Open
Abstract
Precision oncology is driven by biomarkers. For glioblastoma multiforme (GBM), the most common malignant adult primary brain tumor, O6-methylguanine-DNA methyltransferase (MGMT) gene promoter methylation is an important prognostic and treatment clinical biomarker. Time consuming pre-analytical steps such as biospecimen storage, fixation, sampling, and processing are sources of data irreproducibility, and all these pre-analytical variables are confounded by intratumor heterogeneity of MGMT promoter methylation. To assess the effect of pre-analytical variables on GBM DNA methylation, tissue storage/sampling (CryoGrid), sample preparation multi-sonicator (PIXUL), and 5-methylcytosine (5mC) DNA immunoprecipitation (Matrix MeDIP-qPCR/seq) platforms were used. MGMT promoter methylation status assayed by MeDIP-qPCR was validated with methylation specific PCR (MS-PCR). MGMT promoter methylation levels in frozen and formalin fixed paraffin embedded (FFPE) sample pairs were not statistically different, confirming reliability of FFPEs for MGMT promoter methylation analysis. Warm ex-vivo ischemia (up to 4hrs at 37oC) and 3 cycles of repeated sample thawing and freezing did not statistically impact 5mC at MGMT promoter, exon, and enhancer regions, indicating the resistance of DNA methylation to common variations in sample processing conditions that might be encountered in research and clinical settings. 26-34% of specimens exhibited intratumor heterogeneity in the MGMT DNA promoter methylation. These data demonstrate that variations in sample fixation, ischemia duration and temperature, and DNA methylation assay technique do not have a statistically significant impact on MGMT promoter methylation assessment. However, intratumor methylation heterogeneity underscores the value of multiple biopsies at different GBM geographic tumor sites in the evaluation of MGMT promoter methylation status. Matrix-MeDIP-seq analysis revealed that MGMT promoter methylation status clustered with other differentially methylated genomic loci (e.g. HOXA and lncRNAs) that are resilient to variation in the above pre-analytical conditions. These observations offer new opportunities to develop more granular data-based epigenetic GBM biomarkers. In this regard, the high throughput CryoGrid-PIXUL-Matrix toolbox could be useful.
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Affiliation(s)
- Karol Bomsztyk
- UW Medicine South Lake Union, University of Washington, Seattle, WA 98109, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; Matchstick Technologies, Inc, Kirkland, WA 98033, USA.
| | - Daniel Mar
- UW Medicine South Lake Union, University of Washington, Seattle, WA 98109, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Oleg Denisenko
- UW Medicine South Lake Union, University of Washington, Seattle, WA 98109, USA
| | - Suzanne Powell
- Department of Neuropathology, Houston Methodist Hospital, Houston, Texas 77030, USA
| | - Monika Vishnoi
- Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Zheng Yin
- Department of Systems Medicine and Bioengineering, Houston Methodist Neil Cancer Center, Houston, TX, 77030, USA
| | - Jennifer Delegard
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | - Caroline Hadley
- Department of Neurosurgery, University of New Mexico, Albuquerque, NM, 87106, USA
| | - Nitin Tandon
- Department of Neurosurgery, McGovern Medical School at UT Health, Houston, TX, 77030
| | - Akash Patel
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX, 77584, USA
| | - Anoop Patel
- Department of Neurosurgery, Duke University, Durham, NC, 27710
| | - Richard G Ellenbogen
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | - Rohan Ramakrishna
- Department of Neurological Surgery, Weill Cornell Medicine, New York, NY 10065, USA
| | - Robert Rostomily
- Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA; Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA,; Department of Neurological Surgery, Weill Cornell Medicine, New York, NY 10065, USA
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3
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Laisné M, Lupien M, Vallot C. Epigenomic heterogeneity as a source of tumour evolution. Nat Rev Cancer 2024:10.1038/s41568-024-00757-9. [PMID: 39414948 DOI: 10.1038/s41568-024-00757-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/16/2024] [Indexed: 10/18/2024]
Abstract
In the past decade, remarkable progress in cancer medicine has been achieved by the development of treatments that target DNA sequence variants. However, a purely genetic approach to treatment selection is hampered by the fact that diverse cell states can emerge from the same genotype. In multicellular organisms, cell-state heterogeneity is driven by epigenetic processes that regulate DNA-based functions such as transcription; disruption of these processes is a hallmark of cancer that enables the emergence of defective cell states. Advances in single-cell technologies have unlocked our ability to quantify the epigenomic heterogeneity of tumours and understand its mechanisms, thereby transforming our appreciation of how epigenomic changes drive cancer evolution. This Review explores the idea that epigenomic heterogeneity and plasticity act as a reservoir of cell states and therefore as a source of tumour evolution. Best practices to quantify epigenomic heterogeneity and explore its various causes and consequences are discussed, including epigenomic reprogramming, stochastic changes and lasting memory. The design of new therapeutic approaches to restrict epigenomic heterogeneity, with the long-term objective of limiting cancer development and progression, is also addressed.
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Affiliation(s)
- Marthe Laisné
- CNRS UMR3244, Institut Curie, PSL University, Paris, France
- Translational Research Department, Institut Curie, PSL University, Paris, France
| | - Mathieu Lupien
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontorio, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontorio, Canada.
- Ontario Institute for Cancer Research, Toronto, Ontorio, Canada.
| | - Céline Vallot
- CNRS UMR3244, Institut Curie, PSL University, Paris, France.
- Translational Research Department, Institut Curie, PSL University, Paris, France.
- Single Cell Initiative, Institut Curie, PSL University, Paris, France.
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4
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Chen JL, Peng PH, Wu HT, Chen DR, Hsieh CY, Chang JS, Lin J, Lin HY, Hsu KW. ALKBH4 functions as a hypoxia-responsive tumor suppressor and inhibits metastasis and tumorigenesis. Cell Oncol (Dordr) 2024:10.1007/s13402-024-01004-x. [PMID: 39400679 DOI: 10.1007/s13402-024-01004-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2024] [Indexed: 10/15/2024] Open
Abstract
PURPOSE The human AlkB homolog (ALKBH) dioxygenase superfamily plays a crucial role in gene regulation and is implicated in cancer progression. Under hypoxic conditions, hypoxia-inducible factors (HIFs) dynamically regulate methylation by controlling various dioxygenases, thereby modulating gene expression. However, the role of hypoxia-responsive AlkB dioxygenase remains unclear. METHODS The molecular events were examined using real-time PCR and Western blot analysis. Tumor cell aggressiveness was evaluated through migration, invasion, MTT, trypan blue exclusion, and colony formation assays. In vivo metastatic models and xenograft experiments were conducted to evaluate tumor progression. RESULTS Here, we examined the expression of the ALKBH superfamily under hypoxic conditions and found that ALKBH4 expression was negatively regulated by hypoxia. Knockdown of ALKBH4 enhanced the epithelial-mesenchymal transition (EMT), cell migration, invasion, and growth in vitro. The silencing of ALKBH4 enhanced metastatic ability and tumor growth in vivo. Conversely, overexpression of ALLKBH4 reversed these observations. Furthermore, overexpression of ALKBH4 significantly reversed hypoxia/HIF-1α-induced EMT, cell migration, invasion, tumor metastasis, and tumorigenicity. Notably, high expression of ALKBH4 was associated with better outcomes in head and neck cancer and breast cancer patients. Enrichment analysis also revealed that ALKBH4 was negatively enriched in hypoxia-related pathways. Clinically, a negative correlation between ALKBH4 and HIF-1α protein expression has been observed in tissues from both head and neck cancers and breast cancers. CONCLUSION These findings collectively suggest that ALKBH4 acts as a tumor suppressor and holds therapeutic potential for hypoxic tumors.
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Affiliation(s)
- Ji-Lin Chen
- Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Pei-Hua Peng
- Drug Development Center, Program for Cancer Biology and Drug Discovery, China Medical University, Taichung, Taiwan
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Han-Tsang Wu
- Cancer Research Center, Changhua Christian Hospital, Changhua, Taiwan
| | - Dar-Ren Chen
- Cancer Research Center, Changhua Christian Hospital, Changhua, Taiwan
- Comprehensive Breast Cancer Center, Changhua Christian Hospital, Changhua, Taiwan
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Ching-Yun Hsieh
- Division of Hematology and Oncology, Department of Internal Medicine, China Medical University Hospital, Taichung City, Taiwan
| | - Jeng-Shou Chang
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Joseph Lin
- Cancer Research Center, Changhua Christian Hospital, Changhua, Taiwan
- Comprehensive Breast Cancer Center, Changhua Christian Hospital, Changhua, Taiwan
| | - Huan-Yu Lin
- Cheng Ching Hospital Chung Kang Cheng Ching Hospital Branch, Taichung, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Kai-Wen Hsu
- Drug Development Center, Program for Cancer Biology and Drug Discovery, China Medical University, Taichung, Taiwan.
- Research Center for Cancer Biology, China Medical University, Taichung City, Taiwan.
- Institute of Translational Medicine and New Drug Development, China Medical University, Taichung City, 40402, Taiwan.
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5
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Iriondo O, Mecenas D, Li Y, Chin CR, Thomas A, Moriarty A, Marker R, Wang YJ, Hendrick H, Amzaleg Y, Ortiz V, MacKay M, Dickerson A, Lee G, Harotoonian S, Benayoun BA, Smith A, Mason CE, Roussos Torres ET, Klotz R, Yu M. Hypoxic Memory Mediates Prolonged Tumor-Intrinsic Type I Interferon Suppression to Promote Breast Cancer Progression. Cancer Res 2024; 84:3141-3157. [PMID: 38990731 PMCID: PMC11444891 DOI: 10.1158/0008-5472.can-23-2028] [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: 07/09/2023] [Revised: 05/03/2024] [Accepted: 07/03/2024] [Indexed: 07/13/2024]
Abstract
Hypoxia is a common feature of many solid tumors due to aberrant proliferation and angiogenesis that is associated with tumor progression and metastasis. Most of the well-known hypoxia effects are mediated through hypoxia-inducible factors (HIF). Identification of the long-lasting effects of hypoxia beyond the immediate HIF-induced alterations could provide a better understanding of hypoxia-driven metastasis and potential strategies to circumvent it. Here, we uncovered a hypoxia-induced mechanism that exerts a prolonged effect to promote metastasis. In breast cancer patient-derived circulating tumor cell lines and common breast cancer cell lines, hypoxia downregulated tumor-intrinsic type I IFN signaling and its downstream antigen presentation (AP) machinery in luminal breast cancer cells, via both HIF-dependent and HIF-independent mechanisms. Hypoxia induced durable IFN/AP suppression in certain cell types that was sustained after returning to normoxic conditions, presenting a "hypoxic memory" phenotype. Hypoxic memory of IFN/AP downregulation was established by specific hypoxic priming, and cells with hypoxic memory had an enhanced ability for tumorigenesis and metastasis. Overexpression of IRF3 enhanced IFN signaling and reduced tumor growth in normoxic, but not hypoxic, conditions. The histone deacetylase inhibitor entinostat upregulated IFN targets and erased the hypoxic memory. These results point to a mechanism by which hypoxia facilitates tumor progression through a long-lasting memory that provides advantages for circulating tumor cells during the metastatic cascade. Significance: Long-term cellular memory of hypoxia leads to sustained suppression of tumor-intrinsic type I IFN signaling and the antigen presentation pathway that facilitates tumorigenesis and metastasis. See related commentary by Purdy and Ford, p. 3125.
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Affiliation(s)
- Oihana Iriondo
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California
- USC Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, California
- Center for Cooperative Research (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Desirea Mecenas
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California
- USC Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | - Yilin Li
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California
- USC Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, California
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
| | - Christopher R Chin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Amal Thomas
- Department of Molecular and Computational Biology, USC Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California
| | - Aidan Moriarty
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, Maryland
- Marlene and Stewart Greenebaum NCI Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland
| | - Rebecca Marker
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, Maryland
- Marlene and Stewart Greenebaum NCI Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland
| | - Yiru J Wang
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, Maryland
- Marlene and Stewart Greenebaum NCI Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland
| | - Haley Hendrick
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, Maryland
- Marlene and Stewart Greenebaum NCI Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland
| | - Yonatan Amzaleg
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California
- USC Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, California
- Center for Craniofacial Molecular Biology, Ostrow School of Dentistry of the University of Southern California, Los Angeles, California
| | - Veronica Ortiz
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California
- USC Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | - Matthew MacKay
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | - Amber Dickerson
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California
- USC Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | - Grace Lee
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California
- USC Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | - Sevana Harotoonian
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | - Bérénice A Benayoun
- USC Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, California
- Department of Molecular and Computational Biology, USC Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California
| | - Andrew Smith
- Department of Molecular and Computational Biology, USC Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Evanthia T Roussos Torres
- USC Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, California
- Department of Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | - Remi Klotz
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California
- USC Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, California
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, Maryland
- Marlene and Stewart Greenebaum NCI Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland
| | - Min Yu
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California
- USC Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, California
- Department of Pharmacology, University of Maryland School of Medicine, Baltimore, Maryland
- Marlene and Stewart Greenebaum NCI Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland
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Chen L, Peng Z, Yang Y, He J, Lv Z, Zheng Q, Lei T, Guo W, Chen Z, Liu Y, Ran Y, Yang J. The neo-potential therapeutic strategy in preeclampsia: Downregulated miR-26a-2-3p motivates endothelial cell injury by targeting 15-LOX-1. Free Radic Biol Med 2024; 225:112-126. [PMID: 39357683 DOI: 10.1016/j.freeradbiomed.2024.09.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 09/16/2024] [Accepted: 09/30/2024] [Indexed: 10/04/2024]
Abstract
Preeclampsia (PE) poses a life-threatening risk for both mothers and babies, and its onset and progression are linked to endothelial injury. The enzyme 15-lipoxygenase-1 (15-LOX-1), critical in arachidonic acid metabolism, is implicated in various diseases, yet its specific role and precise mechanisms in PE remain largely unknown. In this study, we found that 15-LOX-1 and its main metabolite, 15-HETE, were significantly increased in both the placenta and serum of PE patients. This increase was accompanied by elevated levels of endothelial injury markers, including intercellular adhesion molecule-1 (ICAM-1) and vascular cell adhesion molecule-1 (VCAM-1). A positive correlation between 15-LOX-1 and those markers in the placenta. In Alox15-/- mice, Alox15 deficiency reduced endothelial cell injury in PE-like mice induced by L-NAME. In vitro studies showed that hypoxia-induced upregulation of 15-LOX-1 reduced the cell viability, migration, and angiogenesis of human umbilical vein endothelial cells (HUVECs), while increasing apoptosis and inflammatory cell adhesion. Mechanistically, the p38 MAPK pathway was identified as a downstream target of 15-LOX-1. Knocking down 15-LOX-1 or inhibiting p38 MAPK activation improved endothelial cell injury in hypoxia-treated HUVECs. Furthermore, downregulation of miR-26a-2-3p was found to correlate negatively and colocalize with 15-LOX-1 upregulation in the placenta of PE patients. Luciferase reporter assays further confirmed that miR-26a-2-3p directly bind to the 3'UTR of 15-LOX-1, targeting its expression. Moreover, miR-26a-2-3p agomir ameliorated the PE-like phenotype in mice through the 15-LOX-1/p38 MAPK axis, improving endothelial dysfunction. Therefore, our study provides novel insights into the pathogenesis of PE and highlight modulating the miR-26a-2-3p/15-LOX-1/p38 MAPK axis as a potential therapeutic target for PE.
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Affiliation(s)
- Lin Chen
- Department of Pharmacy, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Department of Pharmacy, Chongqing Health Center for Women and Children, Chongqing, China; Chongqing Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, China
| | - Zhe Peng
- Department of Pharmacy, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Department of Pharmacy, Chongqing Health Center for Women and Children, Chongqing, China
| | - Yang Yang
- Department of Pharmacy, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Department of Pharmacy, Chongqing Health Center for Women and Children, Chongqing, China
| | - Jungong He
- Chongqing Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, China
| | - Zongjie Lv
- Department of Pharmacy, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Department of Pharmacy, Chongqing Health Center for Women and Children, Chongqing, China
| | - Qixue Zheng
- Chongqing Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, China
| | - Tiantian Lei
- Department of Pharmacy, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Department of Pharmacy, Chongqing Health Center for Women and Children, Chongqing, China
| | - Wenjia Guo
- Department of Pharmacy, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Department of Pharmacy, Chongqing Health Center for Women and Children, Chongqing, China
| | - Zhen Chen
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Yong Liu
- Department of Pharmacy, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Department of Pharmacy, Chongqing Health Center for Women and Children, Chongqing, China.
| | - Yajuan Ran
- Department of Pharmacy, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - Junqing Yang
- Department of Pharmacy, Women and Children's Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Biochemistry and Molecular Pharmacology, Chongqing Medical University, Chongqing, China.
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7
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Sacco JL, Gomez EW. Epithelial-Mesenchymal Plasticity and Epigenetic Heterogeneity in Cancer. Cancers (Basel) 2024; 16:3289. [PMID: 39409910 PMCID: PMC11475326 DOI: 10.3390/cancers16193289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Revised: 09/10/2024] [Accepted: 09/23/2024] [Indexed: 10/20/2024] Open
Abstract
The tumor microenvironment comprises various cell types and experiences dynamic alterations in physical and mechanical properties as cancer progresses. Intratumoral heterogeneity is associated with poor prognosis and poses therapeutic challenges, and recent studies have begun to identify the cellular mechanisms that contribute to phenotypic diversity within tumors. This review will describe epithelial-mesenchymal (E/M) plasticity and its contribution to phenotypic heterogeneity in tumors as well as how epigenetic factors, such as histone modifications, histone modifying enzymes, DNA methylation, and chromatin remodeling, regulate and maintain E/M phenotypes. This review will also report how mechanical properties vary across tumors and regulate epigenetic modifications and E/M plasticity. Finally, it highlights how intratumoral heterogeneity impacts therapeutic efficacy and provides potential therapeutic targets to improve cancer treatments.
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Affiliation(s)
- Jessica L. Sacco
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA;
| | - Esther W. Gomez
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA;
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
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8
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de la Calle-Fabregat C, Calafell-Segura J, Gardet M, Dunsmore G, Mulder K, Ciudad L, Silvin A, Moreno-Càceres J, Corbí ÁL, Muñoz-Pinedo C, Michels J, Gouy S, Dutertre CA, Rodríguez-Ubreva J, Ginhoux F, Ballestar E. NF-κB and TET2 promote macrophage reprogramming in hypoxia that overrides the immunosuppressive effects of the tumor microenvironment. SCIENCE ADVANCES 2024; 10:eadq5226. [PMID: 39292770 PMCID: PMC11409945 DOI: 10.1126/sciadv.adq5226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 08/12/2024] [Indexed: 09/20/2024]
Abstract
Macrophages orchestrate tissue homeostasis and immunity. In the tumor microenvironment (TME), macrophage presence is largely associated with poor prognosis because of their reprogramming into immunosuppressive cells. We investigated the effects of hypoxia, a TME-associated feature, on the functional, epigenetic, and transcriptional reprogramming of macrophages and found that hypoxia boosts their immunogenicity. Hypoxic inflammatory macrophages are characterized by a cluster of proinflammatory genes undergoing ten-eleven translocation-mediated DNA demethylation and overexpression. These genes are regulated by NF-κB, while HIF1α dominates the transcriptional reprogramming, demonstrated through ChIP-seq and pharmacological inhibition. In bladder and ovarian carcinomas, hypoxic inflammatory macrophages are enriched in immune-infiltrated tumors, correlating with better patient prognoses. Coculture assays and cell-cell communication analyses support that hypoxic-activated macrophages enhance T cell-mediated responses. The NF-κB-associated hypomethylation signature is displayed by a subset of hypoxic inflammatory macrophages, isolated from ovarian tumors. Our results challenge paradigms regarding the effects of hypoxia on macrophages and highlight actionable target cells to modulate anticancer immune responses.
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Affiliation(s)
- Carlos de la Calle-Fabregat
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- INSERM UMR1015, Gustave Roussy Cancer Campus, 94805 Villejuif, France
| | - Josep Calafell-Segura
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain
| | - Margaux Gardet
- INSERM UMR1015, Gustave Roussy Cancer Campus, 94805 Villejuif, France
| | - Garett Dunsmore
- INSERM UMR1015, Gustave Roussy Cancer Campus, 94805 Villejuif, France
| | - Kevin Mulder
- INSERM UMR1015, Gustave Roussy Cancer Campus, 94805 Villejuif, France
| | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain
| | - Aymeric Silvin
- INSERM UMR1015, Gustave Roussy Cancer Campus, 94805 Villejuif, France
| | - Joaquim Moreno-Càceres
- Preclinical and Experimental Research in Thoracic Tumors (PReTT), Oncobell Program, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ángel L. Corbí
- Myeloid Cell Laboratory, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - Cristina Muñoz-Pinedo
- Preclinical and Experimental Research in Thoracic Tumors (PReTT), Oncobell Program, Institut d’Investigació Biomèdica de Bellvitge (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Judith Michels
- INSERM UMR1186, Integrative Tumor Immunology and Immunotherapy, Gustave Roussy, Faculté de Médecine, Université Paris-Saclay, 94805 Villejuif, France
- Département de Médecine Oncologique, Gustave Roussy, 94805 Villejuif, France
| | - Sébastien Gouy
- Department of Surgical Oncology, Gustave Roussy, 94805 Villejuif, France
| | | | - Javier Rodríguez-Ubreva
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain
| | - Florent Ginhoux
- INSERM UMR1015, Gustave Roussy Cancer Campus, 94805 Villejuif, France
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- Epigenetics in Inflammatory and Metabolic Diseases Laboratory, Health Science Center (HSC), East China Normal University (ECNU), Shanghai 200241, China
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9
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Xun Z, Zhou H, Shen M, Liu Y, Sun C, Du Y, Jiang Z, Yang L, Zhang Q, Lin C, Hu Q, Ye Y, Han L. Identification of Hypoxia-ALCAM high Macrophage- Exhausted T Cell Axis in Tumor Microenvironment Remodeling for Immunotherapy Resistance. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309885. [PMID: 38956900 PMCID: PMC11434037 DOI: 10.1002/advs.202309885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 04/02/2024] [Indexed: 07/04/2024]
Abstract
Although hypoxia is known to be associated with immune resistance, the adaptability to hypoxia by different cell populations in the tumor microenvironment and the underlying mechanisms remain elusive. This knowledge gap has hindered the development of therapeutic strategies to overcome tumor immune resistance induced by hypoxia. Here, bulk, single-cell, and spatial transcriptomics are integrated to characterize hypoxia associated with immune escape during carcinogenesis and reveal a hypoxia-based intercellular communication hub consisting of malignant cells, ALCAMhigh macrophages, and exhausted CD8+ T cells around the tumor boundary. A hypoxic microenvironment promotes binding of HIF-1α complex is demonstrated to the ALCAM promoter therefore increasing its expression in macrophages, and the ALCAMhigh macrophages co-localize with exhausted CD8+ T cells in the tumor spatial microenvironment and promote T cell exhaustion. Preclinically, HIF-1ɑ inhibition reduces ALCAM expression in macrophages and exhausted CD8+ T cells and potentiates T cell antitumor function to enhance immunotherapy efficacy. This study reveals the systematic landscape of hypoxia at single-cell resolution and spatial architecture and highlights the effect of hypoxia on immunotherapy resistance through the ALCAMhigh macrophage-exhausted T cell axis, providing a novel immunotherapeutic strategy to overcome hypoxia-induced resistance in cancers.
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Affiliation(s)
- Zhenzhen Xun
- Center for Immune‐Related Diseases at Shanghai Institute of ImmunologyDepartment of GastroenterologyRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025China
- Shanghai Institute of ImmunologyState Key Laboratory of Systems Medicine for CancerDepartment of Immunology and MicrobiologyShanghai Jiao Tong University School of MedicineShanghai200025China
| | - Huanran Zhou
- Department of EndocrinologyThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui230001China
| | - Mingyi Shen
- Center for Immune‐Related Diseases at Shanghai Institute of ImmunologyDepartment of GastroenterologyRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025China
- Shanghai Institute of ImmunologyState Key Laboratory of Systems Medicine for CancerDepartment of Immunology and MicrobiologyShanghai Jiao Tong University School of MedicineShanghai200025China
| | - Yao Liu
- Department of Hepatobiliary SurgeryCentre for Leading Medicine and Advanced Technologies of IHMThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefei230001China
| | - Chengcao Sun
- Department of Molecular and Cellular OncologyThe University of Texas MD Anderson Cancer CenterHoustonTX77030USA
| | - Yanhua Du
- Center for Immune‐Related Diseases at Shanghai Institute of ImmunologyDepartment of GastroenterologyRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025China
| | - Zhou Jiang
- Department of Molecular and Cellular OncologyThe University of Texas MD Anderson Cancer CenterHoustonTX77030USA
| | - Liuqing Yang
- Department of Molecular and Cellular OncologyThe University of Texas MD Anderson Cancer CenterHoustonTX77030USA
| | - Qing Zhang
- Simmons Comprehensive Cancer CenterDepartment of PathologyUniversity of Texas Southwestern Medical CenterDallasTX75390USA
| | - Chunru Lin
- Department of Molecular and Cellular OncologyThe University of Texas MD Anderson Cancer CenterHoustonTX77030USA
| | - Qingsong Hu
- Department of Hepatobiliary SurgeryCentre for Leading Medicine and Advanced Technologies of IHMThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefei230001China
| | - Youqiong Ye
- Center for Immune‐Related Diseases at Shanghai Institute of ImmunologyDepartment of GastroenterologyRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025China
- Shanghai Institute of ImmunologyState Key Laboratory of Systems Medicine for CancerDepartment of Immunology and MicrobiologyShanghai Jiao Tong University School of MedicineShanghai200025China
| | - Leng Han
- Brown Center for ImmunotherapySchool of MedicineIndiana UniversityIndianapolisIN46202USA
- Department of Biostatistics and Health Data ScienceSchool of MedicineIndiana UniversityIndianapolisIN46202USA
- Department of Biochemistry and Molecular BiologyMcGovern Medical School at The University of Texas Health Science Center at HoustonHoustonTX77030USA
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10
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Kundu P, Jain R, Kanuri NN, Arimappamagan A, Santosh V, Kondaiah P. DNA Methylation in Recurrent Glioblastomas: Increased TEM8 Expression Activates the Src/PI3K/AKT/GSK-3β/B-Catenin Pathway. Cancer Genomics Proteomics 2024; 21:485-501. [PMID: 39191501 PMCID: PMC11363927 DOI: 10.21873/cgp.20466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/20/2024] [Accepted: 06/10/2024] [Indexed: 08/29/2024] Open
Abstract
BACKGROUND/AIM Glioblastomas (GBM) are infiltrative malignant brain tumors which mostly recur within a year's time following surgical resection and chemo-radiation therapy. Studies on glioblastoma cells following radio-chemotherapy, have been demonstrated to induce trans-differentiation, cellular plasticity, activation of DNA damage response and stemness. As glioblastomas are heterogenous tumors that develop treatment resistance and plasticity, we investigated if there exist genome-wide DNA methylation changes in recurrent tumors. MATERIALS AND METHODS Utilizing genome-wide DNA methylation arrays, we compared the DNA methylation profile of 11 primary (first occurrence) tumors with 13 recurrent (relapsed) GBM, to delineate the contribution of epigenetic changes associated with therapy exposure, therapy resistance, and relapse of disease. RESULTS Our data revealed 1,224 hypermethylated- and 526 hypomethylated-probes in recurrent glioblastomas compared to primary disease. We found differential methylation of solute carrier and ion channel genes, interleukin receptor/ligand genes, tumor-suppressor genes and genes associated with metastasis. We functionally characterized one such hypomethylated-up-regulated gene, namely anthrax toxin receptor 1/tumor endothelial marker 8 (ANTXR1/TEM8), whose expression was validated to be significantly up-regulated in recurrent glioblastomas compared to primary tumors and confirmed by immunohistochemistry. Using overexpression and knockdown approaches, we showed that TEM8 induces proliferation, invasion, migration, and chemo-radioresistance in glioblastoma cells. Additionally, we demonstrated a novel mechanism of β-catenin stabilization and activation of the β-catenin transcriptional program due to TEM8 overexpression via a Src/PI3K/AKT/GSK3β/β-catenin pathway. CONCLUSION We report genome-wide DNA methylation changes in recurrent GBM and suggest involvement of the TEM8 gene in GBM recurrence and progression.
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Affiliation(s)
- Paramita Kundu
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
- Breast Cancer Now Toby Robins Research Centre, Department of Breast Research, The Institute of Cancer Research, London, U.K
| | - Ruchi Jain
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
- Al Jalila Genomics Centre, Al Jalila Children's Hospital, Dubai, United Arab Emirates
| | - Nandaki Nag Kanuri
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore, India
| | | | - Vani Santosh
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Paturu Kondaiah
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India;
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11
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Rath SK, Nyamsuren G, Tampe B, Yu DSW, Hulshoff MS, Schlösser D, Maamari S, Zeisberg M, Zeisberg EM. Loss of tet methyl cytosine dioxygenase 3 (TET3) enhances cardiac fibrosis via modulating the DNA damage repair response. Clin Epigenetics 2024; 16:119. [PMID: 39192299 DOI: 10.1186/s13148-024-01719-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 07/29/2024] [Indexed: 08/29/2024] Open
Abstract
BACKGROUND Cardiac fibrosis is the hallmark of all forms of chronic heart disease. Activation and proliferation of cardiac fibroblasts are the prime mediators of cardiac fibrosis. Existing studies show that ROS and inflammatory cytokines produced during fibrosis not only signal proliferative stimuli but also contribute to DNA damage. Therefore, as a prerequisite to maintain sustained proliferation in fibroblasts, activation of distinct DNA repair mechanism is essential. RESULT In this study, we report that TET3, a DNA demethylating enzyme, which has been shown to be reduced in cardiac fibrosis and to exert antifibrotic effects does so not only through its demethylating activity but also through maintaining genomic integrity by facilitating error-free homologous recombination (HR) repair of DNA damage. Using both in vitro and in vivo models of cardiac fibrosis as well as data from human heart tissue, we demonstrate that the loss of TET3 in cardiac fibroblasts leads to spontaneous DNA damage and in the presence of TGF-β to a shift from HR to the fast but more error-prone non-homologous end joining repair pathway. This shift contributes to increased fibroblast proliferation in a fibrotic environment. In vitro experiments showed TET3's recruitment to H2O2-induced DNA double-strand breaks (DSBs) in mouse cardiac fibroblasts, promoting HR repair. Overexpressing TET3 counteracted TGF-β-induced fibroblast proliferation and restored HR repair efficiency. Extending these findings to human cardiac fibrosis, we confirmed TET3 expression loss in fibrotic hearts and identified a negative correlation between TET3 levels, fibrosis markers, and DNA repair pathway alteration. CONCLUSION Collectively, our findings demonstrate TET3's pivotal role in modulating DDR and fibroblast proliferation in cardiac fibrosis and further highlight TET3 as a potential therapeutic target.
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Affiliation(s)
- Sandip Kumar Rath
- Department of Cardiology and Pneumology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
- DZHK (German Center for Cardiovascular Research, Partner Site Lower Saxony, Göttingen, Germany
| | - Gunsmaa Nyamsuren
- Department of Nephrology and Rheumatology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Björn Tampe
- Department of Nephrology and Rheumatology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - David Sung-Wen Yu
- Department of Radiation Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Melanie S Hulshoff
- Department of Cardiology and Pneumology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
- DZHK (German Center for Cardiovascular Research, Partner Site Lower Saxony, Göttingen, Germany
| | - Denise Schlösser
- Department of Cardiology and Pneumology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Sabine Maamari
- Department of Cardiology and Pneumology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
- DZHK (German Center for Cardiovascular Research, Partner Site Lower Saxony, Göttingen, Germany
| | - Michael Zeisberg
- Department of Nephrology and Rheumatology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
- DZHK (German Center for Cardiovascular Research, Partner Site Lower Saxony, Göttingen, Germany
| | - Elisabeth M Zeisberg
- Department of Cardiology and Pneumology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany.
- DZHK (German Center for Cardiovascular Research, Partner Site Lower Saxony, Göttingen, Germany.
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12
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Kong Y, Ji J, Zhan X, Yan W, Liu F, Ye P, Wang S, Tai J. Tet1-mediated 5hmC regulates hippocampal neuroinflammation via wnt signaling as a novel mechanism in obstructive sleep apnoea leads to cognitive deficit. J Neuroinflammation 2024; 21:208. [PMID: 39169375 PMCID: PMC11340128 DOI: 10.1186/s12974-024-03189-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 07/29/2024] [Indexed: 08/23/2024] Open
Abstract
BACKGROUND Obstructive sleep apnoea (OSA) is a sleep-disordered breathing characterized by intermittent hypoxia (IH) that may cause cognitive dysfunction. However, the impact of IH on molecular processes involved in cognitive function remains unclear. METHODS C57BL / 6 J mice were exposed to either normoxia (control) or IH for 6 weeks. DNA hydroxymethylation was quantified by hydroxymethylated DNA immunoprecipitation (hMeDIP) sequencing. ten-eleven translocation 1 (Tet1) was knocked down by lentivirus. Specifically, cognitive function was assessed by behavioral experiments, pathological features were assessed by HE staining, the hippocampal DNA hydroxymethylation was examined by DNA dot blot and immunohistochemical staining, while the Wnt signaling pathway and its downstream effects were studied using qRT-PCR, immunofluorescence staining, and Luminex liquid suspension chip analysis. RESULTS IH mice showed pathological changes and cognitive dysfunction in the hippocampus. Compared with the control group, IH mice exhibited global DNA hydroxylmethylation in the hippocampus, and the expression of three hydroxylmethylases increased significantly. The Wnt signaling pathway was activated, and the mRNA and 5hmC levels of Wnt3a, Ccnd2, and Prickle2 were significantly up-regulated. Further caused downstream neurogenesis abnormalities and neuroinflammatory activation, manifested as increased expression of IBA1 (a marker of microglia), GFAP (a marker of astrocytes), and DCX (a marker of immature neurons), as well as a range of inflammatory cytokines (e.g. TNFa, IL3, IL9, and IL17A). After Tet1 knocked down, the above indicators return to normal. CONCLUSION Activation of Wnt signaling pathway by hippocampal Tet1 is associated with cognitive dysfunction induced by IH.
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Affiliation(s)
- Yaru Kong
- Children's Hospital Capital Institute of Pediatrics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100020, China
- Graduate School of Peking Union Medical College, Beijing, 100730, China
- Department of Otolaryngology, Head and Neck Surgery, Children's Hospital Capital Institute of Paediatrics, Beijing, 100020, China
| | - Jie Ji
- Department of Otolaryngology, Head and Neck Surgery, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Xiaojun Zhan
- Department of Otolaryngology, Head and Neck Surgery, Children's Hospital Capital Institute of Paediatrics, Beijing, 100020, China
| | - Weiheng Yan
- Children's Hospital Capital Institute of Pediatrics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100020, China
- Graduate School of Peking Union Medical College, Beijing, 100730, China
- Department of Otolaryngology, Head and Neck Surgery, Children's Hospital Capital Institute of Paediatrics, Beijing, 100020, China
| | - Fan Liu
- Children's Hospital Capital Institute of Pediatrics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100020, China
- Graduate School of Peking Union Medical College, Beijing, 100730, China
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Pengfei Ye
- Department of Otolaryngology, Head and Neck Surgery, Children's Hospital Capital Institute of Paediatrics, Beijing, 100020, China
| | - Shan Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China.
| | - Jun Tai
- Children's Hospital Capital Institute of Pediatrics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100020, China.
- Department of Otolaryngology, Head and Neck Surgery, Children's Hospital Capital Institute of Paediatrics, Beijing, 100020, China.
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13
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Li Y, Fan Y, Ye S, Xu L, Wang G, Lu Y, Huang S, Zhang Y. Biomedical application of microalgal-biomaterials hybrid system. Biotechnol J 2024; 19:e2400325. [PMID: 39167555 DOI: 10.1002/biot.202400325] [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: 05/15/2024] [Revised: 07/14/2024] [Accepted: 07/16/2024] [Indexed: 08/23/2024]
Abstract
Microalgae are a group of microorganisms containing chlorophyll A, which are highly photosynthetic and rich in nutrients. And they can produce multiple bioactive substances (peptides, proteins, polysaccharides, and fatty acids) for biomedical applications. Despite the unique advantages of microalgae-based biotherapy, the insufficient treatment efficiency limits its further application. With the development of nanotechnology, the combination of microalgae and biomaterials can improve therapeutic efficacies, which has attracted increasing attention. In this microalgal-biomaterials hybrid system, biomaterials with excellent optical and magnetic properties play an important role in biological therapy. Microalgae, as a natural vehicle, can increase oxygen content and alleviate hypoxia in diseased areas, further enhancing therapeutic effects. In this review, the synergistic therapeutic effects of microalgal-biomaterials hybrid system in different diseases (cancer, myocardial infarction, ischemia stroke, chronic infection, and intestinal diseases) are comprehensively summarized.
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Affiliation(s)
- Yize Li
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, China
| | - Yali Fan
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, China
| | - Shuo Ye
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, China
| | - Lingyun Xu
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, China
| | - Gezhen Wang
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, China
| | - Yuli Lu
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, China
| | - Suxiang Huang
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, China
| | - Yingying Zhang
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, China
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14
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An HR, Kim WG, Lee YM, Sung TY, Song DE. Comparison of TERT and 5-Hydroxymethylcytocine immunohistochemistry in various thyroid carcinomas. Ann Diagn Pathol 2024; 71:152290. [PMID: 38552304 DOI: 10.1016/j.anndiagpath.2024.152290] [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: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 06/09/2024]
Abstract
Telomerase reverse transcriptase (TERT) promoter mutation is associated with an aggressive clinical course in thyroid carcinomas. Therefore, detection of TERT promoter mutation is essential for proper patient management. 5-Hydroxymethylcytosine (5hmC) is an epigenetic marker involved in the DNA demethylation pathway, and its loss has been observed in various tumors. Loss of 5hmC has also been reported in thyroid carcinomas and is presented as a possible predictive biomarker for TERT promoter mutation and worse prognosis. This study evaluated the expression of TERT and 5hmC by immunohistochemistry (IHC) in 105 patients (44 in the TERT mutant group and 61 in the TERT wild group) with various thyroid carcinomas. H-scores were calculated using an image analyzer. The median H-scores of TERT IHC were significantly higher in the TERT mutant group than in the TERT wild group (47.15 vs. 9.80). The sensitivity and specificity of TERT IHC for predicting TERT promoter mutations were 65.9 and 65.7 %, respectively. Regardless of TERT promoter mutation status, the 5hmC H-scores were markedly lower in all subtypes of thyroid carcinomas compared to those in their normal counterparts. Significant differences in 5hmC H-scores were observed between N0 and N1 in total thyroid carcinomas, but not within the papillary thyroid carcinoma subgroup. In conclusion, TERT and 5hmC IHC have limitations in predicting the presence of TERT promoter mutations. The expression of 5hmC was downregulated in various thyroid carcinomas compared to that in normal and benign lesions, but comprehensive further studies are required to elucidate the role of 5hmC in thyroid carcinomas.
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Affiliation(s)
- Hyeong Rok An
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea.
| | - Won Gu Kim
- Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea.
| | - Yu-Mi Lee
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea.
| | - Tae-Yon Sung
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea.
| | - Dong Eun Song
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea.
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15
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Kakani P, Dhamdhere SG, Pant D, Joshi R, Mishra J, Samaiya A, Shukla S. Hypoxia-induced CTCF promotes EMT in breast cancer. Cell Rep 2024; 43:114367. [PMID: 38900639 DOI: 10.1016/j.celrep.2024.114367] [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: 10/27/2022] [Revised: 05/23/2024] [Accepted: 05/31/2024] [Indexed: 06/22/2024] Open
Abstract
Cancer cells experiencing hypoxic stress employ epithelial-mesenchymal transition (EMT) to undergo metastasis through rewiring of the chromatin landscape, epigenetics, and importantly, gene expression. Here, we showed that hypoxia modulates the epigenetic landscape on CTCF promoter and upregulates its expression. Hypoxia-driven epigenetic regulation, specifically DNA demethylation mediated by TET2, is a prerequisite for CTCF induction. Mechanistically, in hypoxic conditions, Hypoxia-inducible factor 1-alpha (HIF1α) binds to the unmethylated CTCF promoter, causing transcriptional upregulation. Further, we uncover the pivotal role of CTCF in promoting EMT as loss of CTCF abrogated invasiveness of hypoxic breast cancer cells. These findings highlight the functional contribution of HIF1α-CTCF axis in promoting EMT in hypoxic breast cancer cells. Lastly, CTCF expression is alleviated and the potential for EMT is diminished when the HIF1α binding is particularly disrupted through the dCas9-DNMT3A system-mediated maintenance of DNA methylation on the CTCF promoter. This axis may offer a unique therapeutic target in breast cancer.
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Affiliation(s)
- Parik Kakani
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh 462066, India
| | - Shruti Ganesh Dhamdhere
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh 462066, India
| | - Deepak Pant
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh 462066, India
| | - Rushikesh Joshi
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh 462066, India
| | - Jharna Mishra
- Department of Pathology, Bansal Hospital, Bhopal, Madhya Pradesh 462016, India
| | - Atul Samaiya
- Department of Surgical Oncology, Bansal Hospital, Bhopal, Madhya Pradesh 462016, India
| | - Sanjeev Shukla
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh 462066, India.
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16
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Ci X, Chen S, Zhu R, Zarif M, Jain R, Guo W, Ramotar M, Gong L, Xu W, Singh O, Mansouri S, Zadeh G, Wei GH, Xu W, Bristow R, Berlin A, Koritzinsky M, van der Kwast T, He HH. Oral pimonidazole unveils clinicopathologic and epigenetic features of hypoxic tumour aggressiveness in localized prostate cancer. BMC Cancer 2024; 24:744. [PMID: 38890593 PMCID: PMC11186205 DOI: 10.1186/s12885-024-12505-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 06/11/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Tumor hypoxia is associated with prostate cancer (PCa) treatment resistance and poor prognosis. Pimonidazole (PIMO) is an investigational hypoxia probe used in clinical trials. A better understanding of the clinical significance and molecular alterations underpinning PIMO-labeled tumor hypoxia is needed for future clinical application. Here, we investigated the clinical significance and molecular alterations underpinning PIMO-labeled tumor hypoxia in patients with localized PCa, in order to apply PIMO as a prognostic tool and to identify potential biomarkers for future clinical translation. METHODS A total of 39 patients with localized PCa were recruited and administered oral PIMO before undergoing radical prostatectomy (RadP). Immunohistochemical staining for PIMO was performed on 37 prostatectomy specimens with staining patterns evaluated and clinical association analyzed. Whole genome bisulfite sequencing was performed using laser-capture of microdissected specimen sections comparing PIMO positive and negative tumor areas. A hypoxia related methylation molecular signature was generated by integrating the differentially methylated regions with previously established RNA-seq datasets. RESULTS Three PIMO staining patterns were distinguished: diffuse, focal, and comedo-like. The comedo-like staining pattern was more commonly associated with adverse pathology. PIMO-defined hypoxia intensity was positively correlated with advanced pathologic stage, tumor invasion, and cribriform and intraductal carcinoma morphology. The generated DNA methylation signature was found to be a robust hypoxia biomarker, which could risk-stratify PCa patients across multiple clinical datasets, as well as be applicable in other cancer types. CONCLUSIONS Oral PIMO unveiled clinicopathologic features of disease aggressiveness in localized PCa. The generated DNA methylation signature is a novel and robust hypoxia biomarker that has the potential for future clinical translation.
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Affiliation(s)
- Xinpei Ci
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Sujun Chen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Present Address: West China School of Public Health, West China Fourth Hospital, and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, China
| | - Rui Zhu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Mojgan Zarif
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Rahi Jain
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Wangyuan Guo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Matthew Ramotar
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Linsey Gong
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Wenjie Xu
- MOE Key Laboratory of Metabolism and Molecular Medicine and Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, and Fudan University Shanghai Cancer Center, Shanghai Medical College of Fudan University, Shanghai, China
| | - Olivia Singh
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Sheila Mansouri
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Gelareh Zadeh
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Gong-Hong Wei
- MOE Key Laboratory of Metabolism and Molecular Medicine and Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, and Fudan University Shanghai Cancer Center, Shanghai Medical College of Fudan University, Shanghai, China
| | - Wei Xu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Robert Bristow
- Division of Cancer Sciences, University of Manchester, Manchester, UK
- Christie NHS Trust and CRUK Manchester Institute and Cancer Centre, Manchester, UK
| | - Alejandro Berlin
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
| | - Marianne Koritzinsky
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada.
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada.
| | - Theodorus van der Kwast
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Division of Anatomic Pathology, Laboratory Medicine Program, University Health Network, Toronto, ON, Canada.
| | - Housheng Hansen He
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
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17
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Sekine H, Takeda H, Takeda N, Kishino A, Anzawa H, Isagawa T, Ohta N, Murakami S, Iwaki H, Kato N, Kimura S, Liu Z, Kato K, Katsuoka F, Yamamoto M, Miura F, Ito T, Takahashi M, Izumi Y, Fujita H, Yamagata H, Bamba T, Akaike T, Suzuki N, Kinoshita K, Motohashi H. PNPO-PLP axis senses prolonged hypoxia in macrophages by regulating lysosomal activity. Nat Metab 2024; 6:1108-1127. [PMID: 38822028 DOI: 10.1038/s42255-024-01053-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 04/18/2024] [Indexed: 06/02/2024]
Abstract
Oxygen is critical for all metazoan organisms on the earth and impacts various biological processes in physiological and pathological conditions. While oxygen-sensing systems inducing acute hypoxic responses, including the hypoxia-inducible factor pathway, have been identified, those operating in prolonged hypoxia remain to be elucidated. Here we show that pyridoxine 5'-phosphate oxidase (PNPO), which catalyses bioactivation of vitamin B6, serves as an oxygen sensor and regulates lysosomal activity in macrophages. Decreased PNPO activity under prolonged hypoxia reduced an active form of vitamin B6, pyridoxal 5'-phosphate (PLP), and inhibited lysosomal acidification, which in macrophages led to iron dysregulation, TET2 protein loss and delayed resolution of the inflammatory response. Among PLP-dependent metabolism, supersulfide synthesis was suppressed in prolonged hypoxia, resulting in the lysosomal inhibition and consequent proinflammatory phenotypes of macrophages. The PNPO-PLP axis creates a distinct layer of oxygen sensing that gradually shuts down PLP-dependent metabolism in response to prolonged oxygen deprivation.
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Affiliation(s)
- Hiroki Sekine
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan.
| | - Haruna Takeda
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Norihiko Takeda
- Division of Cardiology and Metabolism, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Japan
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Akihiro Kishino
- Department of Gene Expression Regulation, IDAC, Tohoku University, Sendai, Japan
| | - Hayato Anzawa
- Department of System Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, Japan
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Takayuki Isagawa
- Division of Cardiology and Metabolism, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Japan
- Data Science Center, Jichi Medical University, Shimotsuke, Japan
| | - Nao Ohta
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shohei Murakami
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hideya Iwaki
- Department of Gene Expression Regulation, IDAC, Tohoku University, Sendai, Japan
| | - Nobufumi Kato
- Department of Gene Expression Regulation, IDAC, Tohoku University, Sendai, Japan
| | - Shu Kimura
- Department of Gene Expression Regulation, IDAC, Tohoku University, Sendai, Japan
| | - Zun Liu
- Department of Gene Expression Regulation, IDAC, Tohoku University, Sendai, Japan
| | - Koichiro Kato
- Division of Oxygen Biology, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Fumiki Katsuoka
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Department of Biochemistry and Molecular Biology, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Masatomo Takahashi
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yoshihiro Izumi
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hiroyuki Fujita
- Advanced Research Laboratory, Canon Medical Systems Corporation, Otawara, Japan
| | - Hitoshi Yamagata
- Advanced Research Laboratory, Canon Medical Systems Corporation, Otawara, Japan
| | - Takeshi Bamba
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Takaaki Akaike
- Department of Environmental Medicine and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Norio Suzuki
- Division of Oxygen Biology, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kengo Kinoshita
- Department of System Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, Japan
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Laboratory, Canon Medical Systems Corporation, Otawara, Japan
| | - Hozumi Motohashi
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan.
- Department of Gene Expression Regulation, IDAC, Tohoku University, Sendai, Japan.
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18
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Venken T, Miller IS, Arijs I, Thomas V, Barat A, Betge J, Zhan T, Gaiser T, Ebert MP, O'Farrell AC, Prehn J, Klinger R, O'Connor DP, Moulton B, Murphy V, Serna G, Nuciforo PG, McDermott R, Bird B, Leonard G, Grogan L, Horgan A, Schulte N, Moehler M, Lambrechts D, Byrne AT. Analysis of cell free DNA to predict outcome to bevacizumab therapy in colorectal cancer patients. NPJ Genom Med 2024; 9:33. [PMID: 38811554 PMCID: PMC11137102 DOI: 10.1038/s41525-024-00415-x] [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: 09/22/2023] [Accepted: 05/02/2024] [Indexed: 05/31/2024] Open
Abstract
To predict outcome to combination bevacizumab (BVZ) therapy, we employed cell-free DNA (cfDNA) to determine chromosomal instability (CIN), nucleosome footprints (NF) and methylation profiles in metastatic colorectal cancer (mCRC) patients. Low-coverage whole-genome sequencing (LC-WGS) was performed on matched tumor and plasma samples, collected from 74 mCRC patients from the AC-ANGIOPREDICT Phase II trial (NCT01822444), and analysed for CIN and NFs. A validation cohort of plasma samples from the University Medical Center Mannheim (UMM) was similarly profiled. 61 AC-ANGIOPREDICT plasma samples collected before and following BVZ treatment were selected for targeted methylation sequencing. Using cfDNA CIN profiles, AC-ANGIOPREDICT samples were subtyped with 92.3% accuracy into low and high CIN clusters, with good concordance observed between matched plasma and tumor. Improved survival was observed in CIN-high patients. Plasma-based CIN clustering was validated in the UMM cohort. Methylation profiling identified differences in CIN-low vs. CIN high (AUC = 0.87). Moreover, significant methylation score decreases following BVZ was associated with improved outcome (p = 0.013). Analysis of CIN, NFs and methylation profiles from cfDNA in plasma samples facilitates stratification into CIN clusters which inform patient response to treatment.
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Affiliation(s)
- Tom Venken
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for Cancer Biology, Leuven, Belgium
| | - Ian S Miller
- Precision Cancer Medicine Group, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Ingrid Arijs
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for Cancer Biology, Leuven, Belgium
| | - Valentina Thomas
- Precision Cancer Medicine Group, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Ana Barat
- Centre for Systems Medicine, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Johannes Betge
- Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Junior Clinical Cooperation Unit Translational Gastrointestinal Oncology and Preclinical Models, German Cancer Research Center (DKFZ), Heidelberg, Germany
- DKFZ-Hector Cancer Institute at University Medical Center Mannheim, Mannheim, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Tianzuo Zhan
- Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Timo Gaiser
- Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Matthias P Ebert
- Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- DKFZ-Hector Cancer Institute at University Medical Center Mannheim, Mannheim, Germany
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Alice C O'Farrell
- Precision Cancer Medicine Group, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Jochen Prehn
- Centre for Systems Medicine, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Rut Klinger
- UCD Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Darran P O'Connor
- Department of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | | | | | - Garazi Serna
- Val d'Hebron Institute of Oncology, Barcelona, Spain
| | | | - Ray McDermott
- Cancer Trials Ireland, Dublin, Ireland
- Department of Medical Oncology, Tallaght University Hospital, Dublin, Ireland
- Department of Medical Oncology, St. Vincent's University Hospital, Dublin, Ireland
| | - Brian Bird
- Bon Secours Cork Cancer Centre, Bon Secours Hospital Cork, Cork, Ireland
| | | | - Liam Grogan
- Medical Oncology Department, Beaumont Hospital, Dublin, Ireland
| | - Anne Horgan
- Department of Medical Oncology, South East Cancer Center, University Hospital Waterford, Waterford, Ireland
| | - Nadine Schulte
- Department of Medicine II, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Markus Moehler
- Department of Medicine, Johannes-Gutenberg University Clinic, Mainz, Germany
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium.
- VIB Center for Cancer Biology, Leuven, Belgium.
| | - Annette T Byrne
- Precision Cancer Medicine Group, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland.
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19
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Soliman SHA, Iwanaszko M, Zheng B, Gold S, Howard BC, Das M, Chakrabarty RP, Chandel NS, Shilatifard A. Transcriptional elongation control of hypoxic response. Proc Natl Acad Sci U S A 2024; 121:e2321502121. [PMID: 38564636 PMCID: PMC11009653 DOI: 10.1073/pnas.2321502121] [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: 12/06/2023] [Accepted: 02/23/2024] [Indexed: 04/04/2024] Open
Abstract
The release of paused RNA polymerase II (RNAPII) from promoter-proximal regions is tightly controlled to ensure proper regulation of gene expression. The elongation factor PTEF-b is known to release paused RNAPII via phosphorylation of the RNAPII C-terminal domain by its cyclin-dependent kinase component, CDK9. However, the signal and stress-specific roles of the various RNAPII-associated macromolecular complexes containing PTEF-b/CDK9 are not yet clear. Here, we identify and characterize the CDK9 complex required for transcriptional response to hypoxia. Contrary to previous reports, our data indicate that a CDK9 complex containing BRD4 but not AFF1/4 is essential for this hypoxic stress response. We demonstrate that BRD4 bromodomains (BET) are dispensable for the release of paused RNAPII at hypoxia-activated genes and that BET inhibition by JQ1 is insufficient to impair hypoxic gene response. Mechanistically, we demonstrate that the C-terminal region of BRD4 is required for Polymerase-Associated Factor-1 Complex (PAF1C) recruitment to establish an elongation-competent RNAPII complex at hypoxia-responsive genes. PAF1C disruption using a small-molecule inhibitor (iPAF1C) impairs hypoxia-induced, BRD4-mediated RNAPII release. Together, our results provide insight into potentially targetable mechanisms that control the hypoxia-responsive transcriptional elongation.
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Affiliation(s)
- Shimaa Hassan AbdelAziz Soliman
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
| | - Marta Iwanaszko
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
| | - Bin Zheng
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
| | - Sarah Gold
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
| | - Benjamin Charles Howard
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
| | - Madhurima Das
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
| | - Ram Prosad Chakrabarty
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
- Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University, Chicago, IL60611
| | - Navdeep S. Chandel
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
- Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University, Chicago, IL60611
| | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
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20
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Meng WY, Wang ZX, Zhang Y, Hou Y, Xue JH. Epigenetic marks or not? The discovery of novel DNA modifications in eukaryotes. J Biol Chem 2024; 300:106791. [PMID: 38403247 PMCID: PMC11065753 DOI: 10.1016/j.jbc.2024.106791] [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: 10/29/2023] [Revised: 01/24/2024] [Accepted: 02/04/2024] [Indexed: 02/27/2024] Open
Abstract
DNA modifications add another layer of complexity to the eukaryotic genome to regulate gene expression, playing critical roles as epigenetic marks. In eukaryotes, the study of DNA epigenetic modifications has been confined to 5mC and its derivatives for decades. However, rapid developing approaches have witnessed the expansion of DNA modification reservoirs during the past several years, including the identification of 6mA, 5gmC, 4mC, and 4acC in diverse organisms. However, whether these DNA modifications function as epigenetic marks requires careful consideration. In this review, we try to present a panorama of all the DNA epigenetic modifications in eukaryotes, emphasizing recent breakthroughs in the identification of novel DNA modifications. The characterization of their roles in transcriptional regulation as potential epigenetic marks is summarized. More importantly, the pathways for generating or eliminating these DNA modifications, as well as the proteins involved are comprehensively dissected. Furthermore, we briefly discuss the potential challenges and perspectives, which should be taken into account while investigating novel DNA modifications.
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Affiliation(s)
- Wei-Ying Meng
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital affiliated to Tongji University, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zi-Xin Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital affiliated to Tongji University, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yunfang Zhang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yujun Hou
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.
| | - Jian-Huang Xue
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital affiliated to Tongji University, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.
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21
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Bomsztyk K, Mar D, Denisenko O, Powell S, Vishnoi M, Delegard J, Patel A, Ellenbogen RG, Ramakrishna R, Rostomily R. Analysis of gliomas DNA methylation: Assessment of pre-analytical variables. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586350. [PMID: 38586048 PMCID: PMC10996653 DOI: 10.1101/2024.03.26.586350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Precision oncology is driven by molecular biomarkers. For glioblastoma multiforme (GBM), the most common malignant adult primary brain tumor, O6-methylguanine-DNA methyltransferase ( MGMT ) gene DNA promoter methylation is an important prognostic and treatment clinical biomarker. Time consuming pre-analytical steps such as biospecimen storage before fixing, sampling, and processing are major sources of errors and batch effects, that are further confounded by intra-tumor heterogeneity of MGMT promoter methylation. To assess the effect of pre-analytical variables on GBM DNA methylation, tissue storage/sampling (CryoGrid), sample preparation multi-sonicator (PIXUL) and 5-methylcytosine (5mC) DNA immunoprecipitation (Matrix MeDIP-qPCR/seq) platforms were used. MGMT promoter CpG methylation was examined in 173 surgical samples from 90 individuals, 50 of these were used for intra-tumor heterogeneity studies. MGMT promoter methylation levels in paired frozen and formalin fixed paraffin embedded (FFPE) samples were very close, confirming suitability of FFPE for MGMT promoter methylation analysis in clinical settings. Matrix MeDIP-qPCR yielded similar results to methylation specific PCR (MS-PCR). Warm ex-vivo ischemia (37°C up to 4hrs) and 3 cycles of repeated sample thawing and freezing did not alter 5mC levels at MGMT promoter, exon and upstream enhancer regions, demonstrating the resistance of DNA methylation to the most common variations in sample processing conditions that might be encountered in research and clinical settings. 20-30% of specimens exhibited intratumor heterogeneity in the MGMT DNA promoter methylation. Collectively these data demonstrate that variations in sample fixation, ischemia duration and temperature, and DNA methylation assay technique do not have significant impact on assessment of MGMT promoter methylation status. However, intratumor methylation heterogeneity underscores the need for histologic verification and value of multiple biopsies at different GBM geographic tumor sites in assessment of MGMT promoter methylation. Matrix-MeDIP-seq analysis revealed that MGMT promoter methylation status clustered with other differentially methylated genomic loci (e.g. HOXA and lncRNAs), that are likewise resilient to variation in above post-resection pre-analytical conditions. These MGMT -associated global DNA methylation patterns offer new opportunities to validate more granular data-based epigenetic GBM clinical biomarkers where the CryoGrid-PIXUL-Matrix toolbox could prove to be useful.
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22
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Huang W, Zhang L, Sun J, Sun Y, Gong L, Ge S, Zheng Y, Gao W, Wei X. Hypoxia Reversion by Low-Immunogenic Ultra-Acid-Sensitive Comicelles of Protein-Polymer Conjugates Sensitizes Tumors to Photodynamic Therapy. J Am Chem Soc 2024; 146:7543-7554. [PMID: 38469664 DOI: 10.1021/jacs.3c13501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Hypoxia is characteristic of the tumor microenvironment, which is correlated with resistance to photodynamic therapy (PDT), radiotherapy, chemotherapy, and immunotherapy. Catalase is potentially useful to catalyze the conversion of endogenous H2O2 to O2 for hypoxia reversion. However, the efficient delivery of catalase into the hypoxia regions of tumors is a huge challenge. Here, we report the self-assembly of ultra-acid-sensitive polymer conjugates of catalase and albumin into nanomicelles that are responsive to the acidic tumor microenvironment. The immunogenicity of catalase is mitigated by the presence of albumin, which reduces the cross-linking of catalase with B cell receptors, resulting in improved pharmacokinetics. The ultra acid sensitivity of the nanomicelles makes it possible to efficiently escape the lysosomal degradation after endocytosis and permeate into the interior of tumors to reverse hypoxia in vitro and in vivo. In mice bearing triple-negative breast cancer, the nanomicelles loaded with a photosensitizer effectively accumulate and penetrate into the whole tumors to generate a sufficient amount of O2 to reverse hypoxia, leading to enhanced efficacy of PDT without detectable side effects. These findings provide a general strategy of self-assembly to design low-immunogenic ultra-acid-sensitive comicelles of protein-polymer conjugates to reverse tumor hypoxia, which sensitizes tumors to PDT.
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Affiliation(s)
- Wenchao Huang
- Institute of Medical Technology and Cancer Hospital, Peking University, Beijing 100191, China
- Institute of Advanced Clinical Medicine, Peking University, Beijing 100191, China
- Biomedical Engineering Department, Peking University, Beijing 100191, China
| | - Longshuai Zhang
- Institute of Advanced Clinical Medicine, Peking University, Beijing 100191, China
- Biomedical Engineering Department, Peking University, Beijing 100191, China
- Peking University International Cancer Institute, Beijing 100191, China
- Peking University-Yunnan Baiyao International Medical Research Center, Beijing 100191, China
| | - Jiawei Sun
- Institute of Medical Technology and Cancer Hospital, Peking University, Beijing 100191, China
- Institute of Advanced Clinical Medicine, Peking University, Beijing 100191, China
- Biomedical Engineering Department, Peking University, Beijing 100191, China
- Peking University International Cancer Institute, Beijing 100191, China
- Peking University-Yunnan Baiyao International Medical Research Center, Beijing 100191, China
| | - Yuanzi Sun
- Institute of Medical Technology and Cancer Hospital, Peking University, Beijing 100191, China
- Institute of Advanced Clinical Medicine, Peking University, Beijing 100191, China
- Biomedical Engineering Department, Peking University, Beijing 100191, China
- Peking University International Cancer Institute, Beijing 100191, China
- Peking University-Yunnan Baiyao International Medical Research Center, Beijing 100191, China
| | - Like Gong
- Institute of Medical Technology and Cancer Hospital, Peking University, Beijing 100191, China
- Institute of Advanced Clinical Medicine, Peking University, Beijing 100191, China
- Biomedical Engineering Department, Peking University, Beijing 100191, China
- Peking University International Cancer Institute, Beijing 100191, China
- Peking University-Yunnan Baiyao International Medical Research Center, Beijing 100191, China
| | - Sisi Ge
- Institute of Medical Technology and Cancer Hospital, Peking University, Beijing 100191, China
- Institute of Advanced Clinical Medicine, Peking University, Beijing 100191, China
- Biomedical Engineering Department, Peking University, Beijing 100191, China
| | - Yinghao Zheng
- Institute of Medical Technology and Cancer Hospital, Peking University, Beijing 100191, China
- Institute of Advanced Clinical Medicine, Peking University, Beijing 100191, China
- Biomedical Engineering Department, Peking University, Beijing 100191, China
| | - Weiping Gao
- Institute of Medical Technology and Cancer Hospital, Peking University, Beijing 100191, China
- Institute of Advanced Clinical Medicine, Peking University, Beijing 100191, China
- Biomedical Engineering Department, Peking University, Beijing 100191, China
- Peking University International Cancer Institute, Beijing 100191, China
- Peking University-Yunnan Baiyao International Medical Research Center, Beijing 100191, China
| | - Xunbin Wei
- Institute of Medical Technology and Cancer Hospital, Peking University, Beijing 100191, China
- Institute of Advanced Clinical Medicine, Peking University, Beijing 100191, China
- Biomedical Engineering Department, Peking University, Beijing 100191, China
- Peking University International Cancer Institute, Beijing 100191, China
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23
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Franken A, Bila M, Mechels A, Kint S, Van Dessel J, Pomella V, Vanuytven S, Philips G, Bricard O, Xiong J, Boeckx B, Hatse S, Van Brussel T, Schepers R, Van Aerde C, Geurs S, Vandecaveye V, Hauben E, Vander Poorten V, Verbandt S, Vandereyken K, Qian J, Tejpar S, Voet T, Clement PM, Lambrechts D. CD4 + T cell activation distinguishes response to anti-PD-L1+anti-CTLA4 therapy from anti-PD-L1 monotherapy. Immunity 2024; 57:541-558.e7. [PMID: 38442708 DOI: 10.1016/j.immuni.2024.02.007] [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: 12/26/2022] [Revised: 11/30/2023] [Accepted: 02/08/2024] [Indexed: 03/07/2024]
Abstract
Cancer patients often receive a combination of antibodies targeting programmed death-ligand 1 (PD-L1) and cytotoxic T lymphocyte antigen-4 (CTLA4). We conducted a window-of-opportunity study in head and neck squamous cell carcinoma (HNSCC) to examine the contribution of anti-CTLA4 to anti-PD-L1 therapy. Single-cell profiling of on- versus pre-treatment biopsies identified T cell expansion as an early response marker. In tumors, anti-PD-L1 triggered the expansion of mostly CD8+ T cells, whereas combination therapy expanded both CD4+ and CD8+ T cells. Such CD4+ T cells exhibited an activated T helper 1 (Th1) phenotype. CD4+ and CD8+ T cells co-localized with and were surrounded by dendritic cells expressing T cell homing factors or antibody-producing plasma cells. T cell receptor tracing suggests that anti-CTLA4, but not anti-PD-L1, triggers the trafficking of CD4+ naive/central-memory T cells from tumor-draining lymph nodes (tdLNs), via blood, to the tumor wherein T cells acquire a Th1 phenotype. Thus, CD4+ T cell activation and recruitment from tdLNs are hallmarks of early response to anti-PD-L1 plus anti-CTLA4 in HNSCC.
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Affiliation(s)
- Amelie Franken
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium; VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Michel Bila
- Laboratory of Experimental Oncology (LEO), Department of Oncology, KU Leuven, 3000 Leuven, Belgium; Department of General Medical Oncology, UZ Leuven, 3000 Leuven, Belgium; Department of Oral and Maxillofacial Surgery, UZ Leuven, Leuven 3000, Belgium
| | - Aurelie Mechels
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium; VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Sam Kint
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium; KU Leuven Institute for Single Cell Omics (LISCO), Leuven 3000, Belgium
| | - Jeroen Van Dessel
- Department of Oral and Maxillofacial Surgery, UZ Leuven, Leuven 3000, Belgium
| | | | - Sebastiaan Vanuytven
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium; KU Leuven Institute for Single Cell Omics (LISCO), Leuven 3000, Belgium
| | - Gino Philips
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium; VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Orian Bricard
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium; VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Jieyi Xiong
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium; VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Bram Boeckx
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium; VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Sigrid Hatse
- Laboratory of Experimental Oncology (LEO), Department of Oncology, KU Leuven, 3000 Leuven, Belgium; Department of General Medical Oncology, UZ Leuven, 3000 Leuven, Belgium
| | - Thomas Van Brussel
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium; VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Rogier Schepers
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium; VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Cedric Van Aerde
- Department of Imaging and Pathology, KU Leuven, UZ Leuven, Leuven 3000, Belgium
| | - Sarah Geurs
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium; KU Leuven Institute for Single Cell Omics (LISCO), Leuven 3000, Belgium; Department of Biomolecular Medicine, UZ Ghent, Ghent 9052, Belgium
| | | | - Esther Hauben
- Otorhinolaryngology, Head and Neck Surgery, Leuven 3000, Belgium
| | - Vincent Vander Poorten
- Otorhinolaryngology, Head and Neck Surgery, Leuven 3000, Belgium; Department of Oncology, Section Head and Neck Oncology, Leuven 3000, Belgium
| | - Sara Verbandt
- Digestive Oncology, KU Leuven, UZ Leuven, Leuven 3000, Belgium
| | - Katy Vandereyken
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium; KU Leuven Institute for Single Cell Omics (LISCO), Leuven 3000, Belgium
| | - Junbin Qian
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Sabine Tejpar
- Digestive Oncology, KU Leuven, UZ Leuven, Leuven 3000, Belgium
| | - Thierry Voet
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium; KU Leuven Institute for Single Cell Omics (LISCO), Leuven 3000, Belgium
| | - Paul M Clement
- Laboratory of Experimental Oncology (LEO), Department of Oncology, KU Leuven, 3000 Leuven, Belgium; Department of General Medical Oncology, UZ Leuven, 3000 Leuven, Belgium.
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium; VIB Center for Cancer Biology, Leuven 3000, Belgium; KU Leuven Institute for Single Cell Omics (LISCO), Leuven 3000, Belgium.
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24
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Kriukienė E, Tomkuvienė M, Klimašauskas S. 5-Hydroxymethylcytosine: the many faces of the sixth base of mammalian DNA. Chem Soc Rev 2024; 53:2264-2283. [PMID: 38205583 DOI: 10.1039/d3cs00858d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Epigenetic phenomena play a central role in cell regulatory processes and are important factors for understanding complex human disease. One of the best understood epigenetic mechanisms is DNA methylation. In the mammalian genome, cytosines (C) in CpG dinucleotides were long known to undergo methylation at the 5-position of the pyrimidine ring (mC). Later it was found that mC can be oxidized to 5-hydroxymethylcytosine (hmC) or even further to 5-formylcytosine (fC) and to 5-carboxylcytosine (caC) by the action of 2-oxoglutarate-dependent dioxygenases of the TET family. These findings unveiled a long elusive mechanism of active DNA demethylation and bolstered a wave of studies in the area of epigenetic regulation in mammals. This review is dedicated to critical assessment of recent data on biochemical and chemical aspects of the formation and conversion of hmC in DNA, analytical techniques used for detection and mapping of this nucleobase in mammalian genomes as well as epigenetic roles of hmC in DNA replication, transcription, cell differentiation and human disease.
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Affiliation(s)
- Edita Kriukienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Miglė Tomkuvienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Saulius Klimašauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
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25
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Du S, Zhou X, Zheng B. Beyond Traditional Medicine: EVs-Loaded Hydrogels as a Game Changer in Disease Therapeutics. Gels 2024; 10:162. [PMID: 38534580 DOI: 10.3390/gels10030162] [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: 12/31/2023] [Revised: 01/29/2024] [Accepted: 02/06/2024] [Indexed: 03/28/2024] Open
Abstract
Extracellular vesicles (EVs), especially exosomes, have shown great therapeutic potential in the treatment of diseases, as they can target cells or tissues. However, the therapeutic effect of EVs is limited due to the susceptibility of EVs to immune system clearance during transport in vivo. Hydrogels have become an ideal delivery platform for EVs due to their good biocompatibility and porous structure. This article reviews the preparation and application of EVs-loaded hydrogels as a cell-free therapy strategy in the treatment of diseases. The article also discusses the challenges and future outlook of EVs-loaded hydrogels.
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Affiliation(s)
- Shutong Du
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Xiaohu Zhou
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Bo Zheng
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518132, China
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26
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Zhu C, Du Y, Huai Q, Fang N, Xu W, Yang J, Li X, Zhang Y, Zhang X, Dai H, Li X, Wang H, Dai Y. The Identification of Gamma-Glutamyl Hydrolase in Uterine Corpus Endometrial Carcinoma: a Predictive Model and Machine Learning. Reprod Sci 2024; 31:532-549. [PMID: 37798609 DOI: 10.1007/s43032-023-01363-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 09/14/2023] [Indexed: 10/07/2023]
Abstract
BACKGROUND Poor neoplastic differentiation contributes to the rapid progression of uterine corpus endometrial carcinoma (UCEC). Thus, it is essential to identify candidate genes, clarifying the carcinogenesis and progression of UCEC. METHODS We screened genes that affect differentiation and prognosis in UCEC. Least absolute selection and shrinkage operator (LASSO) regression, univariate Cox, and multivariate Cox proportional risk regression analyses were performed to screen out γ-glutamyl hydrolase (GGH) as the candidate gene. The clinical value of GGH on prognosis was evaluated. The relationship between GGH and immune infiltration was assessed by CIBERSORT, EPIC, ssGSEA, unsupervised clustering and immunohistochemistry (IHC). Additionally, we investigated the effect of GGH knockdown in vitro. RESULTS Among the GGH, CDKN2A, and SIX1 genes, the impact of GGH was predominant on immune infiltration in UCEC. A nomogram containing GGH and other clinical features showed good predictive performance via curve analysis (DCA). In the functional analysis, GGH affected differentiation, tumour proliferation, and immune regulation. The immunosuppressive components were enriched in the GGH-high group, with poor immunotherapy efficacy. The study suggests that GGH may influence the progression of UCEC by regulating the glycolytic process. CONCLUSIONS GGH is closely associated with various immune cell infiltrations. Our study demonstrates the prognostic role of GGH in carcinogenesis in UCEC.
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Affiliation(s)
- Cheng Zhu
- Department of Medical Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Yishan Du
- Department of Geriatrics, Affiliated Provincial Hospital of Anhui Medical University, Hefei, 230001, China
| | - Qian Huai
- Department of Medical Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Nana Fang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, 230032, China
| | - Wentao Xu
- Department of Medical Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Jing Yang
- Department of Breast Surgery, Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, 230036, China
| | - Xingyu Li
- Department of Medical Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Yanyan Zhang
- Department of Medical Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Xu Zhang
- Department of Medical Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Hanren Dai
- Department of Medical Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Xiaolei Li
- Department of Medical Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China.
| | - Hua Wang
- Department of Medical Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China.
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, 230032, China.
| | - Ying Dai
- Department of Medical Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China.
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27
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Liu K, Xu Y. Downregulation of TET2 Contributes to Nasal Polypogenesis Through Hypoxia-Inducible Factor 1α-Mediated Epithelial-to-Mesenchymal Transition. Clin Exp Otorhinolaryngol 2024; 17:64-77. [PMID: 38228132 PMCID: PMC10933810 DOI: 10.21053/ceo.2023.01340] [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: 09/23/2023] [Revised: 12/16/2023] [Accepted: 12/28/2023] [Indexed: 01/18/2024] Open
Abstract
OBJECTIVES Hypoxia-inducible factor 1α (HIF1α) and Tet methylcytosine dioxygenase 2 (TET2) have been reported to mediate nasal polypogenesis through the epithelial-to-mesenchymal transition (EMT). Additionally, HIF1α can regulate the expression and function of TET2. However, the precise mechanism of how TET2 regulates the EMT through HIF1α mediation in nasal epithelial cells is still poorly understood. METHODS Nasal tissue samples were collected from patients with chronic rhinosinusitis (CRS) with nasal polyps (CRSwNP), CRS without nasal polyps (CRSsNP), and controls. The expression of HIF1α and TET2 was detected using Western blotting and immunohistochemistry. EMT markers (E-cadherin and vimentin) were also evaluated by immunohistochemistry. Primary human nasal epithelial cells (hNECs) were stimulated with CoCl2 to mimic hypoxia. Vitamin C (VC), a TET2 non-specific activator, and small interfering RNA (siRNA) transfection of TET2 were used to further determine the role of TET2 in hypoxia-induced EMT. Finally, reactive oxygen species (ROS) and Nrf2 were measured to explore the downstream consequences of TET2 in hypoxic hNECs. RESULTS TET2 levels were lower in the nasal epithelium of CRSwNP patients and were positively correlated with E-cadherin but negatively correlated with vimentin in CRS. However, HIF1α exhibited the opposite pattern and was negatively correlated with TET2 expression. CoCl2-simulated hypoxia led to EMT and increased HIF1α in hNECs in vitro, with simultaneous downregulation of TET2 expression. Addition of VC activated TET2 expression in hNECs, but inhibited EMT and HIF1α expression. Furthermore, siRNA knockdown of TET2 contributed to the EMT in CoCl2-simulated hNECs despite the addition of VC. Finally, TET2 regulated the EMT in hypoxic hNECs through Nrf2 expression and ROS generation. CONCLUSION TET2 was negatively correlated with HIF1α and EMT in vivo. TET2 was downregulated by HIF1α, resulting in the EMT in CoCl2-hypoxic hNECs via regulation of oxidative stress in vitro. Hence, TET2 might provide a new therapeutic approach for CRSwNP.
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Affiliation(s)
- Kunyu Liu
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
- Department of Rhinology and Allergy, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan, China
- Research Institute of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yu Xu
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
- Department of Rhinology and Allergy, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan, China
- Research Institute of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
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28
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Treadway CJ, Boyer JA, Yang S, Yang H, Liu M, Li Z, Cheng M, Marzluff WF, Ye D, Xiong Y, Baldwin AS, Zhang Q, Brown NG. Using NMR to Monitor TET-Dependent Methylcytosine Dioxygenase Activity and Regulation. ACS Chem Biol 2024; 19:15-21. [PMID: 38193366 PMCID: PMC11075173 DOI: 10.1021/acschembio.3c00619] [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] [Indexed: 01/10/2024]
Abstract
The active removal of DNA methylation marks is governed by the ten-eleven translocation (TET) family of enzymes (TET1-3), which iteratively oxidize 5-methycytosine (5mC) into 5-hydroxymethycytosine (5hmC), and then 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). TET proteins are frequently mutated in myeloid malignancies or inactivated in solid tumors. These methylcytosine dioxygenases are α-ketoglutarate (αKG)-dependent and are, therefore, sensitive to metabolic homeostasis. For example, TET2 is activated by vitamin C (VC) and inhibited by specific oncometabolites. However, understanding the regulation of the TET2 enzyme by different metabolites and its activity remains challenging because of limitations in the methods used to simultaneously monitor TET2 substrates, products, and cofactors during catalysis. Here, we measure TET2-dependent activity in real time using NMR. Additionally, we demonstrate that in vitro activity of TET2 is highly dependent on the presence of VC in our system and is potently inhibited by an intermediate metabolite of the TCA cycle, oxaloacetate (OAA). Despite these opposing effects on TET2 activity, the binding sites of VC and OAA on TET2 are shared with αKG. Overall, our work suggests that NMR can be effectively used to monitor TET2 catalysis and illustrates how TET activity is regulated by metabolic and cellular conditions at each oxidation step.
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Affiliation(s)
- Colton J. Treadway
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Joshua A Boyer
- Department. of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Shiyue Yang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Hui Yang
- Molecular & Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai College of Medicine, Fudan University, Shanghai 200032, China
- Present address: Department of Neurosurgery, Huashan Hospital, Institute for Translational Brain Research, Shanghai College of Medicine, Fudan University, Shanghai, 200032, China
| | - Mengxi Liu
- Molecular & Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai College of Medicine, Fudan University, Shanghai 200032, China
- Present address: Plexium, Inc., San Diego, CA 92121, United States
| | - Zhijun Li
- Department. of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Meng Cheng
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - William F. Marzluff
- Department. of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Dan Ye
- Molecular & Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai College of Medicine, Fudan University, Shanghai 200032, China
| | - Yue Xiong
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
- Present address: Cullgen, Inc., 12730 High Bluff Drive, San Diego, CA, 92130, United States
| | - Albert S. Baldwin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Qi Zhang
- Department. of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Nicholas G. Brown
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
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29
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Shi C, Liu X, Han SS, Tang YF, Zeng HL, Du ML, Yang Y, Jia JN, Shi Q, Hou FG. Mechanism of Preventing Recurrence of Stage II-III Colorectal Cancer Metastasis with Immuno-inflammatory and Hypoxic Microenvironment by a Four Ingredients Chinese Herbal Formula: A Bioinformatics and Network Pharmacology Analysis. Curr Pharm Des 2024; 30:2007-2026. [PMID: 38867534 DOI: 10.2174/0113816128294401240523092259] [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: 11/22/2023] [Revised: 03/21/2024] [Accepted: 04/03/2024] [Indexed: 06/14/2024]
Abstract
BACKGROUND Colorectal Cancer (CRC) is one of the top three malignancies with the highest incidence and mortality. OBJECTIVE The study aimed to identify the effect of Traditional Chinese Medicine (TCM) on postoperative patients with stage II-III CRC and explore the core herb combination and its mechanism. METHODS An observational cohort study was conducted on patients diagnosed with stage II-III CRC from January 2016 to January 2021. The primary outcome was disease-free survival, which was compared between the patients who received TCM or not, and the secondary outcome was the hazard ratio. The relevance principle was used to obtain the candidate herb combinations, and the core combination was evaluated through an assessment of efficacy and representativeness. Then, biological processes and signaling pathways associated with CRC were obtained by Gene Ontology function, Kyoto Encyclopedia of Gene and Genomes pathway, and Wikipathway. Furthermore, hub genes were screened by the Kaplan-Meier estimator, and molecular docking was employed to predict the binding sites of key ingredients to hub genes. The correlation analysis was employed for the correlations between the hub genes and tumor-infiltrating immune cells and hypoxiarelated genes. Ultimately, a quantitative polymerase chain reaction was performed to verify the regulation of hub genes by their major ingredients. RESULTS A total of 707 patients were included. TCM could decrease the metastatic recurrence associated with stage II-III CRC (HR: 0.61, log-rank P < 0.05). Among those patients in the TCM group, the core combination was Baizhu → Yinchen, Chenpi, and Fuling (C combination), and its antitumor mechanism was most likely related to the regulation of BCL2L1, XIAP, and TOP1 by its key ingredients, quercetin and tangeretin. The expression of these genes was significantly correlated with both tumor-infiltrating immune cells and hypoxia- related genes. In addition, quercetin and tangeretin down-regulated the mRNA levels of BCL2L1, XIAP, and TOP1, thereby inhibiting the growth of HCT116 cells. CONCLUSION Overall, a combination of four herbs, Baizhu → Yinchen, Chenpi, and Fuling, could reduce metastatic recurrence in postoperative patients with stage II-III CRC. The mechanism may be related to the regulation of BCL2L1, XIAP, and TOP1 by its key ingredients quercetin and tangeretin.
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Affiliation(s)
- Chuan Shi
- Oncology Department III, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, China
| | - Xing Liu
- Department of Central Laboratory Medicine, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, China
| | - Su-Su Han
- Oncology Department III, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, China
| | - Yu-Fei Tang
- Oncology Department III, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, China
| | - Hai-Lun Zeng
- Oncology Department III, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, China
| | - Mei-Lu Du
- Oncology Department III, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, China
| | - Yi Yang
- Oncology Department III, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, China
| | - Jia-Ning Jia
- Oncology Department III, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, China
| | - Qi Shi
- Oncology Department III, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, China
| | - Feng-Gang Hou
- Oncology Department III, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, China
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30
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Verdikt R, Thienpont B. Epigenetic remodelling under hypoxia. Semin Cancer Biol 2024; 98:1-10. [PMID: 38029868 DOI: 10.1016/j.semcancer.2023.10.005] [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: 08/21/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023]
Abstract
Hypoxia is intrinsic to tumours and contributes to malignancy and metastasis while hindering the efficiency of existing treatments. Epigenetic mechanisms play a crucial role in the regulation of hypoxic cancer cell programs, both in the initial phases of sensing the decrease in oxygen levels and during adaptation to chronic lack of oxygen. During the latter, the epigenetic regulation of tumour biology intersects with hypoxia-sensitive transcription factors in a complex network of gene regulation that also involves metabolic reprogramming. Here, we review the current literature on the epigenetic control of gene programs in hypoxic cancer cells. We highlight common themes and features of such epigenetic remodelling and discuss their relevance for the development of therapeutic strategies.
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Affiliation(s)
- Roxane Verdikt
- Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Department of Human Genetics, KU Leuven, Leuven, Belgium; KU Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Belgium
| | - Bernard Thienpont
- Department of Human Genetics, KU Leuven, Leuven, Belgium; KU Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Belgium; KU Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium.
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31
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Radak Z, Pan L, Zhou L, Mozaffaritabar S, Gu Y, A Pinho R, Zheng X, Ba X, Boldogh I. Epigenetic and "redoxogenetic" adaptation to physical exercise. Free Radic Biol Med 2024; 210:65-74. [PMID: 37977212 DOI: 10.1016/j.freeradbiomed.2023.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/03/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Abstract
Exercise-induced adaptation is achieved by altering the epigenetic landscape of the entire genome leading to the expression of genes involved in various processes including regulatory, metabolic, adaptive, immune, and myogenic functions. Clinical and experimental data suggest that the methylation pattern/levels of promoter/enhancer is not linearly correlated with gene expression and proteome levels during physical activity implying a level of complexity and interplay with other regulatory modulators. It has been shown that a higher level of physical fitness is associated with a slower DNA methylation-based aging clock. There is strong evidence supporting exercise-induced ROS being a key regulatory mediator through overlapping events, both as signaling entities and through oxidative modifications to various protein mediators and DNA molecules. ROS generated by physical activity shapes epigenome both directly and indirectly, a complexity we are beginning to unravel within the epigenetic arrangement. Oxidative modification of guanine to 8-oxoguanine is a non-genotoxic alteration, does not distort DNA helix and serves as an epigenetic-like mark. The reader and eraser of oxidized guanine is the 8-oxoguanine DNA glycosylase 1, contributing to changes in gene expression. In fact, it can modulate methylation patterns of promoters/enhancers consequently leading to multiple phenotypic changes. Here, we provide evidence and discuss the potential roles of exercise-induced ROS in altering cytosine methylation patterns during muscle adaptation processes.
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Affiliation(s)
- Zsolt Radak
- Research Center for Molecular Exercise Science, Hungarian University of Sport Science, 1123, Budapest, Hungary; Faculty of Sport Sciences, Waseda University, Tokorozawa, 359-1192, Japan.
| | - Lang Pan
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, TX77555, USA
| | - Lei Zhou
- Research Center for Molecular Exercise Science, Hungarian University of Sport Science, 1123, Budapest, Hungary
| | - Soroosh Mozaffaritabar
- Research Center for Molecular Exercise Science, Hungarian University of Sport Science, 1123, Budapest, Hungary
| | - Yaodong Gu
- Faculty of Sports Science, Ningbo University, Ningbo, China
| | - Ricardo A Pinho
- Laboratory of Exercise Biochemistry in Health, Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, Brazil
| | - Xu Zheng
- Key Laboratory of Molecular Epigenetics of Ministry of Education, School of Life Science, Northeast Normal University, Changchun, Jilin, China; Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, TX77555, USA
| | - Xueqing Ba
- Key Laboratory of Molecular Epigenetics of Ministry of Education, School of Life Science, Northeast Normal University, Changchun, Jilin, China; Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, TX77555, USA
| | - Istvan Boldogh
- Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, Galveston, TX77555, USA
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32
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Salmerón-Bárcenas EG, Zacapala-Gómez AE, Torres-Rojas FI, Antonio-Véjar V, Ávila-López PA, Baños-Hernández CJ, Núñez-Martínez HN, Dircio-Maldonado R, Martínez-Carrillo DN, Ortiz-Ortiz J, Jiménez-Wences H. TET Enzymes and 5hmC Levels in Carcinogenesis and Progression of Breast Cancer: Potential Therapeutic Targets. Int J Mol Sci 2023; 25:272. [PMID: 38203443 PMCID: PMC10779134 DOI: 10.3390/ijms25010272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Breast Cancer (BC) was the most common female cancer in incidence and mortality worldwide in 2020. Similarly, BC was the top female cancer in the USA in 2022. Risk factors include earlier age at menarche, oral contraceptive use, hormone replacement therapy, high body mass index, and mutations in BRCA1/2 genes, among others. BC is classified into Luminal A, Luminal B, HER2-like, and Basal-like subtypes. These BC subtypes present differences in gene expression signatures, which can impact clinical behavior, treatment response, aggressiveness, metastasis, and survival of patients. Therefore, it is necessary to understand the epigenetic molecular mechanism of transcriptional regulation in BC, such as DNA demethylation. Ten-Eleven Translocation (TET) enzymes catalyze the oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) on DNA, which in turn inhibits or promotes the gene expression. Interestingly, the expression of TET enzymes as well as the levels of the 5hmC epigenetic mark are altered in several types of human cancers, including BC. Several studies have demonstrated that TET enzymes and 5hmC play a key role in the regulation of gene expression in BC, directly (dependent or independent of DNA de-methylation) or indirectly (via interaction with other proteins such as transcription factors). In this review, we describe our recent understanding of the regulatory and physiological function of the TET enzymes, as well as their potential role as biomarkers in BC biology.
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Affiliation(s)
- Eric Genaro Salmerón-Bárcenas
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México C.P. 07360, Mexico; (E.G.S.-B.); (P.A.Á.-L.)
| | - Ana Elvira Zacapala-Gómez
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Guerrero, Chilpancingo C. P. 39090, Guerrero, Mexico; (A.E.Z.-G.); (F.I.T.-R.); (V.A.-V.); (J.O.-O.)
| | - Francisco Israel Torres-Rojas
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Guerrero, Chilpancingo C. P. 39090, Guerrero, Mexico; (A.E.Z.-G.); (F.I.T.-R.); (V.A.-V.); (J.O.-O.)
| | - Verónica Antonio-Véjar
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Guerrero, Chilpancingo C. P. 39090, Guerrero, Mexico; (A.E.Z.-G.); (F.I.T.-R.); (V.A.-V.); (J.O.-O.)
| | - Pedro Antonio Ávila-López
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México C.P. 07360, Mexico; (E.G.S.-B.); (P.A.Á.-L.)
| | - Christian Johana Baños-Hernández
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara C. P. 44340, Jalisco, Mexico;
| | - Hober Nelson Núñez-Martínez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México C. P. 04510, Mexico;
| | - Roberto Dircio-Maldonado
- Laboratorio de Investigación Clínica, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Guerrero, Chilpancingo C. P. 39090, Guerrero, Mexico; (R.D.-M.); (D.N.M.-C.)
| | - Dinorah Nashely Martínez-Carrillo
- Laboratorio de Investigación Clínica, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Guerrero, Chilpancingo C. P. 39090, Guerrero, Mexico; (R.D.-M.); (D.N.M.-C.)
- Laboratorio de Investigación en Biomoléculas, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Guerrero, Chilpancingo C. P. 39090, Guerrero, Mexico
| | - Julio Ortiz-Ortiz
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Guerrero, Chilpancingo C. P. 39090, Guerrero, Mexico; (A.E.Z.-G.); (F.I.T.-R.); (V.A.-V.); (J.O.-O.)
| | - Hilda Jiménez-Wences
- Laboratorio de Investigación Clínica, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Guerrero, Chilpancingo C. P. 39090, Guerrero, Mexico; (R.D.-M.); (D.N.M.-C.)
- Laboratorio de Investigación en Biomoléculas, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Guerrero, Chilpancingo C. P. 39090, Guerrero, Mexico
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Helm M, Bohnsack MT, Carell T, Dalpke A, Entian KD, Ehrenhofer-Murray A, Ficner R, Hammann C, Höbartner C, Jäschke A, Jeltsch A, Kaiser S, Klassen R, Leidel SA, Marx A, Mörl M, Meier JC, Meister G, Rentmeister A, Rodnina M, Roignant JY, Schaffrath R, Stadler P, Stafforst T. Experience with German Research Consortia in the Field of Chemical Biology of Native Nucleic Acid Modifications. ACS Chem Biol 2023; 18:2441-2449. [PMID: 37962075 DOI: 10.1021/acschembio.3c00586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The chemical biology of native nucleic acid modifications has seen an intense upswing, first concerning DNA modifications in the field of epigenetics and then concerning RNA modifications in a field that was correspondingly rebaptized epitranscriptomics by analogy. The German Research Foundation (DFG) has funded several consortia with a scientific focus in these fields, strengthening the traditionally well-developed nucleic acid chemistry community and inciting it to team up with colleagues from the life sciences and data science to tackle interdisciplinary challenges. This Perspective focuses on the genesis, scientific outcome, and downstream impact of the DFG priority program SPP1784 and offers insight into how it fecundated further consortia in the field. Pertinent research was funded from mid-2015 to 2022, including an extension related to the coronavirus pandemic. Despite being a detriment to research activity in general, the pandemic has resulted in tremendously boosted interest in the field of RNA and RNA modifications as a consequence of their widespread and successful use in vaccination campaigns against SARS-CoV-2. Funded principal investigators published over 250 pertinent papers with a very substantial impact on the field. The program also helped to redirect numerous laboratories toward this dynamic field. Finally, SPP1784 spawned initiatives for several funded consortia that continue to drive the fields of nucleic acid modification.
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Affiliation(s)
- Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Thomas Carell
- Department of Chemistry, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Alexander Dalpke
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Karl-Dieter Entian
- Institute for Molecular Biosciences, Goethe-University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | | | - Ralf Ficner
- Institute for Microbiology and Genetics, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Christian Hammann
- Department of Medicine, HMU Health and Medical University, 14471 Potsdam, Germany
| | - Claudia Höbartner
- Institute for Organic Chemistry, Julius-Maximilians-University of Würzburg, 97074 Würzburg, Germany
| | - Andres Jäschke
- Institute for Pharmacy and Molecular Biotechnology, Ruprecht-Karls-University Heidelberg, 69120 Heidelberg, Germany
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Stefanie Kaiser
- Institute for Pharmaceutical Chemistry, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Roland Klassen
- Institute for Biology - Microbiology, University of Kassel, 34132 Kassel, Germany
| | - Sebastian A Leidel
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Andreas Marx
- Department of Chemistry - Organic/Cellular Chemistry, University of Constance, 78457 Constance, Germany
| | - Mario Mörl
- Institute of Biochemistry, University of Leipzig, 04103 Leipzig, Germany
| | - Jochen C Meier
- Department of Cell Physiology, Technical University of Braunschweig, 38106 Brunswick, Germany
| | - Gunter Meister
- Institute of Biochemistry, Genetics and Microbiology - Biochemistry I, University of Regensburg, 93053 Regensburg, Germany
| | - Andrea Rentmeister
- Institute for Biochemistry, Westphalian Wilhelms University Münster, 48149 Münster, Germany
| | - Marina Rodnina
- Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Jean-Yves Roignant
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
- Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Raffael Schaffrath
- Institute for Biology - Microbiology, University of Kassel, 34132 Kassel, Germany
| | - Peter Stadler
- Institute for Computer Science - Bioinformatics, University of Leipzig, 04107 Leipzig, Germany
| | - Thorsten Stafforst
- Interfaculty Institute for Biochemistry, Eberhard Karls University Tübingen, 72074 Tübingen, Germany
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Levallet J, Biojout T, Bazille C, Douyère M, Dubois F, Ferreira DL, Taylor J, Teulier S, Toutain J, Elie N, Bernaudin M, Valable S, Bergot E, Levallet G. Hypoxia-induced activation of NDR2 underlies brain metastases from Non-Small Cell Lung Cancer. Cell Death Dis 2023; 14:823. [PMID: 38092743 PMCID: PMC10719310 DOI: 10.1038/s41419-023-06345-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/12/2023] [Accepted: 11/27/2023] [Indexed: 12/17/2023]
Abstract
The molecular mechanisms induced by hypoxia are misunderstood in non-small cell lung cancer (NSCLC), and above all the hypoxia and RASSF1A/Hippo signaling relationship. We confirmed that human NSCLC (n = 45) as their brain metastases (BM) counterpart are hypoxic since positive with CAIX-antibody (target gene of Hypoxia-inducible factor (HIF)). A severe and prolonged hypoxia (0.2% O2, 48 h) activated YAP (but not TAZ) in Human Bronchial Epithelial Cells (HBEC) lines by downregulating RASSF1A/kinases Hippo (except for NDR2) regardless their promoter methylation status. Subsequently, the NDR2-overactived HBEC cells exacerbated a HIF-1A, YAP and C-Jun-dependent-amoeboid migration, and mainly, support BM formation. Indeed, NDR2 is more expressed in human tumor of metastatic NSCLC than in human localized NSCLC while NDR2 silencing in HBEC lines (by shRNA) prevented the xenograft formation and growth in a lung cancer-derived BM model in mice. Collectively, our results indicated that NDR2 kinase is over-active in NSCLC by hypoxia and supports BM formation. NDR2 expression is thus a useful biomarker to predict the metastases risk in patients with NSCLC, easily measurable routinely by immunohistochemistry on tumor specimens.
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Affiliation(s)
- Jérôme Levallet
- Université de Caen Normandie, CNRS, Normandie Université, ISTCT UMR6030, GIP CYCERON, Caen, F-14074, France
| | - Tiphaine Biojout
- Université de Caen Normandie, CNRS, Normandie Université, ISTCT UMR6030, GIP CYCERON, Caen, F-14074, France
| | - Céline Bazille
- Université de Caen Normandie, CNRS, Normandie Université, ISTCT UMR6030, GIP CYCERON, Caen, F-14074, France
- Department of Pathology, CHU de Caen, Caen, F-14000, France
| | - Manon Douyère
- Université de Caen Normandie, CNRS, Normandie Université, ISTCT UMR6030, GIP CYCERON, Caen, F-14074, France
| | - Fatéméh Dubois
- Université de Caen Normandie, CNRS, Normandie Université, ISTCT UMR6030, GIP CYCERON, Caen, F-14074, France
- Department of Pathology, CHU de Caen, Caen, F-14000, France
- Structure Fédérative D'oncogénétique cyto-MOléculaire du CHU de Caen (SF-MOCAE), CHU de Caen, Caen, F-14000, France
| | - Dimitri Leite Ferreira
- Université de Caen Normandie, CNRS, Normandie Université, ISTCT UMR6030, GIP CYCERON, Caen, F-14074, France
- Department of Pulmonology & Thoracic Oncology, CHU de Caen, Caen, F-14000, France
| | - Jasmine Taylor
- Université de Caen Normandie, CNRS, Normandie Université, ISTCT UMR6030, GIP CYCERON, Caen, F-14074, France
| | - Sylvain Teulier
- Université de Caen Normandie, CNRS, Normandie Université, ISTCT UMR6030, GIP CYCERON, Caen, F-14074, France
- Department of Pulmonology & Thoracic Oncology, CHU de Caen, Caen, F-14000, France
| | - Jérôme Toutain
- CNRS, Université de Caen Normandie, Normandie Université, ISTCT UMR6030, GIP CYCERON, Caen, F-14074, France
| | - Nicolas Elie
- Normandie Univ, UNICAEN, Federative Structure 4207 "Normandie Oncologie", Service Unit PLATON, Virtual'His platform, Caen, France; Normandie Univ, UNICAEN, Service Unit EMERODE, Centre de Microscopie Appliquée à la Biologie, CMABio³, Caen, France
| | - Myriam Bernaudin
- CNRS, Université de Caen Normandie, Normandie Université, ISTCT UMR6030, GIP CYCERON, Caen, F-14074, France
| | - Samuel Valable
- CNRS, Université de Caen Normandie, Normandie Université, ISTCT UMR6030, GIP CYCERON, Caen, F-14074, France
| | - Emmanuel Bergot
- Université de Caen Normandie, CNRS, Normandie Université, ISTCT UMR6030, GIP CYCERON, Caen, F-14074, France
- Department of Pulmonology & Thoracic Oncology, CHU de Caen, Caen, F-14000, France
| | - Guénaëlle Levallet
- Université de Caen Normandie, CNRS, Normandie Université, ISTCT UMR6030, GIP CYCERON, Caen, F-14074, France.
- Department of Pathology, CHU de Caen, Caen, F-14000, France.
- Structure Fédérative D'oncogénétique cyto-MOléculaire du CHU de Caen (SF-MOCAE), CHU de Caen, Caen, F-14000, France.
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Mens DM, van Rees JM, Wilting SM, Verhoef C. Can we use a simple blood test to reduce unnecessary adverse effects from radiotherapy by timely identification of radiotherapy-resistant rectal cancers? MeD-Seq rectal study protocol. BMC Cancer 2023; 23:1187. [PMID: 38049783 PMCID: PMC10696698 DOI: 10.1186/s12885-023-11671-y] [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: 10/19/2023] [Accepted: 11/23/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Chemoradiation therapy (CRT) followed by surgery is currently the standard of care to treat patients with locally advanced rectal cancer (LARC). CRT reduces local recurrences, but is associated with significant damage to the surrounding healthy tissue that can severely impact patients quality of life. Additionally, a proportion of patients (hardly) benefit from CRT. We aim to develop a diagnostic innovation, using DNA-methylation, which can enable a more selective and thereby more effective use of the available therapies for rectal cancer patients. METHODS MeD-Seq Rectal is a prospective single centre, observational study. 75 patients diagnosed with rectal cancer and will receive CRT as neoadjuvant treatment are will be included. DNA-methylation profiling will be performed on liquid biopsies to predict pathological response to CRT. DISCUSSION To data no clinical or image-based features were found that predict response to CRT. we hypothesize that DNA methylation patterns in liquid biopsies may provide a promising and patient-friendly strategy to predict CRT resistance upfront. TRIAL REGISTRATION This trial is registered at ClinicalTrials.gov (NCT06035471).
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Affiliation(s)
- D M Mens
- Erasmus MC University Medical Center, Rotterdam, Netherlands.
| | - J M van Rees
- Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - S M Wilting
- Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - C Verhoef
- Erasmus MC University Medical Center, Rotterdam, Netherlands
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Qin W, Jiang M, Lu S, Hu Y, Gan F, Fang W, Chen D, Bo Z. Effects of external environment on promoter methylation of PIK3R5 and related pathway regulation in steroid-induced femoral head necrosis. ENVIRONMENTAL RESEARCH 2023; 238:117116. [PMID: 37709244 DOI: 10.1016/j.envres.2023.117116] [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: 07/20/2023] [Revised: 09/03/2023] [Accepted: 09/09/2023] [Indexed: 09/16/2023]
Abstract
BACKGROUND Steroid-induced Avascular Necrosis of the Femoral Head (SANFH) is a condition characterized by the necrosis of the femoral head caused by long-term or high-dose hormone usage. Studies have shown that the PI3K/AKT pathway plays a crucial regulatory role in the development of SANFH. The aim of this study is to determine how external environmental factors induce changes in endogenous hormone levels, how these changes lead to steroid-induced femoral head necrosis, and the interrelationship between the changes in PIK3R5 promoter methylation levels and the regulation of the associated signaling pathways. METHODS Femoral head samples underwent molecular sequencing analysis. Candidate genes were screened by differential gene analysis and functional enrichment analysis.Methylation level of candidate gene PIK3R5 was verified by methylation-specific PCR(MS-PCR). SANFH model was constructed in New Zealand white rabbits, and the model results were verified by magnetic resonance imaging (MRI) and haematoxylin-eosin (HE) staining.The expression of PIK3R5, PI3K and AKT in rabbit models and human specimens was verified by real-time fluorescence quantitative PCR(RT-qPCR) and Western Blot(WB), respectively. RESULTS Human femoral head sequencing results indicate distinct differences in the methylation level and mRNA expression of PIK3R5 in SANFH. MS-PCR results showed the methylation level of SANFH patients was significantly higher than that of the control group (P < 0.01). The RT-qPCR results showed that PIK3R5 and PI3K expression levels in the SANFH group were lower than those in the control group (P < 0.05), and the WB experiment results were consistent with the RT-qPCR results. The MRI and HE staining results showed that the rabbit model of SANFH was successfully constructed, and the results of RT-qPCR and WB were consistent with the results of human tissues. CONCLUSION During the occurrence and development of SANFH, PIK3R5 gene regulates the PI3K/AKT pathway through methylation modification, promotes the oxidative stress response of cells, and accelerates the disease process.
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Affiliation(s)
- Wentao Qin
- Department of Bone and Joint Surgery, Guangxi Medical University First Affiliated Hospital, Nanning, China
| | - Mingyang Jiang
- Department of Bone and Joint Surgery, Guangxi Medical University First Affiliated Hospital, Nanning, China
| | - Shenyi Lu
- Department of Rehabilitation, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Yang Hu
- Department of Bone and Joint Surgery, Guangxi Medical University First Affiliated Hospital, Nanning, China; Department of Sports Medicine and Joint Surgery, Nanxishan Hospital of Guangxi Zhuang Autonomous Region, Guilin, China
| | - Fu Gan
- Department of Rehabilitation, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Weijun Fang
- Department of Emergency, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.
| | - Dongxu Chen
- Department of Sports Medicine and Joint Surgery, Nanxishan Hospital of Guangxi Zhuang Autonomous Region, Guilin, China.
| | - Zhandong Bo
- Department of Bone and Joint Surgery, Guangxi Medical University First Affiliated Hospital, Nanning, China.
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Schito L, Rey-Keim S. Hypoxia signaling and metastatic progression. Semin Cancer Biol 2023; 97:42-49. [PMID: 37926346 DOI: 10.1016/j.semcancer.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/07/2023]
Abstract
Disruption of oxygen homeostasis, resulting from an imbalance between O2 supply and demand during malignant proliferation, leads to the development of hypoxic tumor microenvironments that promote the acquisition of aggressive cancer cell phenotypes linked to metastasis and patient mortality. In this review, the mechanistic links between tumor hypoxia and metastatic progression are presented. Current status and perspectives of targeting hypoxia signaling pathways as a strategy to halt cancer cell metastatic activities are emphasized.
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Affiliation(s)
- Luana Schito
- UCD School of Medicine, Belfield, Dublin D04 C7X2, Ireland; UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin D04 C7X2, Ireland.
| | - Sergio Rey-Keim
- UCD School of Medicine, Belfield, Dublin D04 C7X2, Ireland; UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin D04 C7X2, Ireland.
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Chen Y, Xu J, Liu X, Guo L, Yi P, Cheng C. Potential therapies targeting nuclear metabolic regulation in cancer. MedComm (Beijing) 2023; 4:e421. [PMID: 38034101 PMCID: PMC10685089 DOI: 10.1002/mco2.421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/28/2023] [Accepted: 10/12/2023] [Indexed: 12/02/2023] Open
Abstract
The interplay between genetic alterations and metabolic dysregulation is increasingly recognized as a pivotal axis in cancer pathogenesis. Both elements are mutually reinforcing, thereby expediting the ontogeny and progression of malignant neoplasms. Intriguingly, recent findings have highlighted the translocation of metabolites and metabolic enzymes from the cytoplasm into the nuclear compartment, where they appear to be intimately associated with tumor cell proliferation. Despite these advancements, significant gaps persist in our understanding of their specific roles within the nuclear milieu, their modulatory effects on gene transcription and cellular proliferation, and the intricacies of their coordination with the genomic landscape. In this comprehensive review, we endeavor to elucidate the regulatory landscape of metabolic signaling within the nuclear domain, namely nuclear metabolic signaling involving metabolites and metabolic enzymes. We explore the roles and molecular mechanisms through which metabolic flux and enzymatic activity impact critical nuclear processes, including epigenetic modulation, DNA damage repair, and gene expression regulation. In conclusion, we underscore the paramount significance of nuclear metabolic signaling in cancer biology and enumerate potential therapeutic targets, associated pharmacological interventions, and implications for clinical applications. Importantly, these emergent findings not only augment our conceptual understanding of tumoral metabolism but also herald the potential for innovative therapeutic paradigms targeting the metabolism-genome transcriptional axis.
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Affiliation(s)
- Yanjie Chen
- Department of Obstetrics and GynecologyThe Third Affiliated Hospital of Chongqing Medical UniversityChongqingChina
| | - Jie Xu
- Department of Obstetrics and GynecologyThe Third Affiliated Hospital of Chongqing Medical UniversityChongqingChina
| | - Xiaoyi Liu
- Department of Obstetrics and GynecologyThe Third Affiliated Hospital of Chongqing Medical UniversityChongqingChina
| | - Linlin Guo
- Department of Microbiology and ImmunologyThe Indiana University School of MedicineIndianapolisIndianaUSA
| | - Ping Yi
- Department of Obstetrics and GynecologyThe Third Affiliated Hospital of Chongqing Medical UniversityChongqingChina
| | - Chunming Cheng
- Department of Radiation OncologyJames Comprehensive Cancer Center and College of Medicine at The Ohio State UniversityColumbusOhioUSA
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Lee SCES, Pyo AHA, Koritzinsky M. Longitudinal dynamics of the tumor hypoxia response: From enzyme activity to biological phenotype. SCIENCE ADVANCES 2023; 9:eadj6409. [PMID: 37992163 PMCID: PMC10664991 DOI: 10.1126/sciadv.adj6409] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/23/2023] [Indexed: 11/24/2023]
Abstract
Poor oxygenation (hypoxia) is a common spatially heterogeneous feature of human tumors. Biological responses to tumor hypoxia are orchestrated by the decreased activity of oxygen-dependent enzymes. The affinity of these enzymes for oxygen positions them along a continuum of oxygen sensing that defines their roles in launching reactive and adaptive cellular responses. These responses encompass regulation of all steps in the central dogma, with rapid perturbation of the metabolome and proteome followed by more persistent reprogramming of the transcriptome and epigenome. Core hypoxia response genes and pathways are commonly regulated at multiple inflection points, fine-tuning the dependencies on oxygen concentration and hypoxia duration. Ultimately, shifts in the activity of oxygen-sensing enzymes directly or indirectly endow cells with intrinsic hypoxia tolerance and drive processes that are associated with aggressive phenotypes in cancer including angiogenesis, migration, invasion, immune evasion, epithelial mesenchymal transition, and stemness.
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Affiliation(s)
- Sandy Che-Eun S. Lee
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Andrea Hye An Pyo
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Marianne Koritzinsky
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
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40
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Yan M, Cao H, Tao K, Xiao B, Chu Y, Ma D, Huang X, Han Y, Ji T. HDACs alters negatively to the tumor immune microenvironment in gynecologic cancers. Gene 2023; 885:147704. [PMID: 37572797 DOI: 10.1016/j.gene.2023.147704] [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: 03/25/2023] [Revised: 08/03/2023] [Accepted: 08/09/2023] [Indexed: 08/14/2023]
Abstract
The role of histone deacetylases (HDACs) in the tumor immune microenvironment of gynecologic tumors remains unexplored. We integrated data from The Cancer Genome Atlas and Human Protein Atlas to examine HDAC expression in breast, cervical, ovarian, and endometrial cancers. Elevated HDAC expression correlated with poor prognosis and highly malignant cancer subtypes. Gene Set Enrichment Analysis revealed positive associations between HDAC expression and tumor proliferation signature, while negative associations were found with tumor inflammation signature. Increased HDAC expression was linked to reduced infiltration of natural killer (NK), NKT, and CD8+ T cells, along with negative associations with the expression of PSMB10, NKG7, CCL5, CD27, HLA-DQA1, and HLA-DQB1. In a murine 4T1 breast cancer model, treatment with suberoylanilide hydroxamic acid (SAHA; HDAC inhibitor) and PD-1 antibody significantly inhibited tumor growth and infiltration of CD3+ and CD8+ T cells. Real-time polymerase chain reaction revealed upregulated expressions of Psmb10, Nkg7, Ccl5, Cd8a, Cxcr6, and Cxcl9 genes, while Ctnnb1 and Myc genes were inhibited, indicating tumor suppression and immune microenvironment activation. Our study revealed that HDACs play tumor-promoting and immunosuppressive roles in gynecologic cancers, suggesting HDAC inhibitors as potential therapeutic agents for these cancers.
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Affiliation(s)
- Miao Yan
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Heng Cao
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kangjia Tao
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bing Xiao
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yifan Chu
- National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ding Ma
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyuan Huang
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yingyan Han
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Teng Ji
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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Duan H, Wang F, Xu W, Sheng G, Sun Z, Chu H. Recent advances in the nanoarchitectonics of metal-organic frameworks for light-activated tumor therapy. Dalton Trans 2023; 52:16085-16102. [PMID: 37814810 DOI: 10.1039/d3dt02725b] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Metal-organic frameworks (MOFs) have received extensive attention in tumor therapy because of their advantages, including large specific surface area, regular pore size, adjustable shape, and facile functionalization. MOFs are porous materials formed by the coordination bonding of metal clusters and organic ligands. This review summarized the most recent advancements in tumor treatment based on nMOFs. First, we discuss the classification of MOFs, which primarily include the series of isoreticular MOF (IRMOF), zeolitic imidazolate framework (ZIF), coordination pillared-layer (CPL), Materials of Institute Lavoisier (MIL), porous coordination network (PCN), University of Oslo (UiO) and Biological metal-organic frameworks (BioMOFs). Then, we discuss the use of nMOFs in antitumor therapy, including drug delivery strategies, photodynamic therapy (PDT), photothermal therapy (PTT), and combination therapy. Finally, the obstacles and opportunities in nMOFs are discussed.
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Affiliation(s)
- Huijuan Duan
- Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China.
- Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Fang Wang
- Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China.
- Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Weizhe Xu
- Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China.
- Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Gang Sheng
- Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China.
- Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Zhaogang Sun
- Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China.
- Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Hongqian Chu
- Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China.
- Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
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Cheng KCL, Frost JM, Sánchez-Luque FJ, García-Canãdas M, Taylor D, Yang WR, Irayanar B, Sampath S, Patani H, Agger K, Helin K, Ficz G, Burns KH, Ewing A, García-Pérez JL, Branco MR. Vitamin C activates young LINE-1 elements in mouse embryonic stem cells via H3K9me3 demethylation. Epigenetics Chromatin 2023; 16:39. [PMID: 37845773 PMCID: PMC10578016 DOI: 10.1186/s13072-023-00514-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/06/2023] [Indexed: 10/18/2023] Open
Abstract
BACKGROUND Vitamin C (vitC) enhances the activity of 2-oxoglutarate-dependent dioxygenases, including TET enzymes, which catalyse DNA demethylation, and Jumonji-domain histone demethylases. The epigenetic remodelling promoted by vitC improves the efficiency of induced pluripotent stem cell derivation, and is required to attain a ground-state of pluripotency in embryonic stem cells (ESCs) that closely mimics the inner cell mass of the early blastocyst. However, genome-wide DNA and histone demethylation can lead to upregulation of transposable elements (TEs), and it is not known how vitC addition in culture media affects TE expression in pluripotent stem cells. RESULTS Here we show that vitC increases the expression of several TE families, including evolutionarily young LINE-1 (L1) elements, in mouse ESCs. We find that TET activity is dispensable for L1 upregulation, and that instead it occurs largely as a result of H3K9me3 loss mediated by KDM4A/C histone demethylases. Despite increased L1 levels, we did not detect increased somatic insertion rates in vitC-treated cells. Notably, treatment of human ESCs with vitC also increases L1 protein levels, albeit through a distinct, post-transcriptional mechanism. CONCLUSION VitC directly modulates the expression of mouse L1s and other TEs through epigenetic mechanisms, with potential for downstream effects related to the multiple emerging roles of L1s in cellular function.
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Affiliation(s)
- Kevin C L Cheng
- Blizard Institute, Faculty of Medicine and Dentistry, QMUL, London, E1 2AT, UK
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Jennifer M Frost
- Blizard Institute, Faculty of Medicine and Dentistry, QMUL, London, E1 2AT, UK
| | - Francisco J Sánchez-Luque
- Institute of Parasitology and Biomedicine "Lopez-Neyra" (IPBLN), Spanish National Research Council (CSIC), PTS Granada, Granada, Spain
| | - Marta García-Canãdas
- Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research (GENYO), PTS Granada, Granada, Spain
| | - Darren Taylor
- Blizard Institute, Faculty of Medicine and Dentistry, QMUL, London, E1 2AT, UK
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Wan R Yang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Branavy Irayanar
- Blizard Institute, Faculty of Medicine and Dentistry, QMUL, London, E1 2AT, UK
| | - Swetha Sampath
- Blizard Institute, Faculty of Medicine and Dentistry, QMUL, London, E1 2AT, UK
| | - Hemalvi Patani
- Barts Cancer Institute, Faculty of Medicine and Dentistry, QMUL, London, EC1M 6BQ, UK
| | - Karl Agger
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark
| | - Kristian Helin
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark
- The Institute of Cancer Research, London, UK
| | - Gabriella Ficz
- Barts Cancer Institute, Faculty of Medicine and Dentistry, QMUL, London, EC1M 6BQ, UK
| | - Kathleen H Burns
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Adam Ewing
- Mater Research Institute, University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - José L García-Pérez
- Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research (GENYO), PTS Granada, Granada, Spain
| | - Miguel R Branco
- Blizard Institute, Faculty of Medicine and Dentistry, QMUL, London, E1 2AT, UK.
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Shi P, Sun X, Yuan H, Chen K, Bi S, Zhang S. Nanoscale Metal-Organic Frameworks Combined with Metal Nanoparticles and Metal Oxide/Peroxide to Relieve Tumor Hypoxia for Enhanced Photodynamic Therapy. ACS Biomater Sci Eng 2023; 9:5441-5456. [PMID: 37729521 DOI: 10.1021/acsbiomaterials.3c00509] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Photodynamic therapy (PDT) is a clinically approved noninvasive tumor therapy that can selectively kill malignant tumor cells, with promising use in the treatment of various cancers. PDT is typically composed of three important parts: the specific wavelength of light, photosensitizer (PS), and oxygen. With the progressing investigation on PDT treatment, the most recent attention has focused on improving photodynamic efficiency. Tumor hypoxia has always been a critical factor hindering the efficacy of PDT. Nanoscale metal-organic frameworks (nMOF), the fourth generation of PS, present great potential in photodynamic therapy. In particular, nMOF combined with metal nanoparticles and metal oxide/peroxide has demonstrated unique properties for enhanced PDT. The metal and metal oxide nanoparticles can catalyze H2O2 to generate oxygen or automatically produces oxygen, alleviating the hypoxia and improving the photodynamic efficiency. Metal peroxide nanoparticles can spontaneously produce oxygen in water or under acidic conditions. Therefore, this Review summarizes the recent development of nMOF combined with metal nanoparticles (platinum nanoparticles and gold nanoparticles) and metal oxide/peroxide (manganese dioxide, ferric oxide, cerium oxide, calcium peroxide, and magnesium peroxide) for enhanced photodynamic therapy by alleviating tumor hypoxia. Finally, future perspectives of nMOF combined nanomaterials in PDT are put forward.
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Affiliation(s)
- Pengfei Shi
- College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, Shandong 266071, China
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, School of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, Shandong, People's Republic of China
| | - Xinran Sun
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, School of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, Shandong, People's Republic of China
| | - Haoming Yuan
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, School of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, Shandong, People's Republic of China
| | - Kaixiu Chen
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, School of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, Shandong, People's Republic of China
| | - Sai Bi
- College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, Shandong 266071, China
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, School of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, Shandong, People's Republic of China
| | - Shusheng Zhang
- College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, Shandong 266071, China
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, School of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, Shandong, People's Republic of China
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Lu X, Wang X, Gao S, Chen Z, Bai R, Wang Y. Bioparameter-directed nanoformulations as MRI CAs enable the specific visualization of hypoxic tumour. Analyst 2023; 148:4967-4981. [PMID: 37724375 DOI: 10.1039/d3an00972f] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
Abstract
A malignant tumour has hypoxic cells of varying degrees. The more severe the hypoxic degree, the more difficult the prognosis of the tumour and the higher the recurrence rate. Therefore, tumour hypoxia imaging is crucial. Magnetic resonance imaging (MRI) shows its strength in high resolution, depth of penetration and noninvasiveness. However, it needs more excellent contrast agents (CAs) to combat the complex tumour microenvironment (TME) and increased targeting of tumours to enhance clinical safety. Many research studies have focused on developing hypoxia-responsive MRI CAs that take advantage of the unique characteristics of hypoxic tumours. The low oxygen pressure, acidic TME, and up-regulated redox molecule levels found in hypoxic tumours serve as biological stimuli for nanoformulations that can accurately image the hypoxic region. This review highlights the importance of developing bioparameter-directed nanoformulations as MRI CAs for accurate tumour diagnosis. The design strategies and mechanisms of tumour-hypoxia imaging with nanoformulations are exemplified, with a focus on pH-responsiveness, redox-responsiveness, and p(O2)-responsiveness. The promising future of bioparameter-responsive nanoformulations for accurate tumour diagnosis and personalised cancer treatment is discussed.
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Affiliation(s)
- Xinyi Lu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, P. R. China.
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Xin Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, P. R. China.
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Susu Gao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, P. R. China.
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Ziwei Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, P. R. China.
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Ru Bai
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, P. R. China.
| | - Yaling Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, P. R. China.
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Zhang T, Pan Y, Suo M, Lyu M, Lam JWY, Jin Z, Ning S, Tang BZ. Photothermal-Triggered Sulfur Oxide Gas Therapy Augments Type I Photodynamic Therapy for Potentiating Cancer Stem Cell Ablation and Inhibiting Radioresistant Tumor Recurrence. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2304042. [PMID: 37559173 PMCID: PMC10582409 DOI: 10.1002/advs.202304042] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Indexed: 08/11/2023]
Abstract
Despite advances in cancer therapy, the existence of self-renewing cancer stem cells (CSC) can lead to tumor recurrence and radiation resistance, resulting in treatment failure and high mortality in patients. To address this issue, a near-infrared (NIR) laser-induced synergistic therapeutic platform has been developed by incorporating aggregation-induced emission (AIE)-active phototheranostic agents and sulfur dioxide (SO2 ) prodrug into a biocompatible hydrogel, namely TBH, to suppress malignant CSC growth. Outstanding hydroxyl radical (·OH) generation and photothermal effect of the AIE phototheranostic agent actualizes Type I photodynamic therapy (PDT) and photothermal therapy through 660 nm NIR laser irradiation. Meanwhile, a large amount of SO2 is released from the SO2 prodrug in thermo-sensitive TBH gel, which depletes upregulated glutathione in CSC and consequentially promotes ·OH generation for PDT enhancement. Thus, the resulting TBH hydrogel can diminish CSC under 660 nm laser irradiation and finally restrain tumor recurrence after radiotherapy (RT). In comparison, the tumor in the mice that were only treated with RT relapsed rapidly. These findings reveal a double-boosting ·OH generation protocol, and the synergistic combination of AIE-mediated PDT and gas therapy provides a novel strategy for inhibiting CSC growth and cancer recurrence after RT, which presents great potential for clinical treatment.
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Affiliation(s)
- Tianfu Zhang
- School of Biomedical EngineeringGuangzhou Medical UniversityGuangzhou510182China
- Department of Chemistrythe Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstructionand Guangdong‐Hong Kong‐Macro Joint Laboratory of Optoelectronic and Magnetic Functional MaterialsThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong Kong999077China
| | - You Pan
- Guangxi Medical University Cancer HospitalNanning530000China
| | - Meng Suo
- School of Biomedical EngineeringGuangzhou Medical UniversityGuangzhou510182China
| | - Meng Lyu
- Department of Gastrointestinal Surgery & Department of GeriatricsShenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology)ShenzhenGuangdong518020China
| | - Jacky Wing Yip Lam
- Department of Chemistrythe Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstructionand Guangdong‐Hong Kong‐Macro Joint Laboratory of Optoelectronic and Magnetic Functional MaterialsThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong Kong999077China
| | - Zhaokui Jin
- School of Biomedical EngineeringGuangzhou Medical UniversityGuangzhou510182China
| | - Shipeng Ning
- Guangxi Medical University Cancer HospitalNanning530000China
| | - Ben Zhong Tang
- Department of Chemistrythe Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstructionand Guangdong‐Hong Kong‐Macro Joint Laboratory of Optoelectronic and Magnetic Functional MaterialsThe Hong Kong University of Science and TechnologyClear Water BayKowloonHong Kong999077China
- School of Science and EngineeringShenzhen Institute of Aggregate Science and TechnologyThe Chinese University of Hong KongShenzhenGuangdong518172China
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Naas S, Schiffer M, Schödel J. Hypoxia and renal fibrosis. Am J Physiol Cell Physiol 2023; 325:C999-C1016. [PMID: 37661918 DOI: 10.1152/ajpcell.00201.2023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/25/2023] [Accepted: 08/25/2023] [Indexed: 09/05/2023]
Abstract
Renal fibrosis is the final stage of most progressive kidney diseases. Chronic kidney disease (CKD) is associated with high comorbidity and mortality. Thus, preventing fibrosis and thereby preserving kidney function increases the quality of life and prolongs the survival of patients with CKD. Many processes such as inflammation or metabolic stress modulate the progression of kidney fibrosis. Hypoxia has also been implicated in the pathogenesis of renal fibrosis, and oxygen sensing in the kidney is of outstanding importance for the body. The dysregulation of oxygen sensing in the diseased kidney is best exemplified by the loss of stimulation of erythropoietin production from interstitial cells in the fibrotic kidney despite anemia. Furthermore, hypoxia is present in acute or chronic kidney diseases and may affect all cell types present in the kidney including tubular and glomerular cells as well as resident immune cells. Pro- and antifibrotic effects of the transcription factors hypoxia-inducible factors 1 and 2 have been described in a plethora of animal models of acute and chronic kidney diseases, but recent advances in sequencing technologies now allow for novel and deeper insights into the role of hypoxia and its cell type-specific effects on the progression of renal fibrosis, especially in humans. Here, we review existing literature on how hypoxia impacts the development and progression of renal fibrosis.
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Affiliation(s)
- Stephanie Naas
- Department of Nephrology and Hypertension, Uniklinikum Erlangen und Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Mario Schiffer
- Department of Nephrology and Hypertension, Uniklinikum Erlangen und Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Johannes Schödel
- Department of Nephrology and Hypertension, Uniklinikum Erlangen und Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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47
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Arechaga-Ocampo E. Epigenetics as a determinant of radiation response in cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023; 383:145-190. [PMID: 38359968 DOI: 10.1016/bs.ircmb.2023.07.008] [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: 02/17/2024]
Abstract
Radiation therapy is a cornerstone of modern cancer treatment. Treatment is based on depositing focal radiation to the tumor to inhibit cell growth, proliferation and metastasis, and to promote the death of cancer cells. In addition, radiation also affects non-tumor cells in the tumor microenvironmental (TME). Radiation resistance of the tumor cells is the most common cause of treatment failure, allowing survival of cancer cell and subsequent tumor growing. Molecular radioresistance comprises genetic and epigenetic characteristics inherent in cancer cells, or characteristics acquired after exposure to radiation. Furthermore, cancer stem cells (CSCs) and non-tumor cells into the TME as stromal and immune cells have a role in promoting and maintaining radioresistant tumor phenotypes. Different regulatory molecules and pathways distinctive of radiation resistance include DNA repair, survival signaling and cell death pathways. Epigenetic mechanisms are one of the most relevant events that occur after radiotherapy to regulate the expression and function of key genes and proteins in the differential radiation-response. This article reviews recent data on the main molecular mechanisms and signaling pathways related to the biological response to radiotherapy in cancer; highlighting the epigenetic control exerted by DNA methylation, histone marks, chromatin remodeling and m6A RNA methylation on gene expression and activation of signaling pathways related to radiation therapy response.
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Affiliation(s)
- Elena Arechaga-Ocampo
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autonoma Metropolitana, Mexico City, Mexico.
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48
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Humphries S, Bond DR, Germon ZP, Keely S, Enjeti AK, Dun MD, Lee HJ. Crosstalk between DNA methylation and hypoxia in acute myeloid leukaemia. Clin Epigenetics 2023; 15:150. [PMID: 37705055 PMCID: PMC10500762 DOI: 10.1186/s13148-023-01566-x] [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: 07/10/2023] [Accepted: 09/08/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND Acute myeloid leukaemia (AML) is a deadly disease characterised by the uncontrolled proliferation of immature myeloid cells within the bone marrow. Altered regulation of DNA methylation is an important epigenetic driver of AML, where the hypoxic bone marrow microenvironment can help facilitate leukaemogenesis. Thus, interactions between epigenetic regulation and hypoxia signalling will have important implications for AML development and treatment. MAIN BODY This review summarises the importance of DNA methylation and the hypoxic bone marrow microenvironment in the development, progression, and treatment of AML. Here, we focus on the role hypoxia plays on signalling and the subsequent regulation of DNA methylation. Hypoxia is likely to influence DNA methylation through altered metabolic pathways, transcriptional control of epigenetic regulators, and direct effects on the enzymatic activity of epigenetic modifiers. DNA methylation may also prevent activation of hypoxia-responsive genes, demonstrating bidirectional crosstalk between epigenetic regulation and the hypoxic microenvironment. Finally, we consider the clinical implications of these interactions, suggesting that reduced cell cycling within the hypoxic bone marrow may decrease the efficacy of hypomethylating agents. CONCLUSION Hypoxia is likely to influence AML progression through complex interactions with DNA methylation, where the therapeutic efficacy of hypomethylating agents may be limited within the hypoxic bone marrow. To achieve optimal outcomes for AML patients, future studies should therefore consider co-treatments that can promote cycling of AML cells within the bone marrow or encourage their dissociation from the bone marrow.
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Affiliation(s)
- Sam Humphries
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
| | - Danielle R Bond
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
| | - Zacary P Germon
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
| | - Simon Keely
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia
- Immune Health Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
| | - Anoop K Enjeti
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
- Department of Haematology, Calvary Mater Hospital, Waratah, NSW, 2298, Australia
- New South Wales Health Pathology, John Hunter Hospital, New Lambton Heights, NSW, 2305, Australia
| | - Matthew D Dun
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
| | - Heather J Lee
- School of Biomedical Sciences and Pharmacy, The University of Newcastle, Callaghan, NSW, 2308, Australia.
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia.
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49
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Flood D, Lee ES, Taylor CT. Intracellular energy production and distribution in hypoxia. J Biol Chem 2023; 299:105103. [PMID: 37507013 PMCID: PMC10480318 DOI: 10.1016/j.jbc.2023.105103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
The hydrolysis of ATP is the primary source of metabolic energy for eukaryotic cells. Under physiological conditions, cells generally produce more than sufficient levels of ATP to fuel the active biological processes necessary to maintain homeostasis. However, mechanisms underpinning the distribution of ATP to subcellular microenvironments with high local demand remain poorly understood. Intracellular distribution of ATP in normal physiological conditions has been proposed to rely on passive diffusion across concentration gradients generated by ATP producing systems such as the mitochondria and the glycolytic pathway. However, subcellular microenvironments can develop with ATP deficiency due to increases in local ATP consumption. Alternatively, ATP production can be reduced during bioenergetic stress during hypoxia. Mammalian cells therefore need to have the capacity to alter their metabolism and energy distribution strategies to compensate for local ATP deficits while also controlling ATP production. It is highly likely that satisfying the bioenergetic requirements of the cell involves the regulated distribution of ATP producing systems to areas of high ATP demand within the cell. Recently, the distribution (both spatially and temporally) of ATP-producing systems has become an area of intense investigation. Here, we review what is known (and unknown) about intracellular energy production and distribution and explore potential mechanisms through which this targeted distribution can be altered in hypoxia, with the aim of stimulating investigation in this important, yet poorly understood field of research.
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Affiliation(s)
- Darragh Flood
- Conway Institute of Biomolecular and Biomedical Research and School of Medicine, University College Dublin, Dublin, Ireland
| | - Eun Sang Lee
- Conway Institute of Biomolecular and Biomedical Research and School of Medicine, University College Dublin, Dublin, Ireland
| | - Cormac T Taylor
- Conway Institute of Biomolecular and Biomedical Research and School of Medicine, University College Dublin, Dublin, Ireland.
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50
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Pamporaki C, Berends AMA, Filippatos A, Prodanov T, Meuter L, Prejbisz A, Beuschlein F, Fassnacht M, Timmers HJLM, Nölting S, Abhyankar K, Constantinescu G, Kunath C, de Haas RJ, Wang K, Remde H, Bornstein SR, Januszewicz A, Robledo M, Lenders JWM, Kerstens MN, Pacak K, Eisenhofer G. Prediction of metastatic pheochromocytoma and paraganglioma: a machine learning modelling study using data from a cross-sectional cohort. Lancet Digit Health 2023; 5:e551-e559. [PMID: 37474439 PMCID: PMC10565306 DOI: 10.1016/s2589-7500(23)00094-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 03/20/2023] [Accepted: 05/03/2023] [Indexed: 07/22/2023]
Abstract
BACKGROUND Pheochromocytomas and paragangliomas have up to a 20% rate of metastatic disease that cannot be reliably predicted. This study prospectively assessed whether the dopamine metabolite, methoxytyramine, might predict metastatic disease, whether predictions might be improved using machine learning models that incorporate other features, and how machine learning-based predictions compare with predictions made by specialists in the field. METHODS In this machine learning modelling study, we used cross-sectional cohort data from the PMT trial, based in Germany, Poland, and the Netherlands, to prospectively examine the utility of methoxytyramine to predict metastatic disease in 267 patients with pheochromocytoma or paraganglioma and positive biochemical test results at initial screening. Another retrospective dataset of 493 patients with these tumors enrolled under clinical protocols at National Institutes of Health (00-CH-0093) and the Netherlands (PRESCRIPT trial) was used to train and validate machine learning models according to selections of additional features. The best performing machine learning models were then externally validated using data for all patients in the PMT trial. For comparison, 12 specialists provided predictions of metastatic disease using data from the training and external validation datasets. FINDINGS Prospective predictions indicated that plasma methoxytyramine could identify metastatic disease at sensitivities of 52% and specificities of 85%. The best performing machine learning model was based on an ensemble tree classifier algorithm that used nine features: plasma methoxytyramine, metanephrine, normetanephrine, age, sex, previous history of pheochromocytoma or paraganglioma, location and size of primary tumours, and presence of multifocal disease. This model had an area under the receiver operating characteristic curve of 0·942 (95% CI 0·894-0·969) that was larger (p<0·0001) than that of the best performing specialist before (0·815, 0·778-0·853) and after (0·812, 0·781-0·854) provision of SDHB variant data. Sensitivity for prediction of metastatic disease in the external validation cohort reached 83% at a specificity of 92%. INTERPRETATION Although methoxytyramine has some utility for prediction of metastatic pheochromocytomas and paragangliomas, sensitivity is limited. Predictive value is considerably enhanced with machine learning models that incorporate our nine recommended features. Our final model provides a preoperative approach to predict metastases in patients with pheochromocytomas and paragangliomas, and thereby guide individualised patient management and follow-up. FUNDING Deutsche Forschungsgemeinschaft.
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Affiliation(s)
| | - Annika M A Berends
- Department of Endocrinology, Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Angelos Filippatos
- University Hospital Carl Gustav Carus, Institute of Lightweight Engineering and Polymer Technology, TU Dresden, Dresden, Germany; Machine Design Laboratory, Department of Mechanical Engineering & Aeronautics, University of Patras, Patras, Greece
| | - Tamara Prodanov
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Leah Meuter
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | | | - Felix Beuschlein
- Department of Internal Medicine IV, University Hospital LMU, Ludwig Maximilian University of Munich, Munich, Germany; Department of Endocrinology, Diabetology, and Clinical Nutrition, University Hospital, University of Zurich, Zurich, Switzerland
| | - Martin Fassnacht
- Department of Internal Medicine, Division of Endocrinology and Diabetes, University of Würzburg, Würzburg, Germany
| | - Henri J L M Timmers
- Department of Internal Medicine, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Svenja Nölting
- Department of Internal Medicine IV, University Hospital LMU, Ludwig Maximilian University of Munich, Munich, Germany; Department of Endocrinology, Diabetology, and Clinical Nutrition, University Hospital, University of Zurich, Zurich, Switzerland
| | - Kaushik Abhyankar
- University Hospital Carl Gustav Carus, Institute of Lightweight Engineering and Polymer Technology, TU Dresden, Dresden, Germany
| | | | - Carola Kunath
- Department of Medicine III, TU Dresden, Dresden, Germany
| | - Robbert J de Haas
- Department of Radiology, Medical Imaging Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Katharina Wang
- Department of Internal Medicine IV, University Hospital LMU, Ludwig Maximilian University of Munich, Munich, Germany
| | - Hanna Remde
- Department of Internal Medicine, Division of Endocrinology and Diabetes, University of Würzburg, Würzburg, Germany
| | | | | | - Mercedes Robledo
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Programme, Spanish National Cancer Reserch Centre, Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Jacques W M Lenders
- Department of Medicine III, TU Dresden, Dresden, Germany; Department of Internal Medicine, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Michiel N Kerstens
- Department of Endocrinology, Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Karel Pacak
- Section on Medical Neuroendocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Graeme Eisenhofer
- Department of Medicine III, TU Dresden, Dresden, Germany; Institute of Clinical Chemistry and Laboratory Medicine, TU Dresden, Dresden, Germany
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