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Zou X, Liu X, Wang H, Li Z, Zhou C. Characterization of cuproptosis signature in clear cell renal cell carcinoma by single cell and spatial transcriptome analysis. Discov Oncol 2024; 15:300. [PMID: 39044005 PMCID: PMC11266328 DOI: 10.1007/s12672-024-01162-2] [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: 05/03/2024] [Accepted: 07/15/2024] [Indexed: 07/25/2024] Open
Abstract
Cuproptosis is a novel type to regulate cell death with copper-dependent manner, and has been reported to involve in the occurrence and development of various malignant tumors. However, the association between cuproptosis and the tumor microenvironment (TME) of clear cell renal cell carcinoma (ccRCC) remained unclear. To address this question, we integrated the single cell RNA sequencing (scRNA-seq) datasets of ccRCC across different stages, systematically examined the distinctive expression patterns of cuproptosis-related genes (CRGs) within the TME of ccRCC, and explored the crucial signatures using the spatial transcriptome sequencing (ST-seq) dataset. The cuproptosis activities reduced in cancer tissues along with the ccRCC development, and recovered after therapy. We identified HILPDA+ ccRCC1 subtype, characterized with hypoxia, as cuproptosis susceptible cells associated with a better prognosis. The main co-expression modules of HILPDA+ ccRCC1 subtype highlighted the role in anion transport, response to oxygen species and PD-L1-PD-1 pathway. Furthermore, the immunosuppressive cells might interact with HILPDA+ ccRCC1 subtype via HAVCR2-LGALS9, C3-C3AR1, HLA-A-CD8B and HLA-C-CD8A axises to shape the cuproptosis-related TME landscape. In summary, we anticipate that this study will offer valuable insights and potential strategies of cuproptosis for therapy of ccRCC.
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Affiliation(s)
- Xiaohong Zou
- Department of Laboratory Medicine, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518033, China
| | - Xiaoqing Liu
- Department of Laboratory Medicine, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518033, China
| | - Huiting Wang
- Department of Laboratory Medicine, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518033, China
| | - Zhenhua Li
- Department of Laboratory Medicine, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518033, China
| | - Chen Zhou
- Department of Laboratory Medicine, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518033, China.
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2
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You M, Shamseldin HE, Fogle HM, Rushing BR, AlMalki RH, Jaafar A, Hashem M, Abdulwahab F, Rahman AMA, Krupenko NI, Alkuraya FS, Krupenko SA. Further delineation of the phenotypic and metabolomic profile of ALDH1L2-related neurodevelopmental disorder. Clin Genet 2024; 105:488-498. [PMID: 38193334 PMCID: PMC10990829 DOI: 10.1111/cge.14479] [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: 11/09/2023] [Revised: 12/22/2023] [Accepted: 12/28/2023] [Indexed: 01/10/2024]
Abstract
ALDH1L2, a mitochondrial enzyme in folate metabolism, converts 10-formyl-THF (10-formyltetrahydrofolate) to THF (tetrahydrofolate) and CO2. At the cellular level, deficiency of this NADP+-dependent reaction results in marked reduction in NADPH/NADP+ ratio and reduced mitochondrial ATP. Thus far, a single patient with biallelic ALDH1L2 variants and the phenotype of a neurodevelopmental disorder has been reported. Here, we describe another patient with a neurodevelopmental disorder associated with a novel homozygous missense variant in ALDH1L2, Pro133His. The variant caused marked reduction in the ALDH1L2 enzyme activity in skin fibroblasts derived from the patient as probed by 10-FDDF, a stable synthetic analog of 10-formyl-THF. Additional associated abnormalities in these fibroblasts include reduced NADPH/NADP+ ratio and pool of mitochondrial ATP, upregulated autophagy and dramatically altered metabolomic profile. Overall, our study further supports a link between ALDH1L2 deficiency and abnormal neurodevelopment in humans.
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Affiliation(s)
- Mikyoung You
- UNC Nutrition Research Institute, Kannapolis, NC, USA
| | - Hanan E. Shamseldin
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center (KFSHRC), Riyadh, Saudi Arabia
| | - Halle M. Fogle
- UNC Nutrition Research Institute, Kannapolis, NC, USA
- Department of Nutrition, University of North Carolina-Chapel Hill, NC, USA
| | - Blake R. Rushing
- UNC Nutrition Research Institute, Kannapolis, NC, USA
- Department of Nutrition, University of North Carolina-Chapel Hill, NC, USA
| | - Reem H. AlMalki
- Metabolomics Section, Department of Clinical Genomics, Center for Genome Medicine, King Faisal Specialist Hospital and Research Center (KFSHRC), Riyadh, Saudi Arabia
| | - Amal Jaafar
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center (KFSHRC), Riyadh, Saudi Arabia
| | - Mais Hashem
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center (KFSHRC), Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center (KFSHRC), Riyadh, Saudi Arabia
| | - Anas M. Abdel Rahman
- Metabolomics Section, Department of Clinical Genomics, Center for Genome Medicine, King Faisal Specialist Hospital and Research Center (KFSHRC), Riyadh, Saudi Arabia
- Department of Biochemistry and Molecular Medicine, College of Medicine, Al Faisal University, Riyadh, Saudi Arabia
| | - Natalia I. Krupenko
- UNC Nutrition Research Institute, Kannapolis, NC, USA
- Department of Nutrition, University of North Carolina-Chapel Hill, NC, USA
| | - Fowzan S. Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center (KFSHRC), Riyadh, Saudi Arabia
| | - Sergey A. Krupenko
- UNC Nutrition Research Institute, Kannapolis, NC, USA
- Department of Nutrition, University of North Carolina-Chapel Hill, NC, USA
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3
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Becker B, Wottawa F, Bakr M, Koncina E, Mayr L, Kugler J, Yang G, Windross SJ, Neises L, Mishra N, Harris D, Tran F, Welz L, Schwärzler J, Bánki Z, Stengel ST, Ito G, Krötz C, Coleman OI, Jaeger C, Haller D, Paludan SR, Blumberg R, Kaser A, Cicin-Sain L, Schreiber S, Adolph TE, Letellier E, Rosenstiel P, Meiser J, Aden K. Serine metabolism is crucial for cGAS-STING signaling and viral defense control in the gut. iScience 2024; 27:109173. [PMID: 38496294 PMCID: PMC10943449 DOI: 10.1016/j.isci.2024.109173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/27/2023] [Accepted: 02/06/2024] [Indexed: 03/19/2024] Open
Abstract
Inflammatory bowel diseases are characterized by the chronic relapsing inflammation of the gastrointestinal tract. While the molecular causality between endoplasmic reticulum (ER) stress and intestinal inflammation is widely accepted, the metabolic consequences of chronic ER stress on the pathophysiology of IBD remain unclear. By using in vitro, in vivo models, and patient datasets, we identified a distinct polarization of the mitochondrial one-carbon metabolism and a fine-tuning of the amino acid uptake in intestinal epithelial cells tailored to support GSH and NADPH metabolism upon ER stress. This metabolic phenotype strongly correlates with IBD severity and therapy response. Mechanistically, we uncover that both chronic ER stress and serine limitation disrupt cGAS-STING signaling, impairing the epithelial response against viral and bacterial infection and fueling experimental enteritis. Consequently, the antioxidant treatment restores STING function and virus control. Collectively, our data highlight the importance of serine metabolism to allow proper cGAS-STING signaling and innate immune responses upon gut inflammation.
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Affiliation(s)
- Björn Becker
- Luxembourg Institute of Health, Department of Cancer Research, Luxembourg, Luxembourg
| | - Felix Wottawa
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Mohamed Bakr
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Eric Koncina
- Faculty of Science, Technology and Medicine, Department of Life Sciences and Medicine, Université du Luxembourg, Luxembourg, Luxembourg
| | - Lisa Mayr
- Department of Internal Medicine I, Gastroenterology, Hepatology, Metabolism & Endocrinology, Medical University of Innsbruck, Innsbruck, Austria
| | - Julia Kugler
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Guang Yang
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | | | - Laura Neises
- Luxembourg Institute of Health, Department of Cancer Research, Luxembourg, Luxembourg
| | - Neha Mishra
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Danielle Harris
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Florian Tran
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
- Department of Internal Medicine I, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Lina Welz
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
- Department of Internal Medicine I, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Julian Schwärzler
- Department of Internal Medicine I, Gastroenterology, Hepatology, Metabolism & Endocrinology, Medical University of Innsbruck, Innsbruck, Austria
| | - Zoltán Bánki
- Institute of Virology, Department of Hygiene, Microbiology and Public Health, Medical University of Innsbruck, Innsbruck, Austria
| | - Stephanie T. Stengel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Go Ito
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Christina Krötz
- Luxembourg Institute of Health, Department of Cancer Research, Luxembourg, Luxembourg
| | - Olivia I. Coleman
- Chair of Nutrition and Immunology, TUM School of Life Sciences, Technical University of Munich, Luxembourg, Luxembourg
| | - Christian Jaeger
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Dirk Haller
- Chair of Nutrition and Immunology, TUM School of Life Sciences, Technical University of Munich, Luxembourg, Luxembourg
- ZIEL-Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany
| | | | - Richard Blumberg
- Gastroenterology Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Arthur Kaser
- Division of Gastroenterology and Hepatology, Department of Medicine, Addenbrooke’s Hospital, University of Cambridge, Cambridge, England, UK
| | - Luka Cicin-Sain
- Helmholtz Zentrum für Infektionsforschung, Braunschweig, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
- Department of Internal Medicine I, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Timon E. Adolph
- Department of Internal Medicine I, Gastroenterology, Hepatology, Metabolism & Endocrinology, Medical University of Innsbruck, Innsbruck, Austria
| | - Elisabeth Letellier
- Faculty of Science, Technology and Medicine, Department of Life Sciences and Medicine, Université du Luxembourg, Luxembourg, Luxembourg
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Johannes Meiser
- Luxembourg Institute of Health, Department of Cancer Research, Luxembourg, Luxembourg
| | - Konrad Aden
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
- Department of Internal Medicine I, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
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4
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Pang S, Zhao S, Dongye Y, Fan Y, Liu J. Identification and validation of m6A-associated ferroptosis genes in renal clear cell carcinoma. Cell Biol Int 2024. [PMID: 38440906 DOI: 10.1002/cbin.12146] [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: 10/11/2023] [Revised: 01/09/2024] [Accepted: 02/17/2024] [Indexed: 03/06/2024]
Abstract
Urinary cancer is synonymous with clear cell renal cell carcinoma (ccRCC). Unfortunately, existing treatments for this illness are ineffective and unpromising. Finding novel ccRCC biomarkers is crucial to creating successful treatments. The Cancer Genome Atlas provided clear cell renal cell carcinoma transcriptome data. Functional enrichment analysis was performed on ccRCC and control samples' differentially expressed N6-methyladenosine RNA methylation and ferroptosis-related genes (DEMFRGs). Machine learning was used to find and model ccRCC patients' predicted genes. A nomogram was created for clear cell renal cell carcinoma patients. Prognostic genes were enriched. We examined patients' immune profiles by risk score. Our prognostic genes predicted ccRCC treatment drugs. We found 37 DEMFRGs by comparing 1913 differentially expressed ccRCC genes to 202 m6A RNA methylation FRGs. Functional enrichment analysis showed that hypoxia-induced cell death and metabolism pathways were the most differentially expressed methylation functional regulating genes. Five prognostic genes were found by machine learning: TRIB3, CHAC1, NNMT, EGFR, and SLC1A4. An advanced renal cell carcinoma nomogram with age and risk score accurately predicted the outcome. These five prognostic genes were linked to various cancers. Immunological cell number and checkpoint expression differed between high- and low-risk groups. The risk model successfully predicted immunotherapy outcome, showing high-risk individuals had poor results. NIACIN, TAE-684, ROCILETINIB, and others treat ccRCC. We found ccRCC prognostic genes that work. This discovery may lead to new ccRCC treatments.
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Affiliation(s)
- Shuo Pang
- Department of Urology, Qilu Hospital of Shandong University, Jinan, Shandong, P.R. China
- Department of Urinary Surgery, Jinan Third People's Hospital, Jinan, Shandong, P.R. China
| | - Shuo Zhao
- Department of Urology, Qilu Hospital of Shandong University, Jinan, Shandong, P.R. China
| | - Yuxi Dongye
- Department of Urology, Qilu Hospital of Shandong University, Jinan, Shandong, P.R. China
- Department of Urinary Surgery, Jinan Third People's Hospital, Jinan, Shandong, P.R. China
| | - Yidong Fan
- Department of Urology, Qilu Hospital of Shandong University, Jinan, Shandong, P.R. China
| | - Jikai Liu
- Department of Urology, Qilu Hospital of Shandong University, Jinan, Shandong, P.R. China
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5
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Wang M, Li J, Yang X, Yan Q, Wang H, Xu X, Lu Y, Li D, Wang Y, Sun R, Zhang S, Zhang Y, Zhang Z, Meng F, Li Y. Targeting TLK2 inhibits the progression of gastric cancer by reprogramming amino acid metabolism through the mTOR/ASNS axis. Cancer Gene Ther 2023; 30:1485-1497. [PMID: 37542132 DOI: 10.1038/s41417-023-00653-8] [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: 02/20/2023] [Revised: 07/17/2023] [Accepted: 07/27/2023] [Indexed: 08/06/2023]
Abstract
Several recent studies have suggested that TLKs are related to tumor progression. However, the function and mechanism of action of TLK2 in gastric cancer (GC) remain elusive. In this study, TLK2 was found to be significantly upregulated in patients with GC and was identified as an independent prognostic factor for GC. Consistently, TLK2 knockdown markedly reduced the aggressiveness of GC, whereas its overexpression had the opposite effect. IP-MS revealed that the effects of TLK2 on GC were mainly associated with metabolism reprogramming. TLK2 knockdown suppressed amino acid synthesis by downregulating the mTORC1 pathway and ASNS expression in GC cells. Mechanistically, mTORC1 directly interacts with the ASNS protein and inhibits its degradation. Further experiments validated that the ASNS protein was degraded via ubiquitination instead of autophagy. Inhibiting and activating the mTORC1 pathway can upregulate and downregulate ASNS ubiquitination, respectively, and the mTORC1 pathway can reverse the regulatory effects of TLK2 on ASNS. Furthermore, TLK2 was found to regulate the mRNA expression of ASNS. TLK2 directly interacted with ATF4, a transcription factor of ASNS, and promoted its expression. The kinase inhibitor fostamatinib significantly inhibited the proliferative, invasive, and migratory capabilities of GC cells by inhibiting TLK2 activity. Altogether, this study reveals a novel functional relationship between TLK2 and the mTORC1/ASNS axis in GC. Therefore, TLK2 may serve as a potential therapeutic target for GC.
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Affiliation(s)
- Mingliang Wang
- General Surgery Department, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, China
| | - Jing Li
- General Surgery Department, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, China
| | - Xiaodong Yang
- General Surgery Department, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, China
| | - Qiang Yan
- General Surgery Department, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, China
| | - Huizhen Wang
- General Surgery Department, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, China
| | - Xin Xu
- General Surgery Department, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, China
| | - Yida Lu
- General Surgery Department, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, China
| | - Deguan Li
- General Surgery Department, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, China
| | - Yigao Wang
- General Surgery Department, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, China
| | - Ruochuan Sun
- General Surgery Department, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, China
| | - Shangxin Zhang
- General Surgery Department, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, China
| | - Yonghong Zhang
- General Surgery Department, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, China
| | - Zhen Zhang
- General Surgery Department, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, China
| | - Futao Meng
- General Surgery Department, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, China.
- Department of Surgical Oncology, The First Affiliated Hospital of Bengbu Medical College, No. 287 Changhuai Road, Bengbu, China.
| | - Yongxiang Li
- General Surgery Department, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, China.
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Clavería-Cabello A, Herranz JM, Latasa MU, Arechederra M, Uriarte I, Pineda-Lucena A, Prosper F, Berraondo P, Alonso C, Sangro B, García Marin JJ, Martinez-Chantar ML, Ciordia S, Corrales FJ, Francalanci P, Alaggio R, Zucman-Rossi J, Indersie E, Cairo S, Domingo-Sàbat M, Zanatto L, Sancho-Bru P, Armengol C, Berasain C, Fernandez-Barrena MG, Avila MA. Identification and experimental validation of druggable epigenetic targets in hepatoblastoma. J Hepatol 2023; 79:989-1005. [PMID: 37302584 DOI: 10.1016/j.jhep.2023.05.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 04/25/2023] [Accepted: 05/22/2023] [Indexed: 06/13/2023]
Abstract
BACKGROUND & AIMS Hepatoblastoma (HB) is the most frequent childhood liver cancer. Patients with aggressive tumors have limited therapeutic options; therefore, a better understanding of HB pathogenesis is needed to improve treatment. HBs have a very low mutational burden; however, epigenetic alterations are increasingly recognized. We aimed to identify epigenetic regulators consistently dysregulated in HB and to evaluate the therapeutic efficacy of their targeting in clinically relevant models. METHODS We performed a comprehensive transcriptomic analysis of 180 epigenetic genes. Data from fetal, pediatric, adult, peritumoral (n = 72) and tumoral (n = 91) tissues were integrated. Selected epigenetic drugs were tested in HB cells. The most relevant epigenetic target identified was validated in primary HB cells, HB organoids, a patient-derived xenograft model, and a genetic mouse model. Transcriptomic, proteomic and metabolomic mechanistic analyses were performed. RESULTS Altered expression of genes regulating DNA methylation and histone modifications was consistently observed in association with molecular and clinical features of poor prognosis. The histone methyltransferase G9a was markedly upregulated in tumors with epigenetic and transcriptomic traits of increased malignancy. Pharmacological targeting of G9a significantly inhibited growth of HB cells, organoids and patient-derived xenografts. Development of HB induced by oncogenic forms of β-catenin and YAP1 was ablated in mice with hepatocyte-specific deletion of G9a. We observed that HBs undergo significant transcriptional rewiring in genes involved in amino acid metabolism and ribosomal biogenesis. G9a inhibition counteracted these pro-tumorigenic adaptations. Mechanistically, G9a targeting potently repressed the expression of c-MYC and ATF4, master regulators of HB metabolic reprogramming. CONCLUSIONS HBs display a profound dysregulation of the epigenetic machinery. Pharmacological targeting of key epigenetic effectors exposes metabolic vulnerabilities that can be leveraged to improve the treatment of these patients. IMPACT AND IMPLICATIONS In spite of recent advances in the management of hepatoblastoma (HB), treatment resistance and drug toxicity are still major concerns. This systematic study reveals the remarkable dysregulation in the expression of epigenetic genes in HB tissues. Through pharmacological and genetic experimental approaches, we demonstrate that the histone-lysine-methyltransferase G9a is an excellent drug target in HB, which can also be harnessed to enhance the efficacy of chemotherapy. Furthermore, our study highlights the profound pro-tumorigenic metabolic rewiring of HB cells orchestrated by G9a in coordination with the c-MYC oncogene. From a broader perspective, our findings suggest that anti-G9a therapies may also be effective in other c-MYC-dependent tumors.
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Affiliation(s)
| | - Jose Maria Herranz
- Hepatology Program, CIMA, CCUN, University of Navarra, Pamplona, Spain; CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Maria Ujue Latasa
- Hepatology Program, CIMA, CCUN, University of Navarra, Pamplona, Spain; CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Maria Arechederra
- Hepatology Program, CIMA, CCUN, University of Navarra, Pamplona, Spain; CIBERehd, Instituto de Salud Carlos III, Madrid, Spain; Instituto de Investigaciones Sanitarias de Navarra IdiSNA, Pamplona, Spain
| | - Iker Uriarte
- Hepatology Program, CIMA, CCUN, University of Navarra, Pamplona, Spain; CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Felipe Prosper
- Instituto de Investigaciones Sanitarias de Navarra IdiSNA, Pamplona, Spain; Oncohematology Program, CIMA, CCUN, University of Navarra, Pamplona, Spain
| | - Pedro Berraondo
- Immunology and Immunotherapy Program, CIMA, University of Navarra, Pamplona, Spain; CIBERonc, Madrid, Spain
| | | | - Bruno Sangro
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain; Instituto de Investigaciones Sanitarias de Navarra IdiSNA, Pamplona, Spain; Hepatology Unit, CCUN, Navarra University Clinic, Pamplona, Spain
| | - Jose Juan García Marin
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain; Experimental Hepatology and Drug Targeting (HEVEFARM), University of Salamanca, IBSAL, Salamanca, Spain
| | - Maria Luz Martinez-Chantar
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain; Liver Disease Laboratory, Center for Cooperative Research in Biosciences (CICbioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Sergio Ciordia
- Functional Proteomics Laboratory, CNB-CSIC, Madrid, Spain
| | - Fernando José Corrales
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain; Functional Proteomics Laboratory, CNB-CSIC, Madrid, Spain
| | - Paola Francalanci
- Pathology Unit, Children's Hospital Bambino Gesù, IRCCS, Rome, Italy
| | - Rita Alaggio
- Pathology Unit, Children's Hospital Bambino Gesù, IRCCS, Sapienza University, Rome, Italy
| | - Jessica Zucman-Rossi
- Centre de Recherche des Cordeliers, Sorbonne Université, Université de Paris, INSERM, Hôpital Européen Georges Pompidou, Paris, France
| | | | - Stefano Cairo
- XenTech, Evry-Courcouronnes, France; Champions Oncology, Rockville, MD, USA
| | - Montserrat Domingo-Sàbat
- Childhood Liver Oncology Group, Program of Predictive and Personalized Medicine of Cancer (PMPCC), Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Laura Zanatto
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain
| | - Pau Sancho-Bru
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain
| | - Carolina Armengol
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain; Childhood Liver Oncology Group, Program of Predictive and Personalized Medicine of Cancer (PMPCC), Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Carmen Berasain
- Hepatology Program, CIMA, CCUN, University of Navarra, Pamplona, Spain; CIBERehd, Instituto de Salud Carlos III, Madrid, Spain; Instituto de Investigaciones Sanitarias de Navarra IdiSNA, Pamplona, Spain
| | - Maite García Fernandez-Barrena
- Hepatology Program, CIMA, CCUN, University of Navarra, Pamplona, Spain; CIBERehd, Instituto de Salud Carlos III, Madrid, Spain; Instituto de Investigaciones Sanitarias de Navarra IdiSNA, Pamplona, Spain.
| | - Matias Antonio Avila
- Hepatology Program, CIMA, CCUN, University of Navarra, Pamplona, Spain; CIBERehd, Instituto de Salud Carlos III, Madrid, Spain; Instituto de Investigaciones Sanitarias de Navarra IdiSNA, Pamplona, Spain.
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7
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Liu Y, Guo S, Xie W, Yang H, Li W, Zhou N, Yang J, Zhou G, Mao C, Zheng Y. Identification of microRNA editing sites in clear cell renal cell carcinoma. Sci Rep 2023; 13:15117. [PMID: 37704698 PMCID: PMC10499803 DOI: 10.1038/s41598-023-42302-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/07/2023] [Indexed: 09/15/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is a malignant tumor originating from the renal tubular epithelium. Although the microRNAs (miRNAs) transcriptome of ccRCC has been extensively studied, the role of miRNAs editing in ccRCC is largely unknown. By analyzing small RNA sequencing profiles of renal tissues of 154 ccRCC patients and 22 normal controls, we identified 1025 miRNA editing sites from 246 pre-miRNAs. There were 122 editing events with significantly different editing levels in ccRCC compared to normal samples, which include two A-to-I editing events in the seed regions of hsa-mir-376a-3p and hsa-mir-376c-3p, respectively, and one C-to-U editing event in the seed region of hsa-mir-29c-3p. After comparing the targets of the original and edited miRNAs, we found that hsa-mir-376a-1_49g, hsa-mir-376c_48g and hsa-mir-29c_59u had many new targets, respectively. Many of these new targets were deregulated in ccRCC, which might be related to the different editing levels of hsa-mir-376a-3p, hsa-mir-376c-3p, hsa-mir-29c-3p in ccRCC compared to normal controls. Our study sheds new light on miRNA editing events and their potential biological functions in ccRCC.
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Affiliation(s)
- Yulong Liu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Shiyong Guo
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Wenping Xie
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Huaide Yang
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
| | - Wanran Li
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Nan Zhou
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Jun Yang
- School of Criminal Investigation, Yunnan Police College, Kunming, 650223, Yunnan, China
| | - Guangchen Zhou
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Chunyi Mao
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, 650500, Yunnan, China
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Yun Zheng
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
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8
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Miller MJ, Marcotte GR, Basisty N, Wehrfritz C, Ryan ZC, Strub MD, McKeen AT, Stern JI, Nath KA, Rasmussen BB, Judge AR, Schilling B, Ebert SM, Adams CM. The transcription regulator ATF4 is a mediator of skeletal muscle aging. GeroScience 2023; 45:2525-2543. [PMID: 37014538 PMCID: PMC10071239 DOI: 10.1007/s11357-023-00772-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/10/2023] [Indexed: 04/05/2023] Open
Abstract
Aging slowly erodes skeletal muscle strength and mass, eventually leading to profound functional deficits and muscle atrophy. The molecular mechanisms of skeletal muscle aging are not well understood. To better understand mechanisms of muscle aging, we investigated the potential role of ATF4, a transcription regulatory protein that can rapidly promote skeletal muscle atrophy in young animals deprived of adequate nutrition or activity. To test the hypothesis that ATF4 may be involved in skeletal muscle aging, we studied fed and active muscle-specific ATF4 knockout mice (ATF4 mKO mice) at 6 months of age, when wild-type mice have achieved peak muscle mass and function, and at 22 months of age, when wild-type mice have begun to manifest age-related muscle atrophy and weakness. We found that 6-month-old ATF4 mKO mice develop normally and are phenotypically indistinguishable from 6-month-old littermate control mice. However, as ATF4 mKO mice become older, they exhibit significant protection from age-related declines in strength, muscle quality, exercise capacity, and muscle mass. Furthermore, ATF4 mKO muscles are protected from some of the transcriptional changes characteristic of normal muscle aging (repression of certain anabolic mRNAs and induction of certain senescence-associated mRNAs), and ATF4 mKO muscles exhibit altered turnover of several proteins with important roles in skeletal muscle structure and metabolism. Collectively, these data suggest ATF4 as an essential mediator of skeletal muscle aging and provide new insight into a degenerative process that impairs the health and quality of life of many older adults.
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Affiliation(s)
- Matthew J Miller
- Division of Endocrinology, Diabetes, Metabolism and Nutrition, Departments of Medicine and Biochemistry and Molecular Biology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
- University of Iowa, Iowa City, IA, USA
| | - George R Marcotte
- Division of Endocrinology, Diabetes, Metabolism and Nutrition, Departments of Medicine and Biochemistry and Molecular Biology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
- University of Iowa, Iowa City, IA, USA
| | - Nathan Basisty
- Buck Institute for Research on Aging, Novato, CA, USA
- National Institute on Aging, NIH, Baltimore, MD, USA
| | | | - Zachary C Ryan
- Division of Endocrinology, Diabetes, Metabolism and Nutrition, Departments of Medicine and Biochemistry and Molecular Biology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Matthew D Strub
- Division of Endocrinology, Diabetes, Metabolism and Nutrition, Departments of Medicine and Biochemistry and Molecular Biology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | | | - Jennifer I Stern
- Division of Endocrinology, Diabetes, Metabolism and Nutrition, Departments of Medicine and Biochemistry and Molecular Biology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Karl A Nath
- Division of Endocrinology, Diabetes, Metabolism and Nutrition, Departments of Medicine and Biochemistry and Molecular Biology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Blake B Rasmussen
- University of Texas Medical Branch, Galveston, TX, USA
- Emmyon, Inc., Rochester, MN, USA
| | - Andrew R Judge
- University of Florida, Gainesville, FL, USA
- Emmyon, Inc., Rochester, MN, USA
| | | | - Scott M Ebert
- Division of Endocrinology, Diabetes, Metabolism and Nutrition, Departments of Medicine and Biochemistry and Molecular Biology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
- Emmyon, Inc., Rochester, MN, USA.
| | - Christopher M Adams
- Division of Endocrinology, Diabetes, Metabolism and Nutrition, Departments of Medicine and Biochemistry and Molecular Biology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
- Emmyon, Inc., Rochester, MN, USA.
- Iowa City Veterans Affairs Medical Center, Iowa City, IA, USA.
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9
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Melis M, Trasino SE, Tang XH, Rappa A, Zhang T, Qin L, Gudas LJ. Retinoic Acid Receptor β Loss in Hepatocytes Increases Steatosis and Elevates the Integrated Stress Response in Alcohol-Associated Liver Disease. Int J Mol Sci 2023; 24:12035. [PMID: 37569418 PMCID: PMC10418449 DOI: 10.3390/ijms241512035] [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: 06/16/2023] [Revised: 07/18/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
In alcohol-associated liver disease (ALD), hepatic reductions in vitamin A and perturbations in vitamin A metabolism are common. However, the roles that the vitamin A receptors, termed retinoic acid receptors (RARs), may have in preventing the pathophysiology of ALD remains unclear. Our prior data indicate that a RARβ agonist limits the pathology of alcohol-related liver disease. Thus, we generated liver-specific AlbCre-RARβ knockout (BKO) mice and compared them to wild type (WT) mice in an early ALD model. Both strains showed similar blood ethanol concentrations and ETOH-metabolizing enzymes. However, the livers of pair-fed-BKO and ETOH-BKO mice developed higher levels of steatosis and triglycerides than pair-fed-WT and ETOH-WT mice. The increased hepatic steatosis observed in the pair-fed-BKO and ETOH-BKO mice was associated with higher lipid synthesis/trafficking transcripts and lower beta-oxidation transcripts. ETOH-BKO mice also exhibited a higher integrated stress response (ISR) signature, including higher transcript and protein levels of ATF4 and its target, 4-EBP1. In human hepatocytes (HepG2) that lack RARβ (RARβ-KO), ETOH treatments resulted in greater reactive oxygen species compared to their parental cells. Notably, even without ETOH, ATF4 and 4-EBP1 protein levels were higher in the RARβ-KO cells than in their parental cells. These 4-EBP1 increases were greatly attenuated in cultured ATF4-deficient and RARβ/ATF4-deficient HepG2, suggesting that RARβ is a crucial negative regulator of 4-EBP1 through ATF4 in cultured hepatocytes. Here, we identify RARβ as a negative regulator of lipid metabolism and cellular stress in ALD.
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Affiliation(s)
- Marta Melis
- Department of Pharmacology, Weill Cornell Medical College of Cornell University, New York, NY 10065, USA; (M.M.)
| | - Steven E. Trasino
- Department of Pharmacology, Weill Cornell Medical College of Cornell University, New York, NY 10065, USA; (M.M.)
- Nutrition Program, Hunter College, City University of New York, New York, NY 10065, USA
| | - Xiao-Han Tang
- Department of Pharmacology, Weill Cornell Medical College of Cornell University, New York, NY 10065, USA; (M.M.)
| | - Andrew Rappa
- Department of Pharmacology, Weill Cornell Medical College of Cornell University, New York, NY 10065, USA; (M.M.)
| | - Tuo Zhang
- Genomics Resources Core Facility, Weill Cornell Medical College of Cornell University, New York, NY 10065, USA
| | - Lihui Qin
- Division of Anatomic Pathology, New York Presbyterian Hospital, Department of Pathology and Laboratory Medicine, Weill Cornell Medical College of Cornell University, New York, NY 10065, USA
| | - Lorraine J. Gudas
- Department of Pharmacology, Weill Cornell Medical College of Cornell University, New York, NY 10065, USA; (M.M.)
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10
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Abstract
Vitamin A (retinol) is a critical micronutrient required for the control of stem cell functions, cell differentiation, and cell metabolism in many different cell types, both during embryogenesis and in the adult organism. However, we must obtain vitamin A from food sources. Thus, the uptake and metabolism of vitamin A by intestinal epithelial cells, the storage of vitamin A in the liver, and the metabolism of vitamin A in target cells to more biologically active metabolites, such as retinoic acid (RA) and 4-oxo-RA, must be precisely regulated. Here, I will discuss the enzymes that metabolize vitamin A to RA and the cytochrome P450 Cyp26 family of enzymes that further oxidize RA. Because much progress has been made in understanding the regulation of ALDH1a2 (RALDH2) actions in the intestine, one focus of this review is on the metabolism of vitamin A in intestinal epithelial cells and dendritic cells. Another focus is on recent data that 4-oxo-RA is a ligand required for the maintenance of hematopoietic stem cell dormancy and the important role of RARβ (RARB) in these stem cells. Despite this progress, many questions remain in this research area, which links vitamin A metabolism to nutrition, immune functions, developmental biology, and nuclear receptor pharmacology.
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Affiliation(s)
- Lorraine J Gudas
- Department of Pharmacology, and Revlon Pharmaceutical Professor of Pharmacology and Toxicology, Pharmacology Department, and the Meyer Cancer Center of Weill Cornell Medicine of Cornell University, 1300 York Ave, New York, NY 10065
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