1
|
Li Y, Liu J, Yao D, Guo Z, Jiang X, Zhang C, Qu L, Liu Y, Hu Y, Gao L, Wang Y, Xu Y. Elevated aerobic glycolysis driven by p62-mTOR axis promotes arsenic-induced oncogenic phenotypes in human mammary epithelial cells. Arch Toxicol 2024; 98:1369-1381. [PMID: 38485781 DOI: 10.1007/s00204-024-03709-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 02/15/2024] [Indexed: 03/27/2024]
Abstract
Chronic arsenic exposure is considered to increase the risk of breast cancer. p62 is a multifunctional adaptor protein that controls myriad cellular processes and is overexpressed in breast cancer tissues. Although previous studies have indicated the involvement of p62 accumulation in arsenic tumorigenesis, the underlying mechanism remains obscure. Here, we found that 0.1 µM or 0.5 µM arsenite exposure for 24 weeks induced oncogenic phenotypes in human mammary epithelial cells. Elevated aerobic glycolysis, cell proliferation capacity, and activation of p62-mTOR pathway, as indicated by increased protein levels of p62, phosphorylated-mTOR (p-mTOR) and hypoxia-inducible factor 1α (HIF1α), were observed in chronically arsenite-exposed cells, and of note in advance of the onset of oncogenic phenotypes. Moreover, p62 silencing inhibited acquisition of oncogenic phenotypes in arsenite-exposed cells. The protein levels of p-mTOR and HIF1α, as well as aerobic glycolysis and cell proliferation, were suppressed by p62 knockdown. In addition, re-activation of p‑mTOR reversed the inhibitory effects of p62 knockdown. Collectively, our data suggest that p62 exerts an oncogenic role via mTORC1 activation and acts as a key player in glucose metabolism during arsenite-induced malignant transformation, which provides a new mechanistic clue for the arsenite carcinogenesis.
Collapse
Affiliation(s)
- Yongfang Li
- Key Laboratory of Environmental Stress and Chronic Disease Control & Prevention (China Medical University), Ministry of Education, Shenyang, People's Republic of China
- School of Public Health, China Medical University, Shenyang, People's Republic of China
- Key Laboratory of Toxic and Biological Effects of Arsenic (China Medical University), Liaoning Province, Shenyang, People's Republic of China
| | - Jiao Liu
- School of Public Health, China Medical University, Shenyang, People's Republic of China
| | - Dianqi Yao
- Key Laboratory of Environmental Stress and Chronic Disease Control & Prevention (China Medical University), Ministry of Education, Shenyang, People's Republic of China
- School of Public Health, China Medical University, Shenyang, People's Republic of China
- Key Laboratory of Toxic and Biological Effects of Arsenic (China Medical University), Liaoning Province, Shenyang, People's Republic of China
| | - Zijun Guo
- Key Laboratory of Environmental Stress and Chronic Disease Control & Prevention (China Medical University), Ministry of Education, Shenyang, People's Republic of China
- School of Public Health, China Medical University, Shenyang, People's Republic of China
- Key Laboratory of Toxic and Biological Effects of Arsenic (China Medical University), Liaoning Province, Shenyang, People's Republic of China
| | - Xuheng Jiang
- School of Public Health, China Medical University, Shenyang, People's Republic of China
| | - Chengwen Zhang
- Key Laboratory of Environmental Stress and Chronic Disease Control & Prevention (China Medical University), Ministry of Education, Shenyang, People's Republic of China
- School of Public Health, China Medical University, Shenyang, People's Republic of China
- Key Laboratory of Toxic and Biological Effects of Arsenic (China Medical University), Liaoning Province, Shenyang, People's Republic of China
| | - Litong Qu
- Key Laboratory of Environmental Stress and Chronic Disease Control & Prevention (China Medical University), Ministry of Education, Shenyang, People's Republic of China
- School of Public Health, China Medical University, Shenyang, People's Republic of China
- Key Laboratory of Toxic and Biological Effects of Arsenic (China Medical University), Liaoning Province, Shenyang, People's Republic of China
| | - Yuyan Liu
- Department of Clinical Epidemiology, the Fourth Affiliated Hospital, China Medical University, Shenyang, People's Republic of China
| | - Yuxin Hu
- Key Laboratory of Environmental Stress and Chronic Disease Control & Prevention (China Medical University), Ministry of Education, Shenyang, People's Republic of China
- School of Public Health, China Medical University, Shenyang, People's Republic of China
- Key Laboratory of Toxic and Biological Effects of Arsenic (China Medical University), Liaoning Province, Shenyang, People's Republic of China
| | - Lanyue Gao
- Key Laboratory of Environmental Stress and Chronic Disease Control & Prevention (China Medical University), Ministry of Education, Shenyang, People's Republic of China
- School of Public Health, China Medical University, Shenyang, People's Republic of China
- Key Laboratory of Toxic and Biological Effects of Arsenic (China Medical University), Liaoning Province, Shenyang, People's Republic of China
| | - Yi Wang
- Key Laboratory of Environmental Stress and Chronic Disease Control & Prevention (China Medical University), Ministry of Education, Shenyang, People's Republic of China
- School of Public Health, China Medical University, Shenyang, People's Republic of China
- Key Laboratory of Toxic and Biological Effects of Arsenic (China Medical University), Liaoning Province, Shenyang, People's Republic of China
| | - Yuanyuan Xu
- Key Laboratory of Environmental Stress and Chronic Disease Control & Prevention (China Medical University), Ministry of Education, Shenyang, People's Republic of China.
- School of Public Health, China Medical University, Shenyang, People's Republic of China.
- Key Laboratory of Toxic and Biological Effects of Arsenic (China Medical University), Liaoning Province, Shenyang, People's Republic of China.
| |
Collapse
|
2
|
Zhang C, Yu M, Hepperla AJ, Zhang Z, Raj R, Zhong H, Zhou J, Hu L, Fang J, Liu H, Liang Q, Jia L, Liao C, Xi S, Simon JM, Xu K, Liu Z, Nam Y, Kapur P, Zhang Q. Von Hippel Lindau tumor suppressor controls m6A-dependent gene expression in renal tumorigenesis. J Clin Invest 2024; 134:e175703. [PMID: 38618952 PMCID: PMC11014668 DOI: 10.1172/jci175703] [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: 09/11/2023] [Accepted: 03/01/2024] [Indexed: 04/16/2024] Open
Abstract
N6-Methyladenosine (m6A) is the most abundant posttranscriptional modification, and its contribution to cancer evolution has recently been appreciated. Renal cancer is the most common adult genitourinary cancer, approximately 85% of which is accounted for by the clear cell renal cell carcinoma (ccRCC) subtype characterized by VHL loss. However, it is unclear whether VHL loss in ccRCC affects m6A patterns. In this study, we demonstrate that VHL binds and promotes METTL3/METTL14 complex formation while VHL depletion suppresses m6A modification, which is distinctive from its canonical E3 ligase role. m6A RNA immunoprecipitation sequencing (RIP-Seq) coupled with RNA-Seq allows us to identify a selection of genes whose expression may be regulated by VHL-m6A signaling. Specifically, PIK3R3 is identified to be a critical gene whose mRNA stability is regulated by VHL in a m6A-dependent but HIF-independent manner. Functionally, PIK3R3 depletion promotes renal cancer cell growth and orthotopic tumor growth while its overexpression leads to decreased tumorigenesis. Mechanistically, the VHL-m6A-regulated PIK3R3 suppresses tumor growth by restraining PI3K/AKT activity. Taken together, we propose a mechanism by which VHL regulates m6A through modulation of METTL3/METTL14 complex formation, thereby promoting PIK3R3 mRNA stability and protein levels that are critical for regulating ccRCC tumorigenesis.
Collapse
Affiliation(s)
- Cheng Zhang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Miaomiao Yu
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Austin J. Hepperla
- Lineberger Comprehensive Cancer Center, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina, USA
- Department of Genetics, Neuroscience Center and
- UNC Neuroscience Center, Carolina Institute for Developmental Disabilities, UNC, Chapel Hill, North Carolina, USA
| | - Zhao Zhang
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Rishi Raj
- Department of Biochemistry, Department of Biophysics, Simmons Comprehensive Cancer Center and
| | - Hua Zhong
- Department of Pathology, Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jin Zhou
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Lianxin Hu
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jun Fang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Hongyi Liu
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Qian Liang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Liwei Jia
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Chengheng Liao
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Sichuan Xi
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jeremy M. Simon
- Lineberger Comprehensive Cancer Center, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina, USA
- Department of Genetics, Neuroscience Center and
- UNC Neuroscience Center, Carolina Institute for Developmental Disabilities, UNC, Chapel Hill, North Carolina, USA
| | - Kexin Xu
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Zhijie Liu
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Yunsun Nam
- Department of Biochemistry, Department of Biophysics, Simmons Comprehensive Cancer Center and
| | - Payal Kapur
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Kidney Cancer Program, Simmons Comprehensive Cancer Center, Department of Urology
| | - Qing Zhang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| |
Collapse
|
3
|
Wang Z, Yan M, Ye L, Zhou Q, Duan Y, Jiang H, Wang L, Ouyang Y, Zhang H, Shen Y, Ji G, Chen X, Tian Q, Xiao L, Wu Q, Meng Y, Liu G, Ma L, Lei B, Lu Z, Xu D. VHL suppresses autophagy and tumor growth through PHD1-dependent Beclin1 hydroxylation. EMBO J 2024; 43:931-955. [PMID: 38360997 PMCID: PMC10943020 DOI: 10.1038/s44318-024-00051-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/17/2024] Open
Abstract
The Von Hippel-Lindau (VHL) protein, which is frequently mutated in clear-cell renal cell carcinoma (ccRCC), is a master regulator of hypoxia-inducible factor (HIF) that is involved in oxidative stresses. However, whether VHL possesses HIF-independent tumor-suppressing activity remains largely unclear. Here, we demonstrate that VHL suppresses nutrient stress-induced autophagy, and its deficiency in sporadic ccRCC specimens is linked to substantially elevated levels of autophagy and correlates with poorer patient prognosis. Mechanistically, VHL directly binds to the autophagy regulator Beclin1, after its PHD1-mediated hydroxylation on Pro54. This binding inhibits the association of Beclin1-VPS34 complexes with ATG14L, thereby inhibiting autophagy initiation in response to nutrient deficiency. Expression of non-hydroxylatable Beclin1 P54A abrogates VHL-mediated autophagy inhibition and significantly reduces the tumor-suppressing effect of VHL. In addition, Beclin1 P54-OH levels are inversely correlated with autophagy levels in wild-type VHL-expressing human ccRCC specimens, and with poor patient prognosis. Furthermore, combined treatment of VHL-deficient mouse tumors with autophagy inhibitors and HIF2α inhibitors suppresses tumor growth. These findings reveal an unexpected mechanism by which VHL suppresses tumor growth, and suggest a potential treatment for ccRCC through combined inhibition of both autophagy and HIF2α.
Collapse
Affiliation(s)
- Zheng Wang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang University, 310029, Hangzhou, China
- Cancer Center, Zhejiang University, 310029, Hangzhou, Zhejiang, China
| | - Meisi Yan
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Leiguang Ye
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Qimin Zhou
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China
| | - Yuran Duan
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang University, 310029, Hangzhou, China
- Cancer Center, Zhejiang University, 310029, Hangzhou, Zhejiang, China
| | - Hongfei Jiang
- Department of Oncology, Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, 266061, Qingdao, Shandong, China
| | - Lei Wang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang University, 310029, Hangzhou, China
- Cancer Center, Zhejiang University, 310029, Hangzhou, Zhejiang, China
| | - Yuan Ouyang
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Center for Stomatology, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Huahe Zhang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
- NHC Key Laboratory of Cell Transplantation, The First Affiliated Hospital of Harbin Medical University, 150001, Harbin, Heilongjiang Province, China
| | - Yuli Shen
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang University, 310029, Hangzhou, China
- Cancer Center, Zhejiang University, 310029, Hangzhou, Zhejiang, China
| | - Guimei Ji
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang University, 310029, Hangzhou, China
- Cancer Center, Zhejiang University, 310029, Hangzhou, Zhejiang, China
| | - Xiaohan Chen
- Department of Oncology, Harbin Medical University Cancer Hospital, Harbin Medical University, 150001, Harbin, Heilongjiang Province, China
| | - Qi Tian
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang University, 310029, Hangzhou, China
- Cancer Center, Zhejiang University, 310029, Hangzhou, Zhejiang, China
| | - Liwei Xiao
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang University, 310029, Hangzhou, China
- Cancer Center, Zhejiang University, 310029, Hangzhou, Zhejiang, China
| | - Qingang Wu
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang University, 310029, Hangzhou, China
- Cancer Center, Zhejiang University, 310029, Hangzhou, Zhejiang, China
| | - Ying Meng
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang University, 310029, Hangzhou, China
- Cancer Center, Zhejiang University, 310029, Hangzhou, Zhejiang, China
| | - Guijun Liu
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang University, 310029, Hangzhou, China
- Cancer Center, Zhejiang University, 310029, Hangzhou, Zhejiang, China
| | - Leina Ma
- Department of Oncology, Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, 266061, Qingdao, Shandong, China
| | - Bo Lei
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China.
- NHC Key Laboratory of Cell Transplantation, The First Affiliated Hospital of Harbin Medical University, 150001, Harbin, Heilongjiang Province, China.
| | - Zhimin Lu
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang University, 310029, Hangzhou, China.
- Cancer Center, Zhejiang University, 310029, Hangzhou, Zhejiang, China.
| | - Daqian Xu
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang University, 310029, Hangzhou, China.
- Cancer Center, Zhejiang University, 310029, Hangzhou, Zhejiang, China.
| |
Collapse
|
4
|
Hu L, Zhang Y, Guo L, Zhong H, Xie L, Zhou J, Liao C, Yao H, Fang J, Liu H, Zhang C, Zhang H, Zhu X, Luo M, von Kriegsheim A, Li B, Luo W, Zhang X, Chen X, Mendell JT, Xu L, Kapur P, Baldwin AS, Brugarolas J, Zhang Q. Kinome-wide siRNA screen identifies a DCLK2-TBK1 oncogenic signaling axis in clear cell renal cell carcinoma. Mol Cell 2024; 84:776-790.e5. [PMID: 38211588 PMCID: PMC10922811 DOI: 10.1016/j.molcel.2023.12.010] [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: 03/21/2023] [Revised: 10/23/2023] [Accepted: 12/10/2023] [Indexed: 01/13/2024]
Abstract
TANK-binding kinase 1 (TBK1) is a potential therapeutic target in multiple cancers, including clear cell renal cell carcinoma (ccRCC). However, targeting TBK1 in clinical practice is challenging. One approach to overcome this challenge would be to identify an upstream TBK1 regulator that could be targeted therapeutically in cancer specifically. In this study, we perform a kinome-wide small interfering RNA (siRNA) screen and identify doublecortin-like kinase 2 (DCLK2) as a TBK1 regulator in ccRCC. DCLK2 binds to and directly phosphorylates TBK1 on Ser172. Depletion of DCLK2 inhibits anchorage-independent colony growth and kidney tumorigenesis in orthotopic xenograft models. Conversely, overexpression of DCLK2203, a short isoform that predominates in ccRCC, promotes ccRCC cell growth and tumorigenesis in vivo. Mechanistically, DCLK2203 elicits its oncogenic signaling via TBK1 phosphorylation and activation. Taken together, these results suggest that DCLK2 is a TBK1 activator and potential therapeutic target for ccRCC.
Collapse
Affiliation(s)
- Lianxin Hu
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yanfeng Zhang
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lei Guo
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hua Zhong
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ling Xie
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jin Zhou
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chengheng Liao
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hongwei Yao
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jun Fang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hongyi Liu
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Cheng Zhang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hui Zhang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaoqiang Zhu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Maowu Luo
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Alex von Kriegsheim
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Bufan Li
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Weibo Luo
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xuewu Zhang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xian Chen
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Joshua T Mendell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lin Xu
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Payal Kapur
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Albert S Baldwin
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - James Brugarolas
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Qing Zhang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Kidney Cancer Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| |
Collapse
|
5
|
Mazzagatti A, Engel JL, Ly P. Boveri and beyond: Chromothripsis and genomic instability from mitotic errors. Mol Cell 2024; 84:55-69. [PMID: 38029753 PMCID: PMC10842135 DOI: 10.1016/j.molcel.2023.11.002] [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: 09/01/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 12/01/2023]
Abstract
Mitotic cell division is tightly monitored by checkpoints that safeguard the genome from instability. Failures in accurate chromosome segregation during mitosis can cause numerical aneuploidy, which was hypothesized by Theodor Boveri over a century ago to promote tumorigenesis. Recent interrogation of pan-cancer genomes has identified unexpected classes of chromosomal abnormalities, including complex rearrangements arising through chromothripsis. This process is driven by mitotic errors that generate abnormal nuclear structures that provoke extensive yet localized shattering of mis-segregated chromosomes. Here, we discuss emerging mechanisms underlying chromothripsis from micronuclei and chromatin bridges, as well as highlight how this mutational cascade converges on the DNA damage response. A fundamental understanding of these catastrophic processes will provide insight into how initial errors in mitosis can precipitate rapid cancer genome evolution.
Collapse
Affiliation(s)
- Alice Mazzagatti
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Justin L Engel
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Peter Ly
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Cell Biology, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| |
Collapse
|
6
|
Xu L, Ding R, Song S, Liu J, Li J, Ju X, Ju B. Single-cell RNA sequencing reveals the mechanism of PI3K/AKT/mTOR signaling pathway activation in lung adenocarcinoma by KRAS mutation. J Gene Med 2024; 26:e3658. [PMID: 38282149 DOI: 10.1002/jgm.3658] [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: 09/21/2023] [Revised: 11/17/2023] [Accepted: 12/05/2023] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Aberrant activation of the phosphatidlinositol 3-kinase (PI3K)/protein kinase B (AKT)/mammalian target of rapamycin (mTOR) signaling pathway has been shown to play an important role in lung adenocarcinoma (LUAD). The effect of KRAS mutations, one of the important signatures of LUAD, on the PI3K/AKT/mTOR pathway in LUAD remains unclear. METHODS The Seurat package and principal component analysis were used for cell categorization of single-cell RNA sequencing data of LUAD. The AUCell score was used to assess the activity of the PI3K/AKT/mTOR pathway. Meanwhile, using the gene expression profiles and mutation profiles in the The Cancer Genome Atlas dataset, LUAD patients were categorized into KRAS-mutant (KRAS-MT) and KRAS-wild-types (KRAS-WT), and the corresponding enrichment scores were calculated using gene set enrichment analysis analysis. Finally, the subpopulation of cells with the highest pathway activity was identified, the copy number variation profile of this subpopulation was inscribed using the inferCNV package and the CMap database was utilized to make predictions for drugs targeting this subpopulation. RESULTS There is higher PI3K/AKT/mTOR pathway activity in LUAD epithelial cells with KRAS mutations, and high expression of KRAS, PIK3CA, AKT1 and PDPK1. In particular, we found significantly higher levels of pathway activity and associated gene expression in KRAS-MT than in KRAS-WT. We identified the highest pathway activity on a subpopulation of GRB2+ epithelial cells and the presence of amplified genes within its pathway. Finally, drugs were able to target GRB2+ epithelial cell subpopulations, such as wortmannin, palbociclib and angiogenesis inhibitor. CONCLUSIONS The present study provides a basic theory for the activation of the PI3K/AKT/mTOR signaling pathway as a result of KRAS mutations.
Collapse
Affiliation(s)
- Long Xu
- School of Traditional Chinese Medicine, Liaoning University of Traditional Chinese Medicine, Shenyang, China
- Department of Oncology, General Hospital of Northern Theater Command, Shenyang, China
| | - Renquan Ding
- Department of Thoracic Surgery, General Hospital of Northern Theater Command, Shenyang, China
| | - Shuxi Song
- Department of Oncology, General Hospital of Northern Theater Command, Shenyang, China
| | - Junling Liu
- Department of Oncology, General Hospital of Northern Theater Command, Shenyang, China
| | - Jingyu Li
- Department of Oncology, General Hospital of Northern Theater Command, Shenyang, China
| | - Xing Ju
- TCM Innovation Engineering Technology Center, Key Laboratory of Ministry of Education for TCM Viscera-State Theory and Applications, Liaoning University of Traditional Chinese Medicine, Shenyang, China
| | - Baozhao Ju
- School of Traditional Chinese Medicine, Liaoning University of Traditional Chinese Medicine, Shenyang, China
| |
Collapse
|
7
|
Lee S, Son JY, Lee J, Cheong H. Unraveling the Intricacies of Autophagy and Mitophagy: Implications in Cancer Biology. Cells 2023; 12:2742. [PMID: 38067169 PMCID: PMC10706449 DOI: 10.3390/cells12232742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/21/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Autophagy is an essential lysosome-mediated degradation pathway that maintains cellular homeostasis and viability in response to various intra- and extracellular stresses. Mitophagy is a type of autophagy that is involved in the intricate removal of dysfunctional mitochondria during conditions of metabolic stress. In this review, we describe the multifaceted roles of autophagy and mitophagy in normal physiology and the field of cancer biology. Autophagy and mitophagy exhibit dual context-dependent roles in cancer development, acting as tumor suppressors and promoters. We also discuss the important role of autophagy and mitophagy within the cancer microenvironment and how autophagy and mitophagy influence tumor host-cell interactions to overcome metabolic deficiencies and sustain the activity of cancer-associated fibroblasts (CAFs) in a stromal environment. Finally, we explore the dynamic interplay between autophagy and the immune response in tumors, indicating their potential as immunomodulatory targets in cancer therapy. As the field of autophagy and mitophagy continues to evolve, this comprehensive review provides insights into their important roles in cancer and cancer microenvironment.
Collapse
Affiliation(s)
- Sunmi Lee
- Branch of Molecular Cancer Biology, Division of Cancer Biology, Research Institute, National Cancer Center, Goyang-si 10408, Republic of Korea; (S.L.); (J.-Y.S.)
| | - Ji-Yoon Son
- Branch of Molecular Cancer Biology, Division of Cancer Biology, Research Institute, National Cancer Center, Goyang-si 10408, Republic of Korea; (S.L.); (J.-Y.S.)
| | - Jinkyung Lee
- Department of Cancer Biomedical Science, Graduate School of Cancer Science & Policy, National Cancer Center, Goyang-si 10408, Republic of Korea;
| | - Heesun Cheong
- Branch of Molecular Cancer Biology, Division of Cancer Biology, Research Institute, National Cancer Center, Goyang-si 10408, Republic of Korea; (S.L.); (J.-Y.S.)
- Department of Cancer Biomedical Science, Graduate School of Cancer Science & Policy, National Cancer Center, Goyang-si 10408, Republic of Korea;
| |
Collapse
|
8
|
Saberi F, Dehghan Z, Noori E, Zali H. Identification of Renal Transplantation Rejection Biomarkers in Blood Using the Systems Biology Approach. IRANIAN BIOMEDICAL JOURNAL 2023; 27:375-87. [PMID: 38224029 PMCID: PMC10826908 DOI: 10.52547/ibj.3871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 08/19/2023] [Indexed: 01/16/2024]
Abstract
Background Renal transplantation plays an essential role in the quality of life of patients with end-stage renal disease. At least 12% of the renal patients receiving transplantations show graft rejection. One of the methods used to diagnose renal transplantation rejection is renal allograft biopsy. This procedure is associated with some risks such as bleeding and arteriovenous fistula formation. In this study, we applied a bioinformatics approach to identify serum markers for graft rejection in patients receiving a renal transplantation. Methods Transcriptomic data were first retrieved from the blood of renal transplantation rejection patients using the GEO database. The data were then used to construct the protein-protein interaction and gene regulatory networks using Cytoscape software. Next, network analysis was performed to identify hub-bottlenecks, and key blood markers involved in renal graft rejection. Lastly, the gene ontology and functional pathways related to hub-bottlenecks were detected using PANTHER and DAVID servers. Results In PPIN and GRN, SYNCRIP, SQSTM1, GRAMD1A, FAM104A, ND2, TPGS2, ZNF652, RORA, and MALAT1 were the identified critical genes. In GRN, miR-155, miR17, miR146b, miR-200 family, and GATA2 were the factors that regulated critical genes. The MAPK, neurotrophin, and TNF signaling pathways, IL-17, and human cytomegalovirus infection, human papillomavirus infection, and shigellosis were identified as significant pathways involved in graft rejection. Concusion The above-mentioned genes can be used as diagnostic and therapeutic serum markers of transplantation rejection in renal patients. The newly predicted biomarkers and pathways require further studies.
Collapse
Affiliation(s)
- Fatemeh Saberi
- Student Research Committee, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zeinab Dehghan
- Department of Comparative Biomedical Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Effat Noori
- Student Research Committee, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hakimeh Zali
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| |
Collapse
|
9
|
Wang Y, Wang Y, Liu B, Gao X, Li Y, Li F, Zhou H. Mapping the tumor microenvironment in clear cell renal carcinoma by single-cell transcriptome analysis. Front Genet 2023; 14:1207233. [PMID: 37533434 PMCID: PMC10392130 DOI: 10.3389/fgene.2023.1207233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/06/2023] [Indexed: 08/04/2023] Open
Abstract
Introduction: Clear cell renal cell carcinoma (ccRCC) is associated with unfavorable clinical outcomes. To identify viable therapeutic targets, a comprehensive understanding of intratumoral heterogeneity is crucial. In this study, we conducted bioinformatic analysis to scrutinize single-cell RNA sequencing data of ccRCC tumor and para-tumor samples, aiming to elucidate the intratumoral heterogeneity in the ccRCC tumor microenvironment (TME). Methods: A total of 51,780 single cells from seven ccRCC tumors and five para-tumor samples were identified and grouped into 11 cell lineages using bioinformatic analysis. These lineages included tumor cells, myeloid cells, T-cells, fibroblasts, and endothelial cells, indicating a high degree of heterogeneity in the TME. Copy number variation (CNV) analysis was performed to compare CNV frequencies between tumor and normal cells. The myeloid cell population was further re-clustered into three major subgroups: monocytes, macrophages, and dendritic cells. Differential expression analysis, gene ontology, and gene set enrichment analysis were employed to assess inter-cluster and intra-cluster functional heterogeneity within the ccRCC TME. Results: Our findings revealed that immune cells in the TME predominantly adopted an inflammatory suppression state, promoting tumor cell growth and immune evasion. Additionally, tumor cells exhibited higher CNV frequencies compared to normal cells. The myeloid cell subgroups demonstrated distinct functional properties, with monocytes, macrophages, and dendritic cells displaying diverse roles in the TME. Certain immune cells exhibited pro-tumor and immunosuppressive effects, while others demonstrated antitumor and immunostimulatory properties. Conclusion: This study contributes to the understanding of intratumoral heterogeneity in the ccRCC TME and provides potential therapeutic targets for ccRCC treatment. The findings emphasize the importance of considering the diverse functional roles of immune cells in the TME for effective therapeutic interventions.
Collapse
Affiliation(s)
- Yuxiong Wang
- Department of Urology, The First Hospital of Jilin University, Jilin, China
| | - Yishu Wang
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Jilin, China
| | - Bin Liu
- Department of Urology, The First Hospital of Jilin University, Jilin, China
| | - Xin Gao
- Department of Urology, The First Hospital of Jilin University, Jilin, China
| | - Yunkuo Li
- Department of Urology, The First Hospital of Jilin University, Jilin, China
| | - Faping Li
- Department of Urology, The First Hospital of Jilin University, Jilin, China
| | - Honglan Zhou
- Department of Urology, The First Hospital of Jilin University, Jilin, China
| |
Collapse
|
10
|
Tabata M, Sato Y, Kogure Y, McClure MB, Oshikawa-Kumade Y, Saito Y, Shingaki S, Ito Y, Yuasa M, Koya J, Yoshida K, Kohno T, Miyama Y, Morikawa T, Chiba K, Okada A, Ogawa S, Ushiku T, Shiraishi Y, Kume H, Kataoka K. Inter- and intra-tumor heterogeneity of genetic and immune profiles in inherited renal cell carcinoma. Cell Rep 2023; 42:112736. [PMID: 37405915 DOI: 10.1016/j.celrep.2023.112736] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 05/04/2023] [Accepted: 06/19/2023] [Indexed: 07/07/2023] Open
Abstract
Patients with von Hippel-Lindau disease (vHL) are at risk of developing spatially and temporally multiple clear cell renal cell carcinomas (ccRCCs), which offers a valuable opportunity to analyze inter- and intra-tumor heterogeneity of genetic and immune profiles within the same patient. Here, we perform whole-exome and RNA sequencing, digital gene expression, and immunohistochemical analyses for 81 samples from 51 ccRCCs of 10 patients with vHL. Inherited ccRCCs are clonally independent and have less genomic alterations than sporadic ccRCCs. Hierarchical clustering of transcriptome profiles shows two clusters with distinct immune signatures: immune hot and cold clusters. Interestingly, not only samples from the same tumors but also different tumors from the same patients tend to show a similar immune signature, whereas samples from different patients frequently exhibit different signatures. Our findings reveal the genetic and immune landscape of inherited ccRCCs, demonstrating the relevance of host factors in shaping anti-tumor immunity.
Collapse
Affiliation(s)
- Mariko Tabata
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Yusuke Sato
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan.
| | - Yasunori Kogure
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Marni B McClure
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Yuji Oshikawa-Kumade
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; Diagnostic Division, Otsuka Pharmaceutical Co., Ltd., Tokushima 771-0182, Japan
| | - Yuki Saito
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; Department of Gastroenterology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Sumito Shingaki
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Yuta Ito
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; Division of Clinical Oncology and Hematology, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo 105-8471, Japan
| | - Mitsuhiro Yuasa
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Junji Koya
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Kazushi Yoshida
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Yu Miyama
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Teppei Morikawa
- Department of Diagnostic Pathology, NTT Medical Center Tokyo, Tokyo 141-8625, Japan
| | - Kenichi Chiba
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Ai Okada
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan; Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan; Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm 17177, Sweden
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yuichi Shiraishi
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Haruki Kume
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Keisuke Kataoka
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; Division of Hematology, Department of Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan.
| |
Collapse
|
11
|
Lu S, Xu J, Xu Y, Liu Y, Shi D, Wang J, Qiu F. Glycyrol attenuates colon injury via promotion of SQSTM1/p62 ubiquitination and autophagy by inhibiting the ubiquitin-specific protease USP8. J Funct Foods 2023. [DOI: 10.1016/j.jff.2023.105492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023] Open
|
12
|
Hallis SP, Kim JM, Kwak MK. Emerging Role of NRF2 Signaling in Cancer Stem Cell Phenotype. Mol Cells 2023; 46:153-164. [PMID: 36994474 PMCID: PMC10070166 DOI: 10.14348/molcells.2023.2196] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 03/31/2023] Open
Abstract
Cancer stem cells (CSCs) are a small population of tumor cells characterized by self-renewal and differentiation capacity. CSCs are currently postulated as the driving force that induces intra-tumor heterogeneity leading to tumor initiation, metastasis, and eventually tumor relapse. Notably, CSCs are inherently resistant to environmental stress, chemotherapy, and radiotherapy due to high levels of antioxidant systems and drug efflux transporters. In this context, a therapeutic strategy targeting the CSC-specific pathway holds a promising cure for cancer. NRF2 (nuclear factor erythroid 2-like 2; NFE2L2) is a master transcription factor that regulates an array of genes involved in the detoxification of reactive oxygen species/electrophiles. Accumulating evidence suggests that persistent NRF2 activation, observed in multiple types of cancer, supports tumor growth, aggressive malignancy, and therapy resistance. Herein, we describe the core properties of CSCs, focusing on treatment resistance, and review the evidence that demonstrates the roles of NRF2 signaling in conferring unique properties of CSCs and the associated signaling pathways.
Collapse
Affiliation(s)
- Steffanus P. Hallis
- Department of Pharmacy, Graduate School, The Catholic University of Korea, Bucheon 14662, Korea
| | - Jin Myung Kim
- Department of Pharmacy, Graduate School, The Catholic University of Korea, Bucheon 14662, Korea
| | - Mi-Kyoung Kwak
- Department of Pharmacy, Graduate School, The Catholic University of Korea, Bucheon 14662, Korea
- College of Pharmacy, The Catholic University of Korea, Bucheon 14662, Korea
| |
Collapse
|
13
|
Wu Y, Terekhanova NV, Caravan W, Naser Al Deen N, Lal P, Chen S, Mo CK, Cao S, Li Y, Karpova A, Liu R, Zhao Y, Shinkle A, Strunilin I, Weimholt C, Sato K, Yao L, Serasanambati M, Yang X, Wyczalkowski M, Zhu H, Zhou DC, Jayasinghe RG, Mendez D, Wendl MC, Clark D, Newton C, Ruan Y, Reimers MA, Pachynski RK, Kinsinger C, Jewell S, Chan DW, Zhang H, Chaudhuri AA, Chheda MG, Humphreys BD, Mesri M, Rodriguez H, Hsieh JJ, Ding L, Chen F. Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma. Nat Commun 2023; 14:1681. [PMID: 36973268 PMCID: PMC10042888 DOI: 10.1038/s41467-023-37211-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 03/07/2023] [Indexed: 03/29/2023] Open
Abstract
Identifying tumor-cell-specific markers and elucidating their epigenetic regulation and spatial heterogeneity provides mechanistic insights into cancer etiology. Here, we perform snRNA-seq and snATAC-seq in 34 and 28 human clear cell renal cell carcinoma (ccRCC) specimens, respectively, with matched bulk proteogenomics data. By identifying 20 tumor-specific markers through a multi-omics tiered approach, we reveal an association between higher ceruloplasmin (CP) expression and reduced survival. CP knockdown, combined with spatial transcriptomics, suggests a role for CP in regulating hyalinized stroma and tumor-stroma interactions in ccRCC. Intratumoral heterogeneity analysis portrays tumor cell-intrinsic inflammation and epithelial-mesenchymal transition (EMT) as two distinguishing features of tumor subpopulations. Finally, BAP1 mutations are associated with widespread reduction of chromatin accessibility, while PBRM1 mutations generally increase accessibility, with the former affecting five times more accessible peaks than the latter. These integrated analyses reveal the cellular architecture of ccRCC, providing insights into key markers and pathways in ccRCC tumorigenesis.
Collapse
Affiliation(s)
- Yige Wu
- Oncology Division, 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
| | - Nadezhda V Terekhanova
- Oncology Division, 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
| | - Wagma Caravan
- Oncology Division, 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
- Oncology Division, 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
| | - Preet Lal
- Oncology Division, Department of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Siqi Chen
- Oncology Division, 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
| | - Chia-Kuei Mo
- Oncology Division, 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
| | - Song Cao
- Oncology Division, 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
| | - Yize Li
- Oncology Division, 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
| | - Alla Karpova
- Oncology Division, 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
| | - Ruiyang Liu
- Oncology Division, 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
- Oncology Division, Department of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Andrew Shinkle
- Oncology Division, 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
| | - Ilya Strunilin
- Oncology Division, 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
| | - Cody Weimholt
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Kazuhito Sato
- Oncology Division, Department of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Lijun Yao
- Oncology Division, 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
| | - Mamatha Serasanambati
- Oncology Division, Department of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Xiaolu Yang
- Oncology Division, Department of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Matthew Wyczalkowski
- Oncology Division, 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
| | - Houxiang Zhu
- Oncology Division, 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
| | - Daniel Cui Zhou
- Oncology Division, 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
| | - Reyka G Jayasinghe
- Oncology Division, 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
| | - Daniel Mendez
- Oncology Division, Department of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Michael C Wendl
- Oncology Division, 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, 63110, USA
- Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - David Clark
- Department of Pathology, Johns Hopkins University, Baltimore, MD, 21231, USA
| | | | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Melissa A Reimers
- Oncology Division, Department of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Russell K Pachynski
- Oncology Division, Department of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Chris Kinsinger
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Scott Jewell
- Van Andel Institutes, Grand Rapids, MI, 49503, USA
| | - Daniel W Chan
- Department of Pathology, Johns Hopkins University, Baltimore, MD, 21231, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, MD, 21231, USA
| | - Aadel A Chaudhuri
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, 63110, USA
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Milan G Chheda
- Oncology Division, Department of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Benjamin D Humphreys
- Oncology Division, Department of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - James J Hsieh
- Oncology Division, Department of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Li Ding
- Oncology Division, 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, 63110, USA.
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, 63110, USA.
| | - Feng Chen
- Oncology Division, Department of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA.
- Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, 63110, USA.
| |
Collapse
|
14
|
Huang H, Pan R, Wang S, Guan Y, Zhao Y, Liu X. Current and potential roles of RNA modification-mediated autophagy dysregulation in cancer. Arch Biochem Biophys 2023; 736:109542. [PMID: 36758911 DOI: 10.1016/j.abb.2023.109542] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/31/2023] [Accepted: 02/05/2023] [Indexed: 02/09/2023]
Abstract
Autophagy, a cellular lysosomal degradation and survival pathway, supports nutrient recycling and adaptation to metabolic stress and participates in various stages of tumor development, including tumorigenesis, metastasis, and malignant state maintenance. Among the various factors contributing to the dysregulation of autophagy in cancer, RNA modification can regulate autophagy by directly affecting the expression of core autophagy proteins. We propose that autophagy disorder mediated by RNA modification is an important mechanism for cancer development. Therefore, this review mainly discusses the role of RNA modification-mediated autophagy regulation in tumorigenesis. We summarize the molecular basis of autophagy and the core proteins and complexes at different stages of autophagy, especially those involved in cancer development. Moreover, we describe the crosstalk of RNA modification and autophagy and review the recent advances and potential role of the RNA modification/autophagy axis in the development of multiple cancers. Furthermore, the dual role of the RNA modification/autophagy axis in cancer drug resistance is discussed. A comprehensive understanding and extensive exploration of the molecular crosstalk of RNA modifications with autophagy will provide important insights into tumor pathophysiology and provide more options for cancer therapeutic strategies.
Collapse
Affiliation(s)
- Hua Huang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Faculty of Environment and Life, Beijing University of Technology, Beijing, 100124, China
| | - Ruining Pan
- Center of Excellence for Environmental Safety and Biological Effects, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Faculty of Environment and Life, Beijing University of Technology, Beijing, 100124, China
| | - Sijia Wang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Faculty of Environment and Life, Beijing University of Technology, Beijing, 100124, China
| | - Yifei Guan
- Center of Excellence for Environmental Safety and Biological Effects, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Faculty of Environment and Life, Beijing University of Technology, Beijing, 100124, China
| | - Yue Zhao
- Intensive Care Unit, Beijing Tsinghua Changgung Hospital, Beijing, 102218, China.
| | - Xinhui Liu
- Center of Excellence for Environmental Safety and Biological Effects, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Faculty of Environment and Life, Beijing University of Technology, Beijing, 100124, China.
| |
Collapse
|
15
|
Ahmadi-Dehlaghi F, Mohammadi P, Valipour E, Pournaghi P, Kiani S, Mansouri K. Autophagy: A challengeable paradox in cancer treatment. Cancer Med 2023. [PMID: 36760166 DOI: 10.1002/cam4.5577] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/14/2022] [Accepted: 12/21/2022] [Indexed: 02/11/2023] Open
Abstract
OBJECTIVE Autophagy is an intracellular degradation pathway conserved in all eukaryotes from yeast to humans. This process plays a quality-control role by destroying harmful cellular components under normal conditions, maintaining cell survival, and establishing cellular adaptation under stressful conditions. Hence, there are various studies indicating dysfunctional autophagy as a factor involved in the development and progression of various human diseases, including cancer. In addition, the importance of autophagy in the development of cancer has been highlighted by paradoxical roles, as a cytoprotective and cytotoxic mechanism. Despite extensive research in the field of cancer, there are many questions and challenges about the roles and effects suggested for autophagy in cancer treatment. The aim of this study was to provide an overview of the paradoxical roles of autophagy in different tumors and related cancer treatment options. METHODS In this study, to find articles, a search was made in PubMed and Google scholar databases with the keywords Autophagy, Autophagy in Cancer Management, and Drug Design. RESULTS According to the investigation, some studies suggest that several advanced cancers are dependent on autophagy for cell survival, so when cancer cells are exposed to therapy, autophagy is induced and suppresses the anti-cancer effects of therapeutic agents and also results in cell resistance. However, enhanced autophagy from using anti-cancer drugs causes autophagy-mediated cell death in several cancers. Because autophagy also plays roles in both tumor suppression and promotion further research is needed to determine the precise mechanism of this process in cancer treatment. CONCLUSION We concluded in this article, autophagy manipulation may either promote or hinder the growth and development of cancer according to the origin of the cancer cells, the type of cancer, and the behavior of the cancer cells exposed to treatment. Thus, before starting treatment it is necessary to determine the basal levels of autophagy in various cancers.
Collapse
Affiliation(s)
- Farnaz Ahmadi-Dehlaghi
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.,Department of Biology, Payame Noor University, Tehran, Iran
| | - Parisa Mohammadi
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.,Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Elahe Valipour
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Sarah Kiani
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Kamran Mansouri
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| |
Collapse
|
16
|
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: 40] [Impact Index Per Article: 40.0] [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
|
17
|
Gupta S, Sukov WR, Vanderbilt CM, Shen W, Herrera-Hernandez L, Lohse CM, Thompson RH, Boorjian SA, Leibovich BC, Jimenez RE, Cheville JC. A contemporary guide to chromosomal copy number profiling in the diagnosis of renal cell carcinoma. Urol Oncol 2022; 40:512-524. [PMID: 34092479 DOI: 10.1016/j.urolonc.2021.04.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/06/2021] [Accepted: 04/28/2021] [Indexed: 02/07/2023]
Abstract
The routine clinical implementation of molecular methods other than fluorescence in situ hybridization in the evaluation of renal neoplasia is currently limited, as the current standard of care primarily involves a combination of morphologic and immunophenotypic analysis of such tumors. Amongst various molecular techniques, global copy number profiling using single nucleotide polymorphism-based microarrays, colloquially referred to as SNP-arrays, is being increasingly utilized to profile renal tumors, as several subtypes have characteristic recurrent patterns of copy number alterations. Recurrent copy number alterations in common tumor types include loss of chromosome 3p in clear cell renal cell carcinoma (RCC), gain of chromosomes 7 and 17 in papillary RCC and multiple losses in chromosomes 1, 2, 6, 10, 13, 17, and 21 in chromophobe RCC. Such assays are being increasingly utilized in the clinical setting. Herein, we discuss some common clinical applications of such testing that includes high yield diagnostic and prognostic applications. Diagnostic utility includes evaluation of tumor types that are primarily defined by underlying copy number alterations, establishing the underlying subtype in high grade dedifferentiated (unclassified) renal tumors, as well as assessment of loss of heterozygosity, which is an important component in the workup for germline alterations in tumor suppressor genes. Universal adoption of these techniques across clinical laboratories will likely be significantly affected by variables such as cost, reimbursement, and turnaround time.
Collapse
Affiliation(s)
- Sounak Gupta
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN.
| | - William R Sukov
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Chad M Vanderbilt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Wei Shen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | | | - Christine M Lohse
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN
| | | | | | | | - Rafael E Jimenez
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - John C Cheville
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| |
Collapse
|
18
|
Luo M, Ye L, Chang R, Ye Y, Zhang Z, Liu C, Li S, Jing Y, Ruan H, Zhang G, He Y, Liu Y, Xue Y, Chen X, Guo AY, Liu H, Han L. Multi-omics characterization of autophagy-related molecular features for therapeutic targeting of autophagy. Nat Commun 2022; 13:6345. [PMID: 36289218 PMCID: PMC9606020 DOI: 10.1038/s41467-022-33946-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/07/2022] [Indexed: 02/08/2023] Open
Abstract
Autophagy is a major contributor to anti-cancer therapy resistance. Many efforts have been made to understand and overcome autophagy-mediated therapy resistance, but these efforts have been unsuccessful in clinical applications. In this study, we establish an autophagy signature to estimate tumor autophagy status. We then classify approximately 10,000 tumor samples across 33 cancer types from The Cancer Genome Atlas into autophagy score-high and autophagy score-low groups. We characterize the associations between multi-dimensional molecular features and tumor autophagy, and further analyse the effects of autophagy status on drug response. In contrast to the conventional view that the induction of autophagy serves as a key resistance mechanism during cancer therapy, our analysis reveals that autophagy induction may also sensitize cancer cells to anti-cancer drugs. We further experimentally validate this phenomenon for several anti-cancer drugs in vitro and in vivo, and reveal that autophagy inducers potentially sensitizes tumor cells to etoposide through downregulating the expression level of DDIT4. Our study provides a comprehensive landscape of molecular alterations associated with tumor autophagy and highlights an opportunity to leverage multi-omics analysis to utilize multiple drug sensitivity induced by autophagy.
Collapse
Affiliation(s)
- Mei Luo
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Lin Ye
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ruimin Chang
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Youqiong Ye
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhao Zhang
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Chunjie Liu
- Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Shengli Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Ying Jing
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Hang Ruan
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Guanxiong Zhang
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yi He
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yaoming Liu
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Yu Xue
- Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Xiang Chen
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - An-Yuan Guo
- Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Hong Liu
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Leng Han
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA.
- Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX, USA.
| |
Collapse
|
19
|
Abstract
Germline loss-of-function mutations of the VHL tumor suppressor gene cause von Hippel–Lindau disease, which is associated with an increased risk of hemangioblastomas, clear cell renal cell carcinomas (ccRCCs), and paragangliomas. This Review describes mechanisms involving the VHL gene product in oxygen sensing, protein degradation, and tumor development and current therapeutic strategies targeting these mechanisms. The VHL gene product is the substrate recognition subunit of a ubiquitin ligase that targets the α subunit of the heterodimeric hypoxia-inducible factor (HIF) transcription factor for proteasomal degradation when oxygen is present. This oxygen dependence stems from the requirement that HIFα be prolyl-hydroxylated on one (or both) of two conserved prolyl residues by members of the EglN (also called PHD) prolyl hydroxylase family. Deregulation of HIF, and particularly HIF2, drives the growth of VHL-defective ccRCCs. Drugs that inhibit the HIF-responsive gene product VEGF are now mainstays of ccRCC treatment. An allosteric HIF2 inhibitor was recently approved for the treatment of ccRCCs arising in the setting of VHL disease and has advanced to phase III testing for sporadic ccRCCs based on promising phase I/II data. Orally available EglN inhibitors are being tested for the treatment of anemia and ischemia. Five of these agents have been approved for the treatment of anemia in the setting of chronic kidney disease in various countries around the world.
Collapse
|
20
|
Russell RC, Guan KL. The multifaceted role of autophagy in cancer. EMBO J 2022; 41:e110031. [PMID: 35535466 PMCID: PMC9251852 DOI: 10.15252/embj.2021110031] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/20/2022] [Accepted: 04/08/2022] [Indexed: 12/15/2022] Open
Abstract
Autophagy is a cellular degradative pathway that plays diverse roles in maintaining cellular homeostasis. Cellular stress caused by starvation, organelle damage, or proteotoxic aggregates can increase autophagy, which uses the degradative capacity of lysosomal enzymes to mitigate intracellular stresses. Early studies have shown a role for autophagy in the suppression of tumorigenesis. However, work in genetically engineered mouse models and in vitro cell studies have now shown that autophagy can be either cancer-promoting or inhibiting. Here, we summarize the effects of autophagy on cancer initiation, progression, immune infiltration, and metabolism. We also discuss the efforts to pharmacologically target autophagy in the clinic and highlight future areas for exploration.
Collapse
Affiliation(s)
- Ryan C Russell
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.,Center for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - Kun-Liang Guan
- Department of Pharmacology and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| |
Collapse
|
21
|
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
|
22
|
A perspective on the role of autophagy in cancer. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166262. [PMID: 34481059 DOI: 10.1016/j.bbadis.2021.166262] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 12/12/2022]
Abstract
Autophagy refers to a ubiquitous set of catabolic pathways required to achieve proper cellular homeostasis. Aberrant autophagy has been implicated in a multitude of diseases including cancer. In this review, we highlight pioneering and groundbreaking research that centers on delineating the role of autophagy in cancer initiation, proliferation and metastasis. First, we discuss the autophagy-related (ATG) proteins and their respective roles in the de novo formation of autophagosomes and the subsequent delivery of cargo to the lysosome for recycling. Next, we touch upon the history of cancer research that centers upon ATG proteins and regulatory mechanisms that control an appropriate autophagic response and how these are altered in the diseased state. Then, we discuss the various discoveries that led to the idea of autophagy as a double-edged sword when it comes to cancer therapy. This review also briefly narrates how different types of autophagy-selective macroautophagy and chaperone-mediated autophagy, have been linked to different cancers. Overall, these studies build upon a steadfast trajectory that aims to solve the monumentally daunting challenge of finding a cure for many types of cancer by modulating autophagy either through inhibition or induction.
Collapse
|
23
|
Liu PF, Shu CW, Yang HC, Lee CH, Liou HH, Ger LP, Tzeng YDT, Wang WC. Combined Evaluation of MAP1LC3B and SQSTM1 for Biological and Clinical Significance in Ductal Carcinoma of Breast Cancer. Biomedicines 2021; 9:biomedicines9111514. [PMID: 34829743 PMCID: PMC8615094 DOI: 10.3390/biomedicines9111514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/06/2021] [Accepted: 10/17/2021] [Indexed: 01/18/2023] Open
Abstract
Breast cancer is the leading cause of cancer death in women worldwide. The microtubule-associated protein light chain 3B (MAP1LC3B) and adaptor sequestosome 1 (SQSTM1) are two major markers for autophagy. Increased protein levels of MAP1LC3B and SQSTM1 are considered to be causes of autophagy inhibition or activation in various types of cancers. However, the roles of MAP1LC3B and SQSTM1 in breast cancer are still not clear. Using a tissue microarray from 274 breast invasive ductal carcinoma (IDC) patients, we found that tumor tissues showed higher protein levels of MAP1LC3B and cytoplasmic SQSTM1 in comparison to those in adjacent normal tissues. Moreover, high levels of MAP1LC3B were associated with better survival, including disease-specific survival and disease-free survival (DFS) in IDC patients. Furthermore, high co-expression of MAP1LC3B and SQSTM1 was significantly associated with better DFS in IDC patients. Astonishingly, the autophagy inhibitor accumulated the protein levels of MAP1LC3B/SQSTM1 and enhanced the cytotoxic effects of cisplatin and paclitaxel in MCF7 and BT474 breast cancer cell lines, implying that autophagy inhibition might result in poor prognosis and chemosensitivity in IDC. Taken together, high co-expression of MAP1LC3B and SQSTM1 might serve as a potential diagnostic and prognostic biomarker for IDC patients.
Collapse
Affiliation(s)
- Pei-Feng Liu
- Department of Biomedical Science and Environmental Biology, College of Life Science, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (P.-F.L.); (C.-H.L.)
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Chih-Wen Shu
- Institute of BioPharmaceutical Sciences, National Sun Yat-sen University, Kaohsiung 80424, Taiwan;
| | - Hsiu-Chen Yang
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung 81362, Taiwan; (H.-C.Y.); (H.-H.L.); (L.-P.G.)
| | - Cheng-Hsin Lee
- Department of Biomedical Science and Environmental Biology, College of Life Science, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (P.-F.L.); (C.-H.L.)
| | - Huei-Han Liou
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung 81362, Taiwan; (H.-C.Y.); (H.-H.L.); (L.-P.G.)
| | - Luo-Ping Ger
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung 81362, Taiwan; (H.-C.Y.); (H.-H.L.); (L.-P.G.)
| | - Yen-Dun Tony Tzeng
- Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung 81362, Taiwan
- Correspondence: (Y.-D.T.T.); (W.-C.W.); Tel.: +886-07-3422121-73008 (Y.-D.T.T.); +886-06-2812811-57112 (W.-C.W.)
| | - Wen-Ching Wang
- Department of General Surgery, Chi Mei Medical Center, Tainan 71004, Taiwan
- Correspondence: (Y.-D.T.T.); (W.-C.W.); Tel.: +886-07-3422121-73008 (Y.-D.T.T.); +886-06-2812811-57112 (W.-C.W.)
| |
Collapse
|
24
|
Adolphe F, Ferlicot S, Verkarre V, Posseme K, Couvé S, Garnier P, Droin N, Deloger M, Job B, Giraud S, Paillerets BBD, Gardie B, Richard S, Renaud F, Gad S. Germline mutation in the NBR1 gene involved in autophagy detected in a family with renal tumors. Cancer Genet 2021; 258-259:51-56. [PMID: 34488032 DOI: 10.1016/j.cancergen.2021.07.003] [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: 12/08/2020] [Revised: 06/10/2021] [Accepted: 07/26/2021] [Indexed: 01/09/2023]
Abstract
Hereditary Renal Cell Carcinomas (RCC) are caused by mutations in predisposing genes, the major ones including VHL, FLCN, FH and MET. However, many families with inherited RCC have no germline mutation in these genes. Using Whole Exome Sequencing on germline DNA from a family presenting three different histological renal tumors (an angiomyolipoma, a clear-cell RCC and an oncocytic papillary RCC), we identified a frameshift mutation in the Neighbor of BRCA1 gene 1 (NBR1), segregating with the tumors. NBR1 encodes a cargo receptor protein involved in autophagy. Genetic and functional analyses suggested a pathogenic impact of the mutation. Indeed, functional study performed in renal cell lines showed that the mutation alters NBR1 interactions with some of its partners (such as p62/SQSTM1), leading to a dominant negative effect. This results in an altered autophagic process and an increased proliferative capacity in renal cell lines. Our study suggests that NBR1 may be a new predisposing gene for RCC, however its characterization needs to be further investigated in order to confirm its role in renal carcinogenesis.
Collapse
Affiliation(s)
- Florine Adolphe
- EPHE, PSL Université, Paris, France; CNRS UMR 9019, Gustave Roussy, Université Paris-Saclay, UMR 9019 CNRS, 114 rue Edouard Vaillant, Villejuif 94800, France
| | - Sophie Ferlicot
- CNRS UMR 9019, Gustave Roussy, Université Paris-Saclay, UMR 9019 CNRS, 114 rue Edouard Vaillant, Villejuif 94800, France; Département de Pathologie, AP-HP, Université Paris-Saclay, Hôpital de Bicêtre, Le Kremlin-Bicêtre, France; Réseau National de Référence pour Cancers Rares de l'Adulte PREDIR labellisé par l'INCa, Hôpital de Bicêtre, AP-HP, et Service d'Urologie, Le Kremlin-Bicêtre, France
| | - Virginie Verkarre
- Réseau National de Référence pour Cancers Rares de l'Adulte PREDIR labellisé par l'INCa, Hôpital de Bicêtre, AP-HP, et Service d'Urologie, Le Kremlin-Bicêtre, France; Service d'Anatomie et de Cytologie Pathologiques, Hôpital Européen Georges Pompidou, AP-HP centre, Université de Paris, Paris, France; Université de Paris, PARCC, INSERM, Equipe Labellisée par la Ligue contre le Cancer, F-75015 Paris, France
| | - Katia Posseme
- Département de Pathologie, AP-HP, Université Paris-Saclay, Hôpital de Bicêtre, Le Kremlin-Bicêtre, France
| | - Sophie Couvé
- EPHE, PSL Université, Paris, France; CNRS UMR 9019, Gustave Roussy, Université Paris-Saclay, UMR 9019 CNRS, 114 rue Edouard Vaillant, Villejuif 94800, France
| | - Pauline Garnier
- EPHE, PSL Université, Paris, France; CNRS UMR 9019, Gustave Roussy, Université Paris-Saclay, UMR 9019 CNRS, 114 rue Edouard Vaillant, Villejuif 94800, France
| | - Nathalie Droin
- Plateforme de Génomique, Gustave Roussy, Villejuif, France
| | - Marc Deloger
- Plateforme de Bioinformatique, Gustave Roussy, Villejuif, France
| | - Bastien Job
- Plateforme de Bioinformatique, Gustave Roussy, Villejuif, France
| | - Sophie Giraud
- Réseau National de Référence pour Cancers Rares de l'Adulte PREDIR labellisé par l'INCa, Hôpital de Bicêtre, AP-HP, et Service d'Urologie, Le Kremlin-Bicêtre, France; Service de Génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
| | - Brigitte Bressac-de Paillerets
- Réseau National de Référence pour Cancers Rares de l'Adulte PREDIR labellisé par l'INCa, Hôpital de Bicêtre, AP-HP, et Service d'Urologie, Le Kremlin-Bicêtre, France; Département de Biopathologie, Service de Génétique, Gustave Roussy, Villejuif, France
| | - Betty Gardie
- EPHE, PSL Université, Paris, France; L'Institut du Thorax, INSERM, CNRS, Université de Nantes, Nantes, France
| | - Stéphane Richard
- EPHE, PSL Université, Paris, France; CNRS UMR 9019, Gustave Roussy, Université Paris-Saclay, UMR 9019 CNRS, 114 rue Edouard Vaillant, Villejuif 94800, France; Réseau National de Référence pour Cancers Rares de l'Adulte PREDIR labellisé par l'INCa, Hôpital de Bicêtre, AP-HP, et Service d'Urologie, Le Kremlin-Bicêtre, France
| | - Flore Renaud
- EPHE, PSL Université, Paris, France; CNRS UMR 9019, Gustave Roussy, Université Paris-Saclay, UMR 9019 CNRS, 114 rue Edouard Vaillant, Villejuif 94800, France
| | - Sophie Gad
- EPHE, PSL Université, Paris, France; CNRS UMR 9019, Gustave Roussy, Université Paris-Saclay, UMR 9019 CNRS, 114 rue Edouard Vaillant, Villejuif 94800, France.
| |
Collapse
|
25
|
The Pathways Underlying the Multiple Roles of p62 in Inflammation and Cancer. Biomedicines 2021; 9:biomedicines9070707. [PMID: 34206503 PMCID: PMC8301319 DOI: 10.3390/biomedicines9070707] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/09/2021] [Accepted: 06/18/2021] [Indexed: 12/12/2022] Open
Abstract
p62 is a highly conserved, multi-domain, and multi-functional adaptor protein critically involved in several important cellular processes. Via its pronounced domain architecture, p62 binds to numerous interaction partners, thereby influencing key pathways that regulate tissue homeostasis, inflammation, and several common diseases including cancer. Via binding of ubiquitin chains, p62 acts in an anti-inflammatory manner as an adaptor for the auto-, xeno-, and mitophagy-dependent degradation of proteins, pathogens, and mitochondria. Furthermore, p62 is a negative regulator of inflammasome complexes. The transcription factor Nrf2 regulates expression of a bundle of ROS detoxifying genes. p62 activates Nrf2 by interaction with and autophagosomal degradation of the Nrf2 inhibitor Keap1. Moreover, p62 activates mTOR, the central kinase of the mTORC1 sensor complex that controls cell proliferation and differentiation. Through different mechanisms, p62 acts as a positive regulator of the transcription factor NF-κB, a central player in inflammation and cancer development. Therefore, p62 represents not only a cargo receptor for autophagy, but also a central signaling hub, linking several important pro- and anti-inflammatory pathways. This review aims to summarize knowledge about the molecular mechanisms underlying the roles of p62 in health and disease. In particular, different types of tumors are characterized by deregulated levels of p62. The elucidation of how p62 contributes to inflammation and cancer progression at the molecular level might promote the development of novel therapeutic strategies.
Collapse
|
26
|
Gong L, Wang K, Wang M, Hu R, Li H, Gao D, Lin M. CUL5-ASB6 Complex Promotes p62/SQSTM1 Ubiquitination and Degradation to Regulate Cell Proliferation and Autophagy. Front Cell Dev Biol 2021; 9:684885. [PMID: 34164402 PMCID: PMC8215545 DOI: 10.3389/fcell.2021.684885] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/06/2021] [Indexed: 12/30/2022] Open
Abstract
p62/SQSTM1 (sequestosome-1) is a key protein involved in multiple cellular bioprocesses including autophagy, nutrient sensing, cell growth, cell death, and survival. Therefore, it is implicated in human diseases such as obesity and cancer. Here, we show that the CUL5–ASB6 complex is a ubiquitin E3 ligase complex mediating p62 ubiquitination and degradation. Depletion of CUL5 or ASB6 induced p62 accumulation, and overexpression of ASB6 promoted ubiquitination and degradation of p62. Functionally, ASB6 overexpression can inhibit the proliferation of MEF and hepatocellular carcinoma cells by reducing p62 protein level, and impair the occurrence of autophagy. Overall, our study identified a new molecular mechanism regulating p62 stability, which may provide additional insights for understanding the delicate control of p62 and cell proliferation–autophagy control in physiological and pathological settings.
Collapse
Affiliation(s)
- Liyan Gong
- Center for Clinical Research and Translational Medicine, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China.,Department of General Surgery, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China
| | - Kaihua Wang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Mengcheng Wang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ronggui Hu
- University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Huaguang Li
- Center for Clinical Research and Translational Medicine, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China
| | - Daming Gao
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Moubin Lin
- Center for Clinical Research and Translational Medicine, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China.,Department of General Surgery, Yangpu Hospital, Tongji University School of Medicine, Shanghai, China
| |
Collapse
|
27
|
Chargui A, Belaid A, Ndiaye PD, Imbert V, Samson M, Guigonis JM, Tauc M, Peyron JF, Poujeol P, Brest P, Hofman P, Mograbi B. The Carcinogen Cadmium Activates Lysine 63 (K63)-Linked Ubiquitin-Dependent Signaling and Inhibits Selective Autophagy. Cancers (Basel) 2021; 13:2490. [PMID: 34065348 PMCID: PMC8161291 DOI: 10.3390/cancers13102490] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 05/11/2021] [Indexed: 01/18/2023] Open
Abstract
Signaling, proliferation, and inflammation are dependent on K63-linked ubiquitination-conjugation of a chain of ubiquitin molecules linked via lysine 63. However, very little information is currently available about how K63-linked ubiquitination is subverted in cancer. The present study provides, for the first time, evidence that cadmium (Cd), a widespread environmental carcinogen, is a potent activator of K63-linked ubiquitination, independently of oxidative damage, activation of ubiquitin ligase, or proteasome impairment. We show that Cd induces the formation of protein aggregates that sequester and inactivate cylindromatosis (CYLD) and selective autophagy, two tumor suppressors that deubiquitinate and degrade K63-ubiquitinated proteins, respectively. The aggregates are constituted of substrates of selective autophagy-SQSTM1, K63-ubiquitinated proteins, and mitochondria. These protein aggregates also cluster double-membrane remnants, which suggests an impairment in autophagosome maturation. However, failure to eliminate these selective cargos is not due to alterations in the general autophagy process, as degradation of long-lived proteins occurs normally. We propose that the simultaneous disruption of CYLD and selective autophagy by Cd feeds a vicious cycle that further amplifies K63-linked ubiquitination and downstream activation of the NF-κB pathway, processes that support cancer progression. These novel findings link together impairment of selective autophagy, K63-linked ubiquitination, and carcinogenesis.
Collapse
Affiliation(s)
- Abderrahman Chargui
- Université Côte d’Azur, Institute of Research on Cancer and Aging in Nice (IRCAN), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Fédération Hospitalo-Universitaire (FHU) OncoAge, Centre Antoine Lacassagne, F-06189 Nice, France; (A.C.); (A.B.); (P.D.N.); (P.B.); (P.H.)
- Higher School of Agriculture of Kef, University Jendouba, Le Kef and Laboratory of Histology, Embryology and Cell Biology, Faculty of Medicine Tunis, 7110 Le Kef, Tunisia
| | - Amine Belaid
- Université Côte d’Azur, Institute of Research on Cancer and Aging in Nice (IRCAN), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Fédération Hospitalo-Universitaire (FHU) OncoAge, Centre Antoine Lacassagne, F-06189 Nice, France; (A.C.); (A.B.); (P.D.N.); (P.B.); (P.H.)
| | - Papa Diogop Ndiaye
- Université Côte d’Azur, Institute of Research on Cancer and Aging in Nice (IRCAN), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Fédération Hospitalo-Universitaire (FHU) OncoAge, Centre Antoine Lacassagne, F-06189 Nice, France; (A.C.); (A.B.); (P.D.N.); (P.B.); (P.H.)
| | - Véronique Imbert
- Université Côte d’Azur, Centre Méditerranéen de Médecine Moléculaire (C3M), Institut National de la Santé et de la Recherche Médicale (INSERM), F-06204 Nice, France; (V.I.); (J.-F.P.)
| | - Michel Samson
- Université Côte d’Azur, Laboratory Transporter in Imaging and Radiotherapy in Oncology (TIRO), Direction de la Recherche Fondamentale (DRF), Institut des sciences du vivant Fréderic Joliot, Commissariat à l’Energie Atomique et aux énergies alternatives (CEA), F-06107 Nice, France; (M.S.); (J.-M.G.)
| | - Jean-Marie Guigonis
- Université Côte d’Azur, Laboratory Transporter in Imaging and Radiotherapy in Oncology (TIRO), Direction de la Recherche Fondamentale (DRF), Institut des sciences du vivant Fréderic Joliot, Commissariat à l’Energie Atomique et aux énergies alternatives (CEA), F-06107 Nice, France; (M.S.); (J.-M.G.)
| | - Michel Tauc
- Université Côte d’Azur, Laboratoire de Physiomédecine Moléculaire, LP2M, Labex ICST, Centre National de la Recherche Scientifique (CNRS), F-06107 Nice, France; (M.T.); (P.P.)
| | - Jean-François Peyron
- Université Côte d’Azur, Centre Méditerranéen de Médecine Moléculaire (C3M), Institut National de la Santé et de la Recherche Médicale (INSERM), F-06204 Nice, France; (V.I.); (J.-F.P.)
| | - Philippe Poujeol
- Université Côte d’Azur, Laboratoire de Physiomédecine Moléculaire, LP2M, Labex ICST, Centre National de la Recherche Scientifique (CNRS), F-06107 Nice, France; (M.T.); (P.P.)
| | - Patrick Brest
- Université Côte d’Azur, Institute of Research on Cancer and Aging in Nice (IRCAN), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Fédération Hospitalo-Universitaire (FHU) OncoAge, Centre Antoine Lacassagne, F-06189 Nice, France; (A.C.); (A.B.); (P.D.N.); (P.B.); (P.H.)
| | - Paul Hofman
- Université Côte d’Azur, Institute of Research on Cancer and Aging in Nice (IRCAN), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Fédération Hospitalo-Universitaire (FHU) OncoAge, Centre Antoine Lacassagne, F-06189 Nice, France; (A.C.); (A.B.); (P.D.N.); (P.B.); (P.H.)
- Université Côte d’Azur, Laboratory of Clinical and Experimental Pathology, FHU OncoAge, Hospital-Integrated Biobank (BB-0033-00025), Centre Hospitalier Universitaire (CHU) de Nice, F-06001 Nice, France
| | - Baharia Mograbi
- Université Côte d’Azur, Institute of Research on Cancer and Aging in Nice (IRCAN), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Fédération Hospitalo-Universitaire (FHU) OncoAge, Centre Antoine Lacassagne, F-06189 Nice, France; (A.C.); (A.B.); (P.D.N.); (P.B.); (P.H.)
| |
Collapse
|
28
|
Qiu Y, Wang J, Li H, Yang B, Wang J, He Q, Weng Q. Emerging views of OPTN (optineurin) function in the autophagic process associated with disease. Autophagy 2021; 18:73-85. [PMID: 33783320 DOI: 10.1080/15548627.2021.1908722] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Macroautophagy/autophagy is a highly conserved process in eukaryotic cells. It plays a critical role in cellular homeostasis by delivering cytoplasmic cargos to lysosomes for selective degradation. OPTN (optineurin), a well-recognized autophagy receptor, has received considerable attention due to its multiple roles in the autophagic process. OPTN is associated with many human disorders that are closely related to autophagy, such as rheumatoid arthritis, osteoporosis, and nephropathy. Here, we review the function of OPTN as an autophagy receptor at different stages of autophagy, focusing on cargo recognition, autophagosome formation, autophagosome maturation, and lysosomal quality control. OPTN tends to be protective in most autophagy associated diseases, though the molecular mechanism of OPTN regulation in these diseases is not well understood. A comprehensive review of the function of OPTN in autophagy provides valuable insight into the pathogenesis of human diseases related to OPTN and facilitates the discovery of potential key regulators and novel therapeutic targets for disease intervention in patients with autophagic diseases.Abbreviations: ATG: autophagy-related; APAP: acetaminophen; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; CC: coiled-coil; HACE1: HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1; MYO6: myosin VI; IKBKG/NEMO: inhibitor of nuclear factor kappa B kinase regulatory subunit gamma; IKK: IκB kinase; LIR: LC3-interacting region; LZ: leucine zipper; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; NFKB/NF-κB: nuclear factor kappa B subunit; OPTN: optineurin; PIK3C3: phosphatidylinositol 3-kinase catalytic subunit type 3; PINK1: PTEN induced kinase 1; PRKN: parkin RBR E3 ubiquitin protein ligase; RTECs: renal tubular epithelial cells; SQSTM1/p62: sequestosome 1; TBK1: TANK binding kinase 1; TOM1: target of myb1 membrane trafficking protein; UBD: ubiquitin-binding domain; ULK1: unc-51 like autophagy activating kinase 1; WIPI2: WD repeat domain, phosphoinositide interacting 2; ZF: zinc finger.
Collapse
Affiliation(s)
- Yueping Qiu
- Center for Drug Safety Evaluation and Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Jincheng Wang
- Center for Drug Safety Evaluation and Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Hui Li
- Center for Drug Safety Evaluation and Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Bo Yang
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Jiajia Wang
- Center for Drug Safety Evaluation and Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Qiaojun He
- Center for Drug Safety Evaluation and Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, China
| | - Qinjie Weng
- Center for Drug Safety Evaluation and Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, China
| |
Collapse
|
29
|
Abstract
Cells use mitophagy to remove dysfunctional or excess mitochondria, frequently in response to imposed stresses, such as hypoxia and nutrient deprivation. Mitochondrial cargo receptors (MCR) induced by these stresses target mitochondria to autophagosomes through interaction with members of the LC3/GABARAP family. There are a growing number of these MCRs, including BNIP3, BNIP3L, FUNDC1, Bcl2-L-13, FKBP8, Prohibitin-2, and others, in addition to mitochondrial protein targets of PINK1/Parkin phospho-ubiquitination. There is also an emerging link between mitochondrial lipid signaling and mitophagy where ceramide, sphingosine-1-phosphate, and cardiolipin have all been shown to promote mitophagy. Here, we review the upstream signaling mechanisms that regulate mitophagy, including components of the mitochondrial fission machinery, AMPK, ATF4, FoxOs, Sirtuins, and mtDNA release, and address the significance of these pathways for stress responses in tumorigenesis and metastasis. In particular, we focus on how mitophagy modulators intersect with cell cycle control and survival pathways in cancer, including following ECM detachment and during cell migration and metastasis. Finally, we interrogate how mitophagy affects tissue atrophy during cancer cachexia and therapy responses in the clinic.
Collapse
Affiliation(s)
- Logan P Poole
- The Ben May Department for Cancer Research, The Gordon Center for Integrative Sciences, W-338, The University of Chicago, 929 E 57th Street, Chicago, IL, 60637, USA
- The Committee on Cancer Biology, The University of Chicago, Chicago, USA
| | - Kay F Macleod
- The Ben May Department for Cancer Research, The Gordon Center for Integrative Sciences, W-338, The University of Chicago, 929 E 57th Street, Chicago, IL, 60637, USA.
- The Committee on Cancer Biology, The University of Chicago, Chicago, USA.
| |
Collapse
|
30
|
Suares A, Medina MV, Coso O. Autophagy in Viral Development and Progression of Cancer. Front Oncol 2021; 11:603224. [PMID: 33763351 PMCID: PMC7982729 DOI: 10.3389/fonc.2021.603224] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 01/12/2021] [Indexed: 12/12/2022] Open
Abstract
Autophagy is a complex degradative process by which eukaryotic cells capture cytoplasmic components for subsequent degradation through lysosomal hydrolases. Although this catabolic process can be triggered by a great variety of stimuli, action in cells varies according to cellular context. Autophagy has been previously linked to disease development modulation, including cancer. Autophagy helps suppress cancer cell advancement in tumor transformation early stages, while promoting proliferation and metastasis in advanced settings. Oncoviruses are a particular type of virus that directly contribute to cell transformation and tumor development. Extensive molecular studies have revealed complex ways in which autophagy can suppress or improve oncovirus fitness while still regulating viral replication and determining host cell fate. This review includes recent advances in autophagic cellular function and emphasizes its antagonistic role in cancer cells.
Collapse
Affiliation(s)
- Alejandra Suares
- Departamento de Fisiología y Biología Molecular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María Victoria Medina
- Departamento de Fisiología y Biología Molecular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Omar Coso
- Departamento de Fisiología y Biología Molecular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| |
Collapse
|
31
|
Suares A, Medina MV, Coso O. Autophagy in Viral Development and Progression of Cancer. Front Oncol 2021. [DOI: 10.3389/fonc.2021.603224
expr 816899697 + 824303767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
Autophagy is a complex degradative process by which eukaryotic cells capture cytoplasmic components for subsequent degradation through lysosomal hydrolases. Although this catabolic process can be triggered by a great variety of stimuli, action in cells varies according to cellular context. Autophagy has been previously linked to disease development modulation, including cancer. Autophagy helps suppress cancer cell advancement in tumor transformation early stages, while promoting proliferation and metastasis in advanced settings. Oncoviruses are a particular type of virus that directly contribute to cell transformation and tumor development. Extensive molecular studies have revealed complex ways in which autophagy can suppress or improve oncovirus fitness while still regulating viral replication and determining host cell fate. This review includes recent advances in autophagic cellular function and emphasizes its antagonistic role in cancer cells.
Collapse
|
32
|
Ichimiya T, Yamakawa T, Hirano T, Yokoyama Y, Hayashi Y, Hirayama D, Wagatsuma K, Itoi T, Nakase H. Autophagy and Autophagy-Related Diseases: A Review. Int J Mol Sci 2020; 21:ijms21238974. [PMID: 33255983 PMCID: PMC7729615 DOI: 10.3390/ijms21238974] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/19/2020] [Accepted: 11/24/2020] [Indexed: 12/20/2022] Open
Abstract
Autophagy refers to the process involving the decomposition of intracellular components via lysosomes. Autophagy plays an important role in maintaining and regulating cell homeostasis by degrading intracellular components and providing degradation products to cells. In vivo, autophagy has been shown to be involved in the starvation response, intracellular quality control, early development, and cell differentiation. Recent studies have revealed that autophagy dysfunction is implicated in neurodegenerative diseases and tumorigenesis. In addition to the discovery of certain disease-causing autophagy-related mutations and elucidation of the pathogenesis of conditions resulting from the abnormal degradation of selective autophagy substrates, the activation of autophagy is essential for prolonging life and suppressing aging. This article provides a comprehensive review of the role of autophagy in health, physiological function, and autophagy-related disease.
Collapse
Affiliation(s)
- Tadashi Ichimiya
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo 060-8543, Japan; (T.I.); (T.Y.); (T.H.); (Y.Y.); (Y.H.); (D.H.); (K.W.)
- Department of Gastroenterology and Hepatology, Tokyo Medical University, Tokyo 160-0023, Japan;
| | - Tsukasa Yamakawa
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo 060-8543, Japan; (T.I.); (T.Y.); (T.H.); (Y.Y.); (Y.H.); (D.H.); (K.W.)
| | - Takehiro Hirano
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo 060-8543, Japan; (T.I.); (T.Y.); (T.H.); (Y.Y.); (Y.H.); (D.H.); (K.W.)
| | - Yoshihiro Yokoyama
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo 060-8543, Japan; (T.I.); (T.Y.); (T.H.); (Y.Y.); (Y.H.); (D.H.); (K.W.)
| | - Yuki Hayashi
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo 060-8543, Japan; (T.I.); (T.Y.); (T.H.); (Y.Y.); (Y.H.); (D.H.); (K.W.)
| | - Daisuke Hirayama
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo 060-8543, Japan; (T.I.); (T.Y.); (T.H.); (Y.Y.); (Y.H.); (D.H.); (K.W.)
| | - Kohei Wagatsuma
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo 060-8543, Japan; (T.I.); (T.Y.); (T.H.); (Y.Y.); (Y.H.); (D.H.); (K.W.)
| | - Takao Itoi
- Department of Gastroenterology and Hepatology, Tokyo Medical University, Tokyo 160-0023, Japan;
| | - Hiroshi Nakase
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo 060-8543, Japan; (T.I.); (T.Y.); (T.H.); (Y.Y.); (Y.H.); (D.H.); (K.W.)
- Correspondence: ; Tel.: +81-11-611-2111
| |
Collapse
|
33
|
Clerici S, Boletta A. Role of the KEAP1-NRF2 Axis in Renal Cell Carcinoma. Cancers (Basel) 2020; 12:E3458. [PMID: 33233657 PMCID: PMC7699726 DOI: 10.3390/cancers12113458] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/13/2020] [Accepted: 11/18/2020] [Indexed: 12/12/2022] Open
Abstract
NRF2 is a transcription factor that coordinates the antioxidant response in many different tissues, ensuring cytoprotection from endogenous and exogenous stress stimuli. In the kidney, its function is essential in appropriate cellular response to oxidative stress, however its aberrant activation supports progression, metastasis, and resistance to therapies in renal cell carcinoma, similarly to what happens in other nonrenal cancers. While at the moment direct inhibitors of NRF2 are not available, understanding the molecular mechanisms that regulate its hyperactivation in specific tumor types is crucial as it may open new therapeutic perspectives. Here, we focus our attention on renal cell carcinoma, describing how NRF2 hyperactivation can contribute to tumor progression and chemoresistance. Furthermore, we highlight the mechanism whereby the many pathways that are generally altered in these tumors converge to dysregulation of the KEAP1-NRF2 axis.
Collapse
Affiliation(s)
| | - Alessandra Boletta
- IRCCS San Raffaele Scientific Institute, Molecular Basis of Cystic Kidney Diseases, Division of Genetics and Cell Biology, 20132 Milan, Italy;
| |
Collapse
|
34
|
Radovanovic M, Vidicevic S, Tasic J, Tomonjic N, Stanojevic Z, Nikic P, Vuksanovic A, Dzamic Z, Bumbasirevic U, Isakovic A, Trajkovic V. Role of AMPK/mTOR-independent autophagy in clear cell renal cell carcinoma. J Investig Med 2020; 68:1386-1393. [PMID: 33087428 DOI: 10.1136/jim-2020-001524] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2020] [Indexed: 12/20/2022]
Abstract
We examined the status and role of autophagy, a process of lysosomal recycling of cellular material, in clear cell renal cell carcinoma (ccRCC). Paired samples of tumor and adjacent non-malignant tissue were collected from 20 patients with ccRCC after radical nephrectomy. The mRNA levels of apoptosis (BAD, BAX, BCL2, BCLXL, BIM) and autophagy (ATG4, BECN1, GABARAP, p62, UVRAG) regulators were measured by RT-qPCR. The protein levels of autophagosome-associated LC3-II, autophagy receptor p62, apoptotic marker PARP, as well as phosphorylation of autophagy initiator Unc 51-like kinase 1 (ULK1), its activator AMP-activated protein kinase (AMPK) and 4EBP1, the substrate of ULK1 inhibitor mechanistic target of rapamycin (mTOR), were analyzed by immunoblotting. The mRNA levels of pro-apoptotic BAX, anti-apoptotic BCLXL and pro-autophagic ATG4, p62 and UVRAG were higher in ccRCC tumors. Autophagy induction was confirmed by an increase in phospho-ULK1 and degradation of the autophagic target p62, while apoptotic PARP cleavage was unaltered. AMPK phosphorylation was reduced and 4EBP1 phosphorylation was increased in ccRCC tissue. The expression of apoptosis regulators did not correlate with clinicopathological features of ccRCC. Conversely, high mRNA levels of ATG4, GABARAP and p62 were associated with lower tumor stage, as well as with smaller tumor size and better disease-specific 5-year survival (ATG4 and p62). Accordingly, low p62 protein levels, corresponding to increased autophagic flux, were associated with lower tumor stage, reduced metastasis and improved 5-year survival. These data demonstrate that transcriptional induction of autophagy in ccRCC is accompanied by AMPK/mTOR-independent increase in ULK1 activation and autophagic flux, which might slow tumor progression and metastasis independently of apoptosis.
Collapse
Affiliation(s)
| | - Sasenka Vidicevic
- Institute of Medical and Clinical Biochemistry, University of Belgrade Faculty of Medicine, Belgrade, Serbia
| | - Jelena Tasic
- Institute of Medical and Clinical Biochemistry, University of Belgrade Faculty of Medicine, Belgrade, Serbia
| | - Nina Tomonjic
- Institute of Medical and Clinical Biochemistry, University of Belgrade Faculty of Medicine, Belgrade, Serbia
| | - Zeljka Stanojevic
- Institute of Medical and Clinical Biochemistry, University of Belgrade Faculty of Medicine, Belgrade, Serbia
| | - Predrag Nikic
- Clinic of Urology, Clinical Center of Serbia, Belgrade, Serbia
| | | | - Zoran Dzamic
- Clinic of Urology, Clinical Center of Serbia, Belgrade, Serbia
| | | | - Aleksandra Isakovic
- Institute of Medical and Clinical Biochemistry, University of Belgrade Faculty of Medicine, Belgrade, Serbia
| | - Vladimir Trajkovic
- Institute of Microbiology and Immunology, University of Belgrade Faculty of Medicine, Belgrade, Serbia
| |
Collapse
|
35
|
Testa U, Pelosi E, Castelli G. Genetic Alterations in Renal Cancers: Identification of The Mechanisms Underlying Cancer Initiation and Progression and of Therapeutic Targets. MEDICINES (BASEL, SWITZERLAND) 2020; 7:E44. [PMID: 32751108 PMCID: PMC7459851 DOI: 10.3390/medicines7080044] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/19/2020] [Accepted: 07/24/2020] [Indexed: 12/26/2022]
Abstract
Renal cell cancer (RCC) involves three most recurrent sporadic types: clear-cell RCC (70-75%, CCRCC), papillary RCCC (10-15%, PRCC), and chromophobe RCC (5%, CHRCC). Hereditary cases account for about 5% of all cases of RCC and are caused by germline pathogenic variants. Herein, we review how a better understanding of the molecular biology of RCCs has driven the inception of new diagnostic and therapeutic approaches. Genomic research has identified relevant genetic alterations associated with each RCC subtype. Molecular studies have clearly shown that CCRCC is universally initiated by Von Hippel Lindau (VHL) gene dysregulation, followed by different types of additional genetic events involving epigenetic regulatory genes, dictating disease progression, aggressiveness, and differential response to treatments. The understanding of the molecular mechanisms that underlie the development and progression of RCC has considerably expanded treatment options; genomic data might guide treatment options by enabling patients to be matched with therapeutics that specifically target the genetic alterations present in their tumors. These new targeted treatments have led to a moderate improvement of the survival of metastatic RCC patients. Ongoing studies based on the combination of immunotherapeutic agents (immune check inhibitors) with VEGF inhibitors are expected to further improve the survival of these patients.
Collapse
Affiliation(s)
- Ugo Testa
- Department of Oncology, Istituto Superiore di Sanità, Vaile Regina Elena 299, 00161 Rome, Italy; (E.P.); (G.C.)
| | | | | |
Collapse
|
36
|
Chhabra R, Nanjundan M. Lysophosphatidic acid reverses Temsirolimus-induced changes in lipid droplets and mitochondrial networks in renal cancer cells. PLoS One 2020; 15:e0233887. [PMID: 32492043 PMCID: PMC7269261 DOI: 10.1371/journal.pone.0233887] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 05/14/2020] [Indexed: 01/05/2023] Open
Abstract
Increased cytoplasmic lipid droplets (LDs) and elevated AKT/mTOR signaling are characteristics of clear cell renal cell carcinoma (ccRCC). Lysophosphatidic acid (LPA), a potent lipid mitogen generated via autotaxin (elevated in ccRCC), can modulate tumor progression but its role in altering chemotherapeutic sensitivity to mTOR inhibitors is unclear and thus is the focus of the studies presented herein. Using malignant (A-498, 769-P and 786-O) and normal immortalized kidney (HK-2) cell lines, we investigated their cellular responsiveness to Temsirolimus (TEMS, mTOR inhibitor) in the absence or presence of LPA by monitoring alterations in AKT/mTOR pathway mediators (via western blotting), LDs (using LipidTOX and real-time PCR to assess transcript changes in modulators of LD biogenesis/turnover), mitochondrial networks (via immunofluorescence staining for TOM20 and TOM70), as well as cellular viability. We identified that TEMS reduced cellular viability in all renal cell lines, with increased sensitivity in the presence of an autophagy inhibitor. TEMS also altered activation of AKT/mTOR pathway mediators, abundance of LDs, and fragmentation of mitochondrial networks. We observed that these effects were antagonized by LPA. In HK-2 cells, LPA markedly increased LD size and abundance, coinciding with phospho-MAPK and phospho-S6 activation, increased diacylglycerol O-acetyltransferase 2 (DGAT2) mRNA (which produces triacylglycerides), and survival. Inhibiting MAPK partially antagonized LPA-induced LD changes. Collectively, we have identified that LPA can reverse the effects of TEMS by increasing LDs in a MAPK-dependent manner; these results suggest that LPA may contribute to the pathogenesis and chemotherapeutic resistance of ccRCC.
Collapse
Affiliation(s)
- Ravneet Chhabra
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida, United States of America
| | - Meera Nanjundan
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida, United States of America
- * E-mail:
| |
Collapse
|
37
|
Abstract
Clear cell renal cell carcinoma (ccRCC) is characterized by loss of tumor suppressor Von Hippel Lindau (VHL) function, which leads to accumulation of hypoxia inducible factor α (including HIF1α and HIF2α). HIF2α was previously reported to be one of the major oncogenic drivers in ccRCC, however, its therapeutic targets remain challenging. Here we performed a deubiquitinase (DUB) complementary DNA (cDNA) library binding screen and discovered that ubiquitin-specific peptidase 37 (USP37) is a DUB that binds HIF2α and promotes HIF2α deubiquitination. As a result, USP37 promotes HIF2α protein stability in an enzymatically dependent manner, and depletion of USP37 leads to HIF2α down-regulation in ccRCC. Functionally, USP37 depletion causes decreased cell proliferation measured by MTS, two-dimensional (2D) colony formation as well as three-dimensional (3D) anchorage- independent growth. USP37 is also essential for maintaining kidney tumorigenesis in an orthotopic xenograft model and its depletion leads to both decreased primary kidney tumorigenesis and spontaneous lung metastasis. Our results suggest that USP37 is a potential therapeutic target in ccRCC.
Collapse
|
38
|
Panieri E, Telkoparan-Akillilar P, Suzen S, Saso L. The NRF2/KEAP1 Axis in the Regulation of Tumor Metabolism: Mechanisms and Therapeutic Perspectives. Biomolecules 2020; 10:biom10050791. [PMID: 32443774 PMCID: PMC7277620 DOI: 10.3390/biom10050791] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/17/2020] [Accepted: 05/19/2020] [Indexed: 02/07/2023] Open
Abstract
The NRF2/KEAP1 pathway is a fundamental signaling cascade that controls multiple cytoprotective responses through the induction of a complex transcriptional program that ultimately renders cancer cells resistant to oxidative, metabolic and therapeutic stress. Interestingly, accumulating evidence in recent years has indicated that metabolic reprogramming is closely interrelated with the regulation of redox homeostasis, suggesting that the disruption of NRF2 signaling might represent a valid therapeutic strategy against a variety of solid and hematologic cancers. These aspects will be the focus of the present review.
Collapse
Affiliation(s)
- Emiliano Panieri
- Department of Physiology and Pharmacology “Vittorio Erspamer”, Sapienza University of Rome, 00185 Rome, Italy
- Correspondence: (E.P.); (L.S.); Tel.: +39-06-4991-2481 (E.P. & L.S.)
| | - Pelin Telkoparan-Akillilar
- Department of Medical Biology, Faculty of Medicine, Yuksek Ihtisas University, 06520 Balgat, Ankara, Turkey;
| | - Sibel Suzen
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, 06100 Tandogan, Ankara, Turkey;
| | - Luciano Saso
- Department of Physiology and Pharmacology “Vittorio Erspamer”, Sapienza University of Rome, 00185 Rome, Italy
- Correspondence: (E.P.); (L.S.); Tel.: +39-06-4991-2481 (E.P. & L.S.)
| |
Collapse
|
39
|
Chen Y, Li Q, Li Q, Xing S, Liu Y, Liu Y, Chen Y, Liu W, Feng F, Sun H. p62/SQSTM1, a Central but Unexploited Target: Advances in Its Physiological/Pathogenic Functions and Small Molecular Modulators. J Med Chem 2020; 63:10135-10157. [DOI: 10.1021/acs.jmedchem.9b02038] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Ying Chen
- Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, People’s Republic of China
| | - Qi Li
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People’s Republic of China
| | - Qihang Li
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People’s Republic of China
| | - Shuaishuai Xing
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People’s Republic of China
| | - Yang Liu
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People’s Republic of China
| | - Yijun Liu
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People’s Republic of China
| | - Yao Chen
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, People’s Republic of China
| | - Wenyuan Liu
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People’s Republic of China
| | - Feng Feng
- Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, People’s Republic of China
- Jiangsu Food and Pharmaceuticals Science College, Institute of Food and Pharmaceuticals Research, Huaian 223005, People’s Republic of China
| | - Haopeng Sun
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People’s Republic of China
- Jiangsu Food and Pharmaceuticals Science College, Institute of Food and Pharmaceuticals Research, Huaian 223005, People’s Republic of China
| |
Collapse
|
40
|
Macklin PS, Yamamoto A, Browning L, Hofer M, Adam J, Pugh CW. Recent advances in the biology of tumour hypoxia with relevance to diagnostic practice and tissue-based research. J Pathol 2020; 250:593-611. [PMID: 32086807 DOI: 10.1002/path.5402] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 02/18/2020] [Indexed: 02/06/2023]
Abstract
In this review article, we examine the importance of low levels of oxygen (hypoxia) in cancer biology. We provide a brief description of how mammalian cells sense oxygen. The hypoxia-inducible factor (HIF) pathway is currently the best characterised oxygen-sensing system, but recent work has revealed that mammals also use an oxygen-sensing system found in plants to regulate the abundance of some proteins and peptides with an amino-terminal cysteine residue. We discuss how the HIF pathway is affected during the growth of solid tumours, which develop in microenvironments with gradients of oxygen availability. We then introduce the concept of 'pseudohypoxia', a state of constitutive, oxygen-independent HIF system activation that occurs due to oncogenic stimulation in a number of specific tumour types that are of immediate relevance to diagnostic histopathologists. We provide an overview of the different methods of quantifying tumour hypoxia, emphasising the importance of pre-analytic factors in interpreting the results of tissue-based studies. Finally, we review recent approaches to targeting hypoxia/HIF system activation for therapeutic benefit, the application of which may require knowledge of which hypoxia signalling components are being utilised by a given tumour. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
Collapse
Affiliation(s)
- Philip S Macklin
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Atsushi Yamamoto
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lisa Browning
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Monika Hofer
- Department of Neuropathology and Ocular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Julie Adam
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | |
Collapse
|
41
|
Tao M, Liu T, You Q, Jiang Z. p62 as a therapeutic target for tumor. Eur J Med Chem 2020; 193:112231. [PMID: 32193054 DOI: 10.1016/j.ejmech.2020.112231] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/10/2020] [Accepted: 03/10/2020] [Indexed: 12/21/2022]
Abstract
p62/SQSTM1 (hereafter as p62) is a stress-inducible cellular protein, which interacts with various signaling proteins to regulate a variety of cellular functions. Growing lines of evidence supported a critical role of p62 in tumorigenesis, and p62 may become a therapeutic target for tumor. In this review, we summarize biological functions of structural domains of p62, reported bioactive molecules targeting p62, and the relationship between p62 and tumorigenesis.
Collapse
Affiliation(s)
- Mengmin Tao
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Tian Liu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qidong You
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Zhengyu Jiang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| |
Collapse
|
42
|
Mandell MA, Saha B, Thompson TA. The Tripartite Nexus: Autophagy, Cancer, and Tripartite Motif-Containing Protein Family Members. Front Pharmacol 2020; 11:308. [PMID: 32226386 PMCID: PMC7081753 DOI: 10.3389/fphar.2020.00308] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/02/2020] [Indexed: 12/12/2022] Open
Abstract
Autophagy is a cellular degradative process that has multiple important actions in cancer. Autophagy modulation is under consideration as a promising new approach to cancer therapy. However, complete autophagy dysregulation is likely to have substantial undesirable side effects. Thus, more targeted approaches to autophagy modulation may prove clinically beneficial. One potential avenue to achieving this goal is to focus on the actions of tripartite motif-containing protein family members (TRIMs). TRIMs have key roles in an array of cellular processes, and their dysregulation has been extensively linked to cancer risk and prognosis. As detailed here, emerging data shows that TRIMs can play important yet context-dependent roles in controlling autophagy and in the selective targeting of autophagic substrates. This review covers how the autophagy-related actions of TRIM proteins contribute to cancer and the possibility of targeting TRIM-directed autophagy in cancer therapy.
Collapse
Affiliation(s)
- Michael A Mandell
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, United States.,Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, United States
| | - Bhaskar Saha
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, United States
| | - Todd A Thompson
- Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, United States.,Department of Pharmaceutical Sciences, University of New Mexico College of Pharmacy, Albuquerque, NM, United States
| |
Collapse
|
43
|
Wu WL, Papagiannakopoulos T. The Pleiotropic Role of the KEAP1/NRF2 Pathway in Cancer. ANNUAL REVIEW OF CANCER BIOLOGY 2020. [DOI: 10.1146/annurev-cancerbio-030518-055627] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The unregulated proliferative capacity of many tumors is dependent on dysfunctional nutrient utilization and ROS (reactive oxygen species) signaling to sustain a deranged metabolic state. Although it is clear that cancers broadly rely on these survival and signaling pathways, how they achieve these aims varies dramatically. Mutations in the KEAP1/NRF2 pathway represent a potent cancer adaptation to exploit native cytoprotective pathways that involve both nutrient metabolism and ROS regulation. Despite activating these advantageous processes, mutations within KEAP1/ NRF2 are not universally selected for across cancers and instead appear to interact with particular tumor driver mutations and tissues of origin. Here, we highlight the relationship between the KEAP1/NRF2 signaling axis and tumor biology with a focus on genetic mutation, metabolism, immune regulation, and treatment implications and opportunities. Understanding the dysregulation of KEAP1 and NRF2 provides not only insight into a commonly mutated tumor suppressor pathway but also a window into the factors dictating the development and evolution of many cancers.
Collapse
Affiliation(s)
- Warren L. Wu
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | | |
Collapse
|
44
|
Overall tumor genomic instability: an important predictor of recurrence-free survival in patients with localized clear cell renal cell carcinoma. Cancer Biol Ther 2020; 21:424-431. [PMID: 32116106 DOI: 10.1080/15384047.2020.1721251] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Measurement of a tumor's overall genomic instability has gathered recent interest over the identification of specific genomic imbalances, as it may provide a more robust measure of tumor aggressiveness. Here we demonstrate the association of tumor genomic instability in the prediction of disease recurrence in patients with clinically localized clear cell renal cell carcinoma (ccRCC). Genomic copy number analysis was performed using SNP-based microarrays on tumors from 103 ccRCC patients. The number of copy number alterations (CNAs) for each tumor was calculated, and a genomic imbalance threshold (GIT) associated with high stage and high-grade disease was determined. Cox proportional hazards regression analyzes were performed to assess the effect of GIT on recurrence-free survival adjusting for known confounders. In the cohort, copy number losses in chromosome arms 3p, 14q, 6q, 9p, and 1p and gains of 5q and 7p/q were common. CNA burden significantly increased with increasing stage (p < .001) and grade (p < .001). The median CNA burden associated with patients presenting with advanced stage (IV) and high-grade (III/IV) tumors was ≥9, defining the GIT. On regression analysis, GIT was a superior predictor of recurrence (Hazard Ratio 4.44 [CI 1.36-14.48], p = .01) independent of stage, with similar results adjusting for grade. These findings were confirmed using an alternative measure of genomic instability, weighted Genomic Integrity Index. Our data support a key role for genomic instability in ccRCC progression. More importantly, we have identified a GIT (≥ 9 CNAs) that is a superior and independent predictor of disease recurrence in high-risk ccRCC patients.
Collapse
|
45
|
Hu L, Xie H, Liu X, Potjewyd F, James LI, Wilkerson EM, Herring LE, Xie L, Chen X, Cabrera JC, Hong K, Liao C, Tan X, Baldwin AS, Gong K, Zhang Q. TBK1 Is a Synthetic Lethal Target in Cancer with VHL Loss. Cancer Discov 2020; 10:460-475. [PMID: 31810986 PMCID: PMC7058506 DOI: 10.1158/2159-8290.cd-19-0837] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 10/25/2019] [Accepted: 12/03/2019] [Indexed: 11/16/2022]
Abstract
TANK binding kinase 1 (TBK1) is an important kinase involved in the innate immune response. Here we discover that TBK1 is hyperactivated by von Hippel-Lindau (VHL) loss or hypoxia in cancer cells. Tumors from patients with kidney cancer with VHL loss display elevated TBK1 phosphorylation. Loss of TBK1 via genetic ablation, pharmacologic inhibition, or a new cereblon-based proteolysis targeting chimera specifically inhibits VHL-deficient kidney cancer cell growth, while leaving VHL wild-type cells intact. TBK1 depletion also significantly blunts kidney tumorigenesis in an orthotopic xenograft model in vivo. Mechanistically, TBK1 hydroxylation on Proline 48 triggers VHL as well as the phosphatase PPM1B binding that leads to decreased TBK1 phosphorylation. We identify that TBK1 phosphorylates p62/SQSTM1 on Ser366, which is essential for p62 stability and kidney cancer cell proliferation. Our results establish that TBK1, distinct from its role in innate immune signaling, is a synthetic lethal target in cancer with VHL loss. SIGNIFICANCE: The mechanisms that lead to TBK1 activation in cancer and whether this activation is connected to its role in innate immunity remain unclear. Here, we discover that TBK1, distinct from its role in innate immunity, is activated by VHL loss or hypoxia in cancer.See related commentary by Bakouny and Barbie, p. 348.This article is highlighted in the In This Issue feature, p. 327.
Collapse
Affiliation(s)
- Lianxin Hu
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Haibiao Xie
- Department of Urology, Peking University First Hospital, Beijing, China
| | - Xijuan Liu
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Frances Potjewyd
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina
| | - Lindsey I James
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina
| | - Emily M Wilkerson
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina
| | - Laura E Herring
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina
| | - Ling Xie
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina
| | - Xian Chen
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina
| | - Johnny Castillo Cabrera
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Kai Hong
- Department of Medical Ultrasound, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Chengheng Liao
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Xianming Tan
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Albert S Baldwin
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Kan Gong
- Department of Urology, Peking University First Hospital, Beijing, China.
| | - Qing Zhang
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina.
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina
| |
Collapse
|
46
|
Liu X, Simon JM, Xie H, Hu L, Wang J, Zurlo G, Fan C, Ptacek TS, Herring L, Tan X, Li M, Baldwin AS, Kim WY, Wu T, Kirschner MW, Gong K, Zhang Q. Genome-wide Screening Identifies SFMBT1 as an Oncogenic Driver in Cancer with VHL Loss. Mol Cell 2020; 77:1294-1306.e5. [PMID: 32023483 DOI: 10.1016/j.molcel.2020.01.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 11/09/2019] [Accepted: 01/01/2020] [Indexed: 11/15/2022]
Abstract
von Hippel-Lindau (VHL) is a critical tumor suppressor in clear cell renal cell carcinomas (ccRCCs). It is important to identify additional therapeutic targets in ccRCC downstream of VHL loss besides hypoxia-inducible factor 2α (HIF2α). By performing a genome-wide screen, we identified Scm-like with four malignant brain tumor domains 1 (SFMBT1) as a candidate pVHL target. SFMBT1 was considered to be a transcriptional repressor but its role in cancer remains unclear. ccRCC patients with VHL loss-of-function mutations displayed elevated SFMBT1 protein levels. SFMBT1 hydroxylation on Proline residue 651 by EglN1 mediated its ubiquitination and degradation governed by pVHL. Depletion of SFMBT1 abolished ccRCC cell proliferation in vitro and inhibited orthotopic tumor growth in vivo. Integrated analyses of ChIP-seq, RNA-seq, and patient prognosis identified sphingosine kinase 1 (SPHK1) as a key SFMBT1 target gene contributing to its oncogenic phenotype. Therefore, the pVHL-SFMBT1-SPHK1 axis serves as a potential therapeutic avenue for ccRCC.
Collapse
Affiliation(s)
- Xijuan Liu
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Jeremy M Simon
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Haibiao Xie
- Department of Urology, Peking University First Hospital, Beijing, China
| | - Lianxin Hu
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jun Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Giada Zurlo
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Cheng Fan
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Travis S Ptacek
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Laura Herring
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA; UNC Proteomics Core Facility, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Xianming Tan
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Mingjie Li
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Albert S Baldwin
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - William Y Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Tao Wu
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Marc W Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Kan Gong
- Department of Urology, Peking University First Hospital, Beijing, China
| | - Qing Zhang
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
| |
Collapse
|
47
|
Zhang N, Chen S, Jiang G, Wu Y, Shao J, Liu W, Wang X, Na R, Xu J. The study on copy number alteration of clear cell renal cancer in Chinese population. J Cancer 2020; 11:16-24. [PMID: 31892969 PMCID: PMC6930398 DOI: 10.7150/jca.33316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 08/16/2019] [Indexed: 01/24/2023] Open
Abstract
Objectives: Copy number alteration (CNA) is one of the important genetic variations. Although there are many studies on renal cancer CNA, few studies are based on the Chinese population. In our study, our objective is to acquire the whole-genome CNA landscape in Chinese population and explore the tumor risk-associated functional genes in the CNA regions, by detecting whole-genome in the clear cell renal cancer (ccRCC) tissues. Methods: We enrolled 35 formalin fixed paraffin embedded samples, which were processed by Oncoscan assay, and then acquired the data of whole-genome CNA. Then genes annotation and enrichment analyzing were processed. Furthermore, the gene burden and the affected bp (base pair) per Mbp (million bp) regions in whole-genome were analyzed by comparison of different T stage affected by CNA. Results: We acquired the whole-genome CNA landscape by Oncoscan detection, and found out the high-frequency CNA regions which were not reported in previous studies, for example, 11P11, 22q11.23, 20q11.3 (PDRG1), and Xp22.33 so on. During the analyzing of genes annotation and enrichment, we found out some ccRCC functional genes in the CNA regions which might play a role in the biological process, for example, the copy number loss of DNA repair genes (TTC5、PARP2, etc.) and tumor suppressor genes (TADA3, VHL, BAP1, ERC2-IT1, etc.), the copy number gain of oncogenes (ABL2, MET, HUWE1, etc.) and Notch signal pathway genes (MDK, etc.). Besides, gene fusion (GSTTP and GSTTP2) was noticed at 22q11.23 which copy number loss occurred, and the frequency is 46%. And between the different T stage patients affected by CNA, the T2+T3 group carried more high-frequency CNA regions (P-value was 0.012). Conclusions: In this study, the whole-genome ccRCC CNA landscape in Chinese population was acquired, a few functional genes and fusion genes were found out. However, a larger scale of samples is still needed to validate our results.
Collapse
Affiliation(s)
- Ning Zhang
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Siteng Chen
- Department of Urology, Shanghai Gerneral Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guangliang Jiang
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yishuo Wu
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jialiang Shao
- Department of Urology, Shanghai Gerneral Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wennuan Liu
- Program for Personalized Cancer Care, Northshore University HealthSystem, Chicago, IL 60201, USA
| | - Xiang Wang
- Department of Urology, Shanghai Gerneral Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rong Na
- Department of Urology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianfeng Xu
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China.,Program for Personalized Cancer Care, Northshore University HealthSystem, Chicago, IL 60201, USA
| |
Collapse
|
48
|
Erdogan S, Ozcan A, Truong LD. Molecular Pathology of Kidney Tumors. KIDNEY CANCER 2020. [DOI: 10.1007/978-3-030-28333-9_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
49
|
Wang Z, Zhang J, Li M, Kong L, Yu J. The expression of p-p62 and nuclear Nrf2 in esophageal squamous cell carcinoma and association with radioresistance. Thorac Cancer 2019; 11:130-139. [PMID: 31755241 PMCID: PMC6938765 DOI: 10.1111/1759-7714.13252] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/25/2019] [Accepted: 10/27/2019] [Indexed: 12/16/2022] Open
Abstract
Background The roles of p62‐Keap1‐Nrf2 pathway in the radioresistance of esophageal squamous cell carcinoma (ESCC) have not yet been revealed. This study aimed to clarify the expression and correlation of p‐p62 and nuclear Nrf2 and their association with radioresistance in ESCC. Methods This study included 164 cases of inoperable locally advanced ESCC. All patients received concurrent chemoradiotherapy (CCRT). Immunohistochemical staining was used to detect the expression of p‐p62 and nuclear Nrf2. The results were analyzed independently by two pathologists. Results There was no significant relationship between p‐p62 or nuclear Nrf2 and patients' clinical characteristics. Compared to patients with low expression of p‐p62, patients with high expression of p‐p62 showed lower objective response rate (ORR). Similarly, patients with high expression of nuclear Nrf2 exhibited lower ORR compared to those with low expression of nuclear Nrf2. The expression of p‐p62 was positively correlated with that of nuclear Nrf2. Moreover, the correlation coefficient between them was higher among patients showing no response to CCRT. Univariate analysis revealed that higher expression of p‐p62 or nuclear Nrf2 was significantly associated with poorer PFS and OS. Multivariate analysis indicated that the expression of nuclear Nrf2 and treatment response were independent prognostic factors for PFS. Sex, treatment response, expression of p‐p62 and nuclear Nrf2 were independent prognostic factors for OS. Conclusion Higher expression of p‐p62 and nuclear Nrf2 are associated with lower ORR as well as poorer prognosis, which indicates that p62‐Keap1‐Nrf2 pathway might play an essential role in the radioresistance of ESCC. Key points The expression of p‐p62 and nuclear Nrf2 in ESCC show a significant relationship with patients' responses to CCRT and influence the prognosis of ESCC. p62‐Keap1‐Nrf2 pathway might be a new target for radiosensitization in ESCC.
Collapse
Affiliation(s)
- Zhe Wang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Jingze Zhang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Minghuan Li
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Li Kong
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Jinming Yu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| |
Collapse
|
50
|
Benstead-Hume G, Wooller SK, Downs JA, Pearl FMG. Defining Signatures of Arm-Wise Copy Number Change and Their Associated Drivers in Kidney Cancers. Int J Mol Sci 2019; 20:E5762. [PMID: 31744086 PMCID: PMC6887958 DOI: 10.3390/ijms20225762] [Citation(s) in RCA: 5] [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: 09/19/2019] [Revised: 11/13/2019] [Accepted: 11/14/2019] [Indexed: 01/15/2023] Open
Abstract
Using pan-cancer data from The Cancer Genome Atlas (TCGA), we investigated how patterns in copy number alterations in cancer cells vary both by tissue type and as a function of genetic alteration. We find that patterns in both chromosomal ploidy and individual arm copy number are dependent on tumour type. We highlight for example, the significant losses in chromosome arm 3p and the gain of ploidy in 5q in kidney clear cell renal cell carcinoma tissue samples. We find that specific gene mutations are associated with genome-wide copy number changes. Using signatures derived from non-negative factorisation, we also find gene mutations that are associated with particular patterns of ploidy change. Finally, utilising a set of machine learning classifiers, we successfully predicted the presence of mutated genes in a sample using arm-wise copy number patterns as features. This demonstrates that mutations in specific genes are correlated and may lead to specific patterns of ploidy loss and gain across chromosome arms. Using these same classifiers, we highlight which arms are most predictive of commonly mutated genes in kidney renal clear cell carcinoma (KIRC).
Collapse
Affiliation(s)
- Graeme Benstead-Hume
- Bioinformatics Lab, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK; (G.B.-H.); (S.K.W.)
| | - Sarah K. Wooller
- Bioinformatics Lab, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK; (G.B.-H.); (S.K.W.)
| | - Jessica A Downs
- Division of Cancer Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK;
| | - Frances M. G. Pearl
- Bioinformatics Lab, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK; (G.B.-H.); (S.K.W.)
| |
Collapse
|