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Liao H, Chen X, Wang H, Lin Y, Chen L, Yuan K, Liao M, Jiang H, Peng J, Wu Z, Huang J, Li J, Zeng Y. Whole-Genome DNA Methylation Profiling of Intrahepatic Cholangiocarcinoma Reveals Prognostic Subtypes with Distinct Biological Drivers. Cancer Res 2024; 84:1747-1763. [PMID: 38471085 PMCID: PMC11148548 DOI: 10.1158/0008-5472.can-23-3298] [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: 10/23/2023] [Revised: 01/17/2024] [Accepted: 03/08/2024] [Indexed: 03/14/2024]
Abstract
Intrahepatic cholangiocarcinoma (iCCA) is the second most prevalent primary liver cancer. Although the genetic characterization of iCCA has led to targeted therapies for treating tumors with FGFR2 alterations and IDH1/2 mutations, only a limited number of patients can benefit from these strategies. Epigenomic profiles have emerged as potential diagnostic and prognostic biomarkers for improving the treatment of cancers. In this study, we conducted whole-genome bisulfite sequencing on 331 iCCAs integrated with genetic, transcriptomic, and proteomic analyses, demonstrating the existence of four DNA methylation subtypes of iCCAs (S1-S4) that exhibited unique postoperative clinical outcomes. The S1 group was an IDH1/2 mutation-specific subtype with moderate survival. The S2 subtype was characterized by the lowest methylation level and the highest mutational burden among the four subtypes and displayed upregulation of a gene-expression pattern associated with cell cycle/DNA replication. The S3 group was distinguished by high interpatient heterogeneity of tumor immunity, a gene-expression pattern associated with carbohydrate metabolism, and an enrichment of KRAS alterations. Patients with the S2 and S3 subtypes had the shortest survival among the four subtypes. Tumors in the S4 subtype, which had the best prognosis, showed global methylation levels comparable to normal controls, increased FGFR2 fusions/BAP1 mutations, and the highest copy-number variant burdens. Further integrative and functional analyses identified GBP4 demethylation, which is highly prevalent in the S2 and S3 groups, as an epigenetic oncogenic factor that regulates iCCA proliferation, migration, and invasion. Together, this study identifies prognostic methylome alterations and epigenetic drivers in iCCA. SIGNIFICANCE Characterization of the DNA methylome of intrahepatic cholangiocarcinoma integrated with genomic, transcriptomic, and proteomic analyses uncovers molecular mechanisms affected by genome-wide DNA methylation alterations, providing a resource for identifying potential therapeutic targets.
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Affiliation(s)
- Haotian Liao
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xing Chen
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Haichuan Wang
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Youpei Lin
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion, (Ministry of Education), Fudan University, Shanghai, China
| | - Lu Chen
- Department of Hepatobiliary Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Kefei Yuan
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Mingheng Liao
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hanyu Jiang
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jiajie Peng
- School of Computer Science, Northwestern Polytechnical University, Xi'an, Shanxi, China
| | - Zhenru Wu
- Institute of Clinical Pathology, Key Laboratory of Transplant Engineering and Immunology, NHC, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jiwei Huang
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jiaxin Li
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yong Zeng
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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Xie AX, Tansey W, Reznik E. UnitedMet harnesses RNA-metabolite covariation to impute metabolite levels in clinical samples. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.24.24307903. [PMID: 38826234 PMCID: PMC11142294 DOI: 10.1101/2024.05.24.24307903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Comprehensively studying metabolism requires the measurement of metabolite levels. However, in contrast to the broad availability of gene expression data, metabolites are rarely measured in large molecularly-defined cohorts of tissue samples. To address this basic barrier to metabolic discovery, we propose a Bayesian framework ("UnitedMet") which leverages the empirical strength of RNA-metabolite covariation to impute otherwise unmeasured metabolite levels from widely available transcriptomic data. We demonstrate that UnitedMet is equally capable of imputing whole pool sizes as well as the outcomes of isotope tracing experiments. We apply UnitedMet to investigate the metabolic impact of driver mutations in kidney cancer, identifying a novel association between BAP1 and a highly oxidative tumor phenotype. We similarly apply UnitedMet to determine that advanced kidney cancers upregulate oxidative phosphorylation relative to early-stage disease, that oxidative metabolism in kidney cancer is associated with inferior outcomes to combination therapy, and that kidney cancer metastases themselves demonstrate elevated oxidative phosphorylation relative to primary tumors. UnitedMet therefore enables the assessment of metabolic phenotypes in contexts where metabolite measurements were not taken or are otherwise infeasible, opening new avenues for the generation and evaluation of metabolite-centered hypotheses. UnitedMet is open source and publicly available (https://github.com/reznik-lab/UnitedMet).
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Affiliation(s)
- Amy X. Xie
- Computational Oncology Service, Memorial Sloan Kettering Cancer Center, NY NY 10065
- Biochemistry, Structural Biology, Cell Biology, Developmental Biology and Molecular Biology Graduate Program, Weill Cornell Medicine, New York, NY
| | - Wesley Tansey
- Computational Oncology Service, Memorial Sloan Kettering Cancer Center, NY NY 10065
| | - Ed Reznik
- Computational Oncology Service, Memorial Sloan Kettering Cancer Center, NY NY 10065
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Raygada M, John L, Liu A, Schultz J, Thomas BJ, Bernstein D, Miettinen M, Raffeld M, Xi L, Tyagi M, Aldape K, Glod J, Reilly KM, Widemann BC, Wedekind MF. Germline findings in cancer predisposing genes from a small cohort of chordoma patients. J Cancer Res Clin Oncol 2024; 150:227. [PMID: 38700789 PMCID: PMC11068663 DOI: 10.1007/s00432-024-05706-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 03/15/2024] [Indexed: 05/06/2024]
Abstract
INTRODUCTION Chordoma is a rare slow-growing tumor that occurs along the length of the spinal axis and arises from primitive notochordal remnants (Stepanek et al., Am J Med Genet 75:335-336, 1998). Most chordomas are sporadic, but a small percentage of cases are due to hereditary cancer syndromes (HCS) such as tuberous sclerosis 1 and 2 (TSC1/2), or constitutional variants in the gene encoding brachyury T (TBXT) (Pillay et al., Nat Genet 44:1185-1187, 2012; Yang et al., Nat Genet 41:1176-1178, 2009). PURPOSE The genetic susceptibility of these tumors is not well understood; there are only a small number of studies that have performed germline genetic testing in this population. METHODS We performed germline genetic in chordoma patients using genomic DNA extracted by blood or saliva. CONCLUSION We report here a chordoma cohort of 24 families with newly found germline genetic mutations in cancer predisposing genes. We discuss implications for genetic counseling, clinical management, and universal germline genetic testing for cancer patients with solid tumors.
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Affiliation(s)
- Margarita Raygada
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
- NIH Clinical Center (Building 10), 10 Center Drive, Room 1-3750, Bethesda, MD, 20892, USA.
| | - Liny John
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Anne Liu
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Julianne Schultz
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - B J Thomas
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Donna Bernstein
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Markku Miettinen
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Mark Raffeld
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Liqiang Xi
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Manoj Tyagi
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - John Glod
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Karlyne M Reilly
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Brigitte C Widemann
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Mary Frances Wedekind
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
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Lee J, Thuzar M, DiPoto-Brahmbhatt AC, Chaudoir C, Tanner A, Fazili T, Yu X, Constantinescu M, Yeh YA. Clear cell renal cell carcinoma with BAP1 mutation: a report of two cases. AMERICAN JOURNAL OF CLINICAL AND EXPERIMENTAL UROLOGY 2023; 11:429-434. [PMID: 37941648 PMCID: PMC10628621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/31/2023] [Indexed: 11/10/2023]
Abstract
Clear cell renal cell carcinoma is the most common subtype of renal cell carcinomas (RCCs) and accounts for 60%-70% of all RCCs cases in adults. Aberrations in the von Hippel-Lindau (VHL) gene on chromosome 3p occurred in > 90% of clear cell RCCs. Other tumor suppressor genes located on chromosome 3p, such as BAP1, PBRM1, and SETD2, also contribute to tumorigenesis. Clear cell RCCs with both BAP1 and VHL mutations may display distinctive histopathological features. Here, we report two cases of clear cell RCCs with BAP1 mutation. One tumor had VHL, BAP-1, and RAF1 mutations and the tumor nests and alveoli of tumor cells were surrounded by proliferative vessels and the optically clear cytoplasm contained numerous eosinophilic granules and hyaline globules of varying sizes. The other tumor had BAP1 and ATM mutations, and demonstrated clear cells with numerous eosinophilic granules and other typical histopathological features of conventional clear cell RCC. Furthermore, many tumor nodules with dense peripheral lymphocytic infiltrates contained rhabdoid cells. Sarcomatoid cells were also observed. Both tumor cells showed high-grade nuclei. Clear cell RCCs with BAP1 mutation exhibit aggressive clinical behaviors.
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Affiliation(s)
- Jennifer Lee
- Pathology and Laboratory Medicine Service, Overton Brooks VA Medical CenterShreveport, LA, USA
- Department of Pathology and Translational Pathobiology, Louisiana State University Health ShreveportShreveport, LA, USA
| | - Moe Thuzar
- Pathology and Laboratory Medicine Service, Overton Brooks VA Medical CenterShreveport, LA, USA
- Department of Pathology and Translational Pathobiology, Louisiana State University Health ShreveportShreveport, LA, USA
| | - Angela C DiPoto-Brahmbhatt
- Pathology and Laboratory Medicine Service, Overton Brooks VA Medical CenterShreveport, LA, USA
- Department of Pathology and Translational Pathobiology, Louisiana State University Health ShreveportShreveport, LA, USA
| | - Catherine Chaudoir
- Pathology and Laboratory Medicine Service, Overton Brooks VA Medical CenterShreveport, LA, USA
- Department of Pathology and Translational Pathobiology, Louisiana State University Health ShreveportShreveport, LA, USA
| | - Anthony Tanner
- Pathology and Laboratory Medicine Service, Overton Brooks VA Medical CenterShreveport, LA, USA
| | - Tajammul Fazili
- Department of Urology, Overton Brooks VA Medical CenterShreveport, LA, USA
- Department of Urology, Louisiana State University Health ShreveportShreveport, LA, USA
| | - Xiuping Yu
- Department of Urology, Louisiana State University Health ShreveportShreveport, LA, USA
- Department of Biochemistry and Molecular Biology, Louisiana State University Health ShreveportShreveport, LA, USA
| | - Michael Constantinescu
- Pathology and Laboratory Medicine Service, Overton Brooks VA Medical CenterShreveport, LA, USA
- Department of Pathology and Translational Pathobiology, Louisiana State University Health ShreveportShreveport, LA, USA
| | - Y Albert Yeh
- Pathology and Laboratory Medicine Service, Overton Brooks VA Medical CenterShreveport, LA, USA
- Department of Pathology and Translational Pathobiology, Louisiana State University Health ShreveportShreveport, LA, USA
- Department of Urology, Louisiana State University Health ShreveportShreveport, LA, USA
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Lin M, Ta RT, Manning HC. Simplified and highly-reliable automated production of [ 18F]FSPG for clinical studies. EJNMMI Radiopharm Chem 2023; 8:15. [PMID: 37486582 PMCID: PMC10366059 DOI: 10.1186/s41181-023-00200-8] [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: 06/13/2023] [Accepted: 07/13/2023] [Indexed: 07/25/2023] Open
Abstract
BACKGROUND (S)-4-(3-18F-Fluoropropyl)-L-Glutamic Acid ([18F]FSPG) is a positron emission tomography (PET) tracer that specifically targets the cystine/glutamate antiporter (xc-), which is frequently overexpressed in cancer and several neurological disorders. Pilot studies examining the dosimetry and biodistribution of [18F]FSPG in healthy volunteers and tumor detection in patients with non-small cell lung cancer, hepatocellular carcinoma, and brain tumors showed promising results. In particular, low background uptake in the brain, lung, liver, and bowel was observed that further leads to excellent imaging contrasts of [18F]FSPG PET. However, reliable production-scale cGMP-compliant automated procedures for [18F]FSPG production are still lacking to further increase the utility and clinical adoption of this radiotracer. Herein, we report the optimized automated approaches to produce [18F]FSPG through two commercially available radiosynthesizers capable of supporting centralized and large-scale production for clinical use. RESULTS Starting with activity levels of 60-85 GBq, the fully-automated process to produce [18F]FSPG took less than 45 min with average radiochemical yields of 22.56 ± 0.97% and 30.82 ± 1.60% (non-decay corrected) using TRACERlab™ FXFN and FASTlab™, respectively. The radiochemical purities were > 95% and the formulated [18F]FSPG solution was determined to be sterile and colorless with the pH of 6.5-7.5. No radiolysis of the product was observed up to 8 h after final batch formulation. CONCLUSIONS In summary, cGMP-compliant radiosyntheses and quality control of [18F]FSPG have been established on two commercially available synthesizers leveraging high activity concentration and radiochemical purity. While the clinical trials using [18F]FSPG PET are currently underway, the automated approaches reported herein will accelerate the clinical adoption of this radiotracer and warrant centralized and large-scale production of [18F]FSPG.
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Affiliation(s)
- Mai Lin
- Cyclotron Radiochemistry Facility, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Robert T Ta
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - H Charles Manning
- Cyclotron Radiochemistry Facility, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA.
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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Han A, Mukha D, Chua V, Purwin TJ, Tiago M, Modasia B, Baqai U, Aumiller JL, Bechtel N, Hunter E, Danielson M, Terai M, Wedegaertner PB, Sato T, Landreville S, Davies MA, Kurtenbach S, Harbour JW, Schug ZT, Aplin AE. Co-Targeting FASN and mTOR Suppresses Uveal Melanoma Growth. Cancers (Basel) 2023; 15:3451. [PMID: 37444561 PMCID: PMC10341317 DOI: 10.3390/cancers15133451] [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: 06/07/2023] [Revised: 06/25/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Uveal melanoma (UM) displays a high frequency of metastasis; however, effective therapies for metastatic UM are limited. Identifying unique metabolic features of UM may provide a potential targeting strategy. A lipid metabolism protein expression signature was induced in a normal choroidal melanocyte (NCM) line transduced with GNAQ (Q209L), a driver in UM growth and development. Consistently, UM cells expressed elevated levels of fatty acid synthase (FASN) compared to NCMs. FASN upregulation was associated with increased mammalian target of rapamycin (mTOR) activation and sterol regulatory element-binding protein 1 (SREBP1) levels. FASN and mTOR inhibitors alone significantly reduced UM cell growth. Concurrent inhibition of FASN and mTOR further reduced UM cell growth by promoting cell cycle arrest and inhibiting glucose utilization, TCA cycle metabolism, and de novo fatty acid biosynthesis. Our findings indicate that FASN is important for UM cell growth and co-inhibition of FASN and mTOR signaling may be considered for treatment of UM.
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Affiliation(s)
- Anna Han
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA; (A.H.); (V.C.); (T.J.P.); (M.T.); (U.B.); (E.H.)
- Department of Food Science and Human Nutrition, Jeonbuk National University, Jeonju 54896, Jeollabuk-do, Republic of Korea
| | - Dzmitry Mukha
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA 19104, USA; (D.M.); (Z.T.S.)
| | - Vivian Chua
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA; (A.H.); (V.C.); (T.J.P.); (M.T.); (U.B.); (E.H.)
| | - Timothy J. Purwin
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA; (A.H.); (V.C.); (T.J.P.); (M.T.); (U.B.); (E.H.)
| | - Manoela Tiago
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA; (A.H.); (V.C.); (T.J.P.); (M.T.); (U.B.); (E.H.)
| | - Bhavik Modasia
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA; (A.H.); (V.C.); (T.J.P.); (M.T.); (U.B.); (E.H.)
| | - Usman Baqai
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA; (A.H.); (V.C.); (T.J.P.); (M.T.); (U.B.); (E.H.)
| | - Jenna L. Aumiller
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA; (J.L.A.); (P.B.W.)
| | - Nelisa Bechtel
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA; (A.H.); (V.C.); (T.J.P.); (M.T.); (U.B.); (E.H.)
| | - Emily Hunter
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA; (A.H.); (V.C.); (T.J.P.); (M.T.); (U.B.); (E.H.)
| | - Meggie Danielson
- Department of Medical Oncology, Thomas Jefferson University, Philadelphia, PA 19107, USA; (M.D.); (M.T.); (T.S.)
| | - Mizue Terai
- Department of Medical Oncology, Thomas Jefferson University, Philadelphia, PA 19107, USA; (M.D.); (M.T.); (T.S.)
| | - Philip B. Wedegaertner
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA; (J.L.A.); (P.B.W.)
| | - Takami Sato
- Department of Medical Oncology, Thomas Jefferson University, Philadelphia, PA 19107, USA; (M.D.); (M.T.); (T.S.)
| | - Solange Landreville
- Department of Ophthalmology and Otorhinolaryngology-Cervical-Facial Surgery, Faculty of Medicine, Université Laval, Québec, QC G1V 0A6, Canada;
| | - Michael A. Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Stefan Kurtenbach
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL 33101, USA; (S.K.); (J.W.H.)
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33101, USA
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL 33101, USA
| | - J. William Harbour
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL 33101, USA; (S.K.); (J.W.H.)
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33101, USA
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL 33101, USA
- Department of Ophthalmology, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zachary T. Schug
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA 19104, USA; (D.M.); (Z.T.S.)
| | - Andrew E. Aplin
- Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA; (A.H.); (V.C.); (T.J.P.); (M.T.); (U.B.); (E.H.)
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
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Lin M, Ta RT, Manning HC. Simplified and Highly-reliable automated production of [18F]FSPG for clinical studies. RESEARCH SQUARE 2023:rs.3.rs-3031030. [PMID: 37461634 PMCID: PMC10350228 DOI: 10.21203/rs.3.rs-3031030/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Background (S)-4-(3- 18 F-Fluoropropyl)-L-Glutamic Acid ([ 18 F]FSPG) is a positron emission tomography (PET) tracer that specifically targets the cystine/glutamate antiporter (xc-), which is frequently overexpressed in cancer and several neurological disorders. Pilot studies examining the dosimetry and biodistribution of ([ 18 F]FSPG in healthy volunteers and tumor detection in patients with non-small cell lung cancer, hepatocellular carcinoma, and brain tumors showed promising results. In particular, low background uptake in the brain, lung, liver, and bowel was observed that further leads to excellent imaging contrasts of [ 18 F]FSPG PET. However, reliable production-scale cGMP-compliant automated procedures for [ 18 F]FSPG production are still lacking to further increase the utility and clinical adoption of this radiotracer. Herein, we report the optimized automated approaches to produce [ 18 F]FSPG through two commercially available radiosynthesizers capable of supporting centralized and large-scale production for clinical use. Results Starting with activity levels of 60-85 GBq, the fully-automated process to produce [ 18 F]FSPG took less than 45 minutes with average radiochemical yields of 22.56 ± 0.97% and 30.82 ± 1.60% (non-decay corrected) using TRACERlab™ FXFN and FASTlab™, respectively. The radiochemical purities were > 95% and the formulated [ 18 F]FSPG solution was determined to be sterile and colorless with the pH of 6.5-7.5. No radiolysis of the product was observed up to 8 hours after final batch formulation. Conclusions In summary, cGMP-compliant radiosyntheses and quality control of [ 18 F]FSPG have been established on two commercially available synthesizers leveraging high activity concentration and radiochemical purity. While the clinical trials using [ 18 F]FSPG PET are currently underway, the automated approaches reported herein will accelerate the clinical adoption of this radiotracer and warrant centralized and large-scale production of [ 18 F]FSPG.
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Lv Y, Wu M, Wang Z, Wang J. Ferroptosis: From regulation of lipid peroxidation to the treatment of diseases. Cell Biol Toxicol 2023; 39:827-851. [PMID: 36459356 DOI: 10.1007/s10565-022-09778-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/11/2022] [Indexed: 12/04/2022]
Abstract
Ferroptosis is a regulated cell death mainly manifested by iron-dependent lipid peroxide accumulation. The leading cause of ferroptosis is the imbalance of intracellular oxidative systems (e.g., LOXs, POR, ROS) and antioxidant systems (e.g., GSH/GPx4, CoQ10/FSP1, BH4/GCH1), which is regulated by a complex network. In the past decade, this metabolic network has been continuously refined, and the links with various pathophysiological processes have been gradually established. Apoptosis has been regarded as the only form of regulated cell death for a long time, and the application of chemotherapeutic drugs to induce apoptosis of cancer cells is the mainstream method. However, studies have reported that cancer cells' key features are resistance to apoptosis and chemotherapeutics. For high proliferation, cancer cells often have very active lipid metabolism and iron metabolism, which pave the way for ferroptosis. Interestingly, researchers found that drug-resistant or highly aggressive cancer cells are more prone to ferroptosis. Therefore, ferroptosis may be a potential strategy to eliminate cancer cells. In addition, links between ferroptosis and other diseases, such as neurological disorders and ischemia-reperfusion injury, have also been found. Understanding these diseases from the perspective of ferroptosis may provide new insights into clinical treatment. Herein, the metabolic processes in ferroptosis are reviewed, and the potential mechanisms and targets of ferroptosis in different diseases are summarized.
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Affiliation(s)
- Yonghui Lv
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, 518107, China
| | - Meiying Wu
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, 518107, China.
| | - Zhe Wang
- Department of Pathology, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518033, China.
| | - Junqing Wang
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, 518107, China.
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Borea F, Franczak MA, Garcia M, Perrino M, Cordua N, Smolenski RT, Peters GJ, Dziadziuszko R, Santoro A, Zucali PA, Giovannetti E. Target Therapy in Malignant Pleural Mesothelioma: Hope or Mirage? Int J Mol Sci 2023; 24:ijms24119165. [PMID: 37298116 DOI: 10.3390/ijms24119165] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/19/2023] [Accepted: 05/21/2023] [Indexed: 06/12/2023] Open
Abstract
Malignant Pleural Mesothelioma (MPM) is a rare neoplasm that is typically diagnosed in a locally advanced stage, making it not eligible for radical surgery and requiring systemic treatment. Chemotherapy with platinum compounds and pemetrexed has been the only approved standard of care for approximately 20 years, without any relevant therapeutic advance until the introduction of immune checkpoint inhibitors. Nevertheless, the prognosis remains poor, with an average survival of only 18 months. Thanks to a better understanding of the molecular mechanisms underlying tumor biology, targeted therapy has become an essential therapeutic option in several solid malignancies. Unfortunately, most of the clinical trials evaluating potentially targeted drugs for MPM have failed. This review aims to present the main findings of the most promising targeted therapies in MPM, and to explore possible reasons leading to treatments failures. The ultimate goal is to determine whether there is still a place for continued preclinical/clinical research in this area.
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Affiliation(s)
- Federica Borea
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20090 Milan, Italy
- Department of Medical Oncology, Amsterdam University Medical Centers, Location VUmc, Cancer Center Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Marika A Franczak
- Department of Medical Oncology, Amsterdam University Medical Centers, Location VUmc, Cancer Center Amsterdam, 1081 HV Amsterdam, The Netherlands
- Department of Biochemistry, Medical University of Gdansk, 80-210 Gdańsk, Poland
| | - Maria Garcia
- Faculty of Experimental Science, Universidad Francisco de Vitoria, 28223 Madrid, Spain
| | - Matteo Perrino
- IRCCS Humanitas Research Hospital, Humanitas Cancer Center, Via Manzoni 56, Rozzano, 20089 Milan, Italy
| | - Nadia Cordua
- IRCCS Humanitas Research Hospital, Humanitas Cancer Center, Via Manzoni 56, Rozzano, 20089 Milan, Italy
| | - Ryszard T Smolenski
- Department of Biochemistry, Medical University of Gdansk, 80-210 Gdańsk, Poland
| | - Godefridus J Peters
- Department of Medical Oncology, Amsterdam University Medical Centers, Location VUmc, Cancer Center Amsterdam, 1081 HV Amsterdam, The Netherlands
- Department of Biochemistry, Medical University of Gdansk, 80-210 Gdańsk, Poland
| | - Rafal Dziadziuszko
- Department of Oncology and Radiotherapy and Early Phase Clinical Trials Centre, Medical University of Gdansk, 80-210 Gdańsk, Poland
| | - Armando Santoro
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20090 Milan, Italy
- IRCCS Humanitas Research Hospital, Humanitas Cancer Center, Via Manzoni 56, Rozzano, 20089 Milan, Italy
| | - Paolo A Zucali
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20090 Milan, Italy
- IRCCS Humanitas Research Hospital, Humanitas Cancer Center, Via Manzoni 56, Rozzano, 20089 Milan, Italy
| | - Elisa Giovannetti
- Department of Medical Oncology, Amsterdam University Medical Centers, Location VUmc, Cancer Center Amsterdam, 1081 HV Amsterdam, The Netherlands
- Fondazione Pisana per la Scienza, 56017 Pisa, Italy
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10
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Abbassi YA, Le Guin C, Bornfeld N, Bechrakis NE, Zeschnigk M, Lohmann DR. Analysis of uveal melanomas and paired constitutional DNA for exclusion of a BAP1-tumor predisposition syndrome. Fam Cancer 2023; 22:193-202. [PMID: 35920959 PMCID: PMC10020278 DOI: 10.1007/s10689-022-00310-3] [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: 04/13/2022] [Accepted: 07/21/2022] [Indexed: 11/04/2022]
Abstract
Uveal melanoma (UM) is a rare tumor originating from melanocytic cells in the eye. Familial aggregation of UM is rare and can occur as part of the tumor predisposition syndrome BAP1-TPDS. However, family history alone will only identify a subset of patients with BAP1-TPDS. In the present study, we used sequential testing of tumor and blood DNA from UM patients for differential diagnosis of BAP1-TPDS. The study group was an unselected prospective cohort of patients from whom UM tissue was available. First, chromosome 3 status in tumor DNA was determined in all 140 patients who consented to participate. As tumors with disomy 3 rarely show BAP1 alterations, sequence analysis of this gene was performed in the 72 tumors with monosomy 3 (M3) or partial M3 only. We identified oncogenic BAP1 alterations in 52 of these tumors (72%). Targeted sequencing of DNA from matched peripheral blood showed pathogenic variants in two patients (3.8%) thus proving BAP1-TPDS. Only one of these two patients also had a medical history suggestive of this syndrome. Conversely, in three patients known to have had additional tumors before diagnosis of UM, constitutional heterozygosity for a BAP1 mutation was excluded. Altogether, in 50 patients we could exclude BAP1-TPDS with high diagnostic certainty. The results of our study support that genetic testing for BAP1-TPDS should be offered to all patients with UM. Moreover, as genetic information from the tumor can help exclude heritable risk, the strategy for analysis should include efforts to obtain tumor samples for testing.
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Affiliation(s)
- Yasaman Arjmand Abbassi
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Hufelandstr. 55, 45147, Essen, Germany
| | - Claudia Le Guin
- Department of Ophthalmology, University Hospital Essen, University Duisburg-Essen, Hufelandstr. 55, 45147, Essen, Germany
| | - Norbert Bornfeld
- Department of Ophthalmology, University Hospital Essen, University Duisburg-Essen, Hufelandstr. 55, 45147, Essen, Germany
| | - Nikolaos E Bechrakis
- Department of Ophthalmology, University Hospital Essen, University Duisburg-Essen, Hufelandstr. 55, 45147, Essen, Germany
| | - Michael Zeschnigk
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Hufelandstr. 55, 45147, Essen, Germany
| | - Dietmar R Lohmann
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Hufelandstr. 55, 45147, Essen, Germany.
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11
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TSUJI S, IMAI K. Medical application of the monoclonal antibody SKM9-2 against sialylated HEG1, a new precision marker for malignant mesothelioma. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2023; 99:39-47. [PMID: 36775341 PMCID: PMC10020423 DOI: 10.2183/pjab.99.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/28/2022] [Indexed: 06/18/2023]
Abstract
Malignant pleural mesothelioma (MPM) is an aggressive tumor of the pleural cavity. Pathologically distinguishing MPM from other pleural lesions is often difficult. We searched for marker antigens to facilitate the pathological diagnosis of MPM and found useful markers for the pathological detection of malignant mesothelioma. Among them, the anti-mesothelioma monoclonal antibody SKM9-2, which was isolated as a clone binding to specimens of MPM (but not to specimens of lung adenocarcinoma) by immunohistochemical screening, showed higher specificity and sensitivity than traditional mesothelioma markers. SKM9-2 recognizes both sialylated O-glycans and peptide sequences in HEG1, and its glycan modifications are specific to mesothelioma. New effective treatments for MPM are needed because the prognosis of patients with MPM is usually poor. SKM9-2 can be used as a seed for next-generation antibody drugs with strong cytotoxic activities. In this review, we have summarized our research on antibody development for MPM diagnosis and treatment.
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Affiliation(s)
- Shoutaro TSUJI
- Department of Medical Technology & Clinical Engineering, Gunma University of Health and Welfare, Maebashi, Gunma, Japan
| | - Kohzoh IMAI
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
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12
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Caksa S, Baqai U, Aplin AE. The future of targeted kinase inhibitors in melanoma. Pharmacol Ther 2022; 239:108200. [PMID: 35513054 PMCID: PMC10187889 DOI: 10.1016/j.pharmthera.2022.108200] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/20/2022] [Accepted: 04/28/2022] [Indexed: 12/13/2022]
Abstract
Melanoma is a cancer of the pigment-producing cells of the body and its incidence is rising. Targeted inhibitors that act against kinases in the MAPK pathway are approved for BRAF-mutant metastatic cutaneous melanoma and increase patients' survival. Response to these therapies is limited by drug resistance and is less durable than with immune checkpoint inhibition. Conversely, rare melanoma subtypes have few therapeutic options for advanced disease and MAPK pathway targeting agents show minimal anti-tumor effects. Nevertheless, there is a future for targeted kinase inhibitors in melanoma: in new applications such as adjuvant or neoadjuvant therapy and in novel combinations with immunotherapies or other targeted therapies. Pre-clinical studies continue to identify tumor dependencies and their corresponding actionable drug targets, paving the way for rational targeted kinase inhibitor combinations as a personalized medicine approach for melanoma.
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Affiliation(s)
- Signe Caksa
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Usman Baqai
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Andrew E Aplin
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA; Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.
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13
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MBD5 and MBD6 stabilize the BAP1 complex and promote BAP1-dependent cancer. Genome Biol 2022; 23:206. [PMID: 36180891 PMCID: PMC9523997 DOI: 10.1186/s13059-022-02776-x] [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: 04/13/2022] [Accepted: 09/25/2022] [Indexed: 11/19/2022] Open
Abstract
Background BRCA1-associated protein 1 (BAP1) is an ubiquitin carboxy-terminal hydrolase, which forms a multi-protein complex with different epigenetic factors, such as ASXL1-3 and FOXK1/2. At the chromatin level, BAP1 catalyzes the removal of mono-ubiquitination on histone H2AK119 in collaboration with other subunits within the complex and functions as a transcriptional activator in mammalian cells. However, the crosstalk between different subunits and how these subunits impact BAP1’s function remains unclear. Results We report the identification of the methyl-CpG-binding domain proteins 5 and 6 (MBD5 and MBD6) that bind to the C-terminal PHD fingers of the large scaffold subunits ASXL1-3 and stabilize the BAP1 complex at the chromatin. We further identify a novel Drosophila protein, the six-banded (SBA), as an ortholog of human MBD5 and MBD6, and demonstrate that the core modules of the BAP1 complex is structurally and functionally conserved from Drosophila (Calypso/ASX/SBA) to human cells (BAP1/ASXL/MBD). Dysfunction of the BAP1 complex induced by the misregulation/mutations in its subunit(s) are frequent in many human cancers. In BAP1-dependent human cancers, such as small cell lung cancer (SCLC), MBD6 tends to be a part of the predominant complex formed. Therefore, depletion of MBD6 leads to a global loss of BAP1 occupancy at the chromatin, resulting in a reduction of BAP1-dependent gene expression and tumor growth in vitro and in vivo. Conclusions We characterize MBD5 and MBD6 as important regulators of the BAP1 complex and maintain its transcriptional landscape, shedding light on the therapeutic potential of targeting MBD5 and MBD6 in BAP1-dependent human cancers. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02776-x.
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14
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Zhou Y, Fang C, Xu H, Yuan L, Liu Y, Wang X, Zhang A, Shao A, Zhou D. Ferroptosis in glioma treatment: Current situation, prospects and drug applications. Front Oncol 2022; 12:989896. [PMID: 36249003 PMCID: PMC9557197 DOI: 10.3389/fonc.2022.989896] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 09/14/2022] [Indexed: 11/13/2022] Open
Abstract
Ferroptosis is a regulatory form of iron-dependent cell death caused by the accumulation of lipid-based reactive oxygen species (ROS) and differs from apoptosis, pyroptosis, and necrosis. Especially in neoplastic diseases, the susceptibility of tumor cells to ferroptosis affects prognosis and is associated with complex effects. Gliomas are the most common primary intracranial tumors, accounting for disease in 81% of patients with malignant brain tumors. An increasing number of studies have revealed the particular characteristics of iron metabolism in glioma cells. Therefore, agents that target a wide range of molecules involved in ferroptosis may regulate this process and enhance glioma treatment. Here, we review the underlying mechanisms of ferroptosis and summarize the potential therapeutic options for targeting ferroptosis in glioma.
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Affiliation(s)
- Yuhang Zhou
- Health Management Center, Tongde Hospital of Zhejiang Province, Hangzhou, China
- The First Clinical Medical College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Chaoyou Fang
- Department of Neurosurgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Houshi Xu
- Department of Neurosurgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ling Yuan
- Department of Neurosurgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yibo Liu
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaoyu Wang
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Anke Zhang
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- *Correspondence: Anke Zhang, ; Anwen Shao, ; Danyang Zhou,
| | - Anwen Shao
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- *Correspondence: Anke Zhang, ; Anwen Shao, ; Danyang Zhou,
| | - Danyang Zhou
- Health Management Center, Tongde Hospital of Zhejiang Province, Hangzhou, China
- *Correspondence: Anke Zhang, ; Anwen Shao, ; Danyang Zhou,
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15
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Hu D, Zheng Y, Ou X, Zhang L, Du X, Shi S. Integrated analysis of anti-tumor roles of BAP1 in osteosarcoma. Front Oncol 2022; 12:973914. [PMID: 36003792 PMCID: PMC9393745 DOI: 10.3389/fonc.2022.973914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
Background This study aims to screen out differentially expressed genes (DEGs) regulated by BRCA1-associated protein 1 (BAP1) in osteosarcoma cells, and to analyze their biological functions. Methods The microarray dataset GSE23035 of BAP1-knockdown osteosarcoma cells was obtained from Gene Expression Omnibus (GEO) database, consisting of shControl, shBAP1#1 and shBAP1#2 samples. The DEGs between the BAP1-knockdown osteosarcoma cells and the untreated osteosarcoma cells were screened with limma package, and then subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Gene Set Enrichment Analysis (GSEA) was also performed for the three groups of samples. Hub genes in a protein-protein interaction (PPI) network of DEGs was filtered, and then subjected to prognostic analysis and correlation analysis with BAP1 in Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database. Besides, the correlation between BAP1 and biological processes/pathways was analyzed by Gene Set Variation Analysis (GSVA) method and the correlation between BAP1 and immune infiltration by CIBERSORT and ESTIMATE methods. The roles of BAP1 in regulating proliferation and epithelial-mesenchymal transition (EMT) were validated by CCK-8 and western blot. Results 58 upregulated DEGs and 81 downregulated DEGs were obtained with |logFC| ≥ 1 and adj.p < 0.05. Cell cycle, DNA repair, and focal adhesion were associated with BAP1 in datasets. Further, BAP1 was negatively correlated with naïve CD4 T cells infiltration. In vitro, BAP1 inhibited proliferation and EMT. Conclusion BAP1 might be a tumor suppressor in osteosarcoma and a promising therapeutic target.
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16
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Vimercati L, Cavone D, Fortarezza F, Delfino MC, Ficarella R, Gentile A, De Palma A, Marulli G, De Maria L, Caporusso C, Marzullo A, d’Amati A, Romano DE, Caputi A, Sponselli S, Serio G, Pezzuto F. Case report: Mesothelioma and BAP1 tumor predisposition syndrome: Implications for public health. Front Oncol 2022; 12:966063. [PMID: 35992853 PMCID: PMC9386481 DOI: 10.3389/fonc.2022.966063] [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: 06/30/2022] [Accepted: 07/12/2022] [Indexed: 11/17/2022] Open
Abstract
BRCA-1 associated protein 1 (BAP1) tumour predisposition syndrome (TPDS) is a hereditary condition characterised by germline mutation of the tumour suppressor BAP1. This disorder is associated with the development of various benign and malignant tumours, mainly involving the skin, eyes, kidneys, and mesothelium. In this article, we report the case of a man recruited through the Apulia (Southern Italy) Mesothelioma Regional Operational Centre of the National Register of Mesotheliomas, who suffered from uveal melanoma, renal cancer, and mesothelioma, and a familial cluster of BAP1 germline mutations demonstrated by molecular analyses. The family members of the proband developed multiple malignancies. As tumours arising in this context have specific peculiarities in terms of clinical behaviour, identification of this condition through appropriate genetic counselling should be considered for adequate primary, secondary, and tertiary prevention measures for offspring.
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Affiliation(s)
- Luigi Vimercati
- Interdisciplinary Department of Medicine, Occupational Medicine Section Ramazzini, University of Bari Aldo Moro, Bari, Italy
| | - Domenica Cavone
- Interdisciplinary Department of Medicine, Occupational Medicine Section Ramazzini, University of Bari Aldo Moro, Bari, Italy
| | - Francesco Fortarezza
- Pathology Unit, Department of Medicine, School of Medicine and Surgery, University Hospital of Padova, University of Padova, Padova, Italy
| | - Maria Celeste Delfino
- Interdisciplinary Department of Medicine, Occupational Medicine Section Ramazzini, University of Bari Aldo Moro, Bari, Italy
| | - Romina Ficarella
- Medical Genetics Unit, Department of Human Reproductive Medicine, ASL Bari, Bari, Italy
| | - Angela Gentile
- Medical Genetics Unit, Department of Human Reproductive Medicine, ASL Bari, Bari, Italy
| | - Angela De Palma
- Thoracic Surgery Unit, Department of Emergency and Organ Transplantation, University Hospital of Bari, Bari, Italy
| | - Giuseppe Marulli
- Thoracic Surgery Unit, Department of Emergency and Organ Transplantation, University Hospital of Bari, Bari, Italy
| | - Luigi De Maria
- Interdisciplinary Department of Medicine, Occupational Medicine Section Ramazzini, University of Bari Aldo Moro, Bari, Italy
| | - Concetta Caporusso
- Department of Emergency and Organ Transplantation (DETO), Pathological Anatomy Section, University of Bari Aldo Moro, Bari, Italy
| | - Andrea Marzullo
- Department of Emergency and Organ Transplantation (DETO), Pathological Anatomy Section, University of Bari Aldo Moro, Bari, Italy
| | - Antonio d’Amati
- Department of Emergency and Organ Transplantation (DETO), Pathological Anatomy Section, University of Bari Aldo Moro, Bari, Italy
| | - Daniele Egidio Romano
- Department of Emergency and Organ Transplantation (DETO), Pathological Anatomy Section, University of Bari Aldo Moro, Bari, Italy
| | - Antonio Caputi
- Interdisciplinary Department of Medicine, Occupational Medicine Section Ramazzini, University of Bari Aldo Moro, Bari, Italy
| | - Stefania Sponselli
- Interdisciplinary Department of Medicine, Occupational Medicine Section Ramazzini, University of Bari Aldo Moro, Bari, Italy
| | - Gabriella Serio
- Department of Emergency and Organ Transplantation (DETO), Pathological Anatomy Section, University of Bari Aldo Moro, Bari, Italy
| | - Federica Pezzuto
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health (DCTV), Pathology Unit, University of Padova, Padova, Italy
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17
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Molecular Profile and Prognostic Value of BAP1 Mutations in Intrahepatic Cholangiocarcinoma: A Genomic Database Analysis. J Pers Med 2022; 12:jpm12081247. [PMID: 36013199 PMCID: PMC9410256 DOI: 10.3390/jpm12081247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/23/2022] [Accepted: 07/28/2022] [Indexed: 11/26/2022] Open
Abstract
Background. Recent years have witnessed the advent of molecular profiling for intrahepatic cholangiocarcinoma (iCCA), and new techniques have led to the identification of several molecular alterations. Precision oncology approaches have been widely evaluated and are currently under assessment, as shown by the recent development of a wide range of agents targeting Fibroblast Growth Factor Receptor (FGFR) 2, Isocitrate Dehydrogenase 1 (IDH-1), and BRAF. However, several knowledge gaps persist in the understanding of the genomic landscape of this hepatobiliary malignancy. Methods. In the current study, we aimed to comprehensively analyze clinicopathological features of BAP1-mutated iCCA patients in public datasets to increase the current knowledge on the molecular and biological profile of iCCA. Results. The current database study, including 772 iCCAs, identified BAP1 mutations in 120 cases (15.7%). According to our analysis, no differences in terms of overall survival and relapse-free survival were observed between BAP1-mutated and BAP1 wild-type patients receiving radical surgery. In addition, IDH1, PBRM1, and ARID1A mutations were the most commonly co-altered genes in BAP1-mutated iCCAs. Conclusions. The genomic characterization of iCCA is destined to become increasingly important, and more efforts aimed to implement iCCA genomics analysis are warranted.
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18
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Han A, Chua V, Baqai U, Purwin TJ, Bechtel N, Hunter E, Tiago M, Seifert E, Speicher DW, Schug ZT, Harbour JW, Aplin AE. Pyruvate dehydrogenase inactivation causes glycolytic phenotype in BAP1 mutant uveal melanoma. Oncogene 2022; 41:1129-1139. [PMID: 35046531 PMCID: PMC9066178 DOI: 10.1038/s41388-021-02154-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 12/02/2021] [Accepted: 12/10/2021] [Indexed: 12/12/2022]
Abstract
Effective therapeutic options are still lacking for uveal melanoma (UM) patients who develop metastasis. Metastatic traits of UM are linked to BRCA1-associated protein 1 (BAP1) mutations. Cell metabolism is re-programmed in UM with BAP1 mutant UM, but the underlying mechanisms and opportunities for therapeutic intervention remain unclear. BAP1 mutant UM tumors have an elevated glycolytic gene expression signature, with increased expression of pyruvate dehydrogenase (PDH) complex and PDH kinase (PDHK1). Furthermore, BAP1 mutant UM cells showed higher levels of phosphorylated PDHK1 and PDH that was associated with an upregulated glycolytic profile compared to BAP1 wild-type UM cells. Suppressing PDHK1-PDH phosphorylation decreased glycolytic capacity and cell growth, and induced cell cycle arrest of BAP1 mutant UM cells. Our results suggest that PDHK1-PDH phosphorylation is a causative factor of glycolytic phenotypes found in BAP1 mutant UM and propose a therapeutic opportunity for BAP1 mutant UM patients.
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Affiliation(s)
- Anna Han
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
- Department of Food Science and Human Nutrition, Jeonbuk National University, Jeonju, Jeollabuk-do, 54896, Republic of Korea
| | - Vivian Chua
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Usman Baqai
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Timothy J Purwin
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Nelisa Bechtel
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Emily Hunter
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Manoela Tiago
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Erin Seifert
- Department of Pathology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - David W Speicher
- Proteomics and Metabolomics Facility, The Wistar Institute, Philadelphia, PA, 19104, USA
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Zachary T Schug
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - J William Harbour
- Bascom Palmer Eye Institute, Sylvester Comprehensive Cancer Center and Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, 33146, USA
- Department of Ophthalmology, Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Andrew E Aplin
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA.
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA.
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19
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Yan YC, Meng GX, Ding ZN, Liu YF, Chen ZQ, Yan LJ, Yang YF, Liu H, Yang CC, Dong ZR, Hong JG, Li T. Somatic mutation and expression of BAP1 in hepatocellular carcinoma: an indicator for ferroptosis and immune checkpoint inhibitor therapies. J Cancer 2022; 13:88-101. [PMID: 34976173 PMCID: PMC8692694 DOI: 10.7150/jca.65574] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 11/10/2021] [Indexed: 12/16/2022] Open
Abstract
BRCA1-Associated Protein 1 (BAP1) is a deubiquitylase that is found associated with multiprotein complexes that regulate key cellular pathways, and subsequent researches have revealed that BAP1 acts independently as a tumor suppressor. Somatic BAP1 mutations occur in various malignancies, but malignancies arising from mutation of tumor suppressors have unexplained tissue proclivity. Whether somatic mutation or expression alteration of BAP1 in hepatocellular carcinoma (HCC) influence carcinogenesis or immunogenicity is still unknown. In this study, we analyzed RNA expression, immune infiltration, survival and mutation data of HCC from The Cancer Genome Atlas databases. The association between BAP1 and clinicopathological features was further investigated by immunohistochemistry on tissue microarray. We found that the prognosis of patients with high BAP1 expression was significantly worse than that of patients with low BAP1 expression, and multivariate analyses revealed that BAP1 expression was an independent prognostic factor for poor prognosis. HCC with high BAP1 expression was associated with low ESTIMATE Score, recruitment of more tumor-infiltrating macrophage, and elevated levels of tumor mutation burden, microsatellite instability, neoantigen count, as well as programmed death-ligand1 in HCC. In addition, BAP1 mutated HCC showed reduced ability to promote ferroptosis and high BAP1 expression was correlated with ferroptosis. In conclusion, high BAP1 expression reflects immunosuppression and ferroptosis in HCC. BAP1 is a promising prognostic marker for survival of HCC and may act as a complementary indicator for patients to receive ferroptosis-promoting therapy or immunotherapy.
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Affiliation(s)
- Yu-Chuan Yan
- Department of general surgery, Qilu Hospital, Shandong University, Jinan 250012, P.R. China
| | - Guang-Xiao Meng
- Department of general surgery, Qilu Hospital, Shandong University, Jinan 250012, P.R. China
| | - Zi-Niu Ding
- Department of general surgery, Qilu Hospital, Shandong University, Jinan 250012, P.R. China
| | - Yan-Feng Liu
- Department of general surgery, Qilu Hospital, Shandong University, Jinan 250012, P.R. China
| | - Zhi-Qiang Chen
- Department of general surgery, Qilu Hospital, Shandong University, Jinan 250012, P.R. China
| | - Lun-Jie Yan
- Department of general surgery, Qilu Hospital, Shandong University, Jinan 250012, P.R. China
| | - Ya-Fei Yang
- Department of general surgery, Qilu Hospital, Shandong University, Jinan 250012, P.R. China
| | - Hui Liu
- Department of general surgery, Qilu Hospital, Shandong University, Jinan 250012, P.R. China
| | - Chun-Cheng Yang
- Department of general surgery, Qilu Hospital, Shandong University, Jinan 250012, P.R. China
| | - Zhao-Ru Dong
- Department of general surgery, Qilu Hospital, Shandong University, Jinan 250012, P.R. China
| | - Jian-Guo Hong
- Department of general surgery, Qilu Hospital, Shandong University, Jinan 250012, P.R. China
| | - Tao Li
- Department of general surgery, Qilu Hospital, Shandong University, Jinan 250012, P.R. China.,Department of hepatobiliary surgery, The second Hospital of Shandong University, Jinan 250012, P.R. China
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20
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Chua V, Han A, Bechtel N, Purwin TJ, Hunter E, Liao C, Harbour JW, Aplin AE. The AMP-dependent kinase pathway is upregulated in BAP1 mutant uveal melanoma. Pigment Cell Melanoma Res 2021; 35:78-87. [PMID: 34347929 DOI: 10.1111/pcmr.13007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 07/31/2021] [Accepted: 08/02/2021] [Indexed: 02/03/2023]
Abstract
Metastatic uveal melanoma (UM) responds poorly to targeted therapies and immune checkpoint inhibitors. Loss of BRCA1-associated protein 1 (BAP1) via inactivating mutations in the BAP1 gene is associated with UM progression. Thus, molecular alterations caused by BAP1 dysfunction may be novel therapeutic targets for metastatic UM. Here, we found that phosphorylation of AMP-dependent kinase (AMPK) was elevated in BAP1-altered (or mutant) compared to BAP1-unaltered (or wild-type [WT]) UM tumors. As a readout of AMPK pathway activation, phosphorylation of an AMPK downstream effector, acetyl-CoA-carboxylase (ACC), was also elevated. BAP1 re-expression in BAP1-null UM cell lines decreased phospho-AMPK (pAMPK) and phospho-ACC (pACC) levels. AMPK phosphorylation is mediated by calcium/calmodulin dependent protein kinase kinase 2 (CaMKK2) and potentially liver kinase B1 (LKB1) in BAP1 mutant UM cells. Knockdown of AMPKα1/2 reduced the viability of BAP1 mutant UM cells, indicating a survival function of AMPK in BAP1 mutant UM. Our data suggest that the AMPK pathway is an important mechanism mediating the survival of BAP1 mutant UM. Targeting the AMPK pathway may be a novel therapeutic strategy for metastatic UM.
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Affiliation(s)
- Vivian Chua
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Anna Han
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Nelisa Bechtel
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Timothy J Purwin
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Emily Hunter
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Connie Liao
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - J William Harbour
- Bascom Palmer Eye Institute, Sylvester Comprehensive Cancer Center and Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Andrew E Aplin
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA.,Sidney Kimmel Cancer Center, Philadelphia, PA, USA
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21
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Webster BR, Rompre-Brodeur A, Daneshvar M, Pahwa R, Srinivasan R. Kidney cancer: from genes to therapy. Curr Probl Cancer 2021; 45:100773. [PMID: 34261604 DOI: 10.1016/j.currproblcancer.2021.100773] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 06/24/2021] [Accepted: 06/24/2021] [Indexed: 11/30/2022]
Abstract
Renal cell carcinoma incidence is rising worldwide with increasing subtype stratification by the World Health Organization. Each subtype has unique genetic alterations, cell biology changes and clinical findings. Such genetic alterations offer the potential for individualized therapeutic approaches that are rapidly progressing. This review highlights the most common subtypes of renal cell carcinoma, including both hereditary and sporadic forms, with a focus on genetic changes, clinical findings and ongoing clinical trials.
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Affiliation(s)
- Bradley R Webster
- Center for Cancer Research, Urologic Oncology Branch, National Cancer Institute/NIH, 10 Center Drive, CRC Room 2W-5940, Bethesda, MD 20892, USA
| | - Alexis Rompre-Brodeur
- Center for Cancer Research, Urologic Oncology Branch, National Cancer Institute/NIH, 10 Center Drive, CRC Room 2W-5940, Bethesda, MD 20892, USA
| | - Michael Daneshvar
- Center for Cancer Research, Urologic Oncology Branch, National Cancer Institute/NIH, 10 Center Drive, CRC Room 2W-5940, Bethesda, MD 20892, USA
| | - Roma Pahwa
- Center for Cancer Research, Urologic Oncology Branch, National Cancer Institute/NIH, 10 Center Drive, CRC Room 2W-5940, Bethesda, MD 20892, USA
| | - Ramaprasad Srinivasan
- Center for Cancer Research, Urologic Oncology Branch, National Cancer Institute/NIH, 10 Center Drive, CRC Room 2W-5940, Bethesda, MD 20892, USA.
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22
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Han A, Schug ZT, Aplin AE. Metabolic Alterations and Therapeutic Opportunities in Rare Forms of Melanoma. Trends Cancer 2021; 7:671-681. [PMID: 34127435 DOI: 10.1016/j.trecan.2021.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 12/12/2022]
Abstract
Melanoma is derived from melanocytes located in multiple regions of the body. Cutaneous melanoma (CM) represents the major subgroup, but less-common subtypes including uveal melanoma (UM), mucosal melanoma (MM), and acral melanoma (AM) arise that have distinct genetic profiles. Treatments effective for CM are ineffective in UM, AM, and MM, and patient survival remains poor. As reprogrammed cancer metabolism is associated with tumorigenesis, the underlying mechanisms are well studied and provide therapeutic opportunities in many cancers; however, metabolism is less well studied in rarer melanoma subtypes. We summarize current knowledge of the metabolic alterations in rare melanoma and potential applications of targeting cancer metabolism to improve the therapeutic options available to UM, AM, and MM patients.
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Affiliation(s)
- Anna Han
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Zachary T Schug
- Molecular and Cellular Oncogenesis Program, Wistar Institute, Philadelphia, PA19104, USA
| | - Andrew E Aplin
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA; Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.
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23
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Wang Y, Wang F. Post-Translational Modifications of Deubiquitinating Enzymes: Expanding the Ubiquitin Code. Front Pharmacol 2021; 12:685011. [PMID: 34177595 PMCID: PMC8224227 DOI: 10.3389/fphar.2021.685011] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022] Open
Abstract
Post-translational modifications such as ubiquitination play important regulatory roles in several biological processes in eukaryotes. This process could be reversed by deubiquitinating enzymes (DUBs), which remove conjugated ubiquitin molecules from target substrates. Owing to their role as essential enzymes in regulating all ubiquitin-related processes, the abundance, localization, and catalytic activity of DUBs are tightly regulated. Dysregulation of DUBs can cause dramatic physiological consequences and a variety of disorders such as cancer, and neurodegenerative and inflammatory diseases. Multiple factors, such as transcription and translation of associated genes, and the presence of accessory domains, binding proteins, and inhibitors have been implicated in several aspects of DUB regulation. Beyond this level of regulation, emerging studies show that the function of DUBs can be regulated by a variety of post-translational modifications, which significantly affect the abundance, localization, and catalytic activity of DUBs. The most extensively studied post-translational modification of DUBs is phosphorylation. Besides phosphorylation, ubiquitination, SUMOylation, acetylation, oxidation, and hydroxylation are also reported in DUBs. In this review, we summarize the current knowledge on the regulatory effects of post-translational modifications of DUBs.
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Affiliation(s)
- Yanfeng Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Feng Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
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24
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Polycomb-group proteins in the initiation and progression of cancer. J Genet Genomics 2021; 48:433-443. [PMID: 34266781 DOI: 10.1016/j.jgg.2021.03.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/23/2021] [Accepted: 03/28/2021] [Indexed: 12/13/2022]
Abstract
The Polycomb group (PcG) proteins are a family of chromatin regulators and critical for the maintenance of cellular identity. The PcG machinery can be categorized into at least three multi-protein complexes, namely Polycomb Repressive Complex 1 (PRC1), PRC2, and Polycomb Repressive DeUBiquitinase (PR-DUB). Their deregulation has been associated with human cancer initiation and progression. Here we review the updated understanding for PcG proteins in transcription regulation and DNA damage repair and highlight increasing links to the hallmarks in cancer. Accordingly, we discuss some of the recent advances in drug development or strategies against cancers caused by the gain or loss of PcG functions.
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