1
|
Liu X, Zhang HY, Deng HA. Transcriptome and single-cell transcriptomics reveal prognostic value and potential mechanism of anoikis in skin cutaneous melanoma. Discov Oncol 2024; 15:70. [PMID: 38460046 PMCID: PMC10924820 DOI: 10.1007/s12672-024-00926-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/05/2024] [Indexed: 03/11/2024] Open
Abstract
BACKGROUND Skin cutaneous melanoma (SKCM) is a highly lethal cancer, ranking among the top four deadliest cancers. This underscores the urgent need for novel biomarkers for SKCM diagnosis and prognosis. Anoikis plays a vital role in cancer growth and metastasis, and this study aims to investigate its prognostic value and mechanism of action in SKCM. METHODS Utilizing consensus clustering, the SKCM samples were categorized into two distinct clusters A and B based on anoikis-related genes (ANRGs), with the B group exhibiting lower disease-specific survival (DSS). Gene set enrichment between distinct clusters was examined using Gene Set Variation Analysis (GSVA) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. RESULTS We created a predictive model based on three anoikis-related differently expressed genes (DEGs), specifically, FASLG, IGF1, and PIK3R2. Moreover, the mechanism of these prognostic genes within the model was investigated at the cellular level using the single-cell sequencing dataset GSE115978. This analysis revealed that the FASLG gene was highly expressed on cluster 1 of Exhausted CD8( +) T (Tex) cells. CONCLUSIONS In conclusion, we have established a novel classification system for SKCM based on anoikis, which carries substantial clinical implications for SKCM patients. Notably, the elevated expression of the FASLG gene on cluster 1 of Tex cells could significantly impact SKCM prognosis through anoikis, thus offering a promising target for the development of immunotherapy for SKCM.
Collapse
Affiliation(s)
- Xing Liu
- Medical Center of Burn Plastic and Wound Repair, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Hong-Yan Zhang
- Medical Center of Burn Plastic and Wound Repair, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China.
| | - Hong-Ao Deng
- Medical Center of Burn Plastic and Wound Repair, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China.
| |
Collapse
|
2
|
Yin J, Chen Z, You N, Li F, Zhang H, Xue J, Ma H, Zhao Q, Yu L, Zeng S, Zhu F. VARIDT 3.0: the phenotypic and regulatory variability of drug transporter. Nucleic Acids Res 2024; 52:D1490-D1502. [PMID: 37819041 PMCID: PMC10767864 DOI: 10.1093/nar/gkad818] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/01/2023] [Accepted: 09/27/2023] [Indexed: 10/13/2023] Open
Abstract
The phenotypic and regulatory variability of drug transporter (DT) are vital for the understanding of drug responses, drug-drug interactions, multidrug resistances, and so on. The ADME property of a drug is collectively determined by multiple types of variability, such as: microbiota influence (MBI), transcriptional regulation (TSR), epigenetics regulation (EGR), exogenous modulation (EGM) and post-translational modification (PTM). However, no database has yet been available to comprehensively describe these valuable variabilities of DTs. In this study, a major update of VARIDT was therefore conducted, which gave 2072 MBIs, 10 610 TSRs, 46 748 EGRs, 12 209 EGMs and 10 255 PTMs. These variability data were closely related to the transportation of 585 approved and 301 clinical trial drugs for treating 572 diseases. Moreover, the majority of the DTs in this database were found with multiple variabilities, which allowed a collective consideration in determining the ADME properties of a drug. All in all, VARIDT 3.0 is expected to be a popular data repository that could become an essential complement to existing pharmaceutical databases, and is freely accessible without any login requirement at: https://idrblab.org/varidt/.
Collapse
Affiliation(s)
- Jiayi Yin
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Zhen Chen
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
| | - Nanxin You
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
| | - Fengcheng Li
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
- The Children's Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310052, China
| | - Hanyu Zhang
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
| | - Jia Xue
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
| | - Hui Ma
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
| | - Qingwei Zhao
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
| | - Lushan Yu
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
| | - Su Zeng
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| |
Collapse
|
3
|
Shigeta K, Hasegawa M, Hishiki T, Naito Y, Baba Y, Mikami S, Matsumoto K, Mizuno R, Miyajima A, Kikuchi E, Saya H, Kosaka T, Oya M. IDH2 stabilizes HIF-1α-induced metabolic reprogramming and promotes chemoresistance in urothelial cancer. EMBO J 2023; 42:e110620. [PMID: 36637036 PMCID: PMC9929641 DOI: 10.15252/embj.2022110620] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 11/26/2022] [Accepted: 11/29/2022] [Indexed: 01/14/2023] Open
Abstract
Drug resistance contributes to poor therapeutic response in urothelial carcinoma (UC). Metabolomic analysis suggested metabolic reprogramming in gemcitabine-resistant urothelial carcinoma cells, whereby increased aerobic glycolysis and metabolic stimulation of the pentose phosphate pathway (PPP) promoted pyrimidine biosynthesis to increase the production of the gemcitabine competitor deoxycytidine triphosphate (dCTP) that diminishes its therapeutic effect. Furthermore, we observed that gain-of-function of isocitrate dehydrogenase 2 (IDH2) induced reductive glutamine metabolism to stabilize Hif-1α expression and consequently stimulate aerobic glycolysis and PPP bypass in gemcitabine-resistant UC cells. Interestingly, IDH2-mediated metabolic reprogramming also caused cross resistance to CDDP, by elevating the antioxidant defense via increased NADPH and glutathione production. Downregulation or pharmacological suppression of IDH2 restored chemosensitivity. Since the expression of key metabolic enzymes, such as TIGAR, TKT, and CTPS1, were affected by IDH2-mediated metabolic reprogramming and related to poor prognosis in patients, IDH2 might become a new therapeutic target for restoring chemosensitivity in chemo-resistant urothelial carcinoma.
Collapse
Affiliation(s)
- Keisuke Shigeta
- Department of UrologyKeio University School of MedicineTokyoJapan
| | | | - Takako Hishiki
- Department of Clinical and Translational Research centerKeio University School of MedicineTokyoJapan
- Department of BiochemistryKeio University School of MedicineTokyoJapan
| | - Yoshiko Naito
- Department of Clinical and Translational Research centerKeio University School of MedicineTokyoJapan
| | - Yuto Baba
- Department of UrologyKeio University School of MedicineTokyoJapan
| | - Shuji Mikami
- Division of PathologyKeio University School of MedicineTokyoJapan
| | | | - Ryuichi Mizuno
- Department of UrologyKeio University School of MedicineTokyoJapan
| | - Akira Miyajima
- Department of UrologyTokai University School of MedicineTokyoJapan
| | - Eiji Kikuchi
- Department of UrologyKeio University School of MedicineTokyoJapan
- Department of UrologySt. Marianna University School of MedicineKanagawaJapan
| | - Hideyuki Saya
- Department of Clinical and Translational Research centerKeio University School of MedicineTokyoJapan
- Division of Gene RegulationInstitute for Advanced Medical Research, Keio University School of MedicineTokyoJapan
| | - Takeo Kosaka
- Department of UrologyKeio University School of MedicineTokyoJapan
| | - Mototsugu Oya
- Department of UrologyKeio University School of MedicineTokyoJapan
| |
Collapse
|
4
|
Sustained activation of non-canonical NF-κB signalling drives glycolytic reprogramming in doxorubicin-resistant DLBCL. Leukemia 2023; 37:441-452. [PMID: 36446947 DOI: 10.1038/s41375-022-01769-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/11/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022]
Abstract
DLBCL is the most common lymphoma with high tumor heterogeneity. Treatment refractoriness and relapse from R-CHOP therapy in patients remain a clinical problem. Activation of the non-canonical NF-κB pathway is associated with R-CHOP resistance. However, downstream targets of non-canonical NF-κB mediating R-CHOP-induced resistance remains uncharacterized. Here, we identify the common mechanisms underlying both intrinsic and acquired resistance that are induced by doxorubicin, the main cytotoxic component of R-CHOP. We performed global transcriptomic analysis of (1) a panel of resistant versus sensitive and (2) isogenic acquired doxorubicin-resistant DLBCL cell lines following short and chronic exposure to doxorubicin respectively. Doxorubicin-induced stress in resistant cells activates a distinct transcriptional signature that is enriched in metabolic reprogramming and oncogenic signalling. Selective and sustained activation of non-canonical NF-κB signalling in these resistant cells exacerbated their survival by augmenting glycolysis. In response to doxorubicin, p52-RelB complexes transcriptionally activated multiple glycolytic regulators with prognostic significance through increased recruitment at their gene promoters. Targeting p52-RelB and their targets in resistant cells increased doxorubicin sensitivity in vitro and in vivo. Collectively, our study uncovered novel molecular drivers of doxorubicin-induced resistance that are regulated by non-canonical NF-κB pathway. We reveal new avenues of therapeutic targeting for R-CHOP-treated refractory/relapsed DLBCL patients.
Collapse
|