1
|
Feng H, Cao S, Fu S, Liu J, Gao Y, Dong Z, Cai T, Wen L, Xiong Z, Li S, Zhang X, Ma X, Li X. NMRK2 is an efficient diagnostic indicator for Xp11.2 translocation renal cell carcinoma. J Pathol 2024. [PMID: 39092712 DOI: 10.1002/path.6340] [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: 01/15/2024] [Revised: 06/24/2024] [Accepted: 07/02/2024] [Indexed: 08/04/2024]
Abstract
Xp11.2 translocation renal cell carcinomas (tRCC) are a rare and highly malignant type of renal cancer, lacking efficient diagnostic indicators and therapeutic targets. Through the analysis of public databases and our cohort, we identified NMRK2 as a potential diagnostic marker for distinguishing Xp11.2 tRCC from kidney renal clear cell carcinoma (KIRC) and kidney renal papillary cell carcinoma (KIRP) due to its specific upregulation in Xp11.2 tRCC tissues. Mechanistically, we discovered that TFE3 fusion protein binds to the promoter of the NMRK2 gene, leading to its upregulation. Importantly, we established RNA- and protein-based diagnostic methods for identifying Xp11.2 tRCC based on NMRK2 expression levels, and the diagnostic performance of our methods was comparable to a dual-color break-apart fluorescence in situ hybridization assay. Moreover, we successfully identified fresh Xp11.2 tRCC tissues after surgical excision using our diagnostic methods and established an immortalized Xp11.2 tRCC cell line for further research purposes. Functional studies revealed that NMRK2 promotes the progression of Xp11.2 tRCC by upregulating the NAD+/NADH ratio, and supplementation with β-nicotinamide mononucleotide (NMN) or nicotinamide riboside chloride (NR), effectively rescued the phenotypes induced by the knockdown of NMRK2 in Xp11.2 tRCC. Taken together, these data introduce a new diagnostic indicator capable of accurately distinguishing Xp11.2 tRCC and highlight the possibility of developing novel targeted therapeutics. © 2024 The Pathological Society of Great Britain and Ireland.
Collapse
Affiliation(s)
- Huayi Feng
- Chinese PLA Medical School, Beijing, PR China
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, PR China
| | - Shouqing Cao
- College of Graduate, Hebei North University, Zhangjiakou, PR China
| | - Shihui Fu
- Department of Cardiology, Hainan Hospital of Chinese PLA General Hospital, Sanya, PR China
- Department of Geriatric Cardiology, Chinese PLA General Hospital, Beijing, PR China
| | - Junxiao Liu
- Chinese PLA Medical School, Beijing, PR China
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, PR China
| | - Yu Gao
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, PR China
| | - Zhouhuan Dong
- Department of Pathology, The First Medical Center, Chinese PLA General Hospital, Beijing, PR China
| | - Tianwei Cai
- Chinese PLA Medical School, Beijing, PR China
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, PR China
| | - Lequan Wen
- Chinese PLA Medical School, Beijing, PR China
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, PR China
| | - Zhuang Xiong
- Chinese PLA Medical School, Beijing, PR China
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, PR China
| | - Shangwei Li
- Chinese PLA Medical School, Beijing, PR China
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, PR China
| | - Xu Zhang
- Chinese PLA Medical School, Beijing, PR China
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, PR China
| | - Xin Ma
- Chinese PLA Medical School, Beijing, PR China
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, PR China
| | - Xiubin Li
- Department of Urology, The Third Medical Center, Chinese PLA General Hospital, Beijing, PR China
| |
Collapse
|
2
|
Li GX, Chen L, Hsiao Y, Mannan R, Zhang Y, Luo J, Petralia F, Cho H, Hosseini N, Leprevost FDV, Calinawan A, Li Y, Anand S, Dagar A, Geffen Y, Kumar-Sinha C, Chugh S, Le A, Ponce S, Guo S, Zhang C, Schnaubelt M, Al Deen NN, Chen F, Caravan W, Houston A, Hopkins A, Newton CJ, Wang X, Polasky DA, Haynes S, Yu F, Jing X, Chen S, Robles AI, Mesri M, Thiagarajan M, An E, Getz GA, Linehan WM, Hostetter G, Jewell SD, Chan DW, Wang P, Omenn GS, Mehra R, Ricketts CJ, Ding L, Chinnaiyan AM, Cieslik MP, Dhanasekaran SM, Zhang H, Nesvizhskii AI. Comprehensive proteogenomic characterization of rare kidney tumors. Cell Rep Med 2024; 5:101547. [PMID: 38703764 PMCID: PMC11148773 DOI: 10.1016/j.xcrm.2024.101547] [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: 03/20/2023] [Revised: 09/29/2023] [Accepted: 04/10/2024] [Indexed: 05/06/2024]
Abstract
Non-clear cell renal cell carcinomas (non-ccRCCs) encompass diverse malignant and benign tumors. Refinement of differential diagnosis biomarkers, markers for early prognosis of aggressive disease, and therapeutic targets to complement immunotherapy are current clinical needs. Multi-omics analyses of 48 non-ccRCCs compared with 103 ccRCCs reveal proteogenomic, phosphorylation, glycosylation, and metabolic aberrations in RCC subtypes. RCCs with high genome instability display overexpression of IGF2BP3 and PYCR1. Integration of single-cell and bulk transcriptome data predicts diverse cell-of-origin and clarifies RCC subtype-specific proteogenomic signatures. Expression of biomarkers MAPRE3, ADGRF5, and GPNMB differentiates renal oncocytoma from chromophobe RCC, and PIGR and SOSTDC1 distinguish papillary RCC from MTSCC. This study expands our knowledge of proteogenomic signatures, biomarkers, and potential therapeutic targets in non-ccRCC.
Collapse
Affiliation(s)
- Ginny Xiaohe Li
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lijun Chen
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Yi Hsiao
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rahul Mannan
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yuping Zhang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jie Luo
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hanbyul Cho
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Noshad Hosseini
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Anna Calinawan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yize Li
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Shankara Anand
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Aniket Dagar
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yifat Geffen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02115, USA
| | - Chandan Kumar-Sinha
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Seema Chugh
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anne Le
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Sean Ponce
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA
| | - Shenghao Guo
- Department of Biomedical Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA
| | - Cissy Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Michael Schnaubelt
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Nataly Naser Al Deen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Feng Chen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Wagma Caravan
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Andrew Houston
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Alex Hopkins
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Xiaoming Wang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel A Polasky
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sarah Haynes
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xiaojun Jing
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Siqi Chen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | | | - Eunkyung An
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Gad A Getz
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Scott D Jewell
- Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Daniel W Chan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Human Genetics, and School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rohit Mehra
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Christopher J Ricketts
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63130, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marcin P Cieslik
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Saravana M Dhanasekaran
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.
| |
Collapse
|
3
|
Damayanti NP, Cordova RA, Rupert C, Delle Fontane I, Shen L, Orsi S, Klunk AJ, Linehan WM, Staschke KA, Hollenhorst PC, Heppner DE, Pili R. TFE3-Splicing Factor Fusions Represent Functional Drivers and Druggable Targets in Translocation Renal Cell Carcinoma. Cancer Res 2024; 84:1286-1302. [PMID: 38266162 DOI: 10.1158/0008-5472.can-23-1789] [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: 07/10/2023] [Revised: 12/05/2023] [Accepted: 01/22/2024] [Indexed: 01/26/2024]
Abstract
TFE3 is a member of the basic helix-loop-helix leucine zipper MiT transcription factor family, and its chimeric proteins are associated with translocation renal cell carcinoma (tRCC). Despite the variety of gene fusions, most TFE3 fusion partner genes are related to spliceosome machinery. Dissecting the function of TFE3 fused to spliceosome machinery factors (TFE3-SF) could direct the development of effective therapies for this lethal disease, which is refractory to standard treatments for kidney cancer. Here, by using a combination of in silico structure prediction, transcriptome profiling, molecular characterization, and high-throughput high-content screening (HTHCS), we interrogated a number of oncogenic mechanisms of TFE3-SF fusions. TFE3-SF fusions drove the transformation of kidney cells and promoted distinct oncogenic phenotypes in a fusion partner-dependent manner, differentially altering the transcriptome and RNA splicing landscape and activating different oncogenic pathways. Inhibiting TFE3-SF dimerization reversed its oncogenic activity and represented a potential target for therapeutic intervention. Screening the FDA-approved drugs library LOPAC and a small-molecule library (Microsource) using HTHCS combined with FRET technology identified compounds that inhibit TFE3-SF dimerization. Hit compounds were validated in 2D and 3D patient-derived xenograft models expressing TFE3-SF. The antihistamine terfenadine decreased cell proliferation and reduced in vivo tumor growth of tRCC. Overall, these results unmask therapeutic strategies to target TFE3-SF dimerization for treating patients with tRCC. SIGNIFICANCE TFE3-splicing factor fusions possess both transcription and splicing factor functions that remodel the transcriptome and spliceosome and can be targeted with dimerization inhibitors to suppress the growth of translocation renal cell carcinoma.
Collapse
Affiliation(s)
- Nur P Damayanti
- Genitourinary Program, Division of Hematology & Oncology, Indiana University, Indianapolis, Indiana
- Department of Neurosurgery, Division of Neuro-Oncology, Indiana University, Indianapolis, Indiana
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana
| | - Ricardo A Cordova
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana
- Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, Indiana
| | - Christopher Rupert
- Division of Hematology and Oncology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - Ilaria Delle Fontane
- Division of Hematology and Oncology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - Li Shen
- Division of Hematology and Oncology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - Sabrina Orsi
- Division of Hematology and Oncology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - Angela J Klunk
- Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, Indiana
| | - W Marston Linehan
- Urological Oncology Branch, National Cancer Institute, Bethesda, Maryland
| | - Kirk A Staschke
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana
- Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, Indiana
| | - Peter C Hollenhorst
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana
| | - David E Heppner
- Department of Chemistry, University at Buffalo, Buffalo, New York
| | - Roberto Pili
- Genitourinary Program, Division of Hematology & Oncology, Indiana University, Indianapolis, Indiana
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana
- Division of Hematology and Oncology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| |
Collapse
|
4
|
Xhori O, Deol N, Rivera CM, Zavras J, Weil SG, Zafari H, Thierauf JC, Faquin WC, Choy E, Rivera MN, John Iafrate A, Jaquinet A, Troulis MJ. A Comparison of Clear Cell Sarcoma to Jaw and Salivary Tumors Bearing EWS Fusions. Head Neck Pathol 2024; 18:25. [PMID: 38526767 DOI: 10.1007/s12105-024-01625-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/04/2024] [Indexed: 03/27/2024]
Abstract
OBJECTIVE To review tumors identified as "clear cell sarcoma" in order to determine similarities to the rare EWS fusion positive jaw and salivary gland tumors clear cell odontogenic carcinoma (CCOC) and clear cell carcinoma of the salivary gland (CCC). METHODS PubMed was used to collect all reports of clear cell sarcoma (CCS). Search parameters were "clear cell sarcoma" and "CCS." References in the publications were screened and cross-referenced. Data extracted included demographic characteristics, presenting signs and symptoms, radiographic findings, histological and immunohistochemical features and known molecular/genetic aberrations. RESULTS Clear cell sarcoma has several similarities to CCOC and CCC. All three tumor types have similar histologic appearances including the presence of clear cells, as well as similar genetic profiles in that all harbor an EWSR1-CREB family fusions. Additionally, these tumors appear in soft tissue as well as bone, and can have a prolonged clinical course. CCS can appear anywhere in the body, including the head and neck region. All three tumors appear to have a predilection to women, although CCS may have a slight younger age of onset as compared to CCOC and CCC (3rd vs 5th decade of life, respectively). CONCLUSION Gaining a better understanding of the similarities and differences between these three tumors may lead to a better understanding of each one.
Collapse
Affiliation(s)
- Ornela Xhori
- Department of Oral and Maxillofacial Surgery, Massachusetts General Hospital, Boston, MA, 02113, USA
| | - Navkiran Deol
- Harvard School of Dental Medicine, DMD'25, 188 Longwood Avenue, Boston, MA, 02115, USA.
- Department of Oral and Maxillofacial Surgery, Massachusetts General Hospital, Boston, MA, 02113, USA.
| | - Camron M Rivera
- Harvard School of Dental Medicine, DMD'25, 188 Longwood Avenue, Boston, MA, 02115, USA
- Department of Oral and Maxillofacial Surgery, Massachusetts General Hospital, Boston, MA, 02113, USA
| | - Jason Zavras
- Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Sophia G Weil
- Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Hirad Zafari
- Harvard School of Dental Medicine, DMD'25, 188 Longwood Avenue, Boston, MA, 02115, USA
| | - Julia C Thierauf
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02113, USA
| | - William C Faquin
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02113, USA
- Harvard Medical School, 27 Shattuck Street, Boston, MA, 02115, USA
| | - Edwin Choy
- Harvard Medical School, 27 Shattuck Street, Boston, MA, 02115, USA
- Division of Hematology Oncology, Massachusetts General Hospital, Boston, MA, 02113, USA
| | - Miguel N Rivera
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02113, USA
- Harvard Medical School, 27 Shattuck Street, Boston, MA, 02115, USA
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02113, USA
- Harvard Medical School, 27 Shattuck Street, Boston, MA, 02115, USA
| | | | - Maria J Troulis
- Harvard School of Dental Medicine, DMD'25, 188 Longwood Avenue, Boston, MA, 02115, USA
- Department of Oral and Maxillofacial Surgery, Massachusetts General Hospital, Boston, MA, 02113, USA
| |
Collapse
|
5
|
Settembre C, Perera RM. Lysosomes as coordinators of cellular catabolism, metabolic signalling and organ physiology. Nat Rev Mol Cell Biol 2024; 25:223-245. [PMID: 38001393 DOI: 10.1038/s41580-023-00676-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2023] [Indexed: 11/26/2023]
Abstract
Every cell must satisfy basic requirements for nutrient sensing, utilization and recycling through macromolecular breakdown to coordinate programmes for growth, repair and stress adaptation. The lysosome orchestrates these key functions through the synchronised interplay between hydrolytic enzymes, nutrient transporters and signalling factors, which together enable metabolic coordination with other organelles and regulation of specific gene expression programmes. In this Review, we discuss recent findings on lysosome-dependent signalling pathways, focusing on how the lysosome senses nutrient availability through its physical and functional association with mechanistic target of rapamycin complex 1 (mTORC1) and how, in response, the microphthalmia/transcription factor E (MiT/TFE) transcription factors exert feedback regulation on lysosome biogenesis. We also highlight the emerging interactions of lysosomes with other organelles, which contribute to cellular homeostasis. Lastly, we discuss how lysosome dysfunction contributes to diverse disease pathologies and how inherited mutations that compromise lysosomal hydrolysis, transport or signalling components lead to multi-organ disorders with severe metabolic and neurological impact. A deeper comprehension of lysosomal composition and function, at both the cellular and organismal level, may uncover fundamental insights into human physiology and disease.
Collapse
Affiliation(s)
- Carmine Settembre
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy.
- Department of Clinical Medicine and Surgery, Federico II University, Naples, Italy.
| | - Rushika M Perera
- Department of Anatomy, University of California at San Francisco, San Francisco, CA, USA.
- Department of Pathology, University of California at San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA.
| |
Collapse
|
6
|
Prakasam G, Mishra A, Christie A, Miyata J, Carrillo D, Tcheuyap VT, Ye H, Do QN, Wang Y, Reig Torras O, Butti R, Zhong H, Gagan J, Jones KB, Carroll TJ, Modrusan Z, Durinck S, Requena-Komuro MC, Williams NS, Pedrosa I, Wang T, Rakheja D, Kapur P, Brugarolas J. Comparative genomics incorporating translocation renal cell carcinoma mouse model reveals molecular mechanisms of tumorigenesis. J Clin Invest 2024; 134:e170559. [PMID: 38386415 PMCID: PMC10977987 DOI: 10.1172/jci170559] [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: 03/15/2023] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
Translocation renal cell carcinoma (tRCC) most commonly involves an ASPSCR1-TFE3 fusion, but molecular mechanisms remain elusive and animal models are lacking. Here, we show that human ASPSCR1-TFE3 driven by Pax8-Cre (a credentialed clear cell RCC driver) disrupted nephrogenesis and glomerular development, causing neonatal death, while the clear cell RCC failed driver, Sglt2-Cre, induced aggressive tRCC (as well as alveolar soft part sarcoma) with complete penetrance and short latency. However, in both contexts, ASPSCR1-TFE3 led to characteristic morphological cellular changes, loss of epithelial markers, and an epithelial-mesenchymal transition. Electron microscopy of tRCC tumors showed lysosome expansion, and functional studies revealed simultaneous activation of autophagy and mTORC1 pathways. Comparative genomic analyses encompassing an institutional human tRCC cohort (including a hitherto unreported SFPQ-TFEB fusion) and a variety of tumorgraft models (ASPSCR1-TFE3, PRCC-TFE3, SFPQ-TFE3, RBM10-TFE3, and MALAT1-TFEB) disclosed significant convergence in canonical pathways (cell cycle, lysosome, and mTORC1) and less established pathways such as Myc, E2F, and inflammation (IL-6/JAK/STAT3, interferon-γ, TLR signaling, systemic lupus, etc.). Therapeutic trials (adjusted for human drug exposures) showed antitumor activity of cabozantinib. Overall, this study provides insight into MiT/TFE-driven tumorigenesis, including the cell of origin, and characterizes diverse mouse models available for research.
Collapse
Affiliation(s)
- Gopinath Prakasam
- Kidney Cancer Program, Simmons Comprehensive Cancer Center
- Hematology-Oncology Division, Department of Internal Medicine
| | - Akhilesh Mishra
- Kidney Cancer Program, Simmons Comprehensive Cancer Center
- Hematology-Oncology Division, Department of Internal Medicine
| | - Alana Christie
- Kidney Cancer Program, Simmons Comprehensive Cancer Center
- Peter O’ Donnell Jr. School of Public Health
| | - Jeffrey Miyata
- Kidney Cancer Program, Simmons Comprehensive Cancer Center
- Hematology-Oncology Division, Department of Internal Medicine
| | - Deyssy Carrillo
- Kidney Cancer Program, Simmons Comprehensive Cancer Center
- Hematology-Oncology Division, Department of Internal Medicine
| | - Vanina T. Tcheuyap
- Kidney Cancer Program, Simmons Comprehensive Cancer Center
- Hematology-Oncology Division, Department of Internal Medicine
| | - Hui Ye
- Kidney Cancer Program, Simmons Comprehensive Cancer Center
- Hematology-Oncology Division, Department of Internal Medicine
| | | | - Yunguan Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Oscar Reig Torras
- Kidney Cancer Program, Simmons Comprehensive Cancer Center
- Department of Medical Oncology and Translational Genomics and Targeted Therapies in Solid Tumors, Institut d’Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Hospital Clinic de Barcelona, Barcelona, Spain
| | - Ramesh Butti
- Kidney Cancer Program, Simmons Comprehensive Cancer Center
- Hematology-Oncology Division, Department of Internal Medicine
| | - Hua Zhong
- Kidney Cancer Program, Simmons Comprehensive Cancer Center
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jeffrey Gagan
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Kevin B. Jones
- Department of Orthopaedics and Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Thomas J. Carroll
- Department of Molecular Biology and Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Zora Modrusan
- Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing and
| | - Steffen Durinck
- Department of Oncology Bioinformatics, Genentech Inc., South San Francisco, California, USA
| | - Mai-Carmen Requena-Komuro
- Kidney Cancer Program, Simmons Comprehensive Cancer Center
- Hematology-Oncology Division, Department of Internal Medicine
| | | | - Ivan Pedrosa
- Kidney Cancer Program, Simmons Comprehensive Cancer Center
- Department of Radiology, and
- Advanced Imaging Research Center, and
- Department of Urology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Tao Wang
- Kidney Cancer Program, Simmons Comprehensive Cancer Center
- Peter O’ Donnell Jr. School of Public Health
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Dinesh Rakheja
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Payal Kapur
- Kidney Cancer Program, Simmons Comprehensive Cancer Center
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Urology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - James Brugarolas
- Kidney Cancer Program, Simmons Comprehensive Cancer Center
- Hematology-Oncology Division, Department of Internal Medicine
| |
Collapse
|
7
|
Yang S, Ting CY, Lilly MA. The GATOR2 complex maintains lysosomal-autophagic function by inhibiting the protein degradation of MiT/TFEs. Mol Cell 2024; 84:727-743.e8. [PMID: 38325378 PMCID: PMC10940221 DOI: 10.1016/j.molcel.2024.01.012] [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: 01/12/2023] [Revised: 07/31/2023] [Accepted: 01/17/2024] [Indexed: 02/09/2024]
Abstract
Lysosomes are central to metabolic homeostasis. The microphthalmia bHLH-LZ transcription factors (MiT/TFEs) family members MITF, TFEB, and TFE3 promote the transcription of lysosomal and autophagic genes and are often deregulated in cancer. Here, we show that the GATOR2 complex, an activator of the metabolic regulator TORC1, maintains lysosomal function by protecting MiT/TFEs from proteasomal degradation independent of TORC1, GATOR1, and the RAG GTPase. We determine that in GATOR2 knockout HeLa cells, members of the MiT/TFEs family are ubiquitylated by a trio of E3 ligases and are degraded, resulting in lysosome dysfunction. Additionally, we demonstrate that GATOR2 protects MiT/TFE proteins in pancreatic ductal adenocarcinoma and Xp11 translocation renal cell carcinoma, two cancers that are driven by MiT/TFE hyperactivation. In summary, we find that the GATOR2 complex has independent roles in TORC1 regulation and MiT/TFE protein protection and thus is central to coordinating cellular metabolism with control of the lysosomal-autophagic system.
Collapse
Affiliation(s)
- Shu Yang
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chun-Yuan Ting
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mary A Lilly
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
8
|
Wei S, Krause HB, Geynisman DM, Elliott A, Kutikov A, Uzzo RG, Pei J, Barata P, Carneiro B, Heath E, Ryan C, Farrell A, Nabhan C, Ali-Fehmi R, Naqash AR, Argani P, McKay RR. Molecular Characterization of TFE3-Rearranged Renal Cell Carcinoma: A Comparative Study With Papillary and Clear Cell Renal Cell Carcinomas. Mod Pathol 2024; 37:100404. [PMID: 38104891 DOI: 10.1016/j.modpat.2023.100404] [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: 06/04/2023] [Revised: 11/30/2023] [Accepted: 12/06/2023] [Indexed: 12/19/2023]
Abstract
TFE3-rearranged renal cell carcinoma (rRCC) is a rare subtype of renal cell carcinomas belonging to the MiT family translocation RCC. To further elucidate the co-alterations that occur along with TFE3 fusions in rRCC, we characterized the genomic, transcriptional, and immune landscapes in comparison to clear cell (ccRCC) and papillary renal cell carcinoma (pRCC). Next-generation sequencing of RNA (whole transcriptome) and DNA (592-gene panel or whole exome) for rRCC (N = 20), pRCC (N = 20), and ccRCC samples (N = 392) was performed. Patients with rRCC were significantly younger and more frequently female (median 44.5 years, 75.0% female) as compared with patients with pRCC (68.5 years, 25.0% female; P < .05) and ccRCC (62.0 years, 27.8% female; P < .05). A total of 8 unique fusion partners were observed, including a novel fusion with SRRM2::TFE3 in 2 patients. ccRCC exhibited significantly higher mutation rates of VHL (0% rRCC, 0% pRCC, 78.7% ccRCC; P < .05) and PBMR1 (0% rRCC, 5.0% pRCC, 49.4% ccRCC; P < .05). The genomic landscapes of rRCC were sparse with no mutations occurring with a prevalence higher than 10% other than pTERT (18.2% rRCC, 0% pRCC, 9.2% ccRCC). rRCC were associated with significantly less M1 macrophages (0.8%) as compared with pRCC (1.4%) and ccRCC (2.7%) (P < .05), suggesting a cold tumor-immune microenvironment. However, rRCC were more commonly PD-L1+ (rRCC 50%, pRCC 19.0%, ccRCC 12.2%; P < .05). Gene set enrichment analysis showed that rRCC are enriched in genes related to oxidative phosphorylation when compared with both ccRCC and pRCC. Despite having a colder tumor-immune microenvironment than pRCC and ccRCC, increased PDL1+ rates in rRCC suggest a potential benefit from immune checkpoint inhibitor therapy.
Collapse
Affiliation(s)
- Shuanzeng Wei
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania.
| | | | - Daniel M Geynisman
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | | | - Alexander Kutikov
- Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Robert G Uzzo
- Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Jianming Pei
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Pedro Barata
- Division of Solid Tumor Oncology, Department of Medicine, University Hospitals Seidman Cancer Center, Cleveland, Ohio
| | - Benedito Carneiro
- Division of Hematology/Oncology, Department of Medicine, Lifespan Health System, Brown University, Providence, Rhode Islands
| | - Elisabeth Heath
- Department of Oncology, Karmanos Cancer Institute, Detroit, Michigan
| | - Charles Ryan
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, Minnesota
| | | | | | - Rouba Ali-Fehmi
- Department of Pathology, Karmanos Cancer Institute, Detroit, Michigan
| | - Abdul Rafeh Naqash
- Medical Oncology, Stephenson Cancer Center, The University of Oklahoma Health Sciences, Oklahoma City, Oklahoma
| | - Pedram Argani
- Department of Pathology, The Johns Hopkins University School of Medicine, The Johns Hopkins Hospital, Baltimore, Maryland
| | - Rana R McKay
- Department of Medicine, University of California San Diego, San Diego, California
| |
Collapse
|
9
|
Alesi N, Khabibullin D, Rosenthal DM, Akl EW, Cory PM, Alchoueiry M, Salem S, Daou M, Gibbons WF, Chen JA, Zhang L, Filippakis H, Graciotti L, Miceli C, Monfregola J, Vilardo C, Morroni M, Di Malta C, Napolitano G, Ballabio A, Henske EP. TFEB drives mTORC1 hyperactivation and kidney disease in Tuberous Sclerosis Complex. Nat Commun 2024; 15:406. [PMID: 38195686 PMCID: PMC10776564 DOI: 10.1038/s41467-023-44229-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 12/05/2023] [Indexed: 01/11/2024] Open
Abstract
Tuberous Sclerosis Complex (TSC) is caused by TSC1 or TSC2 mutations, leading to hyperactivation of mechanistic target of rapamycin complex 1 (mTORC1) and lesions in multiple organs including lung (lymphangioleiomyomatosis) and kidney (angiomyolipoma and renal cell carcinoma). Previously, we found that TFEB is constitutively active in TSC. Here, we generated two mouse models of TSC in which kidney pathology is the primary phenotype. Knockout of TFEB rescues kidney pathology and overall survival, indicating that TFEB is the primary driver of renal disease in TSC. Importantly, increased mTORC1 activity in the TSC2 knockout kidneys is normalized by TFEB knockout. In TSC2-deficient cells, Rheb knockdown or Rapamycin treatment paradoxically increases TFEB phosphorylation at the mTORC1-sites and relocalizes TFEB from nucleus to cytoplasm. In mice, Rapamycin treatment normalizes lysosomal gene expression, similar to TFEB knockout, suggesting that Rapamycin's benefit in TSC is TFEB-dependent. These results change the view of the mechanisms of mTORC1 hyperactivation in TSC and may lead to therapeutic avenues.
Collapse
Affiliation(s)
- Nicola Alesi
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Damir Khabibullin
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Dean M Rosenthal
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Elie W Akl
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Pieter M Cory
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michel Alchoueiry
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Samer Salem
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Melissa Daou
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - William F Gibbons
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jennifer A Chen
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Long Zhang
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Harilaos Filippakis
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Laura Graciotti
- Section of Experimental and Technical Sciences, Department of Biomedical Sciences and Public Health, School of Medicine, Università Politecnica delle Marche, Ancona, Italy
| | | | | | | | - Manrico Morroni
- Section of Neuroscience and Cell Biology, Department of Experimental and Clinical Medicine, School of Medicine, Università Politecnica delle Marche, Ancona, Italy
| | - Chiara Di Malta
- Telethon Institute of Genetics and Medicine, Naples, Italy
- Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy
| | - Gennaro Napolitano
- Telethon Institute of Genetics and Medicine, Naples, Italy
- Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy
- SSM School for Advanced Studies, Federico II University, Naples, Italy
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine, Naples, Italy.
- Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy.
- SSM School for Advanced Studies, Federico II University, Naples, Italy.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
| | - Elizabeth P Henske
- Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
10
|
Ma Y, Liu Y, Meng H. Prognostic evaluation of oral squamous cell carcinoma based on pleiotrophin, urokinase plasminogen activator, and glycoprotein nonmetastatic melanoma protein B expression. Medicine (Baltimore) 2023; 102:e35634. [PMID: 37960806 PMCID: PMC10637552 DOI: 10.1097/md.0000000000035634] [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: 12/20/2022] [Accepted: 09/22/2023] [Indexed: 11/15/2023] Open
Abstract
This study investigated the expression of pleiotrophin (PTN), urokinase plasminogen activator (uPA), and glycoprotein nonmetastatic melanoma protein B (GPNMB) in oral squamous cell carcinoma (OSCC) tissues and their correlation with prognosis. From February 2017 to January 2020, PTN, uPA, and GPNMB expression in cancer tissues and adjacent tissues of 93 patients with OSCC was determined using immunohistochemistry. The diagnostic value of the combined detection of OSCC and its relationship with clinicopathological characteristics were analyzed, as well as the prognostic potential of PTN, uPA, and GPNMB. Cancer tissues from patients with OSCC exhibited high expression of PTN, uPA, and GPNMB. The AUC for the combined detection of PTN, uPA, and GPNMB for diagnosis and prognosis was greater than that of each index alone. The rates of expression of PTN, uPA, and GPNMB were higher in the death group than in the survival group. Patients with PTN, uPA, and GPNMB expression had lower 3-year survival rates. PTN expression was a risk factor affecting the prognosis of patients with OSCC. The rate of PTN, uPA, and GPNMB expression in OSCC tissues was high, and their expression was related to clinicopathological features such as lymph node metastasis and tumor invasion depth. The combined detection of each index has a predictive value for the prognosis of patients.
Collapse
Affiliation(s)
- Yuxin Ma
- Department of Stomatology, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, Xianning City, Hubei Province, China
| | - Yue Liu
- Department of Stomatology, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, Xianning City, Hubei Province, China
| | - Han Meng
- Department of Stomatology, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, Xianning City, Hubei Province, China
| |
Collapse
|
11
|
Li H, Argani P, Halper-Stromberg E, Lotan TL, Merino MJ, Reuter VE, Matoso A. Positive GPNMB Immunostaining Differentiates Renal Cell Carcinoma With Fibromyomatous Stroma Associated With TSC1/2/MTOR Alterations From Others. Am J Surg Pathol 2023; 47:1267-1273. [PMID: 37661807 PMCID: PMC10592185 DOI: 10.1097/pas.0000000000002117] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Renal cell carcinoma with fibromyomatous stroma (RCCFMS) include ELOC/TCEB1 -mutated renal cell carcinoma (RCC) and those with TSC1/2 / MTOR alterations. Besides morphologic similarity, most of these tumors is known to be diffusely positive for carbonic anhydrase IX and cytokeratin 7 by immunohistochemistry. We previously showed strong and diffuse expression of GPNMB (glycoprotein nonmetastatic B) in translocation RCC and eosinophilic renal neoplasms with known TSC1/2/MTOR alterations. We retrospectively identified molecularly confirmed cases of TCEB1/ELOC -mutated RCC (7 tumors from 7 patients), and RCCFMS with alterations in TSC1/2/MTOR (6 tumors from 5 patients, 1 patient with tuberous sclerosis syndrome). In addition, we included 7 clear cell papillary renal cell tumors (CCPRCTs) and 8 clear cell RCC, as they can also present morphologic overlap with RCCFMS. Morphologically, RCCs with TSC1/2/MTOR alterations and those with TCEB1/ELOC mutations were indistinguishable and characterized by papillary, nested, or tubular architecture, with tumor cells with clear cytoplasm and low nuclear grade. By immunohistochemistry, cytokeratin 7 was positive in 5/7 (71%) of TCEB1/ELOC -mutated RCCs, 6/6 (100%) of RCCs with TSC1/2/mTOR alterations, and 7/7 (100%) of CCPRCTs ( P =not significant). Carbonic anhydrase IX was positive in 7/7 TCEB1/ELOC -mutated RCCs, 6/6 (100%) of RCCs with TSC1/2/MTOR alterations, and 7/7 (100%) of CCPRCTs ( P =NS). GPNMB was strongly and diffusely positive in all tumors with TSC1/2/MTOR alterations (6/6), while negative in all TCEB1/ELOC -mutated RCCs (0/6), or CCPRCTs (0/7) ( P =0.002). Two of 8 clear cell RCC showed focal weak staining, while 6/8 were negative. In conclusion, the results support the use of GPNMB to distinguish RCCFMS with TSC1/2/MTOR alterations from others with similar morphology.
Collapse
Affiliation(s)
- Huili Li
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD, 21231
| | - Pedram Argani
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD, 21231
- Department of Oncology, The Johns Hopkins Medical Institutions, Baltimore, MD, 21231
| | | | - Tamara L. Lotan
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD, 21231
- Department of Oncology, The Johns Hopkins Medical Institutions, Baltimore, MD, 21231
| | - Maria J. Merino
- Translational Surgical Pathology, Laboratory of Pathology, National Institutes of health, Bethesda, MD 20892
| | - Victor E. Reuter
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10021
| | - Andres Matoso
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD, 21231
- Department of Urology, The Johns Hopkins Medical Institutions, Baltimore, MD, 21231
- Department of Oncology, The Johns Hopkins Medical Institutions, Baltimore, MD, 21231
| |
Collapse
|
12
|
Gibbons E, Minor BMN, Hammes SR. Lymphangioleiomyomatosis: where endocrinology, immunology and tumor biology meet. Endocr Relat Cancer 2023; 30:e230102. [PMID: 37410387 PMCID: PMC10529736 DOI: 10.1530/erc-23-0102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/03/2023] [Indexed: 07/07/2023]
Abstract
Abstract Lymphangioleiomyomatosis (LAM) is a cystic lung disease found almost exclusively in genetic females and caused by small clusters of smooth muscle cell tumors containing mutations in one of the two tuberous sclerosis genes (TSC1 or TSC2). Significant advances over the past 2-3 decades have allowed researchers and clinicians to more clearly understand the pathophysiology of LAM, and therefore better diagnose and treat patients with this disease. Despite substantial progress, only one proven treatment for LAM is used in practice: mechanistic target of rapamycin complex 1 (mTORC1) inhibition with medications such as sirolimus. While mTORC1 inhibition effectively slows LAM progression in many patients, it is not curative, is not effective in all patients, and can be associated with significant side effects. Furthermore, the presence of established and accurate biomarkers to follow LAM progression is limited. That said, discovering additional diagnostic and treatment options for LAM is paramount. This review will describe recent advances in LAM research, centering on the origin and nature of the LAM cell, the role of estrogen in LAM progression, the significance of melanocytic marker expression in LAM cells, and the potential roles of the microenvironment in promoting LAM tumor growth. By appreciating these processes in more detail, researchers and caregivers may be afforded novel approaches to aid in the treatment of patients with LAM.
Collapse
Affiliation(s)
- Erin Gibbons
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Rochester Medical Center, Rochester, New York, USA
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Briaunna M. N. Minor
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Rochester Medical Center, Rochester, New York, USA
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Stephen R Hammes
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Rochester Medical Center, Rochester, New York, USA
| |
Collapse
|
13
|
Achom M, Sadagopan A, Bao C, McBride F, Xu Q, Konda P, Tourdot RW, Li J, Nakhoul M, Gallant DS, Ahmed UA, O’Toole J, Freeman D, Mary Lee GS, Hecht JL, Kauffman EC, Einstein DJ, Choueiri TK, Zhang CZ, Viswanathan SR. A genetic basis for cancer sex differences revealed in Xp11 translocation renal cell carcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.04.552029. [PMID: 37577497 PMCID: PMC10418269 DOI: 10.1101/2023.08.04.552029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Xp11 translocation renal cell carcinoma (tRCC) is a female-predominant kidney cancer driven by translocations between the TFE3 gene on chromosome Xp11.2 and partner genes located on either chrX or on autosomes. The rearrangement processes that underlie TFE3 fusions, and whether they are linked to the female sex bias of this cancer, are largely unexplored. Moreover, whether oncogenic TFE3 fusions arise from both the active and inactive X chromosomes in females remains unknown. Here we address these questions by haplotype-specific analyses of whole-genome sequences of 29 tRCC samples from 15 patients and by re-analysis of 145 published tRCC whole-exome sequences. We show that TFE3 fusions universally arise as reciprocal translocations with minimal DNA loss or insertion at paired break ends. Strikingly, we observe a near exact 2:1 female:male ratio in TFE3 fusions arising via X:autosomal translocation (but not via X inversion), which accounts for the female predominance of tRCC. This 2:1 ratio is at least partially attributable to oncogenic fusions involving the inactive X chromosome and is accompanied by partial re-activation of silenced chrX genes on the rearranged chromosome. Our results highlight how somatic alterations involving the X chromosome place unique constraints on tumor initiation and exemplify how genetic rearrangements of the sex chromosomes can underlie cancer sex differences.
Collapse
Affiliation(s)
- Mingkee Achom
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Medicine, Harvard Medical School; Boston, MA, USA
| | - Ananthan Sadagopan
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Chunyang Bao
- Department of Data Science, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital; Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard; Cambridge, MA, USA
| | - Fiona McBride
- Department of Biomedical Informatics, Blavatnik Institute, Harvard Medical School; Boston, MA, USA
| | - Qingru Xu
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Prathyusha Konda
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Medicine, Harvard Medical School; Boston, MA, USA
| | - Richard W. Tourdot
- Department of Data Science, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Biomedical Informatics, Blavatnik Institute, Harvard Medical School; Boston, MA, USA
| | - Jiao Li
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Medicine, Harvard Medical School; Boston, MA, USA
| | - Maria Nakhoul
- Department of Informatics & Analytics, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Daniel S. Gallant
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Usman Ali Ahmed
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Jillian O’Toole
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Dory Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Gwo-Shu Mary Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Jonathan L. Hecht
- Department of Pathology, Beth Israel Deaconess Medical Center; Boston, MA, USA
| | - Eric C Kauffman
- Department of Urology, Roswell Park Comprehensive Cancer Center; Buffalo, New York, USA
| | - David J Einstein
- Division of Medical Oncology, Beth Israel Deaconess Medical Center; Boston, MA, USA
| | - Toni K. Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Medicine, Harvard Medical School; Boston, MA, USA
- Department of Medicine, Brigham and Women’s Hospital; Boston, MA, USA
| | - Cheng-Zhong Zhang
- Department of Data Science, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital; Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard; Cambridge, MA, USA
| | - Srinivas R. Viswanathan
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Medicine, Harvard Medical School; Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard; Cambridge, MA, USA
- Department of Medicine, Brigham and Women’s Hospital; Boston, MA, USA
| |
Collapse
|
14
|
Di Malta C, Zampelli A, Granieri L, Vilardo C, De Cegli R, Cinque L, Nusco E, Pece S, Tosoni D, Sanguedolce F, Sorrentino NC, Merino MJ, Nielsen D, Srinivasan R, Ball MW, Ricketts CJ, Vocke CD, Lang M, Karim B, Lanfrancone L, Schmidt LS, Linehan WM, Ballabio A. TFEB and TFE3 drive kidney cystogenesis and tumorigenesis. EMBO Mol Med 2023; 15:e16877. [PMID: 36987696 PMCID: PMC10165358 DOI: 10.15252/emmm.202216877] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/30/2023] Open
Abstract
Birt-Hogg-Dubé (BHD) syndrome is an inherited familial cancer syndrome characterized by the development of cutaneous lesions, pulmonary cysts, renal tumors and cysts and caused by loss-of-function pathogenic variants in the gene encoding the tumor-suppressor protein folliculin (FLCN). FLCN acts as a negative regulator of TFEB and TFE3 transcription factors, master controllers of lysosomal biogenesis and autophagy, by enabling their phosphorylation by the mechanistic Target Of Rapamycin Complex 1 (mTORC1). We have previously shown that deletion of Tfeb rescued the renal cystic phenotype of kidney-specific Flcn KO mice. Using Flcn/Tfeb/Tfe3 double and triple KO mice, we now show that both Tfeb and Tfe3 contribute, in a differential and cooperative manner, to kidney cystogenesis. Remarkably, the analysis of BHD patient-derived tumor samples revealed increased activation of TFEB/TFE3-mediated transcriptional program and silencing either of the two genes rescued tumorigenesis in human BHD renal tumor cell line-derived xenografts (CDXs). Our findings demonstrate in disease-relevant models that both TFEB and TFE3 are key drivers of renal tumorigenesis and suggest novel therapeutic strategies based on the inhibition of these transcription factors.
Collapse
Affiliation(s)
- Chiara Di Malta
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Medical Genetics Unit, Department of Medical and Translational ScienceFederico II UniversityNaplesItaly
| | - Angela Zampelli
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | - Letizia Granieri
- Department of Experimental OncologyEuropean Institute of Oncology IRCCS (IEO)MilanItaly
| | - Claudia Vilardo
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | | | - Laura Cinque
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | - Edoardo Nusco
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
| | - Salvatore Pece
- Department of Experimental OncologyEuropean Institute of Oncology IRCCS (IEO)MilanItaly
| | - Daniela Tosoni
- Department of Experimental OncologyEuropean Institute of Oncology IRCCS (IEO)MilanItaly
| | | | - Nicolina Cristina Sorrentino
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Department of Clinical Medicine and SurgeryFederico II UniversityNaplesItaly
| | - Maria J Merino
- Laboratory of Pathology, Center for Cancer Research, National Cancer InstituteNational Institutes of HealthBethesdaMDUSA
| | - Deborah Nielsen
- Urologic Oncology Branch, Center for Cancer ResearchNational Cancer Institute, National Institutes of HealthBethesdaMDUSA
| | - Ramaprasad Srinivasan
- Urologic Oncology Branch, Center for Cancer ResearchNational Cancer Institute, National Institutes of HealthBethesdaMDUSA
| | - Mark W Ball
- Urologic Oncology Branch, Center for Cancer ResearchNational Cancer Institute, National Institutes of HealthBethesdaMDUSA
| | - Christopher J Ricketts
- Urologic Oncology Branch, Center for Cancer ResearchNational Cancer Institute, National Institutes of HealthBethesdaMDUSA
| | - Cathy D Vocke
- Urologic Oncology Branch, Center for Cancer ResearchNational Cancer Institute, National Institutes of HealthBethesdaMDUSA
| | - Martin Lang
- Urologic Oncology Branch, Center for Cancer ResearchNational Cancer Institute, National Institutes of HealthBethesdaMDUSA
| | - Baktiar Karim
- Molecular Histopathology LaboratoryFrederick National Laboratory for Cancer ResearchFrederickMDUSA
| | - Luisa Lanfrancone
- Department of Experimental OncologyEuropean Institute of Oncology IRCCS (IEO)MilanItaly
| | - Laura S Schmidt
- Urologic Oncology Branch, Center for Cancer ResearchNational Cancer Institute, National Institutes of HealthBethesdaMDUSA
- Basic Science Program, Frederick National Laboratory for Cancer ResearchNational Cancer InstituteFrederickMDUSA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer ResearchNational Cancer Institute, National Institutes of HealthBethesdaMDUSA
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine (TIGEM)PozzuoliItaly
- Medical Genetics Unit, Department of Medical and Translational ScienceFederico II UniversityNaplesItaly
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTXUSA
- Jan and Dan Duncan Neurological Research InstituteTexas Children's HospitalHoustonTXUSA
| |
Collapse
|
15
|
Lang M, Schmidt LS, Wilson KM, Ricketts CJ, Sourbier C, Vocke CD, Wei D, Crooks DR, Yang Y, Gibbs BK, Zhang X, Klumpp-Thomas C, Chen L, Guha R, Ferrer M, McKnight C, Itkin Z, Wangsa D, Wangsa D, James A, Difilippantonio S, Karim B, Morís F, Ried T, Merino MJ, Srinivasan R, Thomas CJ, Linehan WM. High-throughput and targeted drug screens identify pharmacological candidates against MiT-translocation renal cell carcinoma. J Exp Clin Cancer Res 2023; 42:99. [PMID: 37095531 PMCID: PMC10127337 DOI: 10.1186/s13046-023-02667-4] [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: 12/22/2022] [Accepted: 04/06/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND MiT-Renal Cell Carcinoma (RCC) is characterized by genomic translocations involving microphthalmia-associated transcription factor (MiT) family members TFE3, TFEB, or MITF. MiT-RCC represents a specific subtype of sporadic RCC that is predominantly seen in young patients and can present with heterogeneous histological features making diagnosis challenging. Moreover, the disease biology of this aggressive cancer is poorly understood and there is no accepted standard of care therapy for patients with advanced disease. Tumor-derived cell lines have been established from human TFE3-RCC providing useful models for preclinical studies. METHODS TFE3-RCC tumor derived cell lines and their tissues of origin were characterized by IHC and gene expression analyses. An unbiased high-throughput drug screen was performed to identify novel therapeutic agents for treatment of MiT-RCC. Potential therapeutic candidates were validated in in vitro and in vivo preclinical studies. Mechanistic assays were conducted to confirm the on-target effects of drugs. RESULTS The results of a high-throughput small molecule drug screen utilizing three TFE3-RCC tumor-derived cell lines identified five classes of agents with potential pharmacological efficacy, including inhibitors of phosphoinositide-3-kinase (PI3K) and mechanistic target of rapamycin (mTOR), and several additional agents, including the transcription inhibitor Mithramycin A. Upregulation of the cell surface marker GPNMB, a specific MiT transcriptional target, was confirmed in TFE3-RCC and evaluated as a therapeutic target using the GPNMB-targeted antibody-drug conjugate CDX-011. In vitro and in vivo preclinical studies demonstrated efficacy of the PI3K/mTOR inhibitor NVP-BGT226, Mithramycin A, and CDX-011 as potential therapeutic options for treating advanced MiT-RCC as single agents or in combination. CONCLUSIONS The results of the high-throughput drug screen and validation studies in TFE3-RCC tumor-derived cell lines have provided in vitro and in vivo preclinical data supporting the efficacy of the PI3K/mTOR inhibitor NVP-BGT226, the transcription inhibitor Mithramycin A, and GPNMB-targeted antibody-drug conjugate CDX-011 as potential therapeutic options for treating advanced MiT-RCC. The findings presented here should provide the basis for designing future clinical trials for patients with MiT-driven RCC.
Collapse
Affiliation(s)
- Martin Lang
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, 39100, Italy
| | - Laura S Schmidt
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kelli M Wilson
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Bethesda, MD, USA
| | - Christopher J Ricketts
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Carole Sourbier
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cathy D Vocke
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Darmood Wei
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Daniel R Crooks
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Youfeng Yang
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Benjamin K Gibbs
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xiaohu Zhang
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Bethesda, MD, USA
| | - Carleen Klumpp-Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Bethesda, MD, USA
| | - Lu Chen
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Bethesda, MD, USA
| | - Rajarshi Guha
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Bethesda, MD, USA
| | - Marc Ferrer
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Bethesda, MD, USA
| | - Crystal McKnight
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Bethesda, MD, USA
| | - Zina Itkin
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Bethesda, MD, USA
| | - Darawalee Wangsa
- Genetics Branch, Cancer Genomics Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Danny Wangsa
- Genetics Branch, Cancer Genomics Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amy James
- Laboratory of Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Simone Difilippantonio
- Laboratory of Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Baktir Karim
- Laboratory of Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Francisco Morís
- EntreChem SL, Vivero Ciencias de la Salud, Calle Colegio Santo Domingo Guzmán, Oviedo, AS, 33011, Spain
| | - Thomas Ried
- Genetics Branch, Cancer Genomics Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Maria J Merino
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ramaprasad Srinivasan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Bethesda, MD, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
16
|
Tanaka M, Chuaychob S, Homme M, Yamazaki Y, Lyu R, Yamashita K, Ae K, Matsumoto S, Kumegawa K, Maruyama R, Qu W, Miyagi Y, Yokokawa R, Nakamura T. ASPSCR1::TFE3 orchestrates the angiogenic program of alveolar soft part sarcoma. Nat Commun 2023; 14:1957. [PMID: 37029109 PMCID: PMC10082046 DOI: 10.1038/s41467-023-37049-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/01/2023] [Indexed: 04/09/2023] Open
Abstract
Alveolar soft part sarcoma (ASPS) is a soft part malignancy affecting adolescents and young adults. ASPS is characterized by a highly integrated vascular network, and its high metastatic potential indicates the importance of ASPS's prominent angiogenic activity. Here, we find that the expression of ASPSCR1::TFE3, the fusion transcription factor causatively associated with ASPS, is dispensable for in vitro tumor maintenance; however, it is required for in vivo tumor development via angiogenesis. ASPSCR1::TFE3 is frequently associated with super-enhancers (SEs) upon its DNA binding, and the loss of its expression induces SE-distribution dynamic modification related to genes belonging to the angiogenesis pathway. Using epigenomic CRISPR/dCas9 screening, we identify Pdgfb, Rab27a, Sytl2, and Vwf as critical targets associated with reduced enhancer activities due to the ASPSCR1::TFE3 loss. Upregulation of Rab27a and Sytl2 promotes angiogenic factor-trafficking to facilitate ASPS vascular network construction. ASPSCR1::TFE3 thus orchestrates higher ordered angiogenesis via modulating the SE activity.
Collapse
Affiliation(s)
- Miwa Tanaka
- Division of Carcinogenesis, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.
- Department of Experimental Pathology, Institute of Medical Science, Tokyo Medical University, Tokyo, Japan.
- Project for Cancer Epigenomics, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.
| | - Surachada Chuaychob
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Mizuki Homme
- Division of Carcinogenesis, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Division of Cell Biology, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yukari Yamazaki
- Division of Carcinogenesis, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Department of Experimental Pathology, Institute of Medical Science, Tokyo Medical University, Tokyo, Japan
| | - Ruyin Lyu
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Kyoko Yamashita
- Division of Pathology, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Keisuke Ae
- Department of Orthopedic Oncology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Seiichi Matsumoto
- Department of Orthopedic Oncology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kohei Kumegawa
- Project for Cancer Epigenomics, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Reo Maruyama
- Project for Cancer Epigenomics, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Wei Qu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Yohei Miyagi
- Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, Yokohama, Japan
| | - Ryuji Yokokawa
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Takuro Nakamura
- Division of Carcinogenesis, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.
- Department of Experimental Pathology, Institute of Medical Science, Tokyo Medical University, Tokyo, Japan.
| |
Collapse
|
17
|
Li Y, Lih TSM, Dhanasekaran SM, Mannan R, Chen L, Cieslik M, Wu Y, Lu RJH, Clark DJ, Kołodziejczak I, Hong R, Chen S, Zhao Y, Chugh S, Caravan W, Naser Al Deen N, Hosseini N, Newton CJ, Krug K, Xu Y, Cho KC, Hu Y, Zhang Y, Kumar-Sinha C, Ma W, Calinawan A, Wyczalkowski MA, Wendl MC, Wang Y, Guo S, Zhang C, Le A, Dagar A, Hopkins A, Cho H, Leprevost FDV, Jing X, Teo GC, Liu W, Reimers MA, Pachynski R, Lazar AJ, Chinnaiyan AM, Van Tine BA, Zhang B, Rodland KD, Getz G, Mani DR, Wang P, Chen F, Hostetter G, Thiagarajan M, Linehan WM, Fenyö D, Jewell SD, Omenn GS, Mehra R, Wiznerowicz M, Robles AI, Mesri M, Hiltke T, An E, Rodriguez H, Chan DW, Ricketts CJ, Nesvizhskii AI, Zhang H, Ding L. Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness. Cancer Cell 2023; 41:139-163.e17. [PMID: 36563681 PMCID: PMC9839644 DOI: 10.1016/j.ccell.2022.12.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 08/18/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022]
Abstract
Clear cell renal cell carcinomas (ccRCCs) represent ∼75% of RCC cases and account for most RCC-associated deaths. Inter- and intratumoral heterogeneity (ITH) results in varying prognosis and treatment outcomes. To obtain the most comprehensive profile of ccRCC, we perform integrative histopathologic, proteogenomic, and metabolomic analyses on 305 ccRCC tumor segments and 166 paired adjacent normal tissues from 213 cases. Combining histologic and molecular profiles reveals ITH in 90% of ccRCCs, with 50% demonstrating immune signature heterogeneity. High tumor grade, along with BAP1 mutation, genome instability, increased hypermethylation, and a specific protein glycosylation signature define a high-risk disease subset, where UCHL1 expression displays prognostic value. Single-nuclei RNA sequencing of the adverse sarcomatoid and rhabdoid phenotypes uncover gene signatures and potential insights into tumor evolution. In vitro cell line studies confirm the potential of inhibiting identified phosphoproteome targets. This study molecularly stratifies aggressive histopathologic subtypes that may inform more effective treatment strategies.
Collapse
Affiliation(s)
- Yize Li
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Tung-Shing M Lih
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21213, USA
| | - Saravana M Dhanasekaran
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Rahul Mannan
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lijun Chen
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21213, USA
| | - Marcin Cieslik
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yige Wu
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Rita Jiu-Hsien Lu
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - David J Clark
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21213, USA
| | - Iga Kołodziejczak
- International Institute for Molecular Oncology, 60-203 Poznań, Poland; Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Runyu Hong
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Siqi Chen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Yanyan Zhao
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Seema Chugh
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Wagma Caravan
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Nataly Naser Al Deen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Noshad Hosseini
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Karsten Krug
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Yuanwei Xu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA
| | - Kyung-Cho Cho
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21213, USA
| | - Yingwei Hu
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21213, USA
| | - Yuping Zhang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chandan Kumar-Sinha
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Weiping Ma
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Anna Calinawan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Matthew A Wyczalkowski
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Michael C Wendl
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Mathematics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Yuefan Wang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21213, USA
| | - Shenghao Guo
- Department of Biomedical Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA
| | - Cissy Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21213, USA
| | - Anne Le
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21213, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Aniket Dagar
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alex Hopkins
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hanbyul Cho
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Xiaojun Jing
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Guo Ci Teo
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Wenke Liu
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Melissa A Reimers
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA; Division of Medical Oncology, Department of Medicine, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Russell Pachynski
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA; Division of Medical Oncology, Department of Medicine, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Alexander J Lazar
- Departments of Pathology and Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Brian A Van Tine
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Gad Getz
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Feng Chen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | | | | | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Fenyö
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Scott D Jewell
- Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Gilbert S Omenn
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Human Genetics, and School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rohit Mehra
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Maciej Wiznerowicz
- International Institute for Molecular Oncology, 60-203 Poznań, Poland; Heliodor Swiecicki Clinical Hospital in Poznań, ul. Przybyszewskiego 49, 60-355 Poznań, Poland; Poznań University of Medical Sciences, 61-701 Poznań, Poland
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Eunkyung An
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Daniel W Chan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21213, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christopher J Ricketts
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21213, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21218, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63130, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA.
| |
Collapse
|
18
|
Tang J, Baba M. MiT/TFE Family Renal Cell Carcinoma. Genes (Basel) 2023; 14:genes14010151. [PMID: 36672892 PMCID: PMC9859458 DOI: 10.3390/genes14010151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/09/2023] Open
Abstract
The microphthalmia-associated transcription factor/transcription factor E (MiT/TFE) family of transcription factors are evolutionarily conserved, basic helix-loop-helix leucine zipper (bHLH-Zip) transcription factors, consisting of MITF, TFEB, TFE3, and TFEC. MiT/TFE proteins, with the exception of TFEC, are involved in the development of renal cell carcinoma (RCC). Most of the MiT/TFE transcription factor alterations seen in sporadic RCC cases of MiT family translocation renal cell carcinoma (tRCC) are chimeric proteins generated by chromosomal rearrangements. These chimeric MiT/TFE proteins retain the bHLH-Zip structures and act as oncogenic transcription factors. The germline variant of MITF p.E318K has been reported as a risk factor for RCC. E 318 is present at the SUMOylation consensus site of MITF. The p.E318K variant abrogates SUMOylation on K 316, which results in alteration of MITF transcriptional activity. Only a few cases of MITF p.E318K RCC have been reported, and their clinical features have not yet been fully described. It would be important for clinicians to recognize MITF p.E318K RCC and consider MITF germline testing for undiagnosed familial RCC cases. This review outlines the involvement of the MiT/TFE transcription factors in RCC, both in sporadic and hereditary cases. Further elucidation of the molecular function of the MiT/TFE family is necessary for better diagnosis and treatment of these rare diseases.
Collapse
|
19
|
Qu Y, Wu X, Anwaier A, Feng J, Xu W, Pei X, Zhu Y, Liu Y, Bai L, Yang G, Tian X, Su J, Shi GH, Cao DL, Xu F, Wang Y, Gan HL, Ni S, Sun MH, Zhao JY, Zhang H, Ye D, Ding C. Proteogenomic characterization of MiT family translocation renal cell carcinoma. Nat Commun 2022; 13:7494. [PMID: 36470859 PMCID: PMC9722939 DOI: 10.1038/s41467-022-34460-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 10/26/2022] [Indexed: 12/12/2022] Open
Abstract
Microphthalmia transcription factor (MiT) family translocation renal cell carcinoma (tRCC) is a rare type of kidney cancer, which is not well characterized. Here we show the comprehensive proteogenomic analysis of tRCC tumors and normal adjacent tissues to elucidate the molecular landscape of this disease. Our study reveals that defective DNA repair plays an important role in tRCC carcinogenesis and progression. Metabolic processes are markedly dysregulated at both the mRNA and protein levels. Proteomic and phosphoproteome data identify mTOR signaling pathway as a potential therapeutic target. Moreover, molecular subtyping and immune infiltration analysis characterize the inter-tumoral heterogeneity of tRCC. Multi-omic integration reveals the dysregulation of cellular processes affected by genomic alterations, including oxidative phosphorylation, autophagy, transcription factor activity, and proteasome function. This study represents a comprehensive proteogenomic analysis of tRCC, providing valuable insights into its biological mechanisms, disease diagnosis, and prognostication.
Collapse
Affiliation(s)
- Yuanyuan Qu
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
- Department of Oncology, Shanghai Medical College, Shanghai Genitourinary Cancer Institute, Shanghai, 200032, China
| | - Xiaohui Wu
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
| | - Aihetaimujiang Anwaier
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
- Department of Oncology, Shanghai Medical College, Shanghai Genitourinary Cancer Institute, Shanghai, 200032, China
| | - Jinwen Feng
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
| | - Wenhao Xu
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
- Department of Oncology, Shanghai Medical College, Shanghai Genitourinary Cancer Institute, Shanghai, 200032, China
| | - Xiaoru Pei
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
| | - Yu Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
- Department of Oncology, Shanghai Medical College, Shanghai Genitourinary Cancer Institute, Shanghai, 200032, China
| | - Yang Liu
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
| | - Lin Bai
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
| | - Guojian Yang
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
| | - Xi Tian
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
- Department of Oncology, Shanghai Medical College, Shanghai Genitourinary Cancer Institute, Shanghai, 200032, China
| | - Jiaqi Su
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
- Department of Oncology, Shanghai Medical College, Shanghai Genitourinary Cancer Institute, Shanghai, 200032, China
| | - Guo-Hai Shi
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
- Department of Oncology, Shanghai Medical College, Shanghai Genitourinary Cancer Institute, Shanghai, 200032, China
| | - Da-Long Cao
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
- Department of Oncology, Shanghai Medical College, Shanghai Genitourinary Cancer Institute, Shanghai, 200032, China
| | - Fujiang Xu
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China
| | - Yue Wang
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China
- Department of Oncology, Shanghai Medical College, Shanghai Genitourinary Cancer Institute, Shanghai, 200032, China
| | - Hua-Lei Gan
- Department of Oncology, Shanghai Medical College, Shanghai Genitourinary Cancer Institute, Shanghai, 200032, China
- Tissue Bank & Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Shujuan Ni
- Department of Oncology, Shanghai Medical College, Shanghai Genitourinary Cancer Institute, Shanghai, 200032, China
- Tissue Bank & Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Meng-Hong Sun
- Department of Oncology, Shanghai Medical College, Shanghai Genitourinary Cancer Institute, Shanghai, 200032, China
- Tissue Bank & Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Jian-Yuan Zhao
- Institute for Developmental and Regenerative Cardiovascular Medicine, MOE-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.
| | - Hailiang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China.
- Department of Oncology, Shanghai Medical College, Shanghai Genitourinary Cancer Institute, Shanghai, 200032, China.
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China.
- Department of Oncology, Shanghai Medical College, Shanghai Genitourinary Cancer Institute, Shanghai, 200032, China.
| | - Chen Ding
- Department of Urology, Fudan University Shanghai Cancer Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, and Human Phenome Institute, Fudan University, Shanghai, 200433, China.
| |
Collapse
|
20
|
Asrani K, Woo J, Mendes AA, Schaffer E, Vidotto T, Villanueva CR, Feng K, Oliveira L, Murali S, Liu HB, Salles DC, Lam B, Argani P, Lotan TL. An mTORC1-mediated negative feedback loop constrains amino acid-induced FLCN-Rag activation in renal cells with TSC2 loss. Nat Commun 2022; 13:6808. [PMID: 36357396 PMCID: PMC9649702 DOI: 10.1038/s41467-022-34617-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/01/2022] [Indexed: 11/12/2022] Open
Abstract
The mechanistic target of rapamycin complex 1 (mTORC1) integrates inputs from growth factors and nutrients, but how mTORC1 autoregulates its activity remains unclear. The MiT/TFE transcription factors are phosphorylated and inactivated by mTORC1 following lysosomal recruitment by RagC/D GTPases in response to amino acid stimulation. We find that starvation-induced lysosomal localization of the RagC/D GAP complex, FLCN:FNIP2, is markedly impaired in a mTORC1-sensitive manner in renal cells with TSC2 loss, resulting in unexpected TFEB hypophosphorylation and activation upon feeding. TFEB phosphorylation in TSC2-null renal cells is partially restored by destabilization of the lysosomal folliculin complex (LFC) induced by FLCN mutants and is fully rescued by forced lysosomal localization of the FLCN:FNIP2 dimer. Our data indicate that a negative feedback loop constrains amino acid-induced, FLCN:FNIP2-mediated RagC activity in renal cells with constitutive mTORC1 signaling, and the resulting MiT/TFE hyperactivation may drive oncogenesis with loss of the TSC2 tumor suppressor.
Collapse
Affiliation(s)
- Kaushal Asrani
- grid.21107.350000 0001 2171 9311Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Juhyung Woo
- grid.21107.350000 0001 2171 9311Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Adrianna A. Mendes
- grid.21107.350000 0001 2171 9311Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Ethan Schaffer
- grid.21107.350000 0001 2171 9311Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Thiago Vidotto
- grid.21107.350000 0001 2171 9311Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Clarence Rachel Villanueva
- grid.21107.350000 0001 2171 9311Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Kewen Feng
- grid.21107.350000 0001 2171 9311Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Lia Oliveira
- grid.21107.350000 0001 2171 9311Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Sanjana Murali
- grid.21107.350000 0001 2171 9311Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Hans B. Liu
- grid.21107.350000 0001 2171 9311Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Daniela C. Salles
- grid.21107.350000 0001 2171 9311Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Brandon Lam
- grid.21107.350000 0001 2171 9311Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Pedram Argani
- grid.21107.350000 0001 2171 9311Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Tamara L. Lotan
- grid.21107.350000 0001 2171 9311Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD USA ,grid.21107.350000 0001 2171 9311Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD USA ,grid.21107.350000 0001 2171 9311Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| |
Collapse
|
21
|
MiT translocation renal cell carcinoma: A review of the literature from molecular characterization to clinical management. Biochim Biophys Acta Rev Cancer 2022; 1877:188823. [DOI: 10.1016/j.bbcan.2022.188823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/17/2022] [Accepted: 10/04/2022] [Indexed: 11/23/2022]
|
22
|
A Rag GTPase dimer code defines the regulation of mTORC1 by amino acids. Nat Cell Biol 2022; 24:1394-1406. [PMID: 36097072 PMCID: PMC9481461 DOI: 10.1038/s41556-022-00976-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 07/13/2022] [Indexed: 12/14/2022]
Abstract
Amino acid availability controls mTORC1 activity via a heterodimeric Rag GTPase complex that functions as a scaffold at the lysosomal surface, bringing together mTORC1 with its activators and effectors. Mammalian cells express four Rag proteins (RagA–D) that form dimers composed of RagA/B bound to RagC/D. Traditionally, the Rag paralogue pairs (RagA/B and RagC/D) are referred to as functionally redundant, with the four dimer combinations used interchangeably in most studies. Here, by using genetically modified cell lines that express single Rag heterodimers, we uncover a Rag dimer code that determines how amino acids regulate mTORC1. First, RagC/D differentially define the substrate specificity downstream of mTORC1, with RagD promoting phosphorylation of its lysosomal substrates TFEB/TFE3, while both Rags are involved in the phosphorylation of non-lysosomal substrates such as S6K. Mechanistically, RagD recruits mTORC1 more potently to lysosomes through increased affinity to the anchoring LAMTOR complex. Furthermore, RagA/B specify the signalling response to amino acid removal, with RagB-expressing cells maintaining lysosomal and active mTORC1 even upon starvation. Overall, our findings reveal key qualitative differences between Rag paralogues in the regulation of mTORC1, and underscore Rag gene duplication and diversification as a potentially impactful event in mammalian evolution. Gollwitzer, Grützmacher et al. and Figlia et al. establish that the various Rag GTPase genes and isoforms differentially regulate mTORC1 activity and distinctly modulate the responsiveness of mammalian cells to amino acid availability.
Collapse
|
23
|
Lang M, Pramstaller PP, Pichler I. Crosstalk of organelles in Parkinson's disease - MiT family transcription factors as central players in signaling pathways connecting mitochondria and lysosomes. Mol Neurodegener 2022; 17:50. [PMID: 35842725 PMCID: PMC9288732 DOI: 10.1186/s13024-022-00555-7] [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: 11/10/2021] [Accepted: 07/01/2022] [Indexed: 11/10/2022] Open
Abstract
Living organisms constantly need to adapt to their surrounding environment and have evolved sophisticated mechanisms to deal with stress. Mitochondria and lysosomes are central organelles in the response to energy and nutrient availability within a cell and act through interconnected mechanisms. However, when such processes become overwhelmed, it can lead to pathologies. Parkinson's disease (PD) is a common neurodegenerative disorder (NDD) characterized by proteinaceous intracellular inclusions and progressive loss of dopaminergic neurons, which causes motor and non-motor symptoms. Genetic and environmental factors may contribute to the disease etiology. Mitochondrial dysfunction has long been recognized as a hallmark of PD pathogenesis, and several aspects of mitochondrial biology are impaired in PD patients and models. In addition, defects of the autophagy-lysosomal pathway have extensively been observed in cell and animal models as well as PD patients' brains, where constitutive autophagy is indispensable for adaptation to stress and energy deficiency. Genetic and molecular studies have shown that the functions of mitochondria and lysosomal compartments are tightly linked and influence each other. Connections between these organelles are constituted among others by mitophagy, organellar dynamics and cellular signaling cascades, such as calcium (Ca2+) and mTOR (mammalian target of rapamycin) signaling and the activation of transcription factors. Members of the Microphthalmia-associated transcription factor family (MiT), including MITF, TFE3 and TFEB, play a central role in regulating cellular homeostasis in response to metabolic pressure and are considered master regulators of lysosomal biogenesis. As such, they are part of the interconnection between mitochondria and lysosome functions and therefore represent attractive targets for therapeutic approaches against NDD, including PD. The activation of MiT transcription factors through genetic and pharmacological approaches have shown encouraging results at ameliorating PD-related phenotypes in in vitro and in vivo models. In this review, we summarize the relationship between mitochondrial and autophagy-lysosomal functions in the context of PD etiology and focus on the role of the MiT pathway and its potential as pharmacological target against PD.
Collapse
Affiliation(s)
- Martin Lang
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy.
| | - Peter P Pramstaller
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy.,Department of Neurology, University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Irene Pichler
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| |
Collapse
|
24
|
Funasaki S, Mehanna S, Ma W, Nishizawa H, Kamikubo Y, Sugiyama H, Ikeda S, Motoshima T, Hasumi H, Linehan WM, Schmidt LS, Ricketts C, Suda T, Oike Y, Kamba T, Baba M. Targeting chemoresistance in Xp11.2 translocation renal cell carcinoma using a novel polyamide-chlorambucil conjugate. Cancer Sci 2022; 113:2352-2367. [PMID: 35396773 PMCID: PMC9277412 DOI: 10.1111/cas.15364] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 03/26/2022] [Accepted: 04/02/2022] [Indexed: 11/29/2022] Open
Abstract
Renal cell carcinoma with Xp11.2 translocation involving the TFE3 gene (TFE3-RCC) is a recently identified subset of RCC with unique morphology and clinical presentation. The chimeric PRCC-TFE3 protein produced by Xp11.2 translocation has been shown to transcriptionally activate its downstream target genes that play important roles in carcinogenesis and tumor development of TFE3-RCC. However, the underlying molecular mechanisms remain poorly understood. Here we show that in TFE3-RCC cells, PRCC-TFE3 controls heme oxygenase 1 (HMOX1) expression to confer chemoresistance. Inhibition of HMOX1 sensitized the PRCC-TFE3 expressing cells to genotoxic reagents. We screened for a novel chlorambucil-polyamide conjugate (Chb) to target PRCC-TFE3-dependent transcription, and identified Chb16 as a PRCC-TFE3-dependent transcriptional inhibitor of HMOX1 expression. Treatment of the patient-derived cancer cells with Chb16 exhibited senescence and growth arrest, and increased sensitivity of the TFE3-RCC cells to the genotoxic reagent etoposide. Thus, our data showed that the TFE3-RCC cells acquired chemoresistance through HMOX1 expression and that inhibition of HMOX1 by Chb16 may be an effective therapeutic strategy for TFE3-RCC.
Collapse
Affiliation(s)
- Shintaro Funasaki
- Laboratory of Cancer MetabolismInternational Research Center for Medical Sciences (IRCMS)Kumamoto UniversityKumamotoJapan
| | - Sally Mehanna
- Laboratory of Cancer MetabolismInternational Research Center for Medical Sciences (IRCMS)Kumamoto UniversityKumamotoJapan
| | - Wenjuan Ma
- Laboratory of Cancer MetabolismInternational Research Center for Medical Sciences (IRCMS)Kumamoto UniversityKumamotoJapan
| | - Hidekazu Nishizawa
- Laboratory of Cancer MetabolismInternational Research Center for Medical Sciences (IRCMS)Kumamoto UniversityKumamotoJapan
- Department of UrologyGraduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Yasuhiko Kamikubo
- Department of Human Health ScienceGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Hiroshi Sugiyama
- Department of ChemistryGraduate School of ScienceKyoto UniversityKyotoJapan
| | - Shuji Ikeda
- Department of ChemistryGraduate School of ScienceKyoto UniversityKyotoJapan
| | - Takanobu Motoshima
- Department of UrologyGraduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Hisashi Hasumi
- Department of UrologyGraduate School of MedicineYokohama City UniversityYokohamaJapan
| | - W. Marston Linehan
- Urologic Oncology BranchNational Cancer InstituteNational Institutes of HealthBethesdaMarylandUSA
| | - Laura S. Schmidt
- Urologic Oncology BranchNational Cancer InstituteNational Institutes of HealthBethesdaMarylandUSA
- Basic Science ProgramFrederick National Laboratory for Cancer ResearchNational Cancer InstituteFrederickMarylandUSA
| | - Chris Ricketts
- Urologic Oncology BranchNational Cancer InstituteNational Institutes of HealthBethesdaMarylandUSA
| | - Toshio Suda
- Laboratory of Stem Cell RegulationInternational Research Center for Medical Sciences (IRCMS)Kumamoto UniversityKumamotoJapan
- Cancer Science Institute of SingaporeCentre for Translational MedicineNational University of SingaporeSingapore CitySingapore
| | - Yuichi Oike
- Department of Molecular GeneticsGraduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Tomomi Kamba
- Department of UrologyGraduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Masaya Baba
- Laboratory of Cancer MetabolismInternational Research Center for Medical Sciences (IRCMS)Kumamoto UniversityKumamotoJapan
| |
Collapse
|
25
|
Beck P, Selle B, Madenach L, Jones DTW, Vokuhl C, Gopisetty A, Nabbi A, Brecht IB, Ebinger M, Wegert J, Graf N, Gessler M, Pfister SM, Jäger N. The genomic landscape of pediatric renal cell carcinomas. iScience 2022; 25:104167. [PMID: 35445187 PMCID: PMC9014386 DOI: 10.1016/j.isci.2022.104167] [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: 11/16/2021] [Revised: 03/03/2022] [Accepted: 03/24/2022] [Indexed: 12/08/2022] Open
Abstract
Pediatric renal cell carcinomas (RCC) differ from their adult counterparts not only in histologic subtypes but also in clinical characteristics and outcome. However, the underlying biology is still largely unclear. For this reason, we performed whole-exome and transcriptome sequencing analyses on a cohort of 25 pediatric RCC patients with various histologic subtypes, including 10 MiT family translocation (MiT) and 10 papillary RCCs. In this cohort of pediatric RCC, we find only limited genomic overlap with adult RCC, even within the same histologic subtype. Recurrent somatic mutations in genes not previously reported in RCC were detected, such as in CCDC168, PLEKHA1, VWF, and MAP3K9. Our papillary pediatric RCCs, which represent the largest cohort to date with comprehensive molecular profiling in this age group, appeared as a distinct genomic subtype differing in terms of gene mutations and gene expression patterns not only from MiT-RCC but also from their adult counterparts. WES and RNA-seq of 25 pediatric RCCs with various histologic subtypes Detected only limited genomic overlap with adult RCC Revealed recurrent somatic mutations in genes not previously reported in RCC Discovery of a CRK-PITPNA fusion gene in a pediatric papillary RCC
Collapse
Affiliation(s)
- Pengbo Beck
- Hopp Children's Cancer Center Heidelberg (KiTZ) & Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Barbara Selle
- Hopp Children's Cancer Center Heidelberg (KiTZ) & Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Lukas Madenach
- Hopp Children's Cancer Center Heidelberg (KiTZ) & Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ) & Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Pediatric Glioma Research Group, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christian Vokuhl
- Section of Pediatric Pathology, Department of Pathology, University Hospital Bonn, Bonn, Germany
| | - Apurva Gopisetty
- Hopp Children's Cancer Center Heidelberg (KiTZ) & Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Arash Nabbi
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Ines B Brecht
- Department of Pediatric Oncology and Hematology, University Children's Hospital Tübingen, Tübingen, Germany
| | - Martin Ebinger
- Department of Pediatric Oncology and Hematology, University Children's Hospital Tübingen, Tübingen, Germany
| | - Jenny Wegert
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, Würzburg University & Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - Norbert Graf
- Department of Pediatric Oncology and Hematology, Saarland University, Homburg, Germany
| | - Manfred Gessler
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, Würzburg University & Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ) & Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Natalie Jäger
- Hopp Children's Cancer Center Heidelberg (KiTZ) & Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| |
Collapse
|
26
|
Salles DC, Asrani K, Woo J, Vidotto T, Liu HB, Vidal I, Matoso A, Netto GJ, Argani P, Lotan TL. GPNMB
expression identifies
TSC1
/2/
mTOR
‐associated and
MiT
family translocation‐driven renal neoplasms. J Pathol 2022; 257:158-171. [PMID: 35072947 PMCID: PMC9310781 DOI: 10.1002/path.5875] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/21/2021] [Accepted: 01/22/2022] [Indexed: 11/20/2022]
Abstract
GPNMB (glycoprotein nonmetastatic B) and other TFE3/TFEB transcriptional targets have been proposed as markers for microphthalmia (MiT) translocation renal cell carcinomas (tRCCs). We recently demonstrated that constitutive mTORC1 activation via TSC1/2 loss leads to increased activity of TFE3/TFEB, suggesting that the pathogenesis and molecular markers for tRCCs and TSC1/2‐associated tumors may be overlapping. We examined GPNMB expression in human kidney and angiomyolipoma (AML) cell lines with TSC2 and/or TFE3/TFEB loss produced using CRISPR–Cas9 genome editing as well as in a mouse model of Tsc2 inactivation‐driven renal tumorigenesis. Using an automated immunohistochemistry (IHC) assay for GPNMB, digital image analysis was employed to quantitatively score expression in clear cell RCC (ccRCC, n = 87), papillary RCC (papRCC, n = 53), chromophobe RCC (chRCC, n = 34), oncocytoma (n = 4), TFE3‐ or TFEB‐driven tRCC (n = 56), eosinophilic solid and cystic RCC (ESC, n = 6), eosinophilic vacuolated tumor (EVT, n = 4), and low‐grade oncocytic tumor (LOT, n = 3), as well as AML (n = 29) and perivascular epithelioid cell tumors (PEComas, n = 8). In cell lines, GPNMB was upregulated following TSC2 loss in a MiT/TFE‐ and mTORC1‐dependent fashion. Renal tumors in Tsc2+/− A/J mice showed upregulation of GPNMB compared with normal kidney. Mean GPNMB expression was significantly higher in tRCC than in ccRCC (p < 0.0001), papRCC (p < 0.0001), and chRCC (p < 0.0001). GPNMB expression in TSC1/2/MTOR alteration‐associated renal tumors (including ESC, LOT, AML, and PEComa) was comparable to that in tRCC. The immunophenotype of tRCC and TSC1/2/MTOR alteration‐associated renal tumors is highly overlapping, likely due to the increased activity of TFE3/TFEB in both, revealing an important caveat regarding the use of TFE3/TFEB‐transcriptional targets as diagnostic markers. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
Collapse
Affiliation(s)
- Daniela C. Salles
- Department of Pathology Johns Hopkins University School of Medicine Baltimore MD USA
| | - Kaushal Asrani
- Department of Pathology Johns Hopkins University School of Medicine Baltimore MD USA
| | - Juhyung Woo
- Department of Pathology Johns Hopkins University School of Medicine Baltimore MD USA
| | - Thiago Vidotto
- Department of Pathology Johns Hopkins University School of Medicine Baltimore MD USA
| | - Hans B. Liu
- Department of Pathology Johns Hopkins University School of Medicine Baltimore MD USA
| | - Igor Vidal
- Department of Pathology Johns Hopkins University School of Medicine Baltimore MD USA
| | - Andres Matoso
- Department of Pathology Johns Hopkins University School of Medicine Baltimore MD USA
| | - George J. Netto
- Department of Pathology University of Alabama Birmingham Alabama USA
| | - Pedram Argani
- Department of Pathology Johns Hopkins University School of Medicine Baltimore MD USA
| | - Tamara L. Lotan
- Department of Pathology Johns Hopkins University School of Medicine Baltimore MD USA
- Department of Urology Johns Hopkins University School of Medicine Baltimore MD USA
- Department of Oncology Johns Hopkins University School of Medicine Baltimore MD USA
| |
Collapse
|
27
|
Bakouny Z, Sadagopan A, Ravi P, Metaferia NY, Li J, AbuHammad S, Tang S, Denize T, Garner ER, Gao X, Braun DA, Hirsch L, Steinharter JA, Bouchard G, Walton E, West D, Labaki C, Dudani S, Gan CL, Sethunath V, Carvalho FLF, Imamovic A, Ricker C, Vokes NI, Nyman J, Berchuck JE, Park J, Hirsch MS, Haq R, Mary Lee GS, McGregor BA, Chang SL, Feldman AS, Wu CJ, McDermott DF, Heng DY, Signoretti S, Van Allen EM, Choueiri TK, Viswanathan SR. Integrative clinical and molecular characterization of translocation renal cell carcinoma. Cell Rep 2022; 38:110190. [PMID: 34986355 PMCID: PMC9127595 DOI: 10.1016/j.celrep.2021.110190] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 09/01/2021] [Accepted: 12/08/2021] [Indexed: 02/08/2023] Open
Abstract
Translocation renal cell carcinoma (tRCC) is a poorly characterized subtype of kidney cancer driven by MiT/TFE gene fusions. Here, we define the landmarks of tRCC through an integrative analysis of 152 patients with tRCC identified across genomic, clinical trial, and retrospective cohorts. Most tRCCs harbor few somatic alterations apart from MiT/TFE fusions and homozygous deletions at chromosome 9p21.3 (19.2% of cases). Transcriptionally, tRCCs display a heightened NRF2-driven antioxidant response that is associated with resistance to targeted therapies. Consistently, we find that outcomes for patients with tRCC treated with vascular endothelial growth factor receptor inhibitors (VEGFR-TKIs) are worse than those treated with immune checkpoint inhibitors (ICI). Using multiparametric immunofluorescence, we find that the tumors are infiltrated with CD8+ T cells, though the T cells harbor an exhaustion immunophenotype distinct from that of clear cell RCC. Our findings comprehensively define the clinical and molecular features of tRCC and may inspire new therapeutic hypotheses.
Collapse
Affiliation(s)
- Ziad Bakouny
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA,Harvard Medical School, Boston, MA, USA,Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Ananthan Sadagopan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Praful Ravi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Jiao Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shatha AbuHammad
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA,Harvard Medical School, Boston, MA, USA
| | - Stephen Tang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Thomas Denize
- Harvard Medical School, Boston, MA, USA,Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Emma R. Garner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Xin Gao
- Harvard Medical School, Boston, MA, USA,Department of Internal Medicine, Division of Hematology and Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - David A. Braun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA,Harvard Medical School, Boston, MA, USA,Yale Cancer Center / Department of Medicine, Yale School of Medicine, New Haven, CT
| | - Laure Hirsch
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Harvard Medical School, Boston, MA, USA
| | - John A. Steinharter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gabrielle Bouchard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Emily Walton
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Destiny West
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Chris Labaki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shaan Dudani
- Division of Medical Oncology/Hematology, William Osler Health System, Brampton, ON, Canada
| | - Chun-Loo Gan
- Division of Medical Oncology, Tom Baker Cancer Centre, University of Calgary, AB, Canada
| | | | | | - Alma Imamovic
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Cora Ricker
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Natalie I. Vokes
- Department of Thoracic/Head and Neck Medical Oncology; Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX, USA
| | - Jackson Nyman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jacob E. Berchuck
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jihye Park
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michelle S. Hirsch
- Harvard Medical School, Boston, MA, USA,Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Rizwan Haq
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA,Harvard Medical School, Boston, MA, USA
| | - Gwo-Shu Mary Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Bradley A. McGregor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Steven L. Chang
- Harvard Medical School, Boston, MA, USA,Division of Urology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Adam S. Feldman
- Department of Urology, Massachusetts General Hospital, Boston, MA, USA
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | | | - Daniel Y.C. Heng
- Division of Medical Oncology, Tom Baker Cancer Centre, University of Calgary, AB, Canada
| | - Sabina Signoretti
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA,Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Eliezer M. Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA,Harvard Medical School, Boston, MA, USA
| | - Toni K. Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Harvard Medical School, Boston, MA, USA,Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA,Corresponding authors: Toni K. Choueiri, MD, Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, Massachusetts, 02215 (). Tel: +1 617-632-5456, Srinivas R. Viswanathan, MD, PhD, Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, Massachusetts, 02215 (). Tel: +1 617-632-2429
| | - Srinivas R. Viswanathan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA,Harvard Medical School, Boston, MA, USA,Corresponding authors: Toni K. Choueiri, MD, Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, Massachusetts, 02215 (). Tel: +1 617-632-5456, Srinivas R. Viswanathan, MD, PhD, Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, Massachusetts, 02215 (). Tel: +1 617-632-2429
| |
Collapse
|
28
|
Zhai JP, Liu ZH, Wang HD, Huang GL, Man LB. GPNMB overexpression is associated with extensive bone metastasis and poor prognosis in renal cell carcinoma. Oncol Lett 2021; 23:36. [PMID: 34966452 DOI: 10.3892/ol.2021.13154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 08/02/2021] [Indexed: 12/24/2022] Open
Abstract
Glycoprotein non-metastatic protein B (GPNMB) promotes bone metastasis (BM) in various types of cancer. However, GPNMB expression and its function in patients with renal cell carcinoma (RCC) and BM is still unknown. Therefore, the clinical significance of GPNMB and its biological function in RCC with BM was investigated in the present study. A total of 31 patients with RCC and BM were retrospectively collected. The association between GPNMB protein expression level on the primary tumor and the clinicopathological characteristics of the patients was analyzed. Kaplan-Meier analysis was used to investigate the association between GPNMB expression and the prognosis of the patients. The effects of GPNMB inhibition on cell proliferation, migration and invasion in RCC cells were investigated using short hairpin (sh)RNA. High GPNMB expression level was significantly associated with the number (P=0.001) and the extent of BM (P=0.001), Fuhrman grade (P=0.037), and ERK expression level (P=0.003) of the primary tumor. In addition, GPNMB overexpression was significantly associated with poor prognosis with respect to overall survival time (P=0.001). Furthermore, a specific shRNA sequence targeting the GPNMB gene was constructed and transduced into the ACHN cell line, using a lentivirus vector to obtain a stable cell line with low mRNA expression level of GPNMB. Low GPNMB expression level inhibited RCC cell proliferation, which was measured using a Cell Counting Kit-8 assay. Cell migration and invasion ability was significantly decreased in GPNMB knockdown RCC cells compared with that in cells transduced with the negative control shRNA. In addition, the protein expression levels of phosphorylated ERK were lower in the GPNMB shRNA-transduced ACHN cells compared with those in the control cells. Therefore, these results suggested that GPNMB plays an important role in tumor progression in RCC with BM. Furthermore, it might serve as a predictive marker for BM and as a poor prognostic factor in RCC with BM. GPNMB downregulation suppressed the proliferation, migration and invasion of the RCC cells, which may be mediated through the inhibition of the ERK signaling pathway.
Collapse
Affiliation(s)
- Jian-Po Zhai
- Department of Urology, Beijing Jishuitan Hospital, Beijing 102200, P.R. China
| | - Zhen-Hua Liu
- Department of Urology, Beijing Jishuitan Hospital, Beijing 102200, P.R. China
| | - Hai-Dong Wang
- Department of Urology, Beijing Jishuitan Hospital, Beijing 102200, P.R. China
| | - Guang-Lin Huang
- Department of Urology, Beijing Jishuitan Hospital, Beijing 102200, P.R. China
| | - Li-Bo Man
- Department of Urology, Beijing Jishuitan Hospital, Beijing 102200, P.R. China
| |
Collapse
|
29
|
Integrated exome and RNA sequencing of TFE3-translocation renal cell carcinoma. Nat Commun 2021; 12:5262. [PMID: 34489456 PMCID: PMC8421377 DOI: 10.1038/s41467-021-25618-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 08/21/2021] [Indexed: 02/05/2023] Open
Abstract
TFE3-translocation renal cell carcinoma (TFE3-tRCC) is a rare and heterogeneous subtype of kidney cancer with no standard treatment for advanced disease. We describe comprehensive molecular characteristics of 63 untreated primary TFE3-tRCCs based on whole-exome and RNA sequencing. TFE3-tRCC is highly heterogeneous, both clinicopathologically and genotypically. ASPSCR1-TFE3 fusion and several somatic copy number alterations, including the loss of 22q, are associated with aggressive features and poor outcomes. Apart from tumors with MED15-TFE3 fusion, most TFE3-tRCCs exhibit low PD-L1 expression and low T-cell infiltration. Unsupervised transcriptomic analysis reveals five molecular clusters with distinct angiogenesis, stroma, proliferation and KRAS down signatures, which show association with fusion patterns and prognosis. In line with the aggressive nature, the high angiogenesis/stroma/proliferation cluster exclusively consists of tumors with ASPSCR1-TFE3 fusion. Here, we describe the genomic and transcriptomic features of TFE3-tRCC and provide insights into precision medicine for this disease. TFE3-translocation renal cell carcinoma (TFE3-tRCC) is a rare subtype of kidney cancer with no standard treatment options for the advanced disease. Here, the authors perform genomic and transcriptomic profiling of 63 untreated primary TFE3-tRCC tumours and reveal potential therapeutic targets.
Collapse
|
30
|
TSC2 regulates lysosome biogenesis via a non-canonical RAGC and TFEB-dependent mechanism. Nat Commun 2021; 12:4245. [PMID: 34253722 PMCID: PMC8275687 DOI: 10.1038/s41467-021-24499-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 06/11/2021] [Indexed: 02/06/2023] Open
Abstract
Tuberous Sclerosis Complex (TSC) is caused by TSC1 or TSC2 mutations, resulting in hyperactivation of the mechanistic target of rapamycin complex 1 (mTORC1). Transcription factor EB (TFEB), a master regulator of lysosome biogenesis, is negatively regulated by mTORC1 through a RAG GTPase-dependent phosphorylation. Here we show that lysosomal biogenesis is increased in TSC-associated renal tumors, pulmonary lymphangioleiomyomatosis, kidneys from Tsc2+/- mice, and TSC1/2-deficient cells via a TFEB-dependent mechanism. Interestingly, in TSC1/2-deficient cells, TFEB is hypo-phosphorylated at mTORC1-dependent sites, indicating that mTORC1 is unable to phosphorylate TFEB in the absence of the TSC1/2 complex. Importantly, overexpression of folliculin (FLCN), a GTPase activating protein for RAGC, increases TFEB phosphorylation at the mTORC1 sites in TSC2-deficient cells. Overexpression of constitutively active RAGC is sufficient to relocalize TFEB to the cytoplasm. These findings establish the TSC proteins as critical regulators of lysosomal biogenesis via TFEB and RAGC and identify TFEB as a driver of the proliferation of TSC2-deficient cells.
Collapse
|
31
|
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.
Collapse
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.
| |
Collapse
|
32
|
Chen Y, Yang L, Liu N, Shi Q, Yin X, Han X, Gan W, Li D. NONO-TFE3 fusion promotes aerobic glycolysis and angiogenesis by targeting HIF1A in NONO-TFE3 translocation renal cell carcinoma. Curr Cancer Drug Targets 2021; 21:713-723. [PMID: 33845743 DOI: 10.2174/1568009621666210412115026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 02/17/2021] [Accepted: 03/20/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND NONO-TFE3 translocation renal cell carcinoma (tRCC), one of RCCs associated with Xp11.2 translocation/TFE3 gene fusion (Xp11.2 tRCCs), involves an X chromosome inversion between NONO and TFE3 with the characteristics of endonuclear aggregation of NONO-TFE3 fusion protein. Nowadays, the oncogenic mechanisms of NONO-TFE3 fusion have not been fully elucidated. OBJECTIVE This study aimed at investigating the mechanism of NONO-TFE3 fusion regulating HIF1A as well as the role of HIF-1α in the progression of NONO-TFE3 tRCC under hypoxia. METHODS Immunohistochemistry and Western Blotting assays were performed to profile HIF-1α expression in renal clear cell carcinoma (ccRCC) or in Xp11.2 tRCC. Chromatin immunoprecipitation (ChIP), luciferase reporter assay and real-time quantitative PCR (RT-qPCR) were used to evaluate the regulation of HIF1A expression by NONO-TFE3 fusion. Then, flow cytometry analysis, tube formation assays and cell migration assays were used as well as glucose or lactic acid levels were measured to establish the impact of HIF-1α on the progression of NONO-TFE3 tRCC. Besides, the effect of HIF-1α inhibitor (PX-478) on UOK109 cells was analyzed. RESULTS We found that HIF1A was targeting gene of NONO-TFE3 fusion. In UOK109 cells, which were isolated from NONO-TFE3 tRCC samples, NONO-TFE3 fusion promoted aerobic glycolysis and angiogenesis by up-regulating the expression of HIF-1α under hypoxia. Furthermore, inhibition of HIF-1α mediated by PX-478 suppressed the development of NONO-TFE3 tRCC under hypoxia. CONCLUSION HIF-1α is a potential target for therapy of NONO-TFE3 tRCC under hypoxia.
Collapse
Affiliation(s)
- Yi Chen
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Sciences, Medical School, Nanjing University, Nanjing, Jiangsu 210093. China
| | - Lei Yang
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Sciences, Medical School, Nanjing University, Nanjing, Jiangsu 210093. China
| | - Ning Liu
- Department of Urology, Affiliated Drum Tower Hospital of Medical School of Nanjing University, Nanjing, Jiangsu 210008. China
| | - Qiancheng Shi
- Department of Urology, Affiliated Drum Tower Hospital of Medical School of Nanjing University, Nanjing, Jiangsu 210008. China
| | - Xiaoqin Yin
- Department of Endocrinology, Shanghai Children's Hospital, Shanghai 200000. China
| | - Xiaodong Han
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Sciences, Medical School, Nanjing University, Nanjing, Jiangsu 210093. China
| | - Weidong Gan
- Department of Urology, Affiliated Drum Tower Hospital of Medical School of Nanjing University, Nanjing, Jiangsu 210008. China
| | - Dongmei Li
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Sciences, Medical School, Nanjing University, Nanjing, Jiangsu 210093. China
| |
Collapse
|
33
|
Tsou PS, Sawalha AH. Glycoprotein nonmetastatic melanoma protein B: A key mediator and an emerging therapeutic target in autoimmune diseases. FASEB J 2020; 34:8810-8823. [PMID: 32445534 DOI: 10.1096/fj.202000651] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 05/04/2020] [Indexed: 12/21/2022]
Abstract
The glycoprotein nonmetastatic melanoma protein B (GPNMB, also known as osteoactivin) is highly expressed in many cell types and regulates the homeostasis in various tissues. In different physiological contexts, it functions as a melanosome-associated protein, membrane-bound surface receptor, soluble ligand, or adhesion molecule. Therefore, GPNMB is involved in cell differentiation, migration, inflammation, metabolism, and neuroprotection. Because of its various involvement in different physiological conditions, GPNMB has been implicated in many diseases, including cancer, neurological disorders, and more recently immune-mediated diseases. This review summarizes the regulation and function of GPNMB in normal physiology, and discusses the involvement of GPNMB in disease conditions with a particular focus on its potential role and therapeutic implications in autoimmunity.
Collapse
Affiliation(s)
- Pei-Suen Tsou
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Amr H Sawalha
- Division of Rheumatology, Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA.,Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Lupus Center of Excellence, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| |
Collapse
|
34
|
Choueiri TK, Atkins MB, Bakouny Z, Carlo MI, Drake CG, Jonasch E, Kapur P, Lewis B, Linehan WM, Mitchell MJ, Pal SK, Pels K, Poteat S, Rathmell WK, Rini BI, Signoretti S, Tannir N, Uzzo R, Wood CG, Hammers HJ. Summary From the First Kidney Cancer Research Summit, September 12-13, 2019: A Focus on Translational Research. J Natl Cancer Inst 2020; 113:234-243. [PMID: 32359162 DOI: 10.1093/jnci/djaa064] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/07/2020] [Accepted: 04/24/2020] [Indexed: 12/11/2022] Open
Abstract
Kidney cancer is one of the 10 most common cancers both in the United States and worldwide. Until this year, there had not previously been a conference focused on translational studies in the broad and heterogeneous group of kidney cancers. Therefore, a group of researchers, clinicians, and patient advocates dedicated to renal cell carcinoma launched the Kidney Cancer Research Summit (KCRS) to spur collaboration and further therapeutic advances in these tumors. This commentary aims to summarize the oral presentations and serve as a record for future iterations of this meeting. The KCRS sessions addressed the tumor microenvironment, novel methods of drug delivery, single cell sequencing strategies, novel immune checkpoint blockade and cellular therapies, predictive biomarkers, and rare variants of kidney cancers. In addition, the meeting included 2 sessions to promote scientific mentoring and kidney cancer research collaborations. A subsequent KCRS will be planned for the fall of 2020.
Collapse
Affiliation(s)
- Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Michael B Atkins
- Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Washington, DC
| | - Ziad Bakouny
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Maria I Carlo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charles G Drake
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Eric Jonasch
- Department of Genitourinary Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Payal Kapur
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - W Marston Linehan
- Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michael J Mitchell
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Sumanta K Pal
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Kevin Pels
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - W Kimryn Rathmell
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Brian I Rini
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sabina Signoretti
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Nizar Tannir
- Department of Genitourinary Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robert Uzzo
- Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Christopher G Wood
- Department of Urology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hans J Hammers
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| |
Collapse
|
35
|
Computational analysis of pathological images enables a better diagnosis of TFE3 Xp11.2 translocation renal cell carcinoma. Nat Commun 2020; 11:1778. [PMID: 32286325 PMCID: PMC7156652 DOI: 10.1038/s41467-020-15671-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 03/23/2020] [Indexed: 12/17/2022] Open
Abstract
TFE3 Xp11.2 translocation renal cell carcinoma (TFE3-RCC) generally progresses more aggressively compared with other RCC subtypes, but it is challenging to diagnose TFE3-RCC by traditional visual inspection of pathological images. In this study, we collect hematoxylin and eosin- stained histopathology whole-slide images of 74 TFE3-RCC cases (the largest cohort to date) and 74 clear cell RCC cases (ccRCC, the most common RCC subtype) with matched gender and tumor grade. An automatic computational pipeline is implemented to extract image features. Comparative study identifies 52 image features with significant differences between TFE3-RCC and ccRCC. Machine learning models are built to distinguish TFE3-RCC from ccRCC. Tests of the classification models on an external validation set reveal high accuracy with areas under ROC curve ranging from 0.842 to 0.894. Our results suggest that automatically derived image features can capture subtle morphological differences between TFE3-RCC and ccRCC and contribute to a potential guideline for TFE3-RCC diagnosis. Translocation renal cell carcinoma is an aggressive form of renal cancer that is often misdiagnosed to other subtypes. Here the authors demonstrated that by using machine learning and H&E stained whole-slide images, an accurate diagnose of this particular type of renal cancer can be achieved.
Collapse
|
36
|
Doktorova TY, Oki NO, Mohorič T, Exner TE, Hardy B. A semi-automated workflow for adverse outcome pathway hypothesis generation: The use case of non-genotoxic induced hepatocellular carcinoma. Regul Toxicol Pharmacol 2020; 114:104652. [PMID: 32251711 DOI: 10.1016/j.yrtph.2020.104652] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 01/10/2020] [Accepted: 03/29/2020] [Indexed: 02/07/2023]
Abstract
The utility of the Adverse Outcome Pathway (AOP) concept has been largely recognized by scientists, however, the AOP generation is still mainly done manually by screening through evidence and extracting probable associations. To accelerate this process and increase the reliability, we have developed an semi-automated workflow for AOP hypothesis generation. In brief, association mining methods were applied to high-throughput screening, gene expression, in vivo and disease data present in ToxCast and Comparative Toxicogenomics Database. This was supplemented by pathway mapping using Reactome to fill in gaps and identify events occurring at the cellular/tissue levels. Furthermore, in vivo data from TG-Gates was integrated to finally derive a gene, pathway, biochemical, histopathological and disease network from which specific disease sub-networks can be queried. To test the workflow, non-genotoxic-induced hepatocellular carcinoma (HCC) was selected as a case study. The implementation resulted in the identification of several non-genotoxic-specific HCC-connected genes belonging to cell proliferation, endoplasmic reticulum stress and early apoptosis. Biochemical findings revealed non-genotoxic-specific alkaline phosphatase increase. The explored non-genotoxic-specific histopathology was associated with early stages of hepatic steatosis, transforming into cirrhosis. This work illustrates the utility of computationally predicted constructs in supporting development by using pre-existing knowledge in a fast and unbiased manner.
Collapse
Affiliation(s)
- Tatyana Y Doktorova
- Edelweiss Connect GmbH, Hochbergerstrasse 60C, Technology Park Basel, Basel, Switzerland.
| | - Noffisat O Oki
- American Association for the Advancement of Science, Science & Technology Policy Fellow, USA; National Institutes of Health, Rockville, MD, USA
| | - Tomaž Mohorič
- Edelweiss Connect GmbH, Hochbergerstrasse 60C, Technology Park Basel, Basel, Switzerland
| | - Thomas E Exner
- Edelweiss Connect GmbH, Hochbergerstrasse 60C, Technology Park Basel, Basel, Switzerland
| | - Barry Hardy
- Edelweiss Connect GmbH, Hochbergerstrasse 60C, Technology Park Basel, Basel, Switzerland
| |
Collapse
|
37
|
Horiguchi H, Kadomatsu T, Kurahashi R, Hara C, Miyata K, Baba M, Osumi H, Terada K, Araki K, Takai T, Kamba T, Linehan WM, Moroishi T, Oike Y. Dual functions of angiopoietin-like protein 2 signaling in tumor progression and anti-tumor immunity. Genes Dev 2019; 33:1641-1656. [PMID: 31727773 PMCID: PMC6942048 DOI: 10.1101/gad.329417.119] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 10/07/2019] [Indexed: 12/22/2022]
Abstract
Angiopoietin-like protein 2 (ANGPTL2) is a secreted glycoprotein homologous to angiopoietins. Previous studies suggest that tumor cell-derived ANGPTL2 has tumor-promoting function. Here, we conducted mechanistic analysis comparing ANGPTL2 function in cancer progression in a murine syngeneic model of melanoma and a mouse model of translocation renal cell carcinoma (tRCC). ANGPTL2 deficiency in tumor cells slowed tRCC progression, supporting a tumor-promoting role. However, systemic ablation of ANGPTL2 accelerated tRCC progression, supporting a tumor-suppressing role. The syngeneic model also demonstrated a tumor-suppressing role of ANGPTL2 in host tumor microenvironmental cells. Furthermore, the syngeneic model showed that PDGFRα+ fibroblasts in the tumor microenvironment express abundant ANGPTL2 and contribute to tumor suppression. Moreover, host ANGPTL2 facilitates CD8+ T-cell cross-priming and enhances anti-tumor immune responses. Importantly, ANGPTL2 activates dendritic cells through PIR-B-NOTCH signaling and enhances tumor vaccine efficacy. Our study provides strong evidence that ANGPTL2 can function in either tumor promotion or suppression, depending on what cell type it is expressed in.
Collapse
Affiliation(s)
- Haruki Horiguchi
- Department of Molecular Genetics, Graduate school of Medical science, Kumamoto University, Kumamoto 860-8556, Japan.,Institute of Resource Development and Analysis, Kumamoto University, Kumamoto 860-0811, Japan
| | - Tsuyoshi Kadomatsu
- Department of Molecular Genetics, Graduate school of Medical science, Kumamoto University, Kumamoto 860-8556, Japan.,Center for Metabolic Regulation of Healthy Aging (CMHA), Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Ryoma Kurahashi
- Department of Molecular Genetics, Graduate school of Medical science, Kumamoto University, Kumamoto 860-8556, Japan.,Department of Urology, Graduate school of Medical science, Kumamoto University, Chuo-ku, Kumamoto 860-8556, Japan
| | - Chiaki Hara
- Department of Molecular Genetics, Graduate school of Medical science, Kumamoto University, Kumamoto 860-8556, Japan.,Department of Urology, Graduate school of Medical science, Kumamoto University, Chuo-ku, Kumamoto 860-8556, Japan
| | - Keishi Miyata
- Department of Molecular Genetics, Graduate school of Medical science, Kumamoto University, Kumamoto 860-8556, Japan.,Center for Metabolic Regulation of Healthy Aging (CMHA), Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Masaya Baba
- International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto 860-0811, Japan
| | - Hironobu Osumi
- Department of Molecular Genetics, Graduate school of Medical science, Kumamoto University, Kumamoto 860-8556, Japan.,Department of Thoracic Surgery, Graduate school of Medical science, Kumamoto University, Kumamoto 860-8556, Japan
| | - Kazutoyo Terada
- Department of Molecular Genetics, Graduate school of Medical science, Kumamoto University, Kumamoto 860-8556, Japan.,Center for Metabolic Regulation of Healthy Aging (CMHA), Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Kimi Araki
- Center for Metabolic Regulation of Healthy Aging (CMHA), Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-8556, Japan.,Division of Developmental Genetics, Institute of Resource Development and Analysis, Kumamoto University, Kumamoto 860-0811, Japan
| | - Toshiyuki Takai
- Department of Experimental Immunology, Institute of Development, Aging and Cancer, Tohoku University, Sendai 980-8575, Japan
| | - Tomomi Kamba
- Department of Urology, Graduate school of Medical science, Kumamoto University, Chuo-ku, Kumamoto 860-8556, Japan
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Toshiro Moroishi
- Center for Metabolic Regulation of Healthy Aging (CMHA), Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-8556, Japan.,Department of Molecular Enzymology, Faculty of Life sciences, Kumamoto University, Kumamoto 860-8556, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Kawaguchi 332-0012, Japan
| | - Yuichi Oike
- Department of Molecular Genetics, Graduate school of Medical science, Kumamoto University, Kumamoto 860-8556, Japan.,Center for Metabolic Regulation of Healthy Aging (CMHA), Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-8556, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Agency for Medical Research and Development (AMED), Tokyo 100-0004, Japan
| |
Collapse
|