1
|
Liu S, Li G, Yin X, Zhou Y, Luo D, Yang Z, Zhang J, Wang J. Comprehensive investigation of malignant epithelial cell-related genes in clear cell renal cell carcinoma: development of a prognostic signature and exploration of tumor microenvironment interactions. J Transl Med 2024; 22:607. [PMID: 38951896 PMCID: PMC11218120 DOI: 10.1186/s12967-024-05426-x] [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: 03/19/2024] [Accepted: 06/19/2024] [Indexed: 07/03/2024] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is a prevalent malignancy with complex heterogeneity within epithelial cells, which plays a crucial role in tumor progression and immune regulation. Yet, the clinical importance of the malignant epithelial cell-related genes (MECRGs) in ccRCC remains insufficiently understood. This research aims to undertake a comprehensive investigation into the functions and clinical relevance of malignant epithelial cell-related genes in ccRCC, providing valuable understanding of the molecular mechanisms and offering potential targets for treatment strategies. Using data from single-cell sequencing, we successfully identified 219 MECRGs and established a prognostic model MECRGS (MECRGs' signature) by synergistically analyzing 101 machine-learning models using 10 different algorithms. Remarkably, the MECRGS demonstrated superior predictive performance compared to traditional clinical features and 92 previously published signatures across six cohorts, showcasing its independence and accuracy. Upon stratifying patients into high- and low-MECRGS subgroups using the specified cut-off threshold, we noted that patients with elevated MECRGS scores displayed characteristics of an immune suppressive tumor microenvironment (TME) and showed worse outcomes after immunotherapy. Additionally, we discovered a distinct ccRCC tumor cell subtype characterized by the high expressions of PLOD2 (procollagen-lysine,2-oxoglutarate 5-dioxygenase 2) and SAA1 (Serum Amyloid A1), which we further validated in the Renji tissue microarray (TMA) cohort. Lastly, 'Cellchat' revealed potential crosstalk patterns between these cells and other cell types, indicating their potential role in recruiting CD163 + macrophages and regulatory T cells (Tregs), thereby establishing an immunosuppressive TME. PLOD2 + SAA1 + cancer cells with intricate crosstalk patterns indeed show promise for potential therapeutic interventions.
Collapse
Affiliation(s)
- Songyang Liu
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ge Li
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaomao Yin
- Department of Gastrointestinal Surgery, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yihan Zhou
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Dongmei Luo
- Department of Internal Medicine, Shanghai Gongli Hospital, Second Military Medical University, Shanghai, China
| | - Zhenggang Yang
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jin Zhang
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Jianfeng Wang
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| |
Collapse
|
2
|
Andrzejczak A, Małkiewicz B, Tupikowski K, Ptaszkowski K, Szydełko T, Karabon L. Effect of HVEM/CD160 Variations on the Clear Cell Renal Carcinoma Risk and Overall Survival. Int J Mol Sci 2024; 25:6860. [PMID: 38999968 PMCID: PMC11241222 DOI: 10.3390/ijms25136860] [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: 05/28/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 07/14/2024] Open
Abstract
Renal cell carcinoma (RCC) accounts for approximately 90-95% of all kidney cancers in adults, with clear cell RCC (ccRCC) being the most frequently identified subtype. RCC is known for its responsiveness to immunotherapy, making it an area of significant research interest. Immune checkpoint (IC) molecules, which regulate immune surveillance, are established therapeutic targets in RCC. The aim of this study was to analyze the influence of HVEM and CD160 gene polymorphisms on ccRCC susceptibility and patient overall survival (OS) over a ten-year period of observation. We genotyped three HVEM single nucleotide polymorphisms (SNPs): rs1886730, rs2234167, and rs8725, as well as two CD160 SNPs: rs744877 and rs2231375, in 238 ccRCC patients and 521 controls. Our findings indicated that heterozygosity within rs2231375 and/or rs2234167 increases ccRCC risk. Furthermore, in women, heterozygosity within HVEM SNPs rs8725 and rs1886730 is also associated with an increased ccRCC risk. The presence of a minor allele for rs1886730, rs2234167, rs8725, and rs2231375 was also correlated with certain clinical features of ccRCC. Moreover, rs1886730 was found to be associated with OS. In conclusion, our study highlights an association between HVEM and CD160 polymorphisms and the risk of developing ccRCC as well as OS.
Collapse
Affiliation(s)
- Anna Andrzejczak
- Laboratory of Genetic and Epigenetic of Human Diseases, Department of Experimental Therapy, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland;
| | - Bartosz Małkiewicz
- Department of Minimally Invasive and Robotic Urology, University Center of Excellence in Urology, Wroclaw Medical University, 50-556 Wroclaw, Poland; (B.M.); (T.S.)
| | - Krzysztof Tupikowski
- Subdivision of Urology, Lower Silesian Center for Oncology, Pulmonology and Hematology, 53-413 Wroclaw, Poland;
| | - Kuba Ptaszkowski
- Department of Clinical Biomechanics and Physiotherapy in Motor System Disorders, Wroclaw Medical University, 50-368 Wroclaw, Poland;
| | - Tomasz Szydełko
- Department of Minimally Invasive and Robotic Urology, University Center of Excellence in Urology, Wroclaw Medical University, 50-556 Wroclaw, Poland; (B.M.); (T.S.)
| | - Lidia Karabon
- Laboratory of Genetic and Epigenetic of Human Diseases, Department of Experimental Therapy, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland;
| |
Collapse
|
3
|
Zhang R, Wang H, Cheng X, Fan K, Gao T, Qi X, Gao S, Zheng G, Dong H. High estrogen induces trans-differentiation of vascular smooth muscle cells to a macrophage-like phenotype resulting in aortic inflammation via inhibiting VHL/HIF1a/KLF4 axis. Aging (Albany NY) 2024; 16:9876-9898. [PMID: 38843385 PMCID: PMC11210252 DOI: 10.18632/aging.205904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 04/22/2024] [Indexed: 06/22/2024]
Abstract
Estrogen is thought to have a role in slowing down aging and protecting cardiovascular and cognitive function. However, high doses of estrogen are still positively associated with autoimmune diseases and tumors with systemic inflammation. First, we administered exogenous estrogen to female mice for three consecutive months and found that the aorta of mice on estrogen develops inflammatory manifestations similar to Takayasu arteritis (TAK). Then, in vitro estrogen intervention was performed on mouse aortic vascular smooth muscle cells (MOVAS cells). Stimulated by high concentrations of estradiol, MOVAS cells showed decreased expression of contractile phenotypic markers and increased expression of macrophage-like phenotypic markers. This shift was blocked by tamoxifen and Krüppel-like factor 4 (KLF4) inhibitors and enhanced by Von Hippel-Lindau (VHL)/hypoxia-inducible factor-1α (HIF-1α) interaction inhibitors. It suggests that estrogen-targeted regulation of the VHL/HIF-1α/KLF4 axis induces phenotypic transformation of vascular smooth muscle cells (VSMC). In addition, estrogen-regulated phenotypic conversion of VSMC to macrophages is a key mechanism of estrogen-induced vascular inflammation, which justifies the risk of clinical use of estrogen replacement therapy.
Collapse
MESH Headings
- Kruppel-Like Factor 4
- Animals
- Kruppel-Like Transcription Factors/metabolism
- Kruppel-Like Transcription Factors/genetics
- Macrophages/metabolism
- Macrophages/drug effects
- Mice
- Hypoxia-Inducible Factor 1, alpha Subunit/metabolism
- Hypoxia-Inducible Factor 1, alpha Subunit/genetics
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- Muscle, Smooth, Vascular/drug effects
- Female
- Estrogens/pharmacology
- Von Hippel-Lindau Tumor Suppressor Protein/metabolism
- Von Hippel-Lindau Tumor Suppressor Protein/genetics
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/drug effects
- Cell Transdifferentiation/drug effects
- Phenotype
- Aorta/pathology
- Aorta/drug effects
- Inflammation/metabolism
Collapse
Affiliation(s)
- Ruijing Zhang
- Department of Nephrology, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Heng Wang
- Department of Vascular Surgery, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xing Cheng
- Department of Vascular Surgery, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Keyi Fan
- Department of Vascular Surgery, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Tingting Gao
- Department of Vascular Surgery, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xiaotong Qi
- Department of Vascular Surgery, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Siqi Gao
- Department of Vascular Surgery, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| | - Guoping Zheng
- Department of Vascular Surgery, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
- Centre for Transplant and Renal Research, Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
| | - Honglin Dong
- Department of Vascular Surgery, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, China
| |
Collapse
|
4
|
Coxon M, Dennis MA, Dananberg A, Collins C, Wilson H, Meekma J, Savenkova M, Ng D, Osbron C, Mertz T, Goodman A, Duttke S, Maciejowski J, Roberts S. An impaired ubiquitin-proteasome system increases APOBEC3A abundance. NAR Cancer 2023; 5:zcad058. [PMID: 38155930 PMCID: PMC10753533 DOI: 10.1093/narcan/zcad058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 11/21/2023] [Accepted: 12/08/2023] [Indexed: 12/30/2023] Open
Abstract
Apolipoprotein B messenger RNA (mRNA) editing enzyme, catalytic polypeptide-like (APOBEC) cytidine deaminases cause genetic instability during cancer development. Elevated APOBEC3A (A3A) levels result in APOBEC signature mutations; however, mechanisms regulating A3A abundance in breast cancer are unknown. Here, we show that dysregulating the ubiquitin-proteasome system with proteasome inhibitors, including Food and Drug Administration-approved anticancer drugs, increased A3A abundance in breast cancer and multiple myeloma cell lines. Unexpectedly, elevated A3A occurs via an ∼100-fold increase in A3A mRNA levels, indicating that proteasome inhibition triggers a transcriptional response as opposed to or in addition to blocking A3A degradation. This transcriptional regulation is mediated in part through FBXO22, a protein that functions in SKP1-cullin-F-box ubiquitin ligase complexes and becomes dysregulated during carcinogenesis. Proteasome inhibitors increased cellular cytidine deaminase activity, decreased cellular proliferation and increased genomic DNA damage in an A3A-dependent manner. Our findings suggest that proteasome dysfunction, either acquired during cancer development or induced therapeutically, could increase A3A-induced genetic heterogeneity and thereby influence therapeutic responses in patients.
Collapse
Affiliation(s)
- Margo Coxon
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Madeline A Dennis
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Alexandra Dananberg
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Christopher D Collins
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Hannah E Wilson
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Jordyn Meekma
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Marina I Savenkova
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Daniel Ng
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Chelsea A Osbron
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Tony M Mertz
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
- Department of Microbiology and Molecular Genetics, University of Vermont Cancer Center, University of Vermont, Burlington, VT 05405, USA
| | - Alan G Goodman
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Sascha H Duttke
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - John Maciejowski
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Steven A Roberts
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
- Department of Microbiology and Molecular Genetics, University of Vermont Cancer Center, University of Vermont, Burlington, VT 05405, USA
| |
Collapse
|
5
|
Meng J, Jiang A, Lu X, Gu D, Ge Q, Bai S, Zhou Y, Zhou J, Hao Z, Yan F, Wang L, Wang H, Du J, Liang C. Multiomics characterization and verification of clear cell renal cell carcinoma molecular subtypes to guide precise chemotherapy and immunotherapy. IMETA 2023; 2:e147. [PMID: 38868222 PMCID: PMC10989995 DOI: 10.1002/imt2.147] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 10/21/2023] [Indexed: 06/14/2024]
Abstract
Clear cell renal cell carcinoma (ccRCC) is a heterogeneous tumor with different genetic and molecular alterations. Schemes for ccRCC classification system based on multiomics are urgent, to promote further biological insights. Two hundred and fifty-five ccRCC patients with paired data of clinical information, transcriptome expression profiles, copy number alterations, DNA methylation, and somatic mutations were collected for identification. Bioinformatic analyses were performed based on our team's recently developed R package "MOVICS." With 10 state-of-the-art algorithms, we identified the multiomics subtypes (MoSs) for ccRCC patients. MoS1 is an immune exhausted subtype, presented the poorest prognosis, and might be caused by an exhausted immune microenvironment, activated hypoxia features, but can benefit from PI3K/AKT inhibitors. MoS2 is an immune "cold" subtype, which represented more mutation of VHL and PBRM1, favorable prognosis, and is more suitable for sunitinib therapy. MoS3 is the immune "hot" subtype, and can benefit from the anti-PD-1 immunotherapy. We successfully verified the different molecular features of the three MoSs in external cohorts GSE22541, GSE40435, and GSE53573. Patients that received Nivolumab therapy helped us to confirm that MoS3 is suitable for anti-PD-1 therapy. E-MTAB-3267 cohort also supported the fact that MoS2 patients can respond more to sunitinib treatment. We also confirm that SETD2 is a tumor suppressor in ccRCC, along with the decreased SETD2 protein level in advanced tumor stage, and knock-down of SETD2 leads to the promotion of cell proliferation, migration, and invasion. In summary, we provide novel insights into ccRCC molecular subtypes based on robust clustering algorithms via multiomics data, and encourage future precise treatment of ccRCC patients.
Collapse
Affiliation(s)
- Jialin Meng
- Department of UrologyThe First Affiliated Hospital of Anhui Medical University, Institute of Urology, Anhui Medical University, Anhui Province Key Laboratory of Genitourinary DiseasesAnhui Medical UniversityHefeiChina
| | - Aimin Jiang
- Department of Urology, Changhai HospitalNaval Medical University (Second Military Medical University)ShanghaiChina
| | - Xiaofan Lu
- Department of Cancer and Functional GenomicsInstitute of Genetics and Molecular and Cellular Biology, CNRS/INSERM/UNISTRAIllkirchFrance
| | - Di Gu
- Department of Urology, Changhai HospitalNaval Medical University (Second Military Medical University)ShanghaiChina
| | - Qintao Ge
- Department of UrologyThe First Affiliated Hospital of Anhui Medical University, Institute of Urology, Anhui Medical University, Anhui Province Key Laboratory of Genitourinary DiseasesAnhui Medical UniversityHefeiChina
| | - Suwen Bai
- The Second Affiliated Hospital, School of MedicineThe Chinese University of Hong Kong, Shenzhen & Longgang District People's Hospital of ShenzhenShenzhenChina
| | - Yundong Zhou
- Department of Surgery, Ningbo Medical Center Lihuili HospitalNingbo UniversityNingboZhejiangChina
| | - Jun Zhou
- Department of UrologyThe First Affiliated Hospital of Anhui Medical University, Institute of Urology, Anhui Medical University, Anhui Province Key Laboratory of Genitourinary DiseasesAnhui Medical UniversityHefeiChina
| | - Zongyao Hao
- Department of UrologyThe First Affiliated Hospital of Anhui Medical University, Institute of Urology, Anhui Medical University, Anhui Province Key Laboratory of Genitourinary DiseasesAnhui Medical UniversityHefeiChina
| | - Fangrong Yan
- Research Center of Biostatistics and Computational PharmacyChina Pharmaceutical UniversityNanjingChina
| | - Linhui Wang
- Department of Urology, Changhai HospitalNaval Medical University (Second Military Medical University)ShanghaiChina
| | - Haitao Wang
- Cancer Center, Faculty of Health SciencesUniversity of MacauMacau SARChina
- Present address:
Center for Cancer ResearchBethesdaMarylandUSA
| | - Juan Du
- The Second Affiliated Hospital, School of MedicineThe Chinese University of Hong Kong, Shenzhen & Longgang District People's Hospital of ShenzhenShenzhenChina
| | - Chaozhao Liang
- Department of UrologyThe First Affiliated Hospital of Anhui Medical University, Institute of Urology, Anhui Medical University, Anhui Province Key Laboratory of Genitourinary DiseasesAnhui Medical UniversityHefeiChina
| |
Collapse
|
6
|
Lee J, Thuzar M, DiPoto-Brahmbhatt AC, Chaudoir C, Tanner A, Fazili T, Yu X, Constantinescu M, Yeh YA. Clear cell renal cell carcinoma with BAP1 mutation: a report of two cases. AMERICAN JOURNAL OF CLINICAL AND EXPERIMENTAL UROLOGY 2023; 11:429-434. [PMID: 37941648 PMCID: PMC10628621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/31/2023] [Indexed: 11/10/2023]
Abstract
Clear cell renal cell carcinoma is the most common subtype of renal cell carcinomas (RCCs) and accounts for 60%-70% of all RCCs cases in adults. Aberrations in the von Hippel-Lindau (VHL) gene on chromosome 3p occurred in > 90% of clear cell RCCs. Other tumor suppressor genes located on chromosome 3p, such as BAP1, PBRM1, and SETD2, also contribute to tumorigenesis. Clear cell RCCs with both BAP1 and VHL mutations may display distinctive histopathological features. Here, we report two cases of clear cell RCCs with BAP1 mutation. One tumor had VHL, BAP-1, and RAF1 mutations and the tumor nests and alveoli of tumor cells were surrounded by proliferative vessels and the optically clear cytoplasm contained numerous eosinophilic granules and hyaline globules of varying sizes. The other tumor had BAP1 and ATM mutations, and demonstrated clear cells with numerous eosinophilic granules and other typical histopathological features of conventional clear cell RCC. Furthermore, many tumor nodules with dense peripheral lymphocytic infiltrates contained rhabdoid cells. Sarcomatoid cells were also observed. Both tumor cells showed high-grade nuclei. Clear cell RCCs with BAP1 mutation exhibit aggressive clinical behaviors.
Collapse
Affiliation(s)
- Jennifer Lee
- Pathology and Laboratory Medicine Service, Overton Brooks VA Medical CenterShreveport, LA, USA
- Department of Pathology and Translational Pathobiology, Louisiana State University Health ShreveportShreveport, LA, USA
| | - Moe Thuzar
- Pathology and Laboratory Medicine Service, Overton Brooks VA Medical CenterShreveport, LA, USA
- Department of Pathology and Translational Pathobiology, Louisiana State University Health ShreveportShreveport, LA, USA
| | - Angela C DiPoto-Brahmbhatt
- Pathology and Laboratory Medicine Service, Overton Brooks VA Medical CenterShreveport, LA, USA
- Department of Pathology and Translational Pathobiology, Louisiana State University Health ShreveportShreveport, LA, USA
| | - Catherine Chaudoir
- Pathology and Laboratory Medicine Service, Overton Brooks VA Medical CenterShreveport, LA, USA
- Department of Pathology and Translational Pathobiology, Louisiana State University Health ShreveportShreveport, LA, USA
| | - Anthony Tanner
- Pathology and Laboratory Medicine Service, Overton Brooks VA Medical CenterShreveport, LA, USA
| | - Tajammul Fazili
- Department of Urology, Overton Brooks VA Medical CenterShreveport, LA, USA
- Department of Urology, Louisiana State University Health ShreveportShreveport, LA, USA
| | - Xiuping Yu
- Department of Urology, Louisiana State University Health ShreveportShreveport, LA, USA
- Department of Biochemistry and Molecular Biology, Louisiana State University Health ShreveportShreveport, LA, USA
| | - Michael Constantinescu
- Pathology and Laboratory Medicine Service, Overton Brooks VA Medical CenterShreveport, LA, USA
- Department of Pathology and Translational Pathobiology, Louisiana State University Health ShreveportShreveport, LA, USA
| | - Y Albert Yeh
- Pathology and Laboratory Medicine Service, Overton Brooks VA Medical CenterShreveport, LA, USA
- Department of Pathology and Translational Pathobiology, Louisiana State University Health ShreveportShreveport, LA, USA
- Department of Urology, Louisiana State University Health ShreveportShreveport, LA, USA
| |
Collapse
|
7
|
Kannan MP, Sreeraman S, Somala CS, Kushwah RB, Mani SK, Sundaram V, Thirunavukarasou A. Advancement of targeted protein degradation strategies as therapeutics for undruggable disease targets. Future Med Chem 2023; 15:867-883. [PMID: 37254917 DOI: 10.4155/fmc-2023-0072] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/10/2023] [Indexed: 06/01/2023] Open
Abstract
Targeted protein degradation (TPD) aids in developing novel bifunctional small-molecule degraders and eliminates proteins of interest. The TPD approach shows promising results in oncological, neurogenerative, cardiovascular and gynecological drug development. We provide an overview of technology advancements in TPD, including molecular glues, proteolysis-targeting chimeras (PROTACs), lysosome-targeting chimeras, antibody-based PROTAC, GlueBody PROTAC, autophagy-targeting chimera, autophagosome-tethering compound, autophagy-targeting chimera and chaperone-mediated autophagy-based degraders. Here we discuss the development and evolution of the TPD field, the variety of proteins that PROTACs target and the biological repercussions of their degradation. We particularly highlight the recent improvements in TPD research that utilize autophagy or the endolysosomal pathway, which enables the targeting of undruggable targets.
Collapse
Affiliation(s)
- Mayuri P Kannan
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical & Technical Sciences (SIMATS), Thandalam, Chennai, Tamil Nadu, 602105, India
- B-Aatral Biosciences Private Limited, Bangalore, Karnataka, 560091, India
| | - Sarojini Sreeraman
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical & Technical Sciences (SIMATS), Thandalam, Chennai, Tamil Nadu, 602105, India
- SRIIC Lab, Sri Ramachandra Institute for Higher Education & Research, Chennai, Tamil Nadu, 600116, India
| | - Chaitanya S Somala
- B-Aatral Biosciences Private Limited, Bangalore, Karnataka, 560091, India
| | - Raja Bs Kushwah
- B-Aatral Biosciences Private Limited, Bangalore, Karnataka, 560091, India
- Department of Entomology and Agrilife Research, Texas A&M University, College Station, TX 77843, USA
| | - Saravanan K Mani
- B-Aatral Biosciences Private Limited, Bangalore, Karnataka, 560091, India
- Department of Biotechnology, Bharath Institute of Higher Education and Research, Chennai, Tamil Nadu, 600073, India
| | - Vickram Sundaram
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical & Technical Sciences (SIMATS), Thandalam, Chennai, Tamil Nadu, 602105, India
| | - Anand Thirunavukarasou
- B-Aatral Biosciences Private Limited, Bangalore, Karnataka, 560091, India
- SRIIC Lab, Sri Ramachandra Institute for Higher Education & Research, Chennai, Tamil Nadu, 600116, India
| |
Collapse
|
8
|
Sha J, Fan J, Zhang R, Gu Y, Xu X, Ren S, Gu J. B-cell-specific ablation of β-1,4-galactosyltransferase 1 prevents aging-related IgG glycans changes and improves aging phenotype in mice. J Proteomics 2022; 268:104717. [PMID: 36084919 DOI: 10.1016/j.jprot.2022.104717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/16/2022] [Accepted: 08/25/2022] [Indexed: 10/14/2022]
Abstract
IgG N-glycans levels change with advancing age, making it a potential biomarker of aging. β-1,4-galactosyltransferase (B4GALT) gene expression levels also increase with aging. Ultra performance liquid chromatography (UPLC) was used to examine changes inserum IgG N-glycans at six time points during the aging process. Most serum IgG N-glycans changed with aging in WT but not in CD19-cre B4GALT1 floxed mice. The relative abundance of fucosylated biantennary glycans with or without Neu5Gc structures changed with aging in heterozygous B4GALT1 floxed mice but not in homozygous B4GALT1 floxed mice. Additionally, the aging phenotype was more apparent in WT mice than in B4GALT1 floxed mice. These results demonstrate that fucosylated biantennary glycans and fucosylated biantennary glycans containing N-glycolylneuraminic acid (Neu5Gc)-linked N-acetyllactosamine (LacNAc) were highly associated with aging and were affected by the B4GALT1 floxed mouse genotype. The changing levels of fucosylated monoantennary glycans observed with aging in WT mice was reversed in B4GALT1 floxed mice and was not sex specific. In summary, B-cell-specific ablation of B4GALT1 from a glycoproteomic perspective prevented age-related changes in IgG N-glycans in mice. SIGNIFICANCE: In this study, serum IgG glycoproteomic data in wild-type (WT) and B-cell-specific ablation of β-1,4-galactosyltransferase 1 mice (B4GALT) were analyzed. Results showed that fucosylated biantennary glycans with or without N-glycolylneuraminic acid (Neu5Gc)-linked N-acetyllactosamine (LacNAc) were highly associated with aging and were also affected by the B4GALT1 floxed mouse genotype. In terms of gender-specific information, the trend towards elevated fucosylated monoantennary glycans in WT mice was not seen in CD19-cre B4GALT1 floxed mice in either sex. B-cell-specific ablation of B4GALT1 plays an important role in age-related glycan changes; its specific functions and mechanisms are worthy of in-depth study. Our data suggest that investigating the relationship between galactosylation and aging may help advance the field of glycoproteomics and aging research.
Collapse
Affiliation(s)
- Jichen Sha
- NHC Key Laboratory of Glycoconjugates Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, 130 Dongan Road, Shanghai 200032, China
| | - Jiteng Fan
- NHC Key Laboratory of Glycoconjugates Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, 130 Dongan Road, Shanghai 200032, China
| | - Rongrong Zhang
- NHC Key Laboratory of Glycoconjugates Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, 130 Dongan Road, Shanghai 200032, China
| | - Yong Gu
- NHC Key Laboratory of Glycoconjugates Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, 130 Dongan Road, Shanghai 200032, China
| | - Xiaoyan Xu
- NHC Key Laboratory of Glycoconjugates Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, 130 Dongan Road, Shanghai 200032, China
| | - Shifang Ren
- NHC Key Laboratory of Glycoconjugates Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, 130 Dongan Road, Shanghai 200032, China.
| | - Jianxin Gu
- NHC Key Laboratory of Glycoconjugates Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, 130 Dongan Road, Shanghai 200032, China.
| |
Collapse
|
9
|
McCabe EM, Lee S, Rasmussen TP. Belzutifan (Welireg™) for von Hippel Lindau disease. Trends Pharmacol Sci 2022; 43:882-883. [PMID: 35691787 DOI: 10.1016/j.tips.2022.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/11/2022] [Accepted: 05/17/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Evan M McCabe
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - SooWan Lee
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Theodore P Rasmussen
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, USA.
| |
Collapse
|
10
|
Unal U, Cecener G, Tezcan Unlu H, Aytac Vuruskan B, Efendi Erdem E, Egeli U, Ozturk Nazlioglu H, Kaygisiz O, Tunca B, Vuruskan H. Investigation of VHL gene associated with miR-223 in clear cell renal cell carcinoma. Mol Biol Rep 2021; 49:2073-2083. [PMID: 34851479 DOI: 10.1007/s11033-021-07025-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/26/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND Clear cell type renal cell carcinoma (ccRCC) is the most common renal cell carcinoma (RCC). In this study, we examined the expressions of VHL and miR-223 in ccRCC patients׳ tissues to investigate the possible role in the development of ccRCC. METHODS AND RESULTS This study collected five expression profiles (GSE36139, GSE3, GSE73731, GSE40435, and GSE26032) from Gene Omnibus Data. Expressions of VHL and miR-223 in paraffinized tumor and normal tissues of 100 Turkish patients' ccRCC tissues were determined by bioinformatic data mining and real-time quantitative polymerase chain reaction (qRT-PCR). The VHL gene was subjected to mutational analysis by DNA sequencing, and pVHL was analyzed using western blotting. Our study's t-test and Pearson correlation analysis showed that VHL gene expression in tumoral tissues with a - 0.39-fold decrease was not significantly lower than normal tissues (p = 0.441), and a 0.97-fold increase miR-223 (p = 0.045) was determined by real-time PCR. Also, as a result of DNA sequence analysis performed in the VHL gene, it was found that 26% of the patients have mutations. The mutations for (VHL):c.60C>A (p.Val20=) and (VHL):c.467delA (p.Tyr156Leu) was detected for the first time in Turkish patients. CONCLUSIONS The present study demonstrated that the differences in the expression levels of miR-223 have the potential to be biomarkers to determine the poor prognosis in ccRCC.
Collapse
Affiliation(s)
- Ufuk Unal
- Department of Medical Biology, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey
| | - Gulsah Cecener
- Department of Medical Biology, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey.
| | - Havva Tezcan Unlu
- Department of Medical Biology, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey
| | - Berna Aytac Vuruskan
- Department of Medical Pathology, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey
| | - Ecem Efendi Erdem
- Department of Medical Biology, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey
| | - Unal Egeli
- Department of Medical Biology, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey
| | - Hulya Ozturk Nazlioglu
- Department of Medical Pathology, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey
| | - Onur Kaygisiz
- Department of Urology, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey
| | - Berrin Tunca
- Department of Medical Biology, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey
| | - Hakan Vuruskan
- Department of Urology, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey
| |
Collapse
|