1
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Aparicio B, Theunissen P, Hervas-Stubbs S, Fortes P, Sarobe P. Relevance of mutation-derived neoantigens and non-classical antigens for anticancer therapies. Hum Vaccin Immunother 2024; 20:2303799. [PMID: 38346926 PMCID: PMC10863374 DOI: 10.1080/21645515.2024.2303799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/06/2024] [Indexed: 02/15/2024] Open
Abstract
Efficacy of cancer immunotherapies relies on correct recognition of tumor antigens by lymphocytes, eliciting thus functional responses capable of eliminating tumor cells. Therefore, important efforts have been carried out in antigen identification, with the aim of understanding mechanisms of response to immunotherapy and to design safer and more efficient strategies. In addition to classical tumor-associated antigens identified during the last decades, implementation of next-generation sequencing methodologies is enabling the identification of neoantigens (neoAgs) arising from mutations, leading to the development of new neoAg-directed therapies. Moreover, there are numerous non-classical tumor antigens originated from other sources and identified by new methodologies. Here, we review the relevance of neoAgs in different immunotherapies and the results obtained by applying neoAg-based strategies. In addition, the different types of non-classical tumor antigens and the best approaches for their identification are described. This will help to increase the spectrum of targetable molecules useful in cancer immunotherapies.
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Affiliation(s)
- Belen Aparicio
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
| | - Patrick Theunissen
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
- DNA and RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Sandra Hervas-Stubbs
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
| | - Puri Fortes
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
- DNA and RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- Spanish Network for Advanced Therapies (TERAV ISCIII), Spain
| | - Pablo Sarobe
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
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2
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Bidikian A, Bewersdorf JP, Shallis RM, Getz TM, Stempel JM, Kewan T, Stahl M, Zeidan AM. Targeted therapies for myelodysplastic Syndromes/Neoplasms (MDS): current landscape and future directions. Expert Rev Anticancer Ther 2024. [PMID: 39367718 DOI: 10.1080/14737140.2024.2414071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Revised: 10/01/2024] [Accepted: 10/04/2024] [Indexed: 10/06/2024]
Abstract
INTRODUCTION Myelodysplastic syndromes/neoplasms (MDS) are a heterogeneous group of hematologic malignancies that are stratified into high-risk (HR-MDS) and low-risk (LR-MDS) categories. Until recently LR-MDS has been typically managed by supportive measures and erythropoiesis-stimulating agents (ESAs); whereas, management of HR-MDS, typically included hypomethylating agents and allogeneic hematopoietic stem cell transplant. However, the limited rates and duration of response observed with these interventions prompted the search for targeted therapies to improve the outcomes among patients with MDS. AREAS COVERED Here we review the current landscape of targeted therapies in MDS. These include pyruvate kinase and hypoxia-inducible factor (HIF) activators; TGF-beta, telomerase, BCL2 and isocitrate dehydrogenase (IDH) inhibitors; as well as novel approaches targeting inflammation, pyroptosis, immune evasion and RNA splicing machinery. EXPERT OPINION This review highlights the progress and challenges in MDS treatment. Despite some promising results, many therapies remain in early development or have faced setbacks, emphasizing the need for a more comprehensive understanding of the disease's pathobiology. Continued research into targeted therapies, homogenous clinical trial designs, as well as increased incorporation of molecular prognostic tools and artificial intelligence into trial design are essential for developing effective treatments for MDS and improving patient outcomes.
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Affiliation(s)
- Aram Bidikian
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine and Yale New Haven Hospital, New Haven, CT, USA
| | - Jan P Bewersdorf
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine and Yale New Haven Hospital, New Haven, CT, USA
| | - Rory M Shallis
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine and Yale New Haven Hospital, New Haven, CT, USA
| | - Ted M Getz
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine and Yale New Haven Hospital, New Haven, CT, USA
| | - Jessica M Stempel
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine and Yale New Haven Hospital, New Haven, CT, USA
| | - Tariq Kewan
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine and Yale New Haven Hospital, New Haven, CT, USA
| | - Maximilian Stahl
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amer M Zeidan
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine and Yale New Haven Hospital, New Haven, CT, USA
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3
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Wang P, Chen LL, Xiong Y, Ye D. Metabolite regulation of epigenetics in cancer. Cell Rep 2024; 43:114815. [PMID: 39368084 DOI: 10.1016/j.celrep.2024.114815] [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: 06/23/2024] [Revised: 08/17/2024] [Accepted: 09/17/2024] [Indexed: 10/07/2024] Open
Abstract
The catalytic activity of most epigenetic enzymes requires a metabolite produced by central carbon metabolism as a cofactor or (co-)substrate. The concentrations of these metabolites undergo dynamic changes in response to nutrient levels and environmental conditions, reprogramming metabolic processes and epigenetic landscapes. Abnormal accumulations of epigenetic modulatory metabolites resulting from mutations in metabolic enzymes contribute to tumorigenesis. In this review, we first present the concept that metabolite regulation of gene expression represents an evolutionarily conserved mechanism from prokaryotes to eukaryotes. We then review how individual metabolites affect epigenetic enzymes and cancer development. Lastly, we discuss the advancement of and opportunity for therapeutic targeting of metabolite-epigenetic regulation in cancer therapy.
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Affiliation(s)
- Pu Wang
- Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Lei-Lei Chen
- Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Yue Xiong
- Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China; Cullgen, Inc., 12671 High Bluff Drive, San Diego, CA 92130, USA.
| | - Dan Ye
- Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China.
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4
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Parente AD, Bolland DE, Huisinga KL, Provost JJ. Physiology of malate dehydrogenase and how dysregulation leads to disease. Essays Biochem 2024; 68:121-134. [PMID: 38962852 DOI: 10.1042/ebc20230085] [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: 03/03/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 07/05/2024]
Abstract
Malate dehydrogenase (MDH) is pivotal in mammalian tissue metabolism, participating in various pathways beyond its classical roles and highlighting its adaptability to cellular demands. This enzyme is involved in maintaining redox balance, lipid synthesis, and glutamine metabolism and supports rapidly proliferating cells' energetic and biosynthetic needs. The involvement of MDH in glutamine metabolism underlines its significance in cell physiology. In contrast, its contribution to lipid metabolism highlights its role in essential biosynthetic processes necessary for cell maintenance and proliferation. The enzyme's regulatory mechanisms, such as post-translational modifications, underscore its complexity and importance in metabolic regulation, positioning MDH as a potential target in metabolic dysregulation. Furthermore, the association of MDH with various pathologies, including cancer and neurological disorders, suggests its involvement in disease progression. The overexpression of MDH isoforms MDH1 and MDH2 in cancers like breast, prostate, and pancreatic ductal adenocarcinoma, alongside structural modifications, implies their critical role in the metabolic adaptation of tumor cells. Additionally, mutations in MDH2 linked to pheochromocytomas, paragangliomas, and other metabolic diseases emphasize MDH's role in metabolic homeostasis. This review spotlights MDH's potential as a biomarker and therapeutic target, advocating for further research into its multifunctional roles and regulatory mechanisms in health and disease.
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Affiliation(s)
- Amy D Parente
- Department of Chemistry and Biochemistry, Mercyhurst University, Erie, PA, U.S.A
| | - Danielle E Bolland
- Department of Biology, University of Minnesota Morris, Morris, MN 56267, U.S.A
| | - Kathryn L Huisinga
- Department of Chemistry and Biochemistry, Malone University, Canton, OH 44709, U.S.A
| | - Joseph J Provost
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, U.S.A
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5
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Garcia I, Cornely K, Peterson CN, Berkmen MB. Roles of the oncometabolite enantiomers of 2-hydroxyglutarate and their metabolism by diverse dehydrogenases. Essays Biochem 2024; 68:161-171. [PMID: 38919140 DOI: 10.1042/ebc20230077] [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: 04/30/2024] [Revised: 06/09/2024] [Accepted: 06/11/2024] [Indexed: 06/27/2024]
Abstract
2-Hydroxyglutarate (2HG) is an oncometabolite that can contribute to tumor progression. Two enantiomer forms, L-2HG and D-2HG, arise from independent pathways starting from the precursor α-ketoglutarate (αKG). L-2HG production occurs through the promiscuous activities of malate dehydrogenase (MDH) and lactate dehydrogenase (LDH) under acidic and/or hypoxic conditions. D-2HG frequently accumulates by gain-of-function mutations in the genes encoding two isoforms of isocitrate dehydrogenase (IDH1 and IDH2). Cognate metabolite repair enzymes, L- and D-2-hydroxyglutarate dehydrogenases, oxidize the enantiomers and cause abnormally high 2HG accumulation and disease when mutated. Elevated levels of either oncometabolite affect redox homeostasis, metabolism, and immune system functioning. Moreover, the oncometabolites inhibit several α-ketoglutarate-dependent dioxygenases resulting in epigenetic changes such as DNA and histone hypermethylation as well as deficiencies in DNA repair. L-2HG, and D-2HG in some cases, inhibit degradation of hypoxia-inducible factor (HIF1α), a transcription factor that alters gene expression to adapt to hypoxic conditions, favoring tumorigenesis. Patients with the rare disease 2-hydroxyglutaric aciduria (2HGA) have exceedingly high levels of 2HG, which is neurotoxic, causing developmental delays and brain abnormalities. D-2HG also has specific effects on collagen production and NADPH pools. Recently, D-2HG has been targeted in new chemotherapies aimed at disrupting the gain-of-function IDH1 and IDH2 mutants, resulting in successful clinical trials for several cancers.
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Affiliation(s)
- Ivelitza Garcia
- Department of Chemistry, Allegheny College, Meadville, PA, U.S.A
| | - Kathleen Cornely
- Department of Chemistry and Biochemistry, Providence College, Providence, RI, U.S.A
| | | | - Melanie B Berkmen
- Department of Biochemistry, Chemistry, Environment, and Physics, Suffolk University, Boston, MA, U.S.A
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6
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Zheng X, Zhang S, Ma H, Dong Y, Zheng J, Zeng L, Liu J, Dai Y, Yin Q. Replenishment of TCA cycle intermediates and long-noncoding RNAs regulation in breast cancer. Mol Cell Endocrinol 2024; 592:112321. [PMID: 38936596 DOI: 10.1016/j.mce.2024.112321] [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: 12/02/2023] [Revised: 03/13/2024] [Accepted: 06/24/2024] [Indexed: 06/29/2024]
Abstract
The tricarboxylic acid (TCA) cycle is an essential interface that coordinates cellular metabolism and is as a primary route determining the fate of a variety of fuel sources, including glucose, fatty acid and glutamate. The crosstalk of nutrients replenished TCA cycle regulates breast cancer (BC) progression by changing substrate levels-induced epigenetic alterations, especially the methylation, acetylation, succinylation and lactylation. Long non-coding RNAs (lncRNA) have dual roles in inhibiting or promoting energy reprogramming, and so altering the metabolic flux of fuel sources to the TCA cycle, which may regulate epigenetic modifications at the cellular level of BC. This narrative review discussed the central role of the TCA cycle in interconnecting numerous fuels and the induced epigenetic modifications, and the underlying regulatory mechanisms of lncRNAs in BC.
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Affiliation(s)
- Xuewei Zheng
- Precision Medicine Laboratory, School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
| | - ShunShun Zhang
- Precision Medicine Laboratory, School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
| | - HaoDi Ma
- Precision Medicine Laboratory, School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
| | - Yirui Dong
- Precision Medicine Laboratory, School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
| | - Jiayu Zheng
- Precision Medicine Laboratory, School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
| | - Li Zeng
- Precision Medicine Laboratory, School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
| | - Jiangbo Liu
- Department of General Surgery, First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, China
| | - Yanzhenzi Dai
- Animal Science, School of Biosciences, University of Nottingham, UK.
| | - Qinan Yin
- Precision Medicine Laboratory, School of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China.
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7
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Zschernack V, Thomas C, Schaub C, Kristiansen G, Waha A, Goschzik T, Herrlinger U, Pietsch T. FH-mutant glioma displaying the epigenetic signature of IDH-mutant astrocytomas. J Neuropathol Exp Neurol 2024; 83:887-889. [PMID: 38874462 DOI: 10.1093/jnen/nlae064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024] Open
Affiliation(s)
- Valentina Zschernack
- Department of Neuropathology, DGNN Brain Tumor Reference Center, University Hospital Bonn, Bonn, Germany
| | - Christian Thomas
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Christina Schaub
- Department of Neurooncology, Center for Neurology and Center of Integrated Oncology (CIO), University Hospital Bonn, Bonn, Germany
| | | | - Andreas Waha
- Department of Neuropathology, DGNN Brain Tumor Reference Center, University Hospital Bonn, Bonn, Germany
| | - Tobias Goschzik
- Department of Neuropathology, DGNN Brain Tumor Reference Center, University Hospital Bonn, Bonn, Germany
| | - Ulrich Herrlinger
- Department of Neurooncology, Center for Neurology and Center of Integrated Oncology (CIO), University Hospital Bonn, Bonn, Germany
| | - Torsten Pietsch
- Department of Neuropathology, DGNN Brain Tumor Reference Center, University Hospital Bonn, Bonn, Germany
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8
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Urrutia S, Takahashi K. Precision medicine in AML: overcoming resistance. Int J Hematol 2024; 120:439-454. [PMID: 39085680 DOI: 10.1007/s12185-024-03827-8] [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: 04/19/2024] [Revised: 07/04/2024] [Accepted: 07/24/2024] [Indexed: 08/02/2024]
Abstract
The development of molecularly targeted therapy for acute myeloid leukemia is progressing at an accelerated pace. Therapies targeting FLT3, IDH1, IDH2, and BCL2 have been approved in the last 5 years. As we exploit these biological vulnerabilities, various mechanisms of resistance arise. Emergence of competing clones with different genetic drivers and acquisition of constitutional mutations in the target renders therapies ineffective, and enzymatic isoform changes can lead to reappearance of the disease phenotype. Understanding the timing and circumstances of resistance origination will allow clinicians to develop combinatorial and sequential therapeutic approaches to deepen responses and improve survival. The objective of this review is to illustrate the biological underpinnings of each therapy and the landscape of resistance mechanisms and discuss strategies to overcome on- and off-target resistance.
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Affiliation(s)
- Samuel Urrutia
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, 1901 East Road, 4SCR6.2085, Houston, TX, 77030-4009, USA
| | - Koichi Takahashi
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, USA.
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9
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Li M, Liu J, Weng J, Dong G, Chen X, Cui Y, Ren X, Shen S, Jiang H, Zhang X, Zhao X, Li M, Wang X, Ren H, Li Q, Zhang Y, Cheng Q, Yu Y, Lin S. Unveiling hierarchy and spatial distribution of O 6-methylguanine-DNA methyltransferase promoter methylation in World Health Organization grade 2-3 gliomas. Cancer Sci 2024; 115:3403-3414. [PMID: 39101880 PMCID: PMC11447971 DOI: 10.1111/cas.16268] [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: 03/30/2024] [Revised: 06/13/2024] [Accepted: 06/24/2024] [Indexed: 08/06/2024] Open
Abstract
This study investigated the role of O6-methylguanine-DNA methyltransferase promoter (MGMTp) methylation hierarchy and heterogeneity in grade 2-3 gliomas, focusing on variations in chemotherapy benefits and resection dependency. A cohort of 668 newly diagnosed grade 2-3 gliomas, with comprehensive clinical, radiological, and molecular data, formed the basis of this analysis. The extent of resection was categorized into gross total resection (GTR ≥100%), subtotal resection (STR >90%), and partial resection (PR ≤90%). MGMTp methylation levels were examined using quantitative pyrosequencing. Our findings highlighted the critical role of GTR in improving the prognosis for astrocytomas (IDH1/2-mutant and 1p/19q non-codeleted), contrasting with its lesser significance for oligodendrogliomas (IDH1/2 mutation and 1p/19q codeletion). Oligodendrogliomas demonstrated the highest average MGMTp methylation levels (median: 28%), with a predominant percentage of methylated cases (average methylation levels >20%). Astrocytomas were more common in the low-methylated group (10%-20%), while IDH wild-type gliomas were mostly unmethylated (<10%). Spatial distribution analysis revealed a decrement in frontal lobe involvement from methylated, low-methylated to unmethylated cases (72.8%, 59.3%, and 47.8%, respectively). In contrast, low-methylated and unmethylated cases were more likely to invade the temporal-insular region (19.7%, 34.3%, and 40.4%, respectively). Astrocytomas with intermediate MGMTp methylation were notably associated with temporal-insular involvement, potentially indicating a moderate response to temozolomide and underscoring the importance of aggressive resection strategies. In conclusion, our study elucidates the complex interplay of MGMTp methylation hierarchy and heterogeneity among grade 2-3 gliomas, providing insights into why astrocytomas and IDH wild-type lower-grade glioma might derive less benefit from chemotherapy.
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Affiliation(s)
- Mingxiao Li
- Department of Neurosurgery, China-Japan Friendship Hospital, Beijing, China
- Department of Neurosurgical Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jiang Liu
- Department of Neurosurgery, China-Japan Friendship Hospital, Beijing, China
| | - Jiancong Weng
- Department of Neurosurgery, China-Japan Friendship Hospital, Beijing, China
| | - Gehong Dong
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Xuzhu Chen
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yong Cui
- Department of Neurosurgical Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Xiaohui Ren
- Department of Neurosurgical Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Shaoping Shen
- Department of Neurosurgical Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Haihui Jiang
- Department of Neurosurgery, Peking University Third Hospital, Beijing, China
| | - Xiaokang Zhang
- Department of Neurosurgical Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Xuzhe Zhao
- Department of Neurosurgical Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Ming Li
- Department of Neurosurgical Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Xijie Wang
- Department of Neurosurgical Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Hongxiang Ren
- Department of Neurosurgery, China-Japan Friendship Hospital, Beijing, China
| | - Qiang Li
- Department of Neurosurgery, China-Japan Friendship Hospital, Beijing, China
| | - Yulian Zhang
- Department of Neurosurgery, China-Japan Friendship Hospital, Beijing, China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yanbing Yu
- Department of Neurosurgery, China-Japan Friendship Hospital, Beijing, China
| | - Song Lin
- Department of Neurosurgical Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
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Dunn WG, McLoughlin MA, Vassiliou GS. Clonal hematopoiesis and hematological malignancy. J Clin Invest 2024; 134:e180065. [PMID: 39352393 PMCID: PMC11444162 DOI: 10.1172/jci180065] [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: 10/03/2024] Open
Abstract
Clonal hematopoiesis (CH), the expansion of hematopoietic stem cells and their progeny driven by somatic mutations in leukemia-associated genes, is a common phenomenon that rises in prevalence with advancing age to affect most people older than 70 years. CH remains subclinical in most carriers, but, in a minority, it progresses to a myeloid neoplasm, such as acute myeloid leukemia, myelodysplastic syndrome, or myeloproliferative neoplasm. Over the last decade, advances in our understanding of CH, its molecular landscape, and the risks associated with different driver gene mutations have culminated in recent developments that allow for a more precise estimation of myeloid neoplasia risk in CH carriers. In turn, this is leading to the development of translational and clinical programs to intercept and prevent CH from developing into myeloid neoplasia. Here, we give an overview of the spectrum of CH driver mutations, what is known about their pathophysiology, and how this informs the risk of incident myeloid malignancy.
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Affiliation(s)
- William G. Dunn
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Trust, Cambridge, United Kingdom
| | - Matthew A. McLoughlin
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - George S. Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Trust, Cambridge, United Kingdom
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11
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Ponomarova O, Starbard AN, Belfi A, Anderson AV, Sundaram MV, Walhout AJ. idh-1 neomorphic mutation confers sensitivity to vitamin B12 in Caenorhabditis elegans. Life Sci Alliance 2024; 7:e202402924. [PMID: 39009411 PMCID: PMC11249921 DOI: 10.26508/lsa.202402924] [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: 07/02/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 07/17/2024] Open
Abstract
In humans, a neomorphic isocitrate dehydrogenase mutation (idh-1neo) causes increased levels of cellular D-2-hydroxyglutarate (D-2HG), a proposed oncometabolite. However, the physiological effects of increased D-2HG and whether additional metabolic changes occur in the presence of an idh-1neo mutation are not well understood. We created a Caenorhabditis elegans model to study the effects of the idh-1neo mutation in a whole animal. Comparing the phenotypes exhibited by the idh-1neo to ∆dhgd-1 (D-2HG dehydrogenase) mutant animals, which also accumulate D-2HG, we identified a specific vitamin B12 diet-dependent vulnerability in idh-1neo mutant animals that leads to increased embryonic lethality. Through a genetic screen, we found that impairment of the glycine cleavage system, which generates one-carbon donor units, exacerbates this phenotype. In addition, supplementation with alternate sources of one-carbon donors suppresses the lethal phenotype. Our results indicate that the idh-1neo mutation imposes a heightened dependency on the one-carbon pool and provides a further understanding of how this oncogenic mutation rewires cellular metabolism.
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Affiliation(s)
- Olga Ponomarova
- https://ror.org/0464eyp60 Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- https://ror.org/05fs6jp91 Department of Biochemistry and Molecular Biology, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Alyxandra N Starbard
- https://ror.org/0464eyp60 Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Alexandra Belfi
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Amanda V Anderson
- https://ror.org/05fs6jp91 Department of Biochemistry and Molecular Biology, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Meera V Sundaram
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Albertha Jm Walhout
- https://ror.org/0464eyp60 Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
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12
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Hao J, Huang Z, Zhang S, Song K, Wang J, Gao C, Fang Z, Zhang N. Deciphering the multifaceted roles and clinical implications of 2-hydroxyglutarate in cancer. Pharmacol Res 2024; 209:107437. [PMID: 39349213 DOI: 10.1016/j.phrs.2024.107437] [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: 06/25/2024] [Revised: 09/13/2024] [Accepted: 09/24/2024] [Indexed: 10/02/2024]
Abstract
Increasing evidence indicates that 2-hydroxyglutarate (2HG) is an oncometabolite that drives tumour formation and progression. Due to mutations in isocitrate dehydrogenase (IDH) and the dysregulation of other enzymes, 2HG accumulates significantly in tumour cells. Due to its structural similarity to α-ketoglutarate (αKG), accumulated 2HG leads to the competitive inhibition of αKG-dependent dioxygenases (αKGDs), such as KDMs, TETs, and EGLNs. This inhibition results in epigenetic alterations in both tumour cells and the tumour microenvironment. This review comprehensively discusses the metabolic pathways of 2HG and the subsequent pathways influenced by elevated 2HG levels. We will delve into the molecular mechanisms by which 2HG exerts its oncogenic effects, particularly focusing on epigenetic modifications. This review will also explore the various methods available for the detection of 2HG, emphasising both current techniques and emerging technologies. Furthermore, 2HG shows promise as a biomarker for clinical diagnosis and treatment. By integrating these perspectives, this review aims to provide a comprehensive overview of the current understanding of 2HG in cancer biology, highlight the importance of ongoing research, and discuss future directions for translating these findings into clinical applications.
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Affiliation(s)
- Jie Hao
- Department of Breast Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Ziyi Huang
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Siyue Zhang
- Department of Breast Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Kefan Song
- Department of Urology, Qilu Hospital of Shandong University, Jinan, China
| | - Juncheng Wang
- Advanced Medical Research Institute, Shandong University, Jinan, China
| | - Chao Gao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Zhiqing Fang
- Department of Urology, Qilu Hospital of Shandong University, Jinan, China
| | - Ning Zhang
- Department of Breast Surgery, Qilu Hospital of Shandong University, Jinan, China.
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13
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Roux A, Saadi TA, Luo M, Le PU, Diaz R, Petrecca K. Working towards understanding the natural history and treatment response of noncanonical IDH mutant astrocytomas. Neurochirurgie 2024; 70:101599. [PMID: 39341335 DOI: 10.1016/j.neuchi.2024.101599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2024] [Revised: 09/07/2024] [Accepted: 09/11/2024] [Indexed: 10/01/2024]
Affiliation(s)
- Alexandre Roux
- GHU-Paris Psychiatrie et Neurosciences, Hôpital Sainte Anne, Service de Neurochirurgie, F-75014 Paris, France; Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, IMA-Brain, 75014 Paris, France.
| | - Tariq Al Saadi
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec, Canada
| | - Michael Luo
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec, Canada
| | - Phuong Uyen Le
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec, Canada
| | - Roberto Diaz
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec, Canada
| | - Kevin Petrecca
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec, Canada
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14
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Lacoste J, Haghighi M, Haider S, Reno C, Lin ZY, Segal D, Qian WW, Xiong X, Teelucksingh T, Miglietta E, Shafqat-Abbasi H, Ryder PV, Senft R, Cimini BA, Murray RR, Nyirakanani C, Hao T, McClain GG, Roth FP, Calderwood MA, Hill DE, Vidal M, Yi SS, Sahni N, Peng J, Gingras AC, Singh S, Carpenter AE, Taipale M. Pervasive mislocalization of pathogenic coding variants underlying human disorders. Cell 2024:S0092-8674(24)01021-3. [PMID: 39353438 DOI: 10.1016/j.cell.2024.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 07/22/2024] [Accepted: 09/04/2024] [Indexed: 10/04/2024]
Abstract
Widespread sequencing has yielded thousands of missense variants predicted or confirmed as disease causing. This creates a new bottleneck: determining the functional impact of each variant-typically a painstaking, customized process undertaken one or a few genes and variants at a time. Here, we established a high-throughput imaging platform to assay the impact of coding variation on protein localization, evaluating 3,448 missense variants of over 1,000 genes and phenotypes. We discovered that mislocalization is a common consequence of coding variation, affecting about one-sixth of all pathogenic missense variants, all cellular compartments, and recessive and dominant disorders alike. Mislocalization is primarily driven by effects on protein stability and membrane insertion rather than disruptions of trafficking signals or specific interactions. Furthermore, mislocalization patterns help explain pleiotropy and disease severity and provide insights on variants of uncertain significance. Our publicly available resource extends our understanding of coding variation in human diseases.
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Affiliation(s)
- Jessica Lacoste
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | | | - Shahan Haider
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Chloe Reno
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Dmitri Segal
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Wesley Wei Qian
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Xueting Xiong
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Tanisha Teelucksingh
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | | | | | - Pearl V Ryder
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Rebecca Senft
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Beth A Cimini
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ryan R Murray
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Chantal Nyirakanani
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gregory G McClain
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Frederick P Roth
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada; Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Michael A Calderwood
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David E Hill
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - S Stephen Yi
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA; Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, TX, USA; Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, USA; Interdisciplinary Life Sciences Graduate Programs (ILSGP), College of Natural Sciences, The University of Texas at Austin, Austin, TX, USA
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Quantitative and Computational Biosciences Program, Baylor College of Medicine, Houston, TX, USA
| | - Jian Peng
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | | | | | - Mikko Taipale
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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15
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Broome JA, Nguyen NP, Baumung CRE, Chen VC, Bushnell EAC. Gaining Insight into the Catalytic Mechanism of the R132H IDH1 Mutant: A Synergistic DFT Cluster and Experimental Investigation. Biochemistry 2024. [PMID: 39318042 DOI: 10.1021/acs.biochem.4c00022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2024]
Abstract
Human isocitrate dehydrogenase 1 (IDH1) is an enzyme that is found in humans that plays a critical role in aerobic metabolism. As a part of the citric acid cycle, IDH1 becomes responsible for catalyzing the oxidative decarboxylation of isocitrate to form α-ketoglutarate (αKG), with nicotinamide adenine dinucleotide phosphate (NADP+) as a cofactor. Strikingly, mutations of the IDH1 enzyme have been discovered in several cancers including glioblastoma multiforme (GBM), a highly aggressive form of brain cancer. It has been experimentally determined that single-residue IDH1 mutations occur at a very high frequency in GBM. Specifically, the IDH1 R132H mutation is known to produce (D)2-hydroxyglutarate (2HG), a recognized oncometabolite. Using the previously determined catalytic mechanism of IDH1, a DFT QM model was developed to study the mechanistic properties of IDH1 R132H compared to wild type enzyme. Validating these insights, biochemical in vitro assays of metabolites produced by mutant vs wild type enzymes were measured and compared. From the results discussed herein, we discuss the mechanistic impact of mutations in IDH1 on its ability to catalyze the formation of αKG and 2HG.
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Affiliation(s)
- Joshua A Broome
- Department of Chemistry, Brandon University, 270-18th Street, Brandon, Manitoba R7A 6A9, Canada
| | - Nguyen P Nguyen
- Department of Chemistry, Brandon University, 270-18th Street, Brandon, Manitoba R7A 6A9, Canada
| | - Cassidy R E Baumung
- Department of Chemistry, Brandon University, 270-18th Street, Brandon, Manitoba R7A 6A9, Canada
| | - Vincent C Chen
- Department of Chemistry, Brandon University, 270-18th Street, Brandon, Manitoba R7A 6A9, Canada
| | - Eric A C Bushnell
- Department of Chemistry, Brandon University, 270-18th Street, Brandon, Manitoba R7A 6A9, Canada
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16
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Kierans AS, Lutfi A, Afghan MK, Khan S, Javaid S, Currie BM, Rocca J, Samstein B, Golden E, Popa E, Hissong E, Kasi PM. Spectrum of Findings Seen in Patients With IDH1/2-Mutant Cholangiocarcinoma. Int J Surg Pathol 2024:10668969241271397. [PMID: 39314068 DOI: 10.1177/10668969241271397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
BACKGROUND Cholangiocarcinoma-with a growing incidence rate and poor prognosis-is not an aggressive tumor that is not uncommon. Molecular profiling can reveal actionable aberrations in at least a third of the tumors. This is especially so in the case of intrahepatic cholangiocarcinoma (ICC), where mutations in the isocitrate dehydrogenase 1 and 2 genes (IDH1/2) make up 15%-20% of these tumors. IDH1/2 mutant ICC is a rare disease that has not been adequately reported. To expand the spectrum of findings seen in these patients, we present a single institution case series. METHODS AND RESULTS We descriptively characterize the clinical, radiological, and histopathological findings of 12 such patients. IDH1/2 mutant ICC was found in elderly women, with two-thirds of patients having additional co-mutations. Anecdotally, patients who did receive systemic and/or locoregional therapies had long-term durable outcomes. CONCLUSION Our findings indicate an increasing need to personalize an approach for these patients with specific molecular alterations. With the advent of the IDH1 inhibitor ivosidenib and other inhibitors in this space, IDH1/2 mutation has both prognostic and predictive value. Our series builds upon the patterns and findings seen in these patients.
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Affiliation(s)
| | - Areeb Lutfi
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Maaz Khan Afghan
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Sahrish Khan
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Sana Javaid
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Brian Michael Currie
- Department of Vascular and Interventional Radiology, Weill Cornell Medicine, New York, NY, USA
| | - Juan Rocca
- Division of Liver Transplantation and Hepatobiliary Surgery, Department of Surgery, Weill Cornell Medicine, New York, NY, USA
| | - Benjamin Samstein
- Division of Liver Transplantation and Hepatobiliary Surgery, Department of Surgery, Weill Cornell Medicine, New York, NY, USA
| | - Encouse Golden
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Elizabeta Popa
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Erika Hissong
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Pashtoon Murtaza Kasi
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
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17
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Nakhate V, Lasica AB, Wen PY. The Role of Mutant IDH Inhibitors in the Treatment of Glioma. Curr Neurol Neurosci Rep 2024:10.1007/s11910-024-01378-3. [PMID: 39302605 DOI: 10.1007/s11910-024-01378-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2024] [Indexed: 09/22/2024]
Abstract
PURPOSE OF REVIEW The identification of isocitrate dehydrogenase (IDH) mutations has led to a transformation in our understanding of gliomas and has paved the way to a new era of targeted therapy. In this article, we review the classification of IDH-mutant glioma, standard of care treatment options, clinical evidence for mutant IDH (mIDH) inhibitors, and practical implications of the recent landmark INDIGO trial. RECENT FINDINGS In the phase 3 randomized placebo-controlled INDIGO trial, mIDH1/2 inhibitor vorasidenib increased progression-free survival among non-enhancing grade 2 IDH-mutant gliomas following surgery. This marks the first positive randomized trial of targeted therapy in IDH-mutant glioma, and led to the US Food and Drug Administration's approval of vorasidenib in August 2024 for grade 2 IDH-mutant glioma. Vorasidenib is a well-tolerated treatment that can benefit a subset of patients with IDH-mutant glioma. Targeting mIDH also remains a promising strategy for select groups of patients excluded from the INDIGO trial. Ongoing and future studies, including with new agents and with combination therapy approaches, may expand the benefit and unlock the potential of mIDH inhibitors.
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Affiliation(s)
- Vihang Nakhate
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Pappas Center for Neuro-Oncology, Massachusetts General Hospital, Boston, MA, USA.
| | - Aleksandra B Lasica
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Patrick Y Wen
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
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18
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Tateishi K. Translational Research Platform for Malignant Central Nervous System Tumors. Neurol Med Chir (Tokyo) 2024; 64:323-329. [PMID: 39111869 PMCID: PMC11461184 DOI: 10.2176/jns-nmc.2024-0078] [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: 04/08/2024] [Accepted: 06/12/2024] [Indexed: 09/18/2024] Open
Abstract
Some central nervous system (CNS) malignancies are highly aggressive and urgently need innovative treatment strategies to improve prognosis. A significant concern for therapeutic development is the time-consuming nature of developing treatments for CNS tumors. Therefore, a rapid and efficient translational approach is needed to address this problem. Translational and reverse translational research aims to bridge the gap between laboratory data and clinical applications and has been developed in the field of neuro-oncology. This study presents our translational platform systems for malignant CNS tumors, which combine an intraoperative integrated diagnostic system and comprehensive in vitro and in vivo assay systems. These laboratory systems may contribute to a better understanding of tumor biology and the development of novel therapeutic strategies for the poor prognosis of CNS tumors.
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Affiliation(s)
- Kensuke Tateishi
- Department of Neurosurgery, Graduate School of Medicine, Yokohama City University
- Laboratory of Biopharmaceutical and Regenerative Science, Graduate School of Medical Science, Yokohama City University
- Neurosurgical-Oncology Laboratory, Yokohama City University
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19
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Yu Y, Gan W, Xiong J, Li J. A novel biomarker GATM suppresses proliferation and malignancy of cholangiocarcinoma cells by modulating the JNK/c-Jun signalling pathways. Heliyon 2024; 10:e37344. [PMID: 39296238 PMCID: PMC11408786 DOI: 10.1016/j.heliyon.2024.e37344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 08/30/2024] [Accepted: 09/02/2024] [Indexed: 09/21/2024] Open
Abstract
Background Cholangiocarcinoma (CCA) is the second most common primary malignancy of the liver and is associated with poor prognosis. Despite the emerging role of glycine amidinotransferase (GATM) in cancer development, its function in CCA remains elusive. This study investigated the biological significance and molecular mechanisms of GATM in CCA. Method GATM expression was measured using immunohistochemistry and western blotting. Cell proliferation, migration, and invasion were assessed through CCK-8, EdU, clone formation, wound healing, and Transwell assays. Rescue experiments were performed to determine whether the JNK/c-Jun pathway is involved in GATM-mediated CCA development. Immunoprecipitation and mass spectrometry were performed to screen for proteins that interact with GATM. The role of GATM in vivo was investigated according to the xenograft experiment. Result GATM expression was downregulated in CCA tissues and cells (p < 0.05) and had a significant suppressive effect on CCA cell proliferation, migration, and invasion in vitro as well as on tumour growth in vivo (p < 0.05); conversely, GATM knockdown promoted these phenotypes (p < 0.05). Notably, GATM inhibited the JNK/c-Jun pathway, and JNK activation abrogated GATM's antitumor effects (p < 0.05). Isocitrate dehydrogenase 1 (IDH1) interacts with GATM, and IDH1 knockdown significantly attenuated GATM protein degradation. Overexpression of IDH1 restored the biological function of CCA by reversing the inhibition of JNK/c-Jun pathway phosphorylation by GATM (p < 0.05). Conclusion GATM acts as a tumour suppressor in CCA by regulating the phosphorylation of the JNK/c-Jun pathway. IDH1 interacted with GATM to regulate CCA progression.
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Affiliation(s)
- Yi Yu
- Department of Oncology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Wei Gan
- Department of Thoracic Surgery, Sun Yat-sen University Cancer Centre, Guangzhou City, Guangdong Province, 510060, China
| | - Jianping Xiong
- Department of Oncology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Junhe Li
- Department of Oncology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
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20
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Davies-Jenkins CW, Zöllner HJ, Simicic D, Alcicek S, Edden RAE, Oeltzschner G. Data-driven determination of 1H-MRS basis set composition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.11.612503. [PMID: 39314430 PMCID: PMC11419043 DOI: 10.1101/2024.09.11.612503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Purpose Metabolite amplitude estimates derived from linear combination modeling of MR spectra depend upon the precise list of constituent metabolite basis functions used (the "basis set"). The absence of clear consensus on the "ideal" composition or objective criteria to determine the suitability of a particular basis set contributes to the poor reproducibility of MRS. In this proof-of-concept study, we demonstrate a novel, data-driven approach for deciding the basis-set composition using Bayesian information criteria (BIC). Methods We have developed an algorithm that iteratively adds metabolites to the basis set using iterative modeling, informed by BIC scores. We investigated two quantitative "stopping conditions", referred to as max-BIC and zero-amplitude, and whether to optimize the selection of basis set on a per-spectrum basis or at the group level. The algorithm was tested using two groups of synthetic in-vivo-like spectra representing healthy brain and tumor spectra, respectively, and the derived basis sets (and metabolite amplitude estimates) were compared to the ground truth. Results All derived basis sets correctly identified high-concentration metabolites and provided reasonable fits of the spectra. At the single-spectrum level, the two stopping conditions derived the underlying basis set with 77-87% accuracy. When optimizing across a group, basis set determination accuracy improved to 84-92%. Conclusion Data-driven determination of the basis set composition is feasible. With refinement, this approach could provide a valuable data-driven way to derive or refine basis sets, reducing the operator bias of MRS analyses, enhancing the objectivity of quantitative analyses, and increasing the clinical viability of MRS.
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Affiliation(s)
- Christopher W Davies-Jenkins
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Helge J Zöllner
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Dunja Simicic
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Seyma Alcicek
- Institute of Neuroradiology, University Hospital Frankfurt, Goethe University, Frankfurt/Main, Germany
- University Cancer Center Frankfurt (UCT), Frankfurt/Main, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt/Main, Germany
| | - Richard A E Edden
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Georg Oeltzschner
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD, USA
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21
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Ahmed Adam MA, Robinson M, Schwartz AV, Wells G, Hoang A, Albekioni E, Gallo C, Chao G, Weeks J, Quichocho G, George UZ, House CD, Turcan Ş, Sohl CD. Catalytically distinct IDH1 mutants tune phenotype severity in tumor models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.22.590655. [PMID: 38712107 PMCID: PMC11071412 DOI: 10.1101/2024.04.22.590655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Mutations in isocitrate dehydrogenase 1 (IDH1) impart a neomorphic reaction that produces D-2-hydroxyglutarate (D2HG), which can inhibit DNA demethylases to drive tumorigenesis. Mutations affect residue R132 and display distinct catalytic profiles for D2HG production. We show that catalytic efficiency of D2HG production is greater in IDH1 R132Q than R132H mutants, and expression of R132Q in cellular and xenograft models leads to higher D2HG concentrations in cells, tumors, and sera compared to R132H. Though expression of IDH1 R132Q leads to hypermethylation in DNA damage pathways, DNA hypomethylation is more notable when compared to R132H expression. Transcriptome analysis shows increased expression of many pro-tumor pathways upon expression of IDH1 R132Q versus R132H, including transcripts of EGFR and PI3K signaling pathways. Thus, IDH1 mutants appear to modulate D2HG levels via altered catalysis, resulting in distinct epigenetic and transcriptomic consequences where higher D2HG levels appear to be associated with more aggressive tumors.
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Affiliation(s)
- Mowaffaq Adam Ahmed Adam
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182, USA
- These authors contributed equally: Mowaffaq Adam Ahmed Adam, Mikella Robinson, Ashley Schwartz, Grace Wells
| | - Mikella Robinson
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
- These authors contributed equally: Mowaffaq Adam Ahmed Adam, Mikella Robinson, Ashley Schwartz, Grace Wells
| | - Ashley V. Schwartz
- Computational Science Research Center, San Diego State University, San Diego, CA 92182, USA
- These authors contributed equally: Mowaffaq Adam Ahmed Adam, Mikella Robinson, Ashley Schwartz, Grace Wells
| | - Grace Wells
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182, USA
- These authors contributed equally: Mowaffaq Adam Ahmed Adam, Mikella Robinson, Ashley Schwartz, Grace Wells
| | - An Hoang
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182, USA
| | - Elene Albekioni
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182, USA
| | - Cecilia Gallo
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Grace Chao
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Joi Weeks
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Giovanni Quichocho
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182, USA
| | - Uduak Z. George
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA 92182, USA
- Computational Science Research Center, San Diego State University, San Diego, CA 92182, USA
| | - Carrie D. House
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Şevin Turcan
- Neurology Clinic and National Center for Tumor Diseases, Heidelberg University Hospital and Heidelberg University, 69120 Heidelberg, Germany
| | - Christal D. Sohl
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182, USA
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22
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Gantner BN, Palma FR, Pandkar MR, Sakiyama MJ, Arango D, DeNicola GM, Gomes AP, Bonini MG. Metabolism and epigenetics: drivers of tumor cell plasticity and treatment outcomes. Trends Cancer 2024:S2405-8033(24)00172-9. [PMID: 39277448 DOI: 10.1016/j.trecan.2024.08.005] [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: 03/04/2024] [Revised: 08/01/2024] [Accepted: 08/13/2024] [Indexed: 09/17/2024]
Abstract
Emerging evidence indicates that metabolism not only is a source of energy and biomaterials for cell division but also acts as a driver of cancer cell plasticity and treatment resistance. This is because metabolic changes lead to remodeling of chromatin and reprogramming of gene expression patterns, furthering tumor cell phenotypic transitions. Therefore, the crosstalk between metabolism and epigenetics seems to hold immense potential for the discovery of novel therapeutic targets for various aggressive tumors. Here, we highlight recent discoveries supporting the concept that the cooperation between metabolism and epigenetics enables cancer to overcome mounting treatment-induced pressures. We discuss how specific metabolites contribute to cancer cell resilience and provide perspective on how simultaneously targeting these key forces could produce synergistic therapeutic effects to improve treatment outcomes.
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Affiliation(s)
- Benjamin N Gantner
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Flavio R Palma
- Department of Medicine, Feinberg School of Medicine and Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
| | - Madhura R Pandkar
- Department of Medicine, Feinberg School of Medicine and Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
| | - Marcelo J Sakiyama
- Department of Medicine, Feinberg School of Medicine and Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
| | - Daniel Arango
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Gina M DeNicola
- Department of Metabolism and Physiology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Ana P Gomes
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Marcelo G Bonini
- Department of Medicine, Feinberg School of Medicine and Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
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23
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Baek C, Laurenge A, Touat M. Advances in the treatment of IDH-mutant gliomas. Curr Opin Neurol 2024:00019052-990000000-00194. [PMID: 39253756 DOI: 10.1097/wco.0000000000001316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
PURPOSE OF REVIEW Isocitrate dehydrogenase (IDH) mutation is a defining molecular driver of WHO grade 2-4 astrocytomas and oligodendrogliomas. In this article, we review the recent therapeutic approaches specifically targeting IDH-mutant gliomas and summarize ongoing clinical trials in this population. RECENT FINDINGS The IDH inhibitor vorasidenib recently demonstrated its efficacy after surgical resection in grade 2 IDH-mutated gliomas. Several studies in patients with IDH-mutant gliomas are currently exploring various strategies to target IDH mutations, including the use of small-molecule inhibitors, immunotherapies, peptide vaccines and agents targeting metabolic and epigenomic vulnerabilities. SUMMARY Mutant-IDH targeting holds significant promise in treating progressive or recurrent IDH-mutant gliomas. Recent results with IDH inhibitors will change practice and influence the existing guidelines in a near future.
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Affiliation(s)
- Chooyoung Baek
- Service de Neuro-oncologie, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, AP-HP, Sorbonne Université
| | - Alice Laurenge
- Service de Neuro-oncologie, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, AP-HP, Sorbonne Université
- Institut du Cerveau, Paris Brain Institute (ICM), Inserm, CNRS, Sorbonne Université, AP-HP, SIRIC CURAMUS, Paris, France
| | - Mehdi Touat
- Service de Neuro-oncologie, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, AP-HP, Sorbonne Université
- Institut du Cerveau, Paris Brain Institute (ICM), Inserm, CNRS, Sorbonne Université, AP-HP, SIRIC CURAMUS, Paris, France
- Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA
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24
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McCoy MA, Lu J, Richard Miller F, Soisson SM, Lam MH, Fischer C. Biostructural, biochemical and biophysical studies of mutant IDH1. Nat Commun 2024; 15:7877. [PMID: 39251618 PMCID: PMC11385386 DOI: 10.1038/s41467-024-51692-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/15/2024] [Indexed: 09/11/2024] Open
Abstract
We report bio-structural, bio-chemical and bio-physical evidence demonstrating how small molecules can bind to both wild-type and mutant IDH1, but only inhibit the enzymatic activity of the mutant isoform. Enabled through x-ray crystallography, we characterized a series of small molecule inhibitors that bound to mutant IDH1 differently than the marketed inhibitor Ivosidenib, for which we have determined the x-ray crystal structure. Across the industry several mutant IDH1 inhibitor chemotypes bind to this allosteric IDH1 pocket and selectively inhibit the mutant enzyme. Detailed characterization by a variety of biophysical techniques and NMR studies led us to propose how compounds binding in the allosteric IDH1 R132H pocket inhibit the production of 2-Hydroxy glutarate.
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Affiliation(s)
| | - Jun Lu
- MRL, Merck & Co., Inc., Rahway, NJ, USA
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25
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Tsilimigras DI, Stecko H, Ntanasis-Stathopoulos I, Pawlik TM. Racial and Sex Differences in Genomic Profiling of Intrahepatic Cholangiocarcinoma. Ann Surg Oncol 2024:10.1245/s10434-024-16141-8. [PMID: 39251514 DOI: 10.1245/s10434-024-16141-8] [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: 05/24/2024] [Accepted: 08/22/2024] [Indexed: 09/11/2024]
Abstract
BACKGROUND Racial and sex disparities in the incidence and outcomes of patients with intrahepatic cholangiocarcinoma (iCCA) exist, yet potential genomic variations of iCCA based on race and sex that might be contributing to disparate outcomes have not been well studied. METHODS Data from the American Association for Cancer Research Project GENIE registry (version 15.0) were analyzed to assess genetic variations in iCCA. Adult patients (age >18 years) with histologically confirmed iCCA who underwent next-generation sequencing were included in the analytic cohort. Racial and sex variations in genomic profiling of iCCA were examined. RESULTS The study enrolled 1068 patients from 19 centers (White, 71.9%; Black, 5.1%; Asian, 8.4%, other, 14.6%). The male-to-female ratio was 1:1. The majority of the patients had primary tumors (73.7%), whereas 23.0% had metastatic disease sequenced. While IDH1 mutations occurred more frequently in White versus Black patients (20.8% vs. 5.6%; p = 0.021), FGFR2 mutations tended to be more common among Black versus White populations (27.8% vs. 16.1%; p = 0.08). Males were more likely to have TP53 mutations than females (24.3% vs. 18.2%, p = 0.016), whereas females more frequently had IDH1 (23.3% vs 16.0 %), FGFR2 (21.0% vs. 11.3%), and BAP1 (23.4% vs. 14.5%) mutations than males (all p < 0.05). Marked variations in the prevalence of other common genomic alterations in iCCA were noted across different races and sexes. CONCLUSION Distinct genomic variations exist in iCCA across race and sex. Differences in mutational profiles of iCCA patients highlight the importance of including a diverse patient population in iCCA clinical trials as well as the importance of recognizing different genetic drivers that may be targetable to treat distinct patient cohorts.
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Affiliation(s)
- Diamantis I Tsilimigras
- Department of Surgery, Division of Surgical Oncology, The Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH, USA.
| | - Hunter Stecko
- Department of Surgery, Division of Surgical Oncology, The Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH, USA
| | | | - Timothy M Pawlik
- Department of Surgery, Division of Surgical Oncology, The Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, OH, USA
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26
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Petrak J, Tevosian SG, Richter S, Ghayee HK. Metabolomics and proteomics in pheochromocytoma and paraganglioma: Translating biochemistry and biology to bedside. Best Pract Res Clin Endocrinol Metab 2024:101935. [PMID: 39299859 DOI: 10.1016/j.beem.2024.101935] [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] [Indexed: 09/22/2024]
Abstract
The complexity of omes - the key cellular ensembles (genome and epigenome, transcriptome, proteome, and metabolome) - is becoming increasingly understood in terms of big-data analysis, the omics. Amongst these, proteomics provides a global description of quantitative and qualitative alterations of protein expression (or protein abundance in body fluids) in response to physiologic or pathologic processes while metabolomics offers a functional portrait of the physiological state by quantifying metabolite abundances in biological samples. Here, we summarize how different techniques of proteomic and metabolic analysis can be used to define key biochemical characteristics of pheochromocytomas/paragangliomas (PPGL). The significance of omics in understanding features of PPGL biology that might translate to improved diagnosis and treatment will be highlighted.
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Affiliation(s)
- Jiri Petrak
- BIOCEV, First Faculty of Medicine, Charles University, Vestec, Czech Republic.
| | - Sergei G Tevosian
- Department of Physiological Sciences, University of Florida, Gainesville, FL, USA
| | - Susan Richter
- Institute of Clinical Chemistry and Laboratory Medicine, Medical Faculty Carl Gustav Carus, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Hans K Ghayee
- Department of Medicine, Division of Endocrinology & Metabolism, Malcom Randall VA Medical Center, University of Florida, Gainesville, FL, USA.
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27
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Xu T, Yang J, Li D, Challa M, Zou C, Deng P, Zhang SL, Xu B. Discovery of novel natural-product-derived mutant isocitrate dehydrogenases 1 inhibitors: Structure-based virtual screening, biological evaluation and structure-activity relationship study. Eur J Med Chem 2024; 275:116610. [PMID: 38896992 DOI: 10.1016/j.ejmech.2024.116610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/13/2024] [Accepted: 06/15/2024] [Indexed: 06/21/2024]
Abstract
Mutations in IDH1 are commonly observed across various cancers, causing the conversion of α-KG to 2-HG. Elevated levels of 2-HG disrupt histone and DNA demethylation processes, promoting tumor development. Consequently, there is substantial interest in developing small molecule inhibitors targeting the mutant enzymes. Herein, we report a structure-based high-throughput virtual screening strategy using a natural products library, followed by hit-to-lead optimization. Through this process, we discover a potent compound, named 11s, which exhibited significant inhibition to IDH1 R132H and IDH1 R132C with IC50 values of 124.4 and 95.7 nM, respectively. Furthermore, 11s effectively reduced 2-HG formation, with EC50 values of 182 nM in U87 R132H cell, and 84 nM in HT-1080 cell. In addition, 11s significantly reduced U87 R132H and HT-1080 cell proliferation with GC50 values of 3.48 and 1.38 μM, respectively. PK-PD experiments further confirmed that compound 11s significantly decreased 2-HG formation in an HT-1080 xenograft mouse model, resulting in notable suppression of tumor growth without apparent loss in body weight.
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Affiliation(s)
- Tieling Xu
- Department of Medicinal Chemistry, School of Pharmacy, Chongqing Medical University, Chongqing, 400016, PR China
| | - Junya Yang
- Department of Medicinal Chemistry, School of Pharmacy, Chongqing Medical University, Chongqing, 400016, PR China
| | - Dongsheng Li
- Department of Medicinal Chemistry, School of Pharmacy, Chongqing Medical University, Chongqing, 400016, PR China
| | - Mahesh Challa
- School of Pharmaceutical Sciences, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chongqing University, Chongqing, 401331, PR China
| | - Cheng Zou
- School of Pharmaceutical Sciences, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chongqing University, Chongqing, 401331, PR China
| | - Ping Deng
- Department of Medicinal Chemistry, School of Pharmacy, Chongqing Medical University, Chongqing, 400016, PR China.
| | - Shao-Lin Zhang
- School of Pharmaceutical Sciences, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chongqing University, Chongqing, 401331, PR China.
| | - Biao Xu
- Department of Medicinal Chemistry, School of Pharmacy, Chongqing Medical University, Chongqing, 400016, PR China.
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28
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Huang YR, Fan HQ, Kuang YY, Wang P, Lu S. The Relationship Between the Molecular Phenotypes of Brain Gliomas and the Imaging Features and Sensitivity of Radiotherapy and Chemotherapy. Clin Oncol (R Coll Radiol) 2024; 36:541-551. [PMID: 38821723 DOI: 10.1016/j.clon.2024.05.005] [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: 09/20/2023] [Revised: 02/28/2024] [Accepted: 05/10/2024] [Indexed: 06/02/2024]
Abstract
Gliomas are the most common primary malignant tumors of the brain, accounting for about 80% of all central nervous system malignancies. With the development of molecular biology, the molecular phenotypes of gliomas have been shown to be closely related to the process of diagnosis and treatment. The molecular phenotype of glioma also plays an important role in guiding treatment plans and evaluating treatment effects and prognosis. However, due to the heterogeneity of the tumors and the trauma associated with the surgical removal of tumor tissue, the application of molecular phenotyping in glioma is limited. With the development of imaging technology, functional magnetic resonance imaging (MRI) can provide structural and function information about tumors in a noninvasive and radiation-free manner. MRI is very important for the diagnosis of intracranial lesions. In recent years, with the development of the technology for tumor molecular diagnosis and imaging, the use of molecular phenotype information and imaging procedures to evaluate the treatment outcome of tumors has become a hot topic. By reviewing the related literature on glioma treatment and molecular typing that has been published in the past 20 years, and referring to the latest 2020 NCCN treatment guidelines, summarizing the imaging characteristic and sensitivity of radiotherapy and chemotherapy of different molecular phenotypes of glioma. In this article, we briefly review the imaging characteristics of different molecular phenotypes in gliomas and their relationship with radiosensitivity and chemosensitivity of gliomas.
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Affiliation(s)
- Y-R Huang
- Department of Radiation Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - H-Q Fan
- Department of Radiation Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - Y-Y Kuang
- Department of Radiation Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - P Wang
- Department of Radiation Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China
| | - S Lu
- Department of Radiation Oncology, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang, China.
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29
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Bello RO, Okunlola ST, Kumar N, Victor O, Jimoh TO, Abdulsalam ZN, Kehinde IO, Umar HI. An integrative computational approach for the identification of dual inhibitors of isocitrate dehydrogenase 1 and 2 from phytocompounds of Phyllantus amarus. J Biomol Struct Dyn 2024; 42:7272-7288. [PMID: 37559488 DOI: 10.1080/07391102.2023.2245494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 07/16/2023] [Indexed: 08/11/2023]
Abstract
Genetic alterations of the genes encoding the isocitrate dehydrogenase (IDH) enzymes have been identified in about 20% of acute myeloid leukemia (AML) cases as well as many other forms of cancers. Notable among these alterations are the neomorphic IDH1_R132H and IDH2_R140Q mutations which lead to the production of an oncometabolite. Hence, their inhibition is widely considered a therapeutic strategy in the treatment of many cancers. While many inhibitors of the mutant enzymes have been developed, an inhibitor that is capable of co-inhibiting both enzymes are currently lacking while drug resistance has also limited the clinical usage of previously identified mono inhibitors. Consequently, this study employed molecular modeling approaches, such as molecular docking, molecular mechanics generalized Born Surface area (MM/GBSA), molecular dynamics (MD) simulation, and density functional theory (DFT) analysis to identify potential dual inhibitors of the previously mentioned mutant IDH1/2 from the phytocompounds of Phyllantus amarus. Of the 31 phytocompounds identified, 20 showed good binding affinities for both IDH1 _R132H and IDH2 _R140Q (ranging from -5.2 Kca/mol to -9.6 Kcal/mol) and had desirable pharmacokinetic properties. However, ellagic acid and pinoresinol possessed better pharmacokinetic properties, rendering suitable hits. Investigation of the behavior of the IDH1_R132H and IDH2_R140Q complexes with ellagic acid and pinoresinol via the RMSD, RMSF, and contact map analyses showed that all the complexes-maintained stability throughout the simulation time. Ultimately, ellagic acid and pinoresinol were identified as promising hits for the development of IDH1_R132H and IDH2_R140Q dual inhibitors. However, further experimental studies are needed to confirm their potential as therapies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ridwan Opeyemi Bello
- Department of Biotechnology, School of Life Sciences (SLS), Federal University of Technology Akure, Akure, Ondo State, Nigeria
- Computer-Aided Therapeutic Discovery and Design Platform (CAT2D), School of Life Sciences (SLS), Federal University of Technology Akure, Akure, Ondo State, Nigeria
| | - Salihaat Toyin Okunlola
- Computer-Aided Therapeutic Discovery and Design Platform (CAT2D), School of Life Sciences (SLS), Federal University of Technology Akure, Akure, Ondo State, Nigeria
- Department of Physiology, School of Basic Medical Sciences, Federal University of Technology Akure, Akure, Ondo State, Nigeria
| | - Neeraj Kumar
- Department of Pharmaceutical Chemistry, Bhupal Nobles' College of Pharmacy, Udaipur, Rajasthan, India
| | - Omoboyede Victor
- Computer-Aided Therapeutic Discovery and Design Platform (CAT2D), School of Life Sciences (SLS), Federal University of Technology Akure, Akure, Ondo State, Nigeria
- Department of Biochemistry, School of Life Sciences (SLS), Federal University of Technology Akure, Akure, Ondo State, Nigeria
| | - Tajudeen O Jimoh
- Department of Pharmacognosy and Pharmaceutical Botany, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Islamic University in Uganda, Kampala, Uganda
| | - Zainab Naeem Abdulsalam
- Computer-Aided Therapeutic Discovery and Design Platform (CAT2D), School of Life Sciences (SLS), Federal University of Technology Akure, Akure, Ondo State, Nigeria
| | - Idayat Oyinkansola Kehinde
- Computer-Aided Therapeutic Discovery and Design Platform (CAT2D), School of Life Sciences (SLS), Federal University of Technology Akure, Akure, Ondo State, Nigeria
- Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Nigeria
| | - Haruna Isiyaku Umar
- Computer-Aided Therapeutic Discovery and Design Platform (CAT2D), School of Life Sciences (SLS), Federal University of Technology Akure, Akure, Ondo State, Nigeria
- Department of Biochemistry, School of Life Sciences (SLS), Federal University of Technology Akure, Akure, Ondo State, Nigeria
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30
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Grewal US, Gaddam SJ, Beg MS, Brown TJ. Targeted therapies in advanced biliary malignancies: a clinical review. Expert Rev Anticancer Ther 2024; 24:869-880. [PMID: 39083012 DOI: 10.1080/14737140.2024.2387612] [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: 03/27/2024] [Accepted: 07/30/2024] [Indexed: 08/06/2024]
Abstract
INTRODUCTION Despite several therapeutic advancements, the proportion of patients with advanced biliary tract cancers (BTC) surviving 5 years from diagnosis remains dismal. The increasing recognition of targetable genetic alterations in BTCs has ushered in a new era in the treatment of these patients. Newer therapeutic agents targeting mutations such as isocitrate dehydrogenase (IDH), fibroblastic growth factor receptor (FGFR), human epidermal growth factor receptor (HER), and so on have established a new standard of care for treatment upon progression on frontline therapy in patients with disease harboring these mutations. AREAS COVERED The current review aims to concisely summarize progress with various targeted therapy options for BTC. We also briefly discuss future directions in clinical and translational research for the adoption of a personalized approach for the treatment of unresectable or advanced BTC. EXPERT OPINION Several new agents continue to emerge as feasible treatment options for patients with advanced BTC harboring targetable mutations. There is a growing need to identify mechanisms to conquer primary and acquired resistance to these agents. The identification of potential biomarkers that predict response to targeted therapy may be helpful in adopting a more tailored approach. All patients receiving treatment for advanced BTC should undergo tissue genomic profiling at diagnosis.
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Affiliation(s)
- Udhayvir S Grewal
- Division of Hematology and Oncology, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Shiva J Gaddam
- Division of Hematology and Oncology, Department of Medicine, Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | | | - Timothy J Brown
- Division of Hematology and Medical Oncology, Department of Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
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31
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Zhai Y, Zhang X, Chen Z, Yan D, Zhu L, Zhang Z, Wang X, Tian K, Huang Y, Yang X, Sun W, Wang D, Tsai YH, Luo T, Li G. Global profiling of functional histidines in live cells using small-molecule photosensitizer and chemical probe relay labelling. Nat Chem 2024; 16:1546-1557. [PMID: 38834725 DOI: 10.1038/s41557-024-01545-6] [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: 05/25/2023] [Accepted: 04/26/2024] [Indexed: 06/06/2024]
Abstract
Recent advances in chemical proteomics have focused on developing chemical probes that react with nucleophilic amino acid residues. Although histidine is an attractive candidate due to its importance in enzymatic catalysis, metal binding and protein-protein interaction, its moderate nucleophilicity poses challenges. Its modification is frequently influenced by cysteine and lysine, which results in poor selectivity and narrow proteome coverage. Here we report a singlet oxygen and chemical probe relay labelling method that achieves high selectivity towards histidine. Libraries of small-molecule photosensitizers and chemical probes were screened to optimize histidine labelling, enabling histidine profiling in live cells with around 7,200 unique sites. Using NMR spectroscopy and X-ray crystallography, we characterized the reaction mechanism and the structures of the resulting products. We then applied this method to discover unannotated histidine sites key to enzymatic activity and metal binding in select metalloproteins. This method also revealed the accessibility change of histidine mediated by protein-protein interaction that influences select protein subcellular localization, underscoring its capability in discovering functional histidines.
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Affiliation(s)
- Yansheng Zhai
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Xinyu Zhang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A & F University, Yangling, China
| | - Zijing Chen
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering, Ministry of Education and Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | | | - Lin Zhu
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Zhe Zhang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Xianghe Wang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Kailu Tian
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Yan Huang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Xi Yang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Wen Sun
- State Key Laboratory of Fine Chemicals, Frontiers Science Center for Smart Materials Oriented Chemical Engineering, Dalian University of Technology, Dalian, China
| | - Dong Wang
- Shenzhen University, Shenzhen, China
| | - Yu-Hsuan Tsai
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Tuoping Luo
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering, Ministry of Education and Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Gang Li
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China.
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32
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Zhao W, Ouyang C, Zhang L, Wang J, Zhang J, Zhang Y, Huang C, Xiao Q, Jiang B, Lin F, Zhang C, Zhu M, Xie C, Huang X, Zhang B, Zhao W, He J, Chen S, Liu X, Lin D, Li Q, Wang Z. The proto-oncogene tyrosine kinase c-SRC facilitates glioblastoma progression by remodeling fatty acid synthesis. Nat Commun 2024; 15:7455. [PMID: 39198451 PMCID: PMC11358276 DOI: 10.1038/s41467-024-51444-0] [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: 01/05/2024] [Accepted: 08/08/2024] [Indexed: 09/01/2024] Open
Abstract
Increased fatty acid synthesis benefits glioblastoma malignancy. However, the coordinated regulation of cytosolic acetyl-CoA production, the exclusive substrate for fatty acid synthesis, remains unclear. Here, we show that proto-oncogene tyrosine kinase c-SRC is activated in glioblastoma and remodels cytosolic acetyl-CoA production for fatty acid synthesis. Firstly, acetate is an important substrate for fatty acid synthesis in glioblastoma. c-SRC phosphorylates acetyl-CoA synthetase ACSS2 at Tyr530 and Tyr562 to stimulate the conversion of acetate to acetyl-CoA in cytosol. Secondly, c-SRC inhibits citrate-derived acetyl-CoA synthesis by phosphorylating ATP-citrate lyase ACLY at Tyr682. ACLY phosphorylation shunts citrate to IDH1-catalyzed NADPH production to provide reducing equivalent for fatty acid synthesis. The c-SRC-unresponsive double-mutation of ACSS2 and ACLY significantly reduces fatty acid synthesis and hampers glioblastoma progression. In conclusion, this remodeling fulfills the dual needs of glioblastoma cells for both acetyl-CoA and NADPH in fatty acid synthesis and provides evidence for glioma treatment by c-SRC inhibition.
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Affiliation(s)
- Wentao Zhao
- Department of Neurosurgery and Department of Neuroscience, Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen Key Laboratory of Brain Center, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China.
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China.
| | - Cong Ouyang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Liang Zhang
- Department of Neurosurgery and Department of Neuroscience, Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen Key Laboratory of Brain Center, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Jinyang Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Jiaojiao Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Yan Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Chen Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Qiao Xiao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Bin Jiang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Furong Lin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Cixiong Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Mingxia Zhu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Changchuan Xie
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Xi Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Bingchang Zhang
- Department of Neurosurgery and Department of Neuroscience, Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen Key Laboratory of Brain Center, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Wenpeng Zhao
- Department of Neurosurgery and Department of Neuroscience, Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen Key Laboratory of Brain Center, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Jiawei He
- Department of Neurosurgery and Department of Neuroscience, Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen Key Laboratory of Brain Center, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Sifang Chen
- Department of Neurosurgery and Department of Neuroscience, Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen Key Laboratory of Brain Center, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Xiyao Liu
- Department of Neurosurgery and Department of Neuroscience, Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen Key Laboratory of Brain Center, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Donghai Lin
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory of Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Qinxi Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China.
| | - Zhanxiang Wang
- Department of Neurosurgery and Department of Neuroscience, Fujian Key Laboratory of Brain Tumors Diagnosis and Precision Treatment, Xiamen Key Laboratory of Brain Center, the First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China.
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Dakal TC, Kakde GS, Maurya PK. Genomic, epigenomic and transcriptomic landscape of glioblastoma. Metab Brain Dis 2024:10.1007/s11011-024-01414-8. [PMID: 39180605 DOI: 10.1007/s11011-024-01414-8] [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: 05/23/2024] [Accepted: 08/13/2024] [Indexed: 08/26/2024]
Abstract
The mostly aggressive and extremely malignant type of central nervous system is Glioblastoma (GBM), which is characterized by an extremely short average survival time of lesser than 16 months. The primary cause of this phenomenon can be attributed to the extensively altered genome of GBM, which is characterized by the dysregulation of numerous critical signaling pathways and epigenetics regulations associated with proliferation, cellular growth, survival, and apoptosis. In light of this, different genetic alterations in critical signaling pathways and various epigenetics regulation mechanisms are associated with GBM and identified as distinguishing markers. Such GBM prognostic alterations are identified in PI3K/AKT, p53, RTK, RAS, RB, STAT3 and ZIP4 signaling pathways, metabolic pathway (IDH1/2), as well as alterations in epigenetic regulation genes (MGMT, CDKN2A-p16INK4aCDKN2B-p15INK4b). The exploration of innovative diagnostic and therapeutic approaches that specifically target these pathways is utmost importance to enhance the future medication for GBM. This study provides a comprehensive overview of dysregulated epigenetic mechanisms and signaling pathways due to mutations, methylation, and copy number alterations of in critical genes in GBM with prevalence and emphasizing their significance.
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Affiliation(s)
- Tikam Chand Dakal
- Genome and Computational Biology Lab, Mohanlal Sukhadia, University, Udaipur, Rajasthan, 313001, India.
| | - Ganesh S Kakde
- Department of Biochemistry, Central University of Haryana, Mahendergarh, 123031, Haryana, India
| | - Pawan Kumar Maurya
- Department of Biochemistry, Central University of Haryana, Mahendergarh, 123031, Haryana, India.
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Jiang J, Liu Y. Recent discoveries of Sino-Caucasian differences in the genetics of phaeochromocytomas and paragangliomas. Best Pract Res Clin Endocrinol Metab 2024:101928. [PMID: 39191630 DOI: 10.1016/j.beem.2024.101928] [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] [Indexed: 08/29/2024]
Abstract
Pheochromocytomas and paragangliomas (PPGLs) represent the highest degree of heritability of any known tumor types in humans. Previous studies have characterized a dramatic difference between Chinese and European Caucasians with regards to both genetics and clinical features of PPGLs. The proportion of PGLs in Chinese patients was higher than in Caucasians, and the prevalence of metastasis was much lower in Chinese patients. Compared with Caucasians, there were more pathogenic variants (PVs) found in HRAS and FGFR1, but less in NF1 and SDHB. There were less germline PVs found in Chinese patients. Importantly, in Chinese patients, there was a large proportion of PGLs with PVs found in HRAS and FGFR1, mostly with epinephrine-producing capacity. This finding provided solid evidence that genetics (cluster 1 vs. 2), rather than location (PCC vs. PGL), determines the catecholamine-producing phenotype. Besides, the lower prevalence of SDHB partially explained lower occurrence of metastatic lesions in Chinese patients. These findings underscore the importance of considering ethnic differences when evaluating PPGLs and patient outcomes.
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Affiliation(s)
- Jingjing Jiang
- Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, China.
| | - Yujun Liu
- Department of Urology, Zhongshan Hospital, Fudan University, China.
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35
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Nong T, Mehra S, Taylor J. Common Driver Mutations in AML: Biological Impact, Clinical Considerations, and Treatment Strategies. Cells 2024; 13:1392. [PMID: 39195279 DOI: 10.3390/cells13161392] [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: 07/27/2024] [Revised: 08/17/2024] [Accepted: 08/19/2024] [Indexed: 08/29/2024] Open
Abstract
Next-generation sequencing of samples from patients with acute myeloid leukemia (AML) has revealed several driver gene mutations in adult AML. However, unlike other cancers, AML is defined by relatively few mutations per patient, with a median of 4-5 depending on subtype. In this review, we will discuss the most common driver genes found in patients with AML and focus on the most clinically relevant ones that impact treatment strategies. The most common driver gene mutations in AML occur in NPM1 and FLT3, accounting for ~30% each. There are now targeted therapies being tested or already approved for these driver genes. Menin inhibitors, a novel targeted therapy that blocks the function of the menin protein, are in clinical trials for NPM1 driver gene mutant AML after relapse. A number of FLT3 inhibitors are now approved for FLT3 driver gene mutant AML in combination with chemotherapy in the frontline and also as single agent in relapse. Although mutations in IDH1/2 and TP53 only occur in around 10-20% of patients with AML each, they can affect the treatment strategy due to their association with prognosis and availability of targeted agents. While the impact of other driver gene mutations in AML is recognized, there is a lack of data on the actionable impact of those mutations.
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Affiliation(s)
- Tiffany Nong
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Shefali Mehra
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Justin Taylor
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
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36
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Álvarez-González E, Sierra LM. Tricarboxylic Acid Cycle Relationships with Non-Metabolic Processes: A Short Story with DNA Repair and Its Consequences on Cancer Therapy Resistance. Int J Mol Sci 2024; 25:9054. [PMID: 39201738 PMCID: PMC11355010 DOI: 10.3390/ijms25169054] [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: 07/18/2024] [Revised: 08/08/2024] [Accepted: 08/20/2024] [Indexed: 09/03/2024] Open
Abstract
Metabolic changes involving the tricarboxylic acid (TCA) cycle have been linked to different non-metabolic cell processes. Among them, apart from cancer and immunity, emerges the DNA damage response (DDR) and specifically DNA damage repair. The oncometabolites succinate, fumarate and 2-hydroxyglutarate (2HG) increase reactive oxygen species levels and create pseudohypoxia conditions that induce DNA damage and/or inhibit DNA repair. Additionally, by influencing DDR modulation, they establish direct relationships with DNA repair on at least four different pathways. The AlkB pathway deals with the removal of N-alkylation DNA and RNA damage that is inhibited by fumarate and 2HG. The MGMT pathway acts in the removal of O-alkylation DNA damage, and it is inhibited by the silencing of the MGMT gene promoter by 2HG and succinate. The other two pathways deal with the repair of double-strand breaks (DSBs) but with opposite effects: the FH pathway, which uses fumarate to help with the repair of this damage, and the chromatin remodeling pathway, in which oncometabolites inhibit its repair by impairing the homologous recombination repair (HRR) system. Since oncometabolites inhibit DNA repair, their removal from tumor cells will not always generate a positive response in cancer therapy. In fact, their presence contributes to longer survival and/or sensitization against tumor therapy in some cancer patients.
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Affiliation(s)
- Enol Álvarez-González
- Departamento de Biología Funcional, Área de Genética, University of Oviedo, C/Julián Clavería s/n, 33006 Oviedo, Spain;
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), University of Oviedo, 33006 Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias, Avda. HUCA s/n, 33011 Oviedo, Spain
| | - Luisa María Sierra
- Departamento de Biología Funcional, Área de Genética, University of Oviedo, C/Julián Clavería s/n, 33006 Oviedo, Spain;
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), University of Oviedo, 33006 Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias, Avda. HUCA s/n, 33011 Oviedo, Spain
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Cologni R, Holschbach M, Schneider D, Bier D, Schulze A, Stegmayr C, Endepols H, Ermert J, Neumaier F, Neumaier B. Preparation and Preclinical Evaluation of 18F-Labeled Olutasidenib Derivatives for Non-Invasive Detection of Mutated Isocitrate Dehydrogenase 1 (mIDH1). Molecules 2024; 29:3939. [PMID: 39203017 PMCID: PMC11356819 DOI: 10.3390/molecules29163939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 08/12/2024] [Accepted: 08/16/2024] [Indexed: 09/03/2024] Open
Abstract
Mutations of isocitrate dehydrogenase 1 (IDH1) are key biomarkers for glioma classification, but current methods for detection of mutated IDH1 (mIDH1) require invasive tissue sampling and cannot be used for longitudinal studies. Positron emission tomography (PET) imaging with mIDH1-selective radioligands is a promising alternative approach that could enable non-invasive assessment of the IDH status. In the present work, we developed efficient protocols for the preparation of four 18F-labeled derivatives of the mIDH1-selective inhibitor olutasidenib. All four probes were characterized by cellular uptake studies with U87 glioma cells harboring a heterozygous IDH1 mutation (U87-mIDH) and the corresponding wildtype cells (U87-WT). In addition, the most promising probe was evaluated by PET imaging in healthy mice and mice bearing subcutaneous U87-mIDH and U87-WT tumors. Although all four probes inhibited mIDH1 with variable potencies, only one of them ([18F]mIDH-138) showed significantly higher in vitro uptake into U87-mIDH compared to U87-WT cells. In addition, PET imaging with [18F]mIDH-138 in mice demonstrated good in vivo stability and low non-specific uptake of the probe, but also revealed significantly higher uptake into U87-WT compared to U87-mIDH tumors. Finally, application of a two-tissue compartment model (2TCM) to the PET data indicated that preferential tracer uptake into U87-WT tumors results from higher specific binding rather than from differences in tracer perfusion. In conclusion, these results corroborate recent findings that mIDH1-selective inhibition may not directly correlate with mIDH1-selective target engagement and indicate that in vivo engagement of wildtype and mutated IDH1 may be governed by factors that are not faithfully reproduced by in vitro assays, both of which could complicate development of PET probes.
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Affiliation(s)
- Roberta Cologni
- Institute of Neuroscience and Medicine, Nuclear Chemistry (INM-5), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428 Jülich, Germany; (R.C.); (M.H.); (D.S.); (D.B.); (A.S.); (H.E.); (J.E.); (F.N.)
- Institute of Radiochemistry and Experimental Molecular Imaging, Faculty of Medicine and University Hospital Cologne, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany
| | - Marcus Holschbach
- Institute of Neuroscience and Medicine, Nuclear Chemistry (INM-5), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428 Jülich, Germany; (R.C.); (M.H.); (D.S.); (D.B.); (A.S.); (H.E.); (J.E.); (F.N.)
| | - Daniela Schneider
- Institute of Neuroscience and Medicine, Nuclear Chemistry (INM-5), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428 Jülich, Germany; (R.C.); (M.H.); (D.S.); (D.B.); (A.S.); (H.E.); (J.E.); (F.N.)
| | - Dirk Bier
- Institute of Neuroscience and Medicine, Nuclear Chemistry (INM-5), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428 Jülich, Germany; (R.C.); (M.H.); (D.S.); (D.B.); (A.S.); (H.E.); (J.E.); (F.N.)
| | - Annette Schulze
- Institute of Neuroscience and Medicine, Nuclear Chemistry (INM-5), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428 Jülich, Germany; (R.C.); (M.H.); (D.S.); (D.B.); (A.S.); (H.E.); (J.E.); (F.N.)
| | - Carina Stegmayr
- Institute of Neuroscience and Medicine, Medical Imaging Physics (INM-4), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428 Jülich, Germany;
| | - Heike Endepols
- Institute of Neuroscience and Medicine, Nuclear Chemistry (INM-5), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428 Jülich, Germany; (R.C.); (M.H.); (D.S.); (D.B.); (A.S.); (H.E.); (J.E.); (F.N.)
- Institute of Radiochemistry and Experimental Molecular Imaging, Faculty of Medicine and University Hospital Cologne, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany
- Department of Nuclear Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany
| | - Johannes Ermert
- Institute of Neuroscience and Medicine, Nuclear Chemistry (INM-5), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428 Jülich, Germany; (R.C.); (M.H.); (D.S.); (D.B.); (A.S.); (H.E.); (J.E.); (F.N.)
| | - Felix Neumaier
- Institute of Neuroscience and Medicine, Nuclear Chemistry (INM-5), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428 Jülich, Germany; (R.C.); (M.H.); (D.S.); (D.B.); (A.S.); (H.E.); (J.E.); (F.N.)
- Institute of Radiochemistry and Experimental Molecular Imaging, Faculty of Medicine and University Hospital Cologne, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany
| | - Bernd Neumaier
- Institute of Neuroscience and Medicine, Nuclear Chemistry (INM-5), Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428 Jülich, Germany; (R.C.); (M.H.); (D.S.); (D.B.); (A.S.); (H.E.); (J.E.); (F.N.)
- Institute of Radiochemistry and Experimental Molecular Imaging, Faculty of Medicine and University Hospital Cologne, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany
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38
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Erb HHH, Polishchuk N, Stasyk O, Kahya U, Weigel MM, Dubrovska A. Glutamine Metabolism and Prostate Cancer. Cancers (Basel) 2024; 16:2871. [PMID: 39199642 PMCID: PMC11352381 DOI: 10.3390/cancers16162871] [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: 06/29/2024] [Revised: 08/09/2024] [Accepted: 08/12/2024] [Indexed: 09/01/2024] Open
Abstract
Glutamine (Gln) is a non-essential amino acid that is involved in the development and progression of several malignancies, including prostate cancer (PCa). While Gln is non-essential for non-malignant prostate epithelial cells, PCa cells become highly dependent on an exogenous source of Gln. The Gln metabolism in PCa is tightly controlled by well-described oncogenes such as MYC, AR, and mTOR. These oncogenes contribute to therapy resistance and progression to the aggressive castration-resistant PCa. Inhibition of Gln catabolism impedes PCa growth, survival, and tumor-initiating potential while sensitizing the cells to radiotherapy. Therefore, given its significant role in tumor growth, targeting Gln metabolism is a promising approach for developing new therapeutic strategies. Ongoing clinical trials evaluate the safety and efficacy of Gln catabolism inhibitors in combination with conventional and targeted therapies in patients with various solid tumors, including PCa. Further understanding of how PCa cells metabolically interact with their microenvironment will facilitate the clinical translation of Gln inhibitors and help improve therapeutic outcomes. This review focuses on the role of Gln in PCa progression and therapy resistance and provides insights into current clinical trials.
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Affiliation(s)
- Holger H. H. Erb
- Department of Urology, Technische Universität Dresden, 01307 Dresden, Germany;
| | - Nikita Polishchuk
- Department of Cell Signaling, Institute of Cell Biology, National Academy of Sciences of Ukraine, 79000 Lviv, Ukraine; (N.P.); (O.S.)
| | - Oleh Stasyk
- Department of Cell Signaling, Institute of Cell Biology, National Academy of Sciences of Ukraine, 79000 Lviv, Ukraine; (N.P.); (O.S.)
| | - Uğur Kahya
- OncoRay-National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, 01309 Dresden, Germany; (U.K.); (M.M.W.)
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiooncology-OncoRay, 01328 Dresden, Germany
| | - Matthias M. Weigel
- OncoRay-National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, 01309 Dresden, Germany; (U.K.); (M.M.W.)
| | - Anna Dubrovska
- OncoRay-National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden and Helmholtz-Zentrum Dresden-Rossendorf, 01309 Dresden, Germany; (U.K.); (M.M.W.)
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiooncology-OncoRay, 01328 Dresden, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, 01309 Dresden, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden, 01307 Dresden, Germany
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39
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Batool SM, Escobedo AK, Hsia T, Ekanayake E, Khanna SK, Gamblin AS, Zheng H, Skog J, Miller JJ, Stemmer-Rachamimov AO, Cahill DP, Balaj L, Carter BS. Clinical utility of a blood based assay for the detection of IDH1.R132H-mutant gliomas. Nat Commun 2024; 15:7074. [PMID: 39152110 PMCID: PMC11329733 DOI: 10.1038/s41467-024-51332-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 08/05/2024] [Indexed: 08/19/2024] Open
Abstract
Glioma represents the most common central nervous system neoplasm in adults. Current classification scheme utilizes molecular alterations, particularly IDH1.R132H, to stratify lesions into distinct prognostic groups. Identification of the single nucleotide variant through traditional tissue biopsy assessment poses procedural risks and does not fully reflect the heterogeneous and evolving tumor landscape. Here, we introduce a liquid biopsy assay, mt-IDH1dx. The blood-based test allows minimally invasive detection of tumor-derived extracellular vesicle RNA using only 2 ml plasma volume. We perform rigorous, blinded validation testing across the study population (n = 133), comprising of IDH1.R132H patients (n = 80), IDH1 wild-type gliomas (n = 44), and age matched healthy controls (n = 9). Results from our plasma testing demonstrate an overall sensitivity of 75.0% (95% CI: 64.1%-84.0%), specificity 88.7% (95% CI: 77.0%-95.7%), positive predictive value 90.9%, and negative predictive value 70.1% compared to the tissue gold standard. In addition to fundamental diagnostic applications, the study also highlights the utility of mt-IDH1dx platform for blood-based monitoring and surveillance, offering valuable prognostic information. Finally, the optimized workflow enables rapid and efficient completion of both tumor tissue and plasma testing in under 4 hours from the time of sampling.
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Affiliation(s)
- Syeda Maheen Batool
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ana K Escobedo
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tiffaney Hsia
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Emil Ekanayake
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sirena K Khanna
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Austin S Gamblin
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hui Zheng
- Center for Biostatistics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Johan Skog
- Exosome Diagnostics, a Bio-Techne Brand, Waltham, MA, USA
| | - Julie J Miller
- Translational Neuro-Oncology Laboratory, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Neuro-Oncology, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Daniel P Cahill
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Leonora Balaj
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Bob S Carter
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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40
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Ebrahimi S, Khaleghi Ghadiri M, Stummer W, Gorji A. Enhancing 5-ALA-PDT efficacy against resistant tumor cells: Strategies and advances. Life Sci 2024; 351:122808. [PMID: 38852796 DOI: 10.1016/j.lfs.2024.122808] [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: 04/04/2024] [Revised: 05/20/2024] [Accepted: 06/04/2024] [Indexed: 06/11/2024]
Abstract
As a precursor of protoporphyrin IX (PpIX), an endogenous pro-apoptotic and fluorescent molecule, 5-Aminolevulinic acid (5-ALA) has gained substantial attention for its potential in fluorescence-guided surgery as well as photodynamic therapy (PDT). Moreover, 5-ALA-PDT has been suggested as a promising chemo-radio sensitization therapy for various cancers. However, insufficient 5-ALA-induced PpIX fluorescence and the induction of multiple resistance mechanisms may hinder the 5-ALA-PDT clinical outcome. Reduced efficacy and resistance to 5-ALA-PDT can result from genomic alterations, tumor heterogeneity, hypoxia, activation of pathways related to cell surveillance, production of nitric oxide, and most importantly, deregulated 5-ALA transporter proteins and heme biosynthesis enzymes. Understanding the resistance regulatory mechanisms of 5-ALA-PDT may allow the development of effective personalized cancer therapy. Here, we described the mechanisms underlying resistance to 5-ALA-PTD across various tumor types and explored potential strategies to overcome this resistance. Furthermore, we discussed future approaches that may enhance the efficacy of treatments using 5-ALA-PDT.
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Affiliation(s)
- Safieh Ebrahimi
- Epilepsy Research Center, Münster University, 48149 Münster, Germany; Department of Clinical Biochemistry, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Shefa Neuroscience Research Center, Khatam Alanbia Hospital, Tehran 1996835911, Iran
| | | | - Walter Stummer
- Department of Neurosurgery, Münster University, 48149 Münster, Germany
| | - Ali Gorji
- Epilepsy Research Center, Münster University, 48149 Münster, Germany; Shefa Neuroscience Research Center, Khatam Alanbia Hospital, Tehran 1996835911, Iran; Neuroscience Research Center, Mashhad University of Medical Sciences, 9177948564 Mashhad, Iran.
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41
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Mundhara N, Sadhukhan P. Cracking the Codes behind Cancer Cells' Immune Evasion. Int J Mol Sci 2024; 25:8899. [PMID: 39201585 PMCID: PMC11354234 DOI: 10.3390/ijms25168899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 08/03/2024] [Accepted: 08/09/2024] [Indexed: 09/02/2024] Open
Abstract
Immune evasion is a key phenomenon in understanding tumor recurrence, metastasis, and other critical steps in tumor progression. The tumor microenvironment (TME) is in constant flux due to the tumor's ability to release signals that affect it, while immune cells within it can impact cancer cell behavior. Cancer cells undergo several changes, which can change the enrichment of different immune cells and modulate the activity of existing immune cells in the tumor microenvironment. Cancer cells can evade immune surveillance by downregulating antigen presentation or expressing immune checkpoint molecules. High levels of tumor-infiltrating lymphocytes (TILs) correlate with better outcomes, and robust immune responses can control tumor growth. On the contrary, increased enrichment of Tregs, myeloid-derived suppressor cells, and M2-like anti-inflammatory macrophages can hinder effective immune surveillance and predict poor prognosis. Overall, understanding these immune evasion mechanisms guides therapeutic strategies. Researchers aim to modulate the TME to enhance immune surveillance and improve patient outcomes. In this review article, we strive to summarize the composition of the tumor immune microenvironment, factors affecting the tumor immune microenvironment (TIME), and different therapeutic modalities targeting the immune cells. This review is a first-hand reference to understand the basics of immune surveillance and immune evasion.
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Affiliation(s)
| | - Pritam Sadhukhan
- Department of Oncology, Johns Hopkins University, Baltimore, MD 21287, USA
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Schiff D. Low-Grade Gliomas: A New Mutation, New Targeted Therapy, and Many Questions. Neurology 2024; 103:e209688. [PMID: 39008801 DOI: 10.1212/wnl.0000000000209688] [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: 07/17/2024] Open
Abstract
The discovery in 2008 that many adult gliomas harbor a hitherto unknown mutation in the metabolic gene isocitrate dehydrogenase (IDH) initiated revolutionary advances in our understanding of the biology, and correspondingly our classification, of gliomas. IDH mutations are found in most nonglioblastoma adult gliomas and portend a better prognosis. Massive efforts have unraveled many of the pleiotropic cellular effects of these mutations and spawned several lines of investigation to target the effect to therapeutic benefit. In this article are reviewed the implications of the IDH mutation in gliomas, in particular focusing on recent studies that have culminated in a rare positive phase 3 trial in these generally refractory tumors.
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Affiliation(s)
- David Schiff
- From the Departments of Neurology, Neurological Surgery, and Medicine, University of Virginia Health System
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DiNardo CD, Roboz GJ, Watts JM, Madanat YF, Prince GT, Baratam P, de Botton S, Stein A, Foran JM, Arellano ML, Sallman DA, Hossain M, Marchione DM, Bai X, Patel PA, Kapsalis SM, Garcia-Manero G, Fathi AT. Final phase 1 substudy results of ivosidenib for patients with mutant IDH1 relapsed/refractory myelodysplastic syndrome. Blood Adv 2024; 8:4209-4220. [PMID: 38640348 PMCID: PMC11372395 DOI: 10.1182/bloodadvances.2023012302] [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: 11/29/2023] [Revised: 02/28/2024] [Accepted: 04/09/2024] [Indexed: 04/21/2024] Open
Abstract
ABSTRACT Ivosidenib is a first-in-class mutant isocitrate dehydrogenase 1 (mIDH1) inhibitor with efficacy and tolerability in patients with advanced mIDH1 hematologic malignancies, leading to approval in frontline and relapsed/refractory (R/R) mIDH1 acute myeloid leukemia. We report final data from a phase 1 single-arm substudy of once-daily ivosidenib in patients with R/R mIDH1 myelodysplastic syndrome (MDS) after failure of standard-of-care therapies. Primary objectives were to determine safety, tolerability, and clinical activity. The primary efficacy end point was the complete remission (CR) + partial remission (PR) rate. Nineteen patients were enrolled; 18 were included in the efficacy analysis. Treatment-related adverse events occurred in 8 (42.1%) patients, including a grade 1 QT interval prolongation in 1 (5.3%) patient and grade 2 differentiation syndrome in 2 (10.5%) patients. Rates of CR + PR and objective response (CR + PR + marrow CR) were 38.9% (95% confidence interval [CI], 17.3-64.3) and 83.3% (95% CI, 58.6-96.4), respectively. Kaplan-Meier estimates showed a 68.6% probability of patients in CR achieving a remission duration of ≥5 years, and a median overall survival of 35.7 months. Of note, 71.4% and 75.0% baseline red blood cell (RBC)- and platelet-transfusion-dependent patients, respectively, became transfusion independent (TI; no transfusion for ≥56 days); 81.8% and 100% of baseline RBC and platelet TI patients, respectively, remained TI. One (5.3%) patient proceeded to a hematopoietic stem cell transplant. In conclusion, ivosidenib is clinically active, with durable remissions and a manageable safety profile observed in these patients. This trial was registered at www.ClinicalTrials.gov as #NCT02074839.
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Affiliation(s)
- Courtney D DiNardo
- Department of Leukemia, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Gail J Roboz
- Clinical and Translational Leukemia Programs, Weill Cornell Medicine and New York Presbyterian Hospital, New York, NY
| | - Justin M Watts
- Division of Hematology, University of Miami, Sylvester Comprehensive Cancer Center, Miami, FL
| | - Yazan F Madanat
- Division of Hematology and Oncology, UT Southwestern Medical Center, Dallas, TX
| | - Gabrielle T Prince
- Division of Hematologic Malignancy, Johns Hopkins Hospital, Baltimore, MD
| | - Praneeth Baratam
- Division of Hematology and Oncology, Medical University of South Carolina, Charleston, SC
| | - Stéphane de Botton
- Hematologie Clinique, Institut Gustave Roussy, Villejuif, Faculté Paris-Saclay, Institut Gustave Roussy, Villejuif, France
| | - Anthony Stein
- Division of Leukemia, Department of Hematology & Hematopoietic Cell Transplantation, City of Hope, Duarte, CA
| | - James M Foran
- Division of Hematology & Medical Oncology, Mayo Clinic, Jacksonville, FL
| | - Martha L Arellano
- Department of Hematology and Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA
| | - David A Sallman
- Department of Malignant Hematology, Moffitt Cancer Center, Tampa, FL
| | | | | | | | | | | | - Guillermo Garcia-Manero
- Department of Leukemia, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Amir T Fathi
- Department of Medicine, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA
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Collins M, Gorgoglione R, Impedovo V, Pan X, Chakkarai S, Yi SS, Lodi A, Tiziani S. Exploration of the intracellular chiral metabolome in pediatric BCP-ALL: a pilot study investigating the metabolic phenotype of IgH locus aberrations. Front Oncol 2024; 14:1413264. [PMID: 39161381 PMCID: PMC11332069 DOI: 10.3389/fonc.2024.1413264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 05/13/2024] [Indexed: 08/21/2024] Open
Abstract
Background and aims Aberrations in the immunoglobulin heavy chain (IgH) locus are associated with poor prognosis in pediatric precursor B-cell acute lymphoblastic leukemia (BCP-ALL) patients. The primary objective of this pilot study is to enhance our understanding of the IgH phenotype by exploring the intracellular chiral metabolome. Materials and methods Leukemia cells were isolated from the bone marrow of BCP-ALL pediatric patients at diagnosis. The samples' metabolome and transcriptome were characterized using untargeted chiral metabolomic and next-generation sequencing transcriptomic analyses. Results For the first time D- amino acids were identified in the leukemic cells' intracellular metabolome from the bone marrow niche. Chiral metabolic signatures at diagnosis was indicative of a resistant phenotype. Through integrated network analysis and Pearson correlation, confirmation was obtained regarding the association of the IgH phenotype with several genes linked to poor prognosis. Conclusion The findings of this study have contributed to the understanding that the chiral metabolome plays a role in the poor prognosis observed in an exceptionally rare patient cohort. The findings include elevated D-amino acid incorporation in the IgH group, the emergence of several unknown, potentially enantiomeric, metabolites, and insights into metabolic pathways that all warrant further exploration.
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Affiliation(s)
- Meghan Collins
- Department of Nutritional Sciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX, United States
- Dell Pediatric Research Institute, Dell Medical School, The University of Texas at Austin, Austin, TX, United States
| | - Ruggiero Gorgoglione
- Department of Nutritional Sciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX, United States
- Dell Pediatric Research Institute, Dell Medical School, The University of Texas at Austin, Austin, TX, United States
| | - Valeria Impedovo
- Department of Nutritional Sciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX, United States
- Dell Pediatric Research Institute, Dell Medical School, The University of Texas at Austin, Austin, TX, United States
| | - Xingxin Pan
- Department of Oncology, Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, United States
| | - Sathyaseelan Chakkarai
- Department of Oncology, Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, United States
| | - S. Stephen Yi
- Department of Oncology, Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, United States
- Interdisciplinary Life Sciences Graduate Programs, College of Natural Sciences, The University of Texas at Austin, Austin, TX, United States
- Oden Institute for Computational Engineering and Sciences, and Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Alessia Lodi
- Department of Nutritional Sciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX, United States
- Dell Pediatric Research Institute, Dell Medical School, The University of Texas at Austin, Austin, TX, United States
| | - Stefano Tiziani
- Department of Nutritional Sciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX, United States
- Dell Pediatric Research Institute, Dell Medical School, The University of Texas at Austin, Austin, TX, United States
- Department of Oncology, Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, United States
- Department of Pediatrics, Dell Medical School, The University of Texas at Austin, Austin, TX, United States
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Harrahill NJ, Hadden MK. Small molecules that regulate the N 6-methyladenosine RNA modification as potential anti-cancer agents. Eur J Med Chem 2024; 274:116526. [PMID: 38805939 DOI: 10.1016/j.ejmech.2024.116526] [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: 02/16/2024] [Revised: 05/14/2024] [Accepted: 05/20/2024] [Indexed: 05/30/2024]
Abstract
Epitranscriptomics, the field of post-translational RNA modifications, is a burgeoning domain of research that has recently received significant attention for its role in multiple diseases, including cancer. N6-methyladenosine (m6A) is the most prominent post-translational RNA modification and plays a critical role in RNA transcription, processing, translation, and metabolism. The m6A modification is controlled by three protein classes known as writers (methyltransferases), erasers (demethylases), and readers (m6A-binding proteins). Each class of m6A regulatory proteins has been implicated in cancer initiation and progression. As such, many of these proteins have been identified as potential targets for anti-cancer chemotherapeutics. In this work, we provide an overview of the role m6A-regulating proteins play in cancer and discuss the current state of small molecule therapeutics targeting these proteins.
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Affiliation(s)
- Noah J Harrahill
- Department of Pharmaceutical Sciences, University of Connecticut, 69 N Eagleville Rd, Unit 3092, Storrs, CT, 06269-3092, United States
| | - M Kyle Hadden
- Department of Pharmaceutical Sciences, University of Connecticut, 69 N Eagleville Rd, Unit 3092, Storrs, CT, 06269-3092, United States.
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Mohan A, Quingalahua E, Gunchick V, Paul S, Kumar-Sinha C, Crysler O, Zalupski MM, Sahai V. PARP inhibitor therapy in patients with IDH1 mutated cholangiocarcinoma. Oncologist 2024; 29:725-730. [PMID: 39036962 PMCID: PMC11299928 DOI: 10.1093/oncolo/oyae163] [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: 02/26/2024] [Accepted: 06/06/2024] [Indexed: 07/23/2024] Open
Abstract
BACKGROUND Isocitrate dehydrogenase 1 (IDH1) missense mutations occur at a frequency of 10%-15% in intrahepatic cholangiocarcinoma (iCCA). IDH1 mutations result in accumulation of (R)-2-hydroxyglutarate, an oncometabolite that leads to DNA hypermethylation and impairment of homologous recombination (HR). Impairment of HR results in a "BRCAness" phenotype which may confer sensitivity to poly(ADP ribose) polymerase (PARP) inhibition. METHODS We conducted a retrospective cohort review to identify patients with advanced, IDH1 mutated iCCA treated with a PARP inhibitor (PARPi) at the University of Michigan between 2018 and 2023. Patients are described with respect to prior lines of therapy, response to platinum-based chemotherapy, and progression-free survival (PFS) and overall survival (OS) from the time of PARPi initiation. RESULTS Between 2018 and 2023 we identified 40 patients with IDH1 mutated iCCA of which 6 patients were treated with a PARPi as monotherapy or in combination with an ATR inhibitor or anti-PD-1 immune checkpoint inhibitor. Majority of patients (n = 5) carried an IDH1 R132C mutation per tissue-based next generation sequencing. All patients had previously received at least one line of cisplatin-based systemic therapy for advanced disease prior to treatment with PARPi. PFS and OS from time of PARPi initiation ranged from 1.4 to 18.5 months and 2.8 to 42.4 months, respectively. Best response on PARPi therapy included 2 partial responses. CONCLUSION This is the first case series to describe PARPi treatment in IDH1 mutated iCCA. Results underscore the limitation of PARPi monotherapy, potentially support combined PARPi therapies, and highlight a need for effective treatment options for patients with IDH1 mutated iCCA.
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Affiliation(s)
- Arathi Mohan
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, United States
| | - Elit Quingalahua
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Valerie Gunchick
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, United States
| | - Simi Paul
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Chandan Kumar-Sinha
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, United States
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
| | - Oxana Crysler
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, United States
| | - Mark M Zalupski
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, United States
| | - Vaibhav Sahai
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, United States
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Carosi F, Broseghini E, Fabbri L, Corradi G, Gili R, Forte V, Roncarati R, Filippini DM, Ferracin M. Targeting Isocitrate Dehydrogenase (IDH) in Solid Tumors: Current Evidence and Future Perspectives. Cancers (Basel) 2024; 16:2752. [PMID: 39123479 PMCID: PMC11311780 DOI: 10.3390/cancers16152752] [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: 06/26/2024] [Revised: 07/26/2024] [Accepted: 07/28/2024] [Indexed: 08/12/2024] Open
Abstract
The isocitrate dehydrogenase 1 and 2 (IDH1 and IDH2) enzymes are involved in key metabolic processes in human cells, regulating differentiation, proliferation, and oxidative damage response. IDH mutations have been associated with tumor development and progression in various solid tumors such as glioma, cholangiocarcinoma, chondrosarcoma, and other tumor types and have become crucial markers in molecular classification and prognostic assessment. The intratumoral and serum levels of D-2-hydroxyglutarate (D-2-HG) could serve as diagnostic biomarkers for identifying IDH mutant (IDHmut) tumors. As a result, an increasing number of clinical trials are evaluating targeted treatments for IDH1/IDH2 mutations. Recent studies have shown that the focus of these new therapeutic strategies is not only the neomorphic activity of the IDHmut enzymes but also the epigenetic shift induced by IDH mutations and the potential role of combination treatments. Here, we provide an overview of the current knowledge about IDH mutations in solid tumors, with a particular focus on available IDH-targeted treatments and emerging results from clinical trials aiming to explore IDHmut tumor-specific features and to identify the clinical benefit of IDH-targeted therapies and their combination strategies. An insight into future perspectives and the emerging roles of circulating biomarkers and radiomic features is also included.
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Affiliation(s)
- Francesca Carosi
- Medical Oncology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (F.C.); (L.F.); (G.C.)
| | | | - Laura Fabbri
- Medical Oncology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (F.C.); (L.F.); (G.C.)
| | - Giacomo Corradi
- Medical Oncology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (F.C.); (L.F.); (G.C.)
| | - Riccardo Gili
- Medical Oncology Unit, IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy;
| | - Valentina Forte
- Diagnostic Imaging Unit, Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy;
| | - Roberta Roncarati
- Istituto di Genetica Molecolare “Luigi Luca Cavalli-Sforza”, Consiglio Nazionale delle Ricerche (CNR), 40136 Bologna, Italy;
| | - Daria Maria Filippini
- Medical Oncology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy; (F.C.); (L.F.); (G.C.)
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Manuela Ferracin
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
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Duan H, Li J, Ma J, Chen T, Zhang H, Shang G. Global research development of chondrosarcoma from 2003 to 2022: a bibliometric analysis. Front Pharmacol 2024; 15:1431958. [PMID: 39156101 PMCID: PMC11327078 DOI: 10.3389/fphar.2024.1431958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 07/24/2024] [Indexed: 08/20/2024] Open
Abstract
Background Chondrosarcomas are common primary malignant bone tumors; however, comprehensive bibliometric analysis in this field has not yet been conducted. Therefore, this study aimed to explore the research hotspots and trends in the field of chondrosarcoma through bibliometric analysis to help researchers understand the current status and direction of research in the field. Methods Articles and reviews related to chondrosarcoma published between 2003 and 2022 were retrieved from the Web of Science. Countries, institutions, authors, journals, references, and keywords in this field were visualized and analyzed using CtieSpace and VOSviewer software. Results Between 2003 and 2022, 4,149 relevant articles were found. The number of articles published on chondrosarcoma has increased significantly annually, mainly from 569 institutions in China and the United States, and 81 in other countries. In total, 904 authors participated in the publication of studies related to chondrosarcomas. Over the past 20 years, articles on chondrosarcoma have been published in 958 academic journals, with Skeletal Radiology having the highest number of publications. Furthermore, keywords such as "gene expression," "radiotherapy," "experience," and "apoptosis" have been popular in recent years. Conclusion Over the past 20 years, the global trend in chondrosarcoma research has primarily been clinical research, with basic research as a supplement. In the future, communication and exchange between countries and institutions should be strengthened. Further, the future main research hotspots in the field of chondrosarcoma include mutated genes and signaling pathways, precision surgical treatment, proton therapy, radiation therapy, chemotherapy, immunotherapy, and other aspects.
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Affiliation(s)
| | | | | | | | | | - Guanning Shang
- Department of Bone and Soft Tissue Oncology, Shengjing Hospital of China Medical University, Shenyang, China
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Papageorgakopoulou MA, Bania A, Lagogianni IA, Birmpas K, Assimakopoulou M. The Role of Glia Telomere Dysfunction in the Pathogenesis of Central Nervous System Diseases. Mol Neurobiol 2024; 61:5868-5881. [PMID: 38240992 PMCID: PMC11249767 DOI: 10.1007/s12035-024-03947-6] [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: 10/10/2023] [Accepted: 01/09/2024] [Indexed: 07/16/2024]
Abstract
Maintaining the telomere length is decisive for the viability and homeostasis process of all the cells of an organism, including human glial cells. Telomere shortening of microglial cells has been widely associated with the onset and progression of neurodegenerative diseases such as Parkinson's and Alzheimer's disease. Additionally, traumatic brain injury appears to have a positive correlation with the telomere-shortening process of microglia, and telomere length can be used as a non-invasive biomarker for the clinical management of these patients. Moreover, telomere involvement through telomerase reactivation and homologous recombination also known as the alternative lengthening of telomeres (ALT) has been described in gliomagenesis pathways, and particular focus has been given in the translational significance of these mechanisms in gliomas diagnosis and prognostic classification. Finally, glia telomere shortening is implicated in some psychiatric diseases. Given that telomere dysfunction of glial cells is involved in the central nervous system (CNS) disease pathogenesis, it represents a promising drug target that could lead to the incorporation of new tools in the medicinal arsenal for the management of so far incurable conditions.
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Affiliation(s)
| | - Angelina Bania
- School of Medicine, University of Patras, 26504, Patras, Greece
| | | | | | - Martha Assimakopoulou
- Department of Anatomy, Histology and Embryology, School of Medicine, University of Patras, Preclinical Medicine Department Building, 1 Asklipiou, 26504, Patras, Greece.
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Kosvyra Α, Karadimitris Α, Papaioannou Μ, Chouvarda I. Machine learning and integrative multi-omics network analysis for survival prediction in acute myeloid leukemia. Comput Biol Med 2024; 178:108735. [PMID: 38875909 DOI: 10.1016/j.compbiomed.2024.108735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/14/2024] [Accepted: 06/08/2024] [Indexed: 06/16/2024]
Abstract
BACKGROUND Acute myeloid leukemia (AML) is the most common malignant myeloid disorder in adults and the fifth most common malignancy in children, necessitating advanced technologies for outcome prediction. METHOD This study aims to enhance prognostic capabilities in AML by integrating multi-omics data, especially gene expression and methylation, through network-based feature selection methodologies. By employing artificial intelligence and network analysis, we are exploring different methods to build a machine learning model for predicting AML patient survival. We evaluate the effectiveness of combining omics data, identify the most informative method for network integration and compare the performance with standard feature selection methods. RESULTS Our findings demonstrate that integrating gene expression and methylation data significantly improves prediction accuracy compared to single omics data. Among network integration methods, our study identifies the best approach that improves informative feature selection for predicting patient outcomes in AML. Comparative analyses demonstrate the superior performance of the proposed network-based methods over standard techniques. CONCLUSIONS This research presents an innovative and robust methodology for building a survival prediction model tailored to AML patients. By leveraging multilayer network analysis for feature selection, our approach contributes to improving the understanding and prognostic capabilities in AML and laying the foundation for more effective personalized therapeutic interventions in the future.
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Affiliation(s)
- Α Kosvyra
- Laboratory of Computing, Medical Informatics and Biomedical Imaging Technologies, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece.
| | - Α Karadimitris
- Centre for Haematology and Hugh and Josseline Langmuir Centre for Myeloma Research, Department of Immunology and Inflammation, Imperial College London, Department of Haematology, Hammersmith Hospital, Imperial College Healthcare NHS Trust, Du Cane Road, London, W12 0NN, UK
| | - Μ Papaioannou
- Hematology Unit, 1st Dept of Internal Medicine, AHEPA Hospital, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - I Chouvarda
- Laboratory of Computing, Medical Informatics and Biomedical Imaging Technologies, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
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