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Zheng XJ, Chen Y, Yao L, Li XL, Sun D, Li YQ. Identification of new hub- ferroptosis-related genes in Lupus Nephritis. Autoimmunity 2024; 57:2319204. [PMID: 38409788 DOI: 10.1080/08916934.2024.2319204] [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: 10/26/2023] [Accepted: 02/11/2024] [Indexed: 02/28/2024]
Abstract
Background: Lupus Nephritis (LN) is the primary causation of kidney injury in systemic lupus erythematosus (SLE). Ferroptosis is a programmed cell death. Therefore, understanding the crosstalk between LN and ferroptosis is still a significant challenge. Methods: We obtained the expression profile of LN kidney biopsy samples from the Gene Expression Omnibus database and utilised the R-project software to identify differentially expressed genes (DEGs). Then, we conducted a functional correlation analysis. Ferroptosis-related genes (FRGs) and differentially expressed genes (DEGs) crossover to select FRGs with LN. Afterwards, we used CIBERSORT to assess the infiltration of immune cells in both LN tissues and healthy control samples. Finally, we performed immunohistochemistry on LN human renal tissue. Results: 10619 DEGs screened from the LN biopsy tissue were identified. 22 hub-ferroptosis-related genes with LN (FRGs-LN) were screened out. The CIBERSORT findings revealed that there were significant statistical differences in immune cells between healthy control samples and LN tissues. Immunohistochemistry further demonstrated a significant difference in HRAS, TFRC, ATM, and SRC expression in renal tissue between normal and control groups. Conclusion: We developed a signature that allowed us to identify 22 new biomarkers associated with FRGs-LN. These findings suggest new insights into the pathology and therapeutic potential of LN ferroptosis inhibitors and iron chelators.
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Affiliation(s)
- Xiao-Jie Zheng
- Department of Nephrology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Ying Chen
- Department of Nephrology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Li Yao
- Department of Nephrology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xiao-Li Li
- Department of Nephrology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Da Sun
- Department of Nephrology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Yan-Qiu Li
- Department of Nephrology, The First Affiliated Hospital of China Medical University, Shenyang, China
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Liu M, Hu M, Liu R, Wang L, Wang J, Wang Y, Zhang R, Wang H, Liu M, Zhang Y, Wang L, Pei W, Zhang Y. Unveiling the role of APOM gene in liver cancer: Investigating the impact of hsa-miR-4489/MUC1-mediated ferroptosis on the advancement of hepatocellular carcinoma cells. Gene 2024; 925:148591. [PMID: 38788818 DOI: 10.1016/j.gene.2024.148591] [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: 02/02/2024] [Revised: 05/10/2024] [Accepted: 05/17/2024] [Indexed: 05/26/2024]
Abstract
Primary liver cancer has consistently exhibited a high prevalence and fatality rate, necessitating the investigation of associated diagnostic markers and inhibition mechanisms to effectively mitigate its impact. The significance of apolipoprotein M (ApoM) in impeding the progression of neoplastic ailments is progressively gaining recognition. However, a comprehensive understanding of its underlying mechanism in liver cancer advancement remains to be elucidated. Recent evidence indicates a potential association between ApoM and polyunsaturated fatty acids (PUFAs), with the peroxidation of phospholipids (PLs) containing PUFAs being recognized as a crucial element in the occurrence of ferroptosis. This prompts us to investigate the impact of the APOM gene on the progression of liver cancer through the ferroptosis pathway and elucidate its underlying mechanisms. The findings of this study indicate that the liver cancer cell model, which was genetically modified to overexpress the APOM gene, demonstrated a heightened ferroptosis effect. Moreover, the observed inhibition of the GSH (Glutathione) - GPX4 (Glutathione Peroxidase 4) regulatory axis suggests that the role of this axis in inhibiting ferroptosis is weakened. Through intersection screening and validation, we found that Mucin 1,cell surface associated (MUC1) can inhibit ferroptosis and is regulated by the APOM gene. Bioinformatics analysis and screening identified miR-4489 as a mediator between the two. Experimental results using the dual luciferase reporter gene confirmed that has-miR-4489 targets MUC1's 3'-UTR and inhibits its expression. In conclusion, this study provides evidence that the APOM gene induces a down-regulation in the expression of the ferroptosis-inhibiting gene MUC1, mediated by miR-4489, thereby impeding the advancement of liver cancer cells through the facilitation of ferroptosis.
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Affiliation(s)
- Miaomiao Liu
- Anhui Province Key Laboratory of Biological Macro-molecules Research, Wannan Medical College, Wuhu 241002, PR China; Department of Biochemistry and Molecular Biology, Wannan Medical College, Wuhu 241002, PR China
| | - Mengyu Hu
- Anhui Province Key Laboratory of Biological Macro-molecules Research, Wannan Medical College, Wuhu 241002, PR China
| | - Rong Liu
- Anhui Province Key Laboratory of Biological Macro-molecules Research, Wannan Medical College, Wuhu 241002, PR China
| | - Ling Wang
- Anhui Province Key Laboratory of Biological Macro-molecules Research, Wannan Medical College, Wuhu 241002, PR China
| | - Jingtong Wang
- Anhui Province Key Laboratory of Biological Macro-molecules Research, Wannan Medical College, Wuhu 241002, PR China
| | - Yun Wang
- Anhui Province Key Laboratory of Biological Macro-molecules Research, Wannan Medical College, Wuhu 241002, PR China
| | - Ruixi Zhang
- Anhui Province Key Laboratory of Biological Macro-molecules Research, Wannan Medical College, Wuhu 241002, PR China; Department of Biochemistry and Molecular Biology, Wannan Medical College, Wuhu 241002, PR China
| | - Hui Wang
- Anhui Province Key Laboratory of Biological Macro-molecules Research, Wannan Medical College, Wuhu 241002, PR China
| | - Mengru Liu
- Anhui Province Key Laboratory of Biological Macro-molecules Research, Wannan Medical College, Wuhu 241002, PR China
| | - Yi Zhang
- Anhui Province Key Laboratory of Biological Macro-molecules Research, Wannan Medical College, Wuhu 241002, PR China
| | - Lizhuo Wang
- Anhui Province Key Laboratory of Biological Macro-molecules Research, Wannan Medical College, Wuhu 241002, PR China; Department of Biochemistry and Molecular Biology, Wannan Medical College, Wuhu 241002, PR China
| | - Wenjun Pei
- Anhui Province Key Laboratory of Biological Macro-molecules Research, Wannan Medical College, Wuhu 241002, PR China; Department of Biochemistry and Molecular Biology, Wannan Medical College, Wuhu 241002, PR China.
| | - Yao Zhang
- Anhui Province Key Laboratory of Biological Macro-molecules Research, Wannan Medical College, Wuhu 241002, PR China; Department of Biochemistry and Molecular Biology, Wannan Medical College, Wuhu 241002, PR China.
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Song Y, Song Q, Tan F, Wang Y, Li C, Liao S, Yu K, Mei Z, Lv L. Seliciclib alleviates ulcerative colitis by inhibiting ferroptosis and improving intestinal inflammation. Life Sci 2024; 351:122794. [PMID: 38866218 DOI: 10.1016/j.lfs.2024.122794] [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: 02/04/2024] [Revised: 05/28/2024] [Accepted: 06/04/2024] [Indexed: 06/14/2024]
Abstract
BACKGROUND Ulcerative colitis (UC) is a chronic, recurrent, non-specific inflammatory disease, and the pathogenesis of the disease remains unclear. Ferroptosis is a form of programmed cell death characterized by the accumulation of iron-dependent lipid peroxides, which are simultaneously closely related to reactive oxygen species (ROS). Although seliciclib is highly effective against immune inflammation, its mechanism on colitis is unclear. This study demonstrated that seliciclib administration partially inhibited ferroptosis, alleviating symptoms and inflammation in experimental colitis. METHODS The mouse UC model was induced by 3.0 % dextran sodium sulfate (DSS) for 7 days and treated with seliciclib (10 mg/kg) for 5 days. In the in vitro model, LPS (100 μg/mL) was used for induction and seliciclib (10 μM) was applied for 2 h. Meanwhile, appropriate histopathology, inflammatory response, oxidative stress, and ferroptosis regulators were measured. RESULTS This study primarily investigated the role of seliciclib in regulating ferroptosis in UC. Bioinformatics analysis indicated that Dual oxidase 2 (DUOX2) may serve a role involved in the ferroptosis of UC. The experimental findings demonstrated that seliciclib alleviates symptoms and inflammation in DSS-induced UC mice and partially mitigates the occurrence of ferroptosis both in vivo and in vitro, possibly through the modulation of DUOX2. CONCLUSIONS Ferroptosis is strongly associated with the development of colitis, and seliciclib plays an essential role in ferroptosis and inflammation in UC. The suppression of ferroptosis in the intestinal epithelium could be a therapeutic approach for UC.
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Affiliation(s)
- Ya Song
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, 74 Linjiang Road, Yuzhong, 400010 Chongqing, China.
| | - Qian Song
- The Second College of Clinical Medicine, Chongqing Medical University, 1 Yixue Road, Yuzhong, 400016 Chongqing, China.
| | - Fangyan Tan
- Department of Nephrology, The Second Affiliated Hospital of Chongqing Medical University, 74 Linjiang Road, Yuzhong, 400010 Chongqing, China.
| | - Yanhui Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, 74 Linjiang Road, Yuzhong, 400010 Chongqing, China
| | - Chuanfei Li
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, 74 Linjiang Road, Yuzhong, 400010 Chongqing, China
| | - Shengtao Liao
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, 74 Linjiang Road, Yuzhong, 400010 Chongqing, China.
| | - Keqi Yu
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, 74 Linjiang Road, Yuzhong, 400010 Chongqing, China
| | - Zhechuan Mei
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, 74 Linjiang Road, Yuzhong, 400010 Chongqing, China.
| | - Lin Lv
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, 74 Linjiang Road, Yuzhong, 400010 Chongqing, China.
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Yang G, Yang Y, Song Z, Chen L, Liu F, Li Y, Jiang S, Xue S, Pei J, Wu Y, He Y, Chu B, Wu H. Spliceosomal GTPase Eftud2 deficiency-triggered ferroptosis leads to Purkinje cell degeneration. Neuron 2024:S0896-6273(24)00542-7. [PMID: 39153477 DOI: 10.1016/j.neuron.2024.07.020] [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: 03/21/2023] [Revised: 03/20/2024] [Accepted: 07/23/2024] [Indexed: 08/19/2024]
Abstract
Spliceosomal GTPase elongation factor Tu GTP binding domain containing 2 (EFTUD2) is a causative gene for mandibulofacial dysostosis with microcephaly (MFDM) syndrome comprising cerebellar hypoplasia and motor dysfunction. How EFTUD2 deficiency contributes to these symptoms remains elusive. Here, we demonstrate that specific ablation of Eftud2 in cerebellar Purkinje cells (PCs) in mice results in severe ferroptosis, PC degeneration, dyskinesia, and cerebellar atrophy, which recapitulates phenotypes observed in patients with MFDM. Mechanistically, Eftud2 promotes Scd1 and Gch1 expression, upregulates monounsaturated fatty acid phospholipids, and enhances antioxidant activity, thereby suppressing PC ferroptosis. Importantly, we identified transcription factor Atf4 as a downstream target to regulate anti-ferroptosis effects in PCs in a p53-independent manner. Inhibiting ferroptosis efficiently rescued cerebellar deficits in Eftud2 cKO mice. Our data reveal an important role of Eftud2 in maintaining PC survival, showing that pharmacologically or genetically inhibiting ferroptosis may be a promising therapeutic strategy for EFTUD2 deficiency-induced disorders.
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Affiliation(s)
- Guochao Yang
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, 100850 Beijing, China; Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, 226019 Nantong, China
| | - Yinghong Yang
- Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, 250100 Jinan, China
| | - Zhihong Song
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, 100850 Beijing, China
| | - Liping Chen
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, 100850 Beijing, China
| | - Fengjiao Liu
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, 100850 Beijing, China
| | - Ying Li
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, 100850 Beijing, China
| | - Shaofei Jiang
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, 100850 Beijing, China
| | - Saisai Xue
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, 100850 Beijing, China
| | - Jie Pei
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, 100850 Beijing, China
| | - Yan Wu
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, 100850 Beijing, China
| | - Yuanlin He
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, 211166 Nanjing, China
| | - Bo Chu
- Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, 250100 Jinan, China.
| | - Haitao Wu
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, 100850 Beijing, China; Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, 226019 Nantong, China; Chinese Institute for Brain Research, 102206 Beijing, China.
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Han H, Zhang G, Zhang X, Zhao Q. Nrf2-mediated ferroptosis inhibition: a novel approach for managing inflammatory diseases. Inflammopharmacology 2024:10.1007/s10787-024-01519-7. [PMID: 39126567 DOI: 10.1007/s10787-024-01519-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Accepted: 06/28/2024] [Indexed: 08/12/2024]
Abstract
Inflammatory diseases, including psoriasis, atherosclerosis, rheumatoid arthritis, and ulcerative colitis, are characterized by persistent inflammation. Moreover, the existing treatments for inflammatory diseases only provide temporary relief by controlling symptoms, and treatments of unstable and expensive. Therefore, new therapeutic solutions are urgently needed to address the underlying causes or symptoms of inflammatory diseases. Inflammation frequently coincides with a high level of (reactive oxygen species) ROS activation, serving as a fundamental element in numerous physiological and pathological phenotypes that can result in serious harm to the organism. Given its pivotal role in inflammation, oxidative stress, and ferroptosis, ROS represents a focal node for investigating the (nuclear factor E2-related factor 2) Nrf2 pathway and ferroptosis, both of which are intricately linked to ROS. Ferroptosis is mainly triggered by oxidative stress and involves iron-dependent lipid peroxidation. The transcription factor Nrf2 targets several genes within the ferroptosis pathway. Recent studies have shown that Nrf2 plays a significant role in three key ferroptosis-related routes, including the synthesis and metabolism of glutathione/glutathione peroxidase 4, iron metabolism, and lipid processes. As a result, ferroptosis-related treatments for inflammatory diseases have attracted much attention. Moreover, drugs targeting Nrf2 can be used to manage inflammatory conditions. This review aimed to assess ferroptosis regulation mechanism and the role of Nrf2 in ferroptosis inhibition. Therefore, this review article may provide the basis for more research regarding the treatment of inflammatory diseases through Nrf2-inhibited ferroptosis.
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Affiliation(s)
- Hang Han
- College of Pharmacy, Chongqing Medical University, Chongqing, Chongqing, 400016, China
| | - Guojiang Zhang
- College of Pharmacy, Chongqing Medical University, Chongqing, Chongqing, 400016, China
| | - Xiao Zhang
- College of Pharmacy, Chongqing Medical University, Chongqing, Chongqing, 400016, China.
| | - Qinjian Zhao
- College of Pharmacy, Chongqing Medical University, Chongqing, Chongqing, 400016, China.
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Hou CY, Suo YH, Lv P, Yuan HF, Zhao LN, Wang YF, Zhang HH, Sun J, Sun LL, Lu W, Zhang NN, Yang G, Zhang XD. Aristolochic acids-hijacked p53 promotes liver cancer cell growth by inhibiting ferroptosis. Acta Pharmacol Sin 2024:10.1038/s41401-024-01354-0. [PMID: 39090392 DOI: 10.1038/s41401-024-01354-0] [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: 03/11/2024] [Accepted: 07/02/2024] [Indexed: 08/04/2024] Open
Abstract
Aristolochic acids (AAs) have been identified as a significant risk factor for hepatocellular carcinoma (HCC). Ferroptosis is a type of regulated cell death involved in the tumor development. In this study, we investigated the molecular mechanisms by which AAs enhanced the growth of HCC. By conducting bioinformatics and RNA-Seq analyses, we found that AAs were closely correlated with ferroptosis. The physical interaction between p53 and AAs in HepG2 cells was validated by bioinformatics analysis and SPR assays with the binding pocket sites containing Pro92, Arg174, Asp207, Phe212, and His214 of p53. Based on the binding pocket that interacts with AAs, we designed a mutant and performed RNA-Seq profiling. Interestingly, we found that the binding pocket was responsible for ferroptosis, GADD45A, NRF2, and SLC7A11. Functionally, the interaction disturbed the binding of p53 to the promoter of GADD45A or NRF2, attenuating the role of p53 in enhancing GADD45A and suppressing NRF2; the mutant did not exhibit the same effects. Consequently, this event down-regulated GADD45A and up-regulated NRF2, ultimately inhibiting ferroptosis, suggesting that AAs hijacked p53 to down-regulate GADD45A and up-regulate NRF2 in HepG2 cells. Thus, AAs treatment resulted in the inhibition of ferroptosis via the p53/GADD45A/NRF2/SLC7A11 axis, which led to the enhancement of tumor growth. In conclusion, AAs-hijacked p53 restrains ferroptosis through the GADD45A/NRF2/SLC7A11 axis to enhance tumor growth. Our findings provide an underlying mechanism by which AAs enhance HCC and new insights into p53 in liver cancer. Therapeutically, the oncogene NRF2 is a promising target for liver cancer.
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Affiliation(s)
- Chun-Yu Hou
- National Key Laboratory of Draggability Evaluation and Systematic Translational Medicine, Tianjin's Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, Department of Gastrointestinal Cancer Biology, Tianjin Cancer Institute, Liver Cancer Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Yu-Hong Suo
- Department of Hepatobiliary Oncology, Liver Cancer Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
| | - Pan Lv
- National Key Laboratory of Draggability Evaluation and Systematic Translational Medicine, Tianjin's Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, Department of Gastrointestinal Cancer Biology, Tianjin Cancer Institute, Liver Cancer Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Hong-Feng Yuan
- National Key Laboratory of Draggability Evaluation and Systematic Translational Medicine, Tianjin's Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, Department of Gastrointestinal Cancer Biology, Tianjin Cancer Institute, Liver Cancer Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Li-Na Zhao
- National Key Laboratory of Draggability Evaluation and Systematic Translational Medicine, Tianjin's Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, Department of Gastrointestinal Cancer Biology, Tianjin Cancer Institute, Liver Cancer Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Yu-Fei Wang
- National Key Laboratory of Draggability Evaluation and Systematic Translational Medicine, Tianjin's Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, Department of Gastrointestinal Cancer Biology, Tianjin Cancer Institute, Liver Cancer Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Hui-Hui Zhang
- National Key Laboratory of Draggability Evaluation and Systematic Translational Medicine, Tianjin's Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, Department of Gastrointestinal Cancer Biology, Tianjin Cancer Institute, Liver Cancer Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Jiao Sun
- Department of Hepatobiliary Oncology, Liver Cancer Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
| | - Lin-Lin Sun
- Department of Hepatobiliary Oncology, Liver Cancer Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
| | - Wei Lu
- Department of Hepatobiliary Oncology, Liver Cancer Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
| | - Ning-Ning Zhang
- Department of Hepatobiliary Oncology, Liver Cancer Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China.
| | - Guang Yang
- National Key Laboratory of Draggability Evaluation and Systematic Translational Medicine, Tianjin's Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, Department of Gastrointestinal Cancer Biology, Tianjin Cancer Institute, Liver Cancer Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China.
| | - Xiao-Dong Zhang
- National Key Laboratory of Draggability Evaluation and Systematic Translational Medicine, Tianjin's Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, Department of Gastrointestinal Cancer Biology, Tianjin Cancer Institute, Liver Cancer Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China.
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Chen J, Yang X, Li Q, Ma J, Li H, Wang L, Chen Z, Quan Z. Inhibiting DNA methyltransferase DNMT3B confers protection against ferroptosis in nucleus pulposus and ameliorates intervertebral disc degeneration via upregulating SLC40A1. Free Radic Biol Med 2024; 220:139-153. [PMID: 38705495 DOI: 10.1016/j.freeradbiomed.2024.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/07/2024]
Abstract
Epigenetic changes are important considerations for degenerative diseases. DNA methylation regulates crucial genes by epigenetic mechanism, impacting cell function and fate. DNA presents hypermethylation in degenerated nucleus pulposus (NP) tissue, but its role in intervertebral disc degeneration (IVDD) remains elusive. This study aimed to demonstrate that methyltransferase mediated hypermethylation was responsible for IVDD by integrative bioinformatics and experimental verification. Methyltransferase DNMT3B was highly expressed in severely degenerated NP tissue (involving human and rats) and in-vitro degenerated human NP cells (NPCs). Bioinformatics elucidated that hypermethylated genes were enriched in oxidative stress and ferroptosis, and the ferroptosis suppressor gene SLC40A1 was identified with lower expression and higher methylation in severely degenerated human NP tissue. Cell culture using human NPCs showed that DNMT3B induced ferroptosis and oxidative stress in NPCs by downregulating SLC40A1, promoting a degenerative cell phenotype. An in-vivo rat IVDD model showed that DNA methyltransferase inhibitor 5-AZA alleviated puncture-induced IVDD. Taken together, DNA methyltransferase DNMT3B aggravates ferroptosis and oxidative stress in NPCs via regulating SLC40A1. Epigenetic mechanism within DNA methylation is a promising therapeutic biomarker for IVDD.
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Affiliation(s)
- Jiaxing Chen
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China; Orthopedic Laboratory of Chongqing Medical University, Chongqing, 400016, China
| | - Xinyu Yang
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China; Orthopedic Laboratory of Chongqing Medical University, Chongqing, 400016, China
| | - Qiaochu Li
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China; Orthopedic Laboratory of Chongqing Medical University, Chongqing, 400016, China
| | - Jingjin Ma
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China; Orthopedic Laboratory of Chongqing Medical University, Chongqing, 400016, China
| | - Huanhuan Li
- Department of Emergency, Chongqing University Three Gorges Hospital, Chongqing, 404000, China
| | - Linbang Wang
- Department of Orthopedics, Peking University Third Hospital, Beijing, 100191, China
| | - Zhiyu Chen
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China; Orthopedic Laboratory of Chongqing Medical University, Chongqing, 400016, China
| | - Zhengxue Quan
- Department of Orthopedics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China; Orthopedic Laboratory of Chongqing Medical University, Chongqing, 400016, China.
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8
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Lin X, Shao K, Lin Z, Liang Q, Li X, Chen H, Wu J. Identification of a ferroptosis-related gene signature for the prognosis of pediatric neuroblastoma. Transl Cancer Res 2024; 13:3678-3694. [PMID: 39145053 PMCID: PMC11319987 DOI: 10.21037/tcr-24-269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 05/24/2024] [Indexed: 08/16/2024]
Abstract
Background Ferroptosis-related genes are correlated with the prognosis of patients with neuroblastoma (NB) remains unknown. This study aims to establish a prognostic ferroptosis-related gene model for predicting prognostic value in pediatric NB patients. Methods The gene expression array and clinical characteristics of NB were downloaded from a public database. Correlations between ferroptosis-related genes and drug responses were analyzed by Childhood Cancer Therapeutics. The prognostic model was constructed by least absolute shrinkage and selection operator (LASSO) Cox regression and was validated in NB patients from the ICGC cohort. The survival analysis was performed by Cox regression analysis. single-sample gene set enrichment analysis (ssGSEA) was used to quantify the immune cell infiltration correlation. Results Overall, 70 genes were identified as ferroptosis-related differentially expressed genes (DEGs) from 247 samples. Then, 13 ferroptosis-related genes were correlated with OS in the univariate Cox regression analysis. Five prognostic ferroptosis-related DEGs (pFR-DEGs) (STEAP3, MAP1LC3A, ULK2, MTOR and TUBE1), which were defined as the intersection of DEGs and prognostic ferroptosis-related genes, were identified and utilized to construct the prognostic signature. The correlation between five pFR-DEGs and drug responses was analyzed, and the box plots indicated that MTOR gene expression was highest, suggesting that MTOR expression is related to progressive NB disease. The receiver operating characteristic (ROC) curve showed that the model had moderate predictive power. The survival analysis indicated that the high-risk group had poor overall survival (OS) (P=2.087×10-06). Univariate and multivariate analyses identified the risk score as a significant prognostic risk factor [P=0.003, hazard ratio (HR) =1.933]. Immune cell infiltration correlation analysis showed that the high-risk group was related to more immune cells. Conclusions The present study indicated a difference in ferroptosis-related gene expression between low- and high-risk NB patients. The ferroptosis-related signature could serve as a prognostic prediction tool. Additionally, immune infiltration might play an important role in different risk groups for NB patients.
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Affiliation(s)
- Xijin Lin
- Department of Radiation Oncology, Fujian Children’s Hospital (Fujian Branch of Shanghai Children’s Medical Center), College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
| | - Kongfeng Shao
- Department of Radiation Oncology, Fujian Children’s Hospital (Fujian Branch of Shanghai Children’s Medical Center), College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
| | - Zhuangbin Lin
- Department of Radiation Oncology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Qiandong Liang
- Department of Radiation Oncology, Fujian Children’s Hospital (Fujian Branch of Shanghai Children’s Medical Center), College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
| | - Xiaoyan Li
- Department of Radiation Oncology, Fujian Children’s Hospital (Fujian Branch of Shanghai Children’s Medical Center), College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
| | - Haiyan Chen
- Department of Radiation Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Junxin Wu
- Department of Radiation Oncology, Fujian Children’s Hospital (Fujian Branch of Shanghai Children’s Medical Center), College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
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9
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Liu Q, Lin Z, Yue M, Wu J, Li L, Huang D, Fang Y, Zhang X, Hao T. Identification and validation of ferroptosis related markers in erythrocyte differentiation of umbilical cord blood-derived CD34 + cell by bioinformatic analysis. Front Genet 2024; 15:1365232. [PMID: 39139819 PMCID: PMC11319168 DOI: 10.3389/fgene.2024.1365232] [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: 01/04/2024] [Accepted: 07/09/2024] [Indexed: 08/15/2024] Open
Abstract
Ferroptosis has been observed to play an important role during erythrocyte differentiation (ED). However, the biological gene markers and ferroptosis mechanisms in ED remain unknown. We downloaded the datasets of ED in human umbilical cord blood-derived CD34+ cells from the Gene Expression Omnibus database. Using median differentiation time, the sample was categorized into long and short groups. The differentially expressed ferroptosis-related genes (DE-FRGs) were screened using differential expression analysis. The enrichment analyses and a protein-protein interaction (PPI) network were conducted. To predict the ED stage, a logistic regression model was constructed using the least absolute shrinkage and selection operator (LASSO). Overall, 22 DE-FRGs were identified. Ferroptosis-related pathways were enriched using Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes. Gene Set Enrichment Analysis and Gene Set Variation Analysis revealed the primary involvement of DE-FRGs in JAK-STAT, MAPK, PI3K-AKT-mTORC1, WNT, and NOTCH signaling pathways. Ten-hub DE-FRGs were obtained using PPI analysis. Furthermore, we constructed mRNA-microRNA (miRNA) and mRNA-transcription factor networks. Immune cell infiltration levels differed significantly during ED. LASSO regression analysis established a signature using six DE-FRGs (ATF3, CDH2, CHAC1, DDR2, DPP4, and GDF15) related to the ED stage. Bioinformatic analyses identified ferroptosis-associated genes during ED, which were further validated. Overall, we identified ferroptosis-related genes to predict their correlations in ED. Exploring the underlying mechanisms of ferroptosis may help us better understand pathophysiological changes in ED and provide new evidence for clinical transformation.
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Affiliation(s)
- Qian Liu
- Department of Cardiology, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Ze Lin
- Shantou University Medical College, Shantou, Guangdong, China
| | - Minghui Yue
- Shantou University Medical College, Shantou, Guangdong, China
| | - Jianbo Wu
- Department of Cardiology, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Lei Li
- Department of Cardiology, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Daqi Huang
- Department of Cardiology, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Yipeng Fang
- Department of Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Xin Zhang
- Shantou University Medical College, Shantou, Guangdong, China
- Laboratory of Molecular Cardiology, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Laboratory of Medical Molecular Imaging, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Tao Hao
- Department of Colorectal Surgery, Binzhou Medical University Hospital, Binzhou, Shandong, China
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10
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Wang H, Zhang M, Hu Y, He J, Zhong Y, Dai Y, Wang Q. Deciphering the role of ferroptosis in rheumatoid arthritis: Synovial transcriptome analysis and immune infiltration correlation. Heliyon 2024; 10:e33648. [PMID: 39091931 PMCID: PMC11292532 DOI: 10.1016/j.heliyon.2024.e33648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 06/23/2024] [Accepted: 06/25/2024] [Indexed: 08/04/2024] Open
Abstract
The pathogenesis of rheumatoid arthritis (RA) remains elusive. The initiation of joint degeneration is characterized by the loss of self-tolerance in peripheral joints. Ferroptosis, a form of regulated cell death, holds significant importance in the pathophysiology of inflammatory arthritis, primarily due to iron accumulation and the subsequent lipid peroxidation. The present study investigated the association between synovial lesions and ferroptosis-related genes using previously published data from rheumatoid patients. Transcriptome differential gene analysis was employed to identify ferroptosis-related differentially expressed genes (FRDEGs). To validate FRDEGs and screen hub genes, we used weighted gene co-expression network analysis (WGCNA) and receiver operating characteristic (ROC) curves. Subsequently, immune infiltration analysis and single cell analysis were conducted to investigate the relationship between various synovial tissues cells and FRDEGs. The findings were further confirmed through reverse transcription-quantitative polymerase chain reaction (RT-qPCR), immunohistochemical staining, and immunofluorescence techniques. Upon intersecting DEGs with ferroptosis-related genes, we identified a total of 104 FRDEGs. Through the construction of a protein-protein interaction (PPI) network, we pinpointed the top 20 most highly concentrated genes as hub genes. Subsequent analyses using ROC curve and WGCNA validated eight FRDEGs: TIMP1, JUN, EGFR, SREBF1, ADIPOQ, SCD, AR, and FABP4. Immuno-infiltration analyses revealed significant infiltration of immune cell in RA synovial tissues and their correlations with the FRDEGs. Notably, TIMP1 demonstrated a positive correlation with various immune cell populations. Single-cell sequencing date of RA synovial tissue revealed predominant expression of TIMP1 is in fibroblasts. RT-qPCR, immunohistochemistry, and immunofluorescence analyses confirmed significant upregulation of TIMP1 at both mRNA and protein levels in RA synovial tissues and fibroblast-like synoviocytes (FLS). The findings provide novel insights into pathophysiology of peripheral immune tolerance deficiency in RA. The dysregulation of TIMP1, a gene associated with ferroptosis, was significantly observed in RA patients, suggesting its potential as a promising biomarker and therapeutic target.
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Affiliation(s)
- Hongli Wang
- Department of Rheumatism and Immunology, Peking University Shenzhen Hospital, Shenzhen, China
- The Key Laboratory of Inflammatory and Immunology Diseases, Shenzhen, China
| | - Miaomiao Zhang
- Department of Rheumatism and Immunology, Peking University Shenzhen Hospital, Shenzhen, China
- The Key Laboratory of Inflammatory and Immunology Diseases, Shenzhen, China
| | - Yiping Hu
- Department of Rheumatism and Immunology, Peking University Shenzhen Hospital, Shenzhen, China
- The Key Laboratory of Inflammatory and Immunology Diseases, Shenzhen, China
| | - Juan He
- Department of Rheumatism and Immunology, Peking University Shenzhen Hospital, Shenzhen, China
- The Key Laboratory of Inflammatory and Immunology Diseases, Shenzhen, China
| | - Yuchao Zhong
- Department of Rheumatism and Immunology, Peking University Shenzhen Hospital, Shenzhen, China
- The Key Laboratory of Inflammatory and Immunology Diseases, Shenzhen, China
| | - Yong Dai
- Department of Rheumatism and Immunology, Peking University Shenzhen Hospital, Shenzhen, China
- The Key Laboratory of Inflammatory and Immunology Diseases, Shenzhen, China
| | - Qingwen Wang
- Department of Rheumatism and Immunology, Peking University Shenzhen Hospital, Shenzhen, China
- The Key Laboratory of Inflammatory and Immunology Diseases, Shenzhen, China
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11
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Feng J, Zhang P, Chen K, Huang P, Liang X, Dong J, Zhu B, Fu Z, Deng T, Zhu L, Chen C, Zhang Y. Soot nanoparticles promote ferroptosis in dopaminergic neurons via alteration of m6A RNA methylation in Parkinson's disease. JOURNAL OF HAZARDOUS MATERIALS 2024; 473:134691. [PMID: 38788584 DOI: 10.1016/j.jhazmat.2024.134691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/06/2024] [Accepted: 05/20/2024] [Indexed: 05/26/2024]
Abstract
Soot nanoparticles (SNPs) are black carbon prevalent in atmospheric environment with significant impacts on public health, leading to neurodegenerative diseases including development of Parkinson's disease (PD). This study investigated the effects of SNPs exposure on PD symptoms, employing both in vivo and in vitro PD models. In the in vivo experiments, animal behavior assessments showed that SNPs exposure exacerbated motor and cognitive impairments in PD mice. Molecular biology techniques further unveiled that SNPs aggravated degeneration of dopaminergic neurons. In vitro experiments revealed that SNPs exposure intensified ferroptosis of PD cells by increasing reactive oxygen species and iron ion levels, while reducing glutathione levels and mitochondrial membrane potential. Sequencing tests indicated elevated N6-methyladenosine (m6A) alteration of the ferroptosis-related protein, acyl-CoA synthetase long chain family member 4 (ACSL4). This study demonstrates that SNPs may exacerbate the onset and progression of PD by recruiting YTH domain-containing family protein 1 (YTHDF1) protein, enhancing m6A methylation in the ACSL4 5'UTR, amplifying ACSL4 protein expression, and accelerating the ferroptosis process in dopaminergic neurons. These molecular mechanisms underlying SNPs exacerbation of PD development may provide crucial insights for formulating environmental safety regulations and potential therapeutic strategies addressing PD in populations residing in regions with varied air quality.
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Affiliation(s)
- Jiezhu Feng
- School of Medicine, South China University of Technology, Guangzhou 510006, China; Department of Neurology, Guangdong Neuroscience Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province 510080, China; Guangzhou Key Laboratory of Diagnosis and Treatment for Neurodegenerative Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Guangzhou 510080, China
| | - Piao Zhang
- Department of Neurology, Guangdong Neuroscience Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province 510080, China; Guangzhou Key Laboratory of Diagnosis and Treatment for Neurodegenerative Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Guangzhou 510080, China
| | - Kunlin Chen
- College of Natural Resources and Environment, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Peiting Huang
- Department of Neurology, Guangdong Neuroscience Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province 510080, China; Guangzhou Key Laboratory of Diagnosis and Treatment for Neurodegenerative Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Guangzhou 510080, China
| | - Xiaomei Liang
- Department of Neurology, Guangdong Neuroscience Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province 510080, China; Guangzhou Key Laboratory of Diagnosis and Treatment for Neurodegenerative Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Guangzhou 510080, China
| | - Jiawei Dong
- College of Natural Resources and Environment, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Baoyu Zhu
- Department of Neurology, Guangdong Neuroscience Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province 510080, China; Guangzhou Key Laboratory of Diagnosis and Treatment for Neurodegenerative Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Guangzhou 510080, China
| | - Zhongling Fu
- Department of Neurology, Guangdong Neuroscience Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province 510080, China; Guangzhou Key Laboratory of Diagnosis and Treatment for Neurodegenerative Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Guangzhou 510080, China
| | - Tongtong Deng
- School of Medicine, South China University of Technology, Guangzhou 510006, China; Department of Neurology, Guangdong Neuroscience Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province 510080, China; Guangzhou Key Laboratory of Diagnosis and Treatment for Neurodegenerative Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Guangzhou 510080, China
| | - Linyan Zhu
- Department of Pharmacology, Medical College, Jinan University, Guangzhou 510632, China.
| | - Chengyu Chen
- College of Natural Resources and Environment, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, South China Agricultural University, Guangzhou, Guangdong 510642, China.
| | - Yuhu Zhang
- School of Medicine, South China University of Technology, Guangzhou 510006, China; Department of Neurology, Guangdong Neuroscience Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province 510080, China; Guangzhou Key Laboratory of Diagnosis and Treatment for Neurodegenerative Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Guangzhou 510080, China.
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12
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Yang Y, Zhang T, Li Q, Ling Y, Ma Y, Tao S. SQSTM1 improves acute lung injury via inhibiting airway epithelium ferroptosis in a vitamin D receptor/autophagy-mediated manner. Free Radic Biol Med 2024; 222:588-600. [PMID: 38996820 DOI: 10.1016/j.freeradbiomed.2024.07.009] [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: 02/03/2024] [Revised: 07/06/2024] [Accepted: 07/08/2024] [Indexed: 07/14/2024]
Abstract
Emerging evidence has reported that acute lung injury (ALI), characterized by inflammation and oxidative stress in airway epithelium, is regulated by programmed cell death. Ferroptosis, a regulated form of cell death spurred by uncontrolled lipid peroxidation, has been proven to implicate various diseases. Inhibiting ferroptosis represents a feasible strategy for ALI through the suppression of lipid peroxidation, while the mechanism remains to be further elucidated. Here, we identified Sequestosome 1 (SQSTM1) as a negative regulator of airway epithelium ferroptosis during ALI. SQSTM1 knockdown cells manifested higher sensitivity to ferroptosis. Mechanistically, SQSTM1 was found to directly interact with vitamin D receptor (VDR) through its nuclear receptor (NR) box motif, facilitating its nuclear translocation and initiating autophagy at the transcriptional level. To further validate these findings, an in vivo preventive model utilizing spermidine, a proven inducer of SQSTM1 was established. The results consistently demonstrated that spermidine supplementation significantly induced SQSTM1 and ameliorated ALI by mitigating airway epithelial ferroptosis. Notably, these effects were abrogated in the absence of SQSTM1. Taken together, this study identified SQSTM1 as a negative regulator of airway epithelium ferroptosis in a VDR-mediated autophagy manner, making it a potential therapeutic target for the treatment of ALI.
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Affiliation(s)
- Youjing Yang
- Chongqing Emergency Medical Center, Chongqing University Central Hospital, School of Medicine, Chongqing University, Chongqing, China; Chongqing Key Laboratory of Emergency Medicine, Chongqing, China.
| | - Tao Zhang
- Chongqing Emergency Medical Center, Chongqing University Central Hospital, School of Medicine, Chongqing University, Chongqing, China; Chongqing Key Laboratory of Emergency Medicine, Chongqing, China
| | - Qianmin Li
- Chongqing Emergency Medical Center, Chongqing University Central Hospital, School of Medicine, Chongqing University, Chongqing, China
| | - Yi Ling
- School of Public Health, Medical College of Soochow University, Suzhou, China
| | - Yu Ma
- Chongqing Emergency Medical Center, Chongqing University Central Hospital, School of Medicine, Chongqing University, Chongqing, China; Chongqing Key Laboratory of Emergency Medicine, Chongqing, China
| | - Shasha Tao
- Chongqing Emergency Medical Center, Chongqing University Central Hospital, School of Medicine, Chongqing University, Chongqing, China; Chongqing Key Laboratory of Emergency Medicine, Chongqing, China.
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13
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Fu Y, Xu T, Guo M, Lv W, Ma N, Zhang L. Identification of disulfidptosis- and ferroptosis-related transcripts in periodontitis by bioinformatics analysis and experimental validation. Front Genet 2024; 15:1402663. [PMID: 39045324 PMCID: PMC11263038 DOI: 10.3389/fgene.2024.1402663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 06/18/2024] [Indexed: 07/25/2024] Open
Abstract
Background Disulfidptosis and ferroptosis are forms of programmed cell death that may be associated with the pathogenesis of periodontitis. Our study developed periodontitis-associated biomarkers combining disulfidptosis and ferroptosis, which provides a new perspective on the pathogenesis of periodontitis. Methods Firstly, we obtained the periodontitis dataset from public databases and found disulfidptosis- and ferroptosis-related differentially expressed transcripts based on the disulfidptosis and ferroptosis transcript sets. After that, transcripts that are tissue biomarkers for periodontitis were found using three machine learning methods. We also generated transcript subclusters from two periodontitis microarray datasets: GSE16134 and GSE23586. Furthermore, three transcripts with the best classification efficiency were further screened. Their expression and classification efficacy were validated using qRT-PCR. Finally, periodontal clinical indicators of 32 clinical patients were collected, and the correlation between three transcripts above and periodontal clinical indicators was analyzed. Results We identified six transcripts that are tissue biomarkers for periodontitis, the top three transcripts with the best classification, and delineated two expression patterns in periodontitis. Conclusions Our study found that disulfidptosis and ferroptosis were associated with immune responses and may involve periodontitis genesis.
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Affiliation(s)
| | | | | | | | - Ning Ma
- Hospital of Stomatology, Jilin University, Changchun, China
| | - Li Zhang
- Hospital of Stomatology, Jilin University, Changchun, China
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14
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Han L, He J, Xie H, Gong Y, Xie C. Pan-cell death-related signature reveals tumor immune microenvironment and optimizes personalized therapy alternations in lung adenocarcinoma. Sci Rep 2024; 14:15682. [PMID: 38977778 PMCID: PMC11231366 DOI: 10.1038/s41598-024-66662-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 07/03/2024] [Indexed: 07/10/2024] Open
Abstract
This study constructed a comprehensive analysis of cell death modules in eliminating aberrant cells and remodeling tumor microenvironment (TME). Consensus analysis was performed in 490 lung adenocarcinoma (LUAD) patients based on 4 types of cell death prognostic genes. Intersection method divided these LUAD samples into 5 cell death risk (CDR) clusters, and COX regression analysis were used to construct the CDR signature (CDRSig) with risk scores. Significant differences of TME phenotypes, clinical factors, genome variations, radiosensitivity and immunotherapy sensitivity were observed in different CDR clusters. Patients with higher risk scores in the CDRSig tended to be immune-excluded or immune-desert, and those with lower risk scores were more sensitive to radiotherapy and immunotherapy. The results from mouse model showed that intense expression of the high-risk gene PFKP was associated with low CD8+ T cell infiltration upon radiotherapy and anti-PD-L1 treatment. Deficient assays in vitro confirmed that PFKP downregulation enhanced cGAS/STING pathway activation and radiosensitivity in LUAD cells. In conclusion, our studies originally performed a comprehensive cell death analysis, suggesting the importance of CDR patterns in reprogramming TME and providing novel clues for LUAD personalized therapies.
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Affiliation(s)
- Linzhi Han
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, Hubei, China
| | - Jingyi He
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, Hubei, China
| | - Hongxin Xie
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, Hubei, China
| | - Yan Gong
- Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, Hubei, China.
- Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China.
| | - Conghua Xie
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, Hubei, China.
- Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China.
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15
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Lin Y, Xu J, Gu Q. FerroLigandDB: A Ferroptosis Ligand Database of Structure-Activity Relations. J Chem Inf Model 2024; 64:5052-5062. [PMID: 38885636 DOI: 10.1021/acs.jcim.4c00525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Ferroptosis is an iron-dependent programmed cell death characterized by lipid peroxidation that is linked to the pathophysiological processes in many diseases, such as neurodegenerative diseases, cancers, ischemia-reperfusion injuries, and organ damages. Many proteins are associated with ferroptosis signal transduction pathways. Novel chemical compounds are demanded to explore and regulate these pathways. Therefore, a ferroptosis ligand database, which holds relations among chemical structures, targets, bioactivities, and diseases, is needed for discovering and designing new ferroptosis regulators. This work reports FerroLigandDB, a manually curated database for small-molecular ferroptosis regulators. The database comprises 466 ferroptosis inducer entries (with 380 unique molecular structures) and 539 ferroptosis inhibitor entries (with 468 unique molecular structures) (note: one compound can be recorded as multiple entries due to the different assays). Each ferroptosis ligand entry is detailed with compound IDs, structure attributes, bioactivity values, test objects, target information, associated diseases, and references. The fields in the FerroLigandDB database implicitly contain relationships among chemical structures, bioactivities, targets, and diseases. Thus, FerroLigandDB is a comprehensive resource for scientists to design and discover novel ferroptosis regulators. The user interface of FerroLigandDB is implemented with query features and data visualization facilities. With compound identifiers, the compounds are linked to the records of other chemoinformatics databases (such as PubChem and SciFinder). The FerroLigandDB database is freely accessible at http://ferr.gulab.org.cn/.
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Affiliation(s)
- Yating Lin
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Jun Xu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Qiong Gu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
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16
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Zhu X, Zhang X, Guo J, He L, Wang F, Qiu Z, Li A, Zhang J, Gao F, Li W. Surface Engineering Enhances Vanadium Carbide MXene-Based Nanoplatform Triggered by NIR-II for Cancer Theranostics. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2401655. [PMID: 38966887 DOI: 10.1002/smll.202401655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 06/06/2024] [Indexed: 07/06/2024]
Abstract
Despite the advantages of high tissue penetration depth, selectivity, and non-invasiveness of photothermal therapy for cancer treatment, developing NIR-II photothermal agents with desirable photothermal performance and advanced theranostics ability remains a key challenge. Herein, a universal surface modification strategy is proposed to effectively improve the photothermal performance of vanadium carbide MXene nanosheets (L-V2C) with the removal of surface impurity ions and generation of mesopores. Subsequently, MnOx coating capable of T1-weighted magnetic resonance imaging can be in situ formed through surface redox reaction on L-V2C, and then, stable nanoplatforms (LVM-PEG) under physiological conditions can be obtained after further PEGylation. In the tumor microenvironment irradiated by NIR-II laser, multivalent Mn ions released from LVM-PEG, as a reversible electronic station, can consume the overexpression of glutathione and catalyze a Fenton-like reaction to produce ·OH, resulting in synchronous cellular oxidative damage. Efficient synergistic therapy promotes immunogenic cell death, improving tumor-related immune microenvironment and immunomodulation, and thus, LVM-PEG can demonstrate high accuracy and excellent anticancer efficiency guided by multimodal imaging. As a result, this study provides a new approach for the customization of 2D surface strategies and the study of synergistic therapy mechanisms, highlighting the application of MXene-based materials in the biomedical field.
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Affiliation(s)
- Xiaodong Zhu
- Department of Nanomedicine & Shanghai Key Lab of Cell Engineering, Naval Medical University, Shanghai, 200433, P. R. China
| | - Xide Zhang
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, 200433, P. R. China
| | - Jiahao Guo
- Department of Nanomedicine & Shanghai Key Lab of Cell Engineering, Naval Medical University, Shanghai, 200433, P. R. China
| | - Lei He
- Department of Nanomedicine & Shanghai Key Lab of Cell Engineering, Naval Medical University, Shanghai, 200433, P. R. China
| | - Fuming Wang
- Department of Interventional Radiology, Changhai Hospital, Naval Medical University, Shanghai, P. R. China
| | - Zhiwen Qiu
- Department of Nanomedicine & Shanghai Key Lab of Cell Engineering, Naval Medical University, Shanghai, 200433, P. R. China
| | - Ang Li
- Department of Nanomedicine & Shanghai Key Lab of Cell Engineering, Naval Medical University, Shanghai, 200433, P. R. China
| | - Jing Zhang
- Department of Pathology, Changzheng Hospital, Naval Medical University, Shanghai, 200433, P. R. China
| | - Fu Gao
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, 200433, P. R. China
| | - Wei Li
- Department of Nanomedicine & Shanghai Key Lab of Cell Engineering, Naval Medical University, Shanghai, 200433, P. R. China
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17
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Wang Y, Shen Z, Mo S, Zhang H, Chen J, Zhu C, Lv S, Zhang D, Huang X, Gu Y, Yu X, Ding X, Zhang X. Crosstalk among proximal tubular cells, macrophages, and fibroblasts in acute kidney injury: single-cell profiling from the perspective of ferroptosis. Hum Cell 2024; 37:1039-1055. [PMID: 38753279 PMCID: PMC11194220 DOI: 10.1007/s13577-024-01072-z] [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: 10/20/2023] [Accepted: 04/27/2024] [Indexed: 06/24/2024]
Abstract
The link between ferroptosis, a form of cell death mediated by iron and acute kidney injury (AKI) is recently gaining widespread attention. However, the mechanism of the crosstalk between cells in the pathogenesis and progression of acute kidney injury remains unexplored. In our research, we performed a non-negative matrix decomposition (NMF) algorithm on acute kidney injury single-cell RNA sequencing data based specifically focusing in ferroptosis-associated genes. Through a combination with pseudo-time analysis, cell-cell interaction analysis and SCENIC analysis, we discovered that proximal tubular cells, macrophages, and fibroblasts all showed associations with ferroptosis in different pathways and at various time. This involvement influenced cellular functions, enhancing cellular communication and activating multiple transcription factors. In addition, analyzing bulk expression profiles and marker genes of newly defined ferroptosis subtypes of cells, we have identified crucial cell subtypes, including Egr1 + PTC-C1, Jun + PTC-C3, Cxcl2 + Mac-C1 and Egr1 + Fib-C1. All these subtypes which were found in AKI mice kidneys and played significantly distinct roles from those of normal mice. Moreover, we verified the differential expression of Egr1, Jun, and Cxcl2 in the IRI mouse model and acute kidney injury human samples. Finally, our research presented a novel analysis of the crosstalk of proximal tubular cells, macrophages and fibroblasts in acute kidney injury targeting ferroptosis, therefore, contributing to better understanding the acute kidney injury pathogenesis, self-repairment and acute kidney injury-chronic kidney disease (AKI-CKD) progression.
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Affiliation(s)
- Yulin Wang
- Department of Nephrology, Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Shanghai, 200032, China
- Shanghai Medical Center of Kidney Disease, No. 180 Fenglin Road, Shanghai, 200032, China
- Shanghai Key Laboratory of Kidney and Blood Purification, No. 180 Fenglin Road, Shanghai, 200032, China
| | - Ziyan Shen
- Department of Nephrology, Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Shanghai, 200032, China
- Shanghai Medical Center of Kidney Disease, No. 180 Fenglin Road, Shanghai, 200032, China
- Shanghai Institute of Kidney and Dialysis, No. 180 Fenglin Road, Shanghai, 200032, China
| | - Shaocong Mo
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Han Zhang
- Department of Nephrology, Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Shanghai, 200032, China
- Shanghai Medical Center of Kidney Disease, No. 180 Fenglin Road, Shanghai, 200032, China
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Jing Chen
- Department of Nephrology, Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Shanghai, 200032, China
- Shanghai Medical Center of Kidney Disease, No. 180 Fenglin Road, Shanghai, 200032, China
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Cheng Zhu
- Department of Nephrology, Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Shanghai, 200032, China
- Shanghai Medical Center of Kidney Disease, No. 180 Fenglin Road, Shanghai, 200032, China
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Shiqi Lv
- Department of Nephrology, Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Shanghai, 200032, China
- Shanghai Medical Center of Kidney Disease, No. 180 Fenglin Road, Shanghai, 200032, China
- Shanghai Key Laboratory of Kidney and Blood Purification, No. 180 Fenglin Road, Shanghai, 200032, China
| | - Di Zhang
- Department of Nephrology, Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Shanghai, 200032, China
- Shanghai Medical Center of Kidney Disease, No. 180 Fenglin Road, Shanghai, 200032, China
- Shanghai Key Laboratory of Kidney and Blood Purification, No. 180 Fenglin Road, Shanghai, 200032, China
| | - Xinhui Huang
- Department of Nephrology, Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Shanghai, 200032, China
- Shanghai Medical Center of Kidney Disease, No. 180 Fenglin Road, Shanghai, 200032, China
- Shanghai Key Laboratory of Kidney and Blood Purification, No. 180 Fenglin Road, Shanghai, 200032, China
| | - Yulu Gu
- Division of Nephrology, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou, 213100, Jiangsu, China
| | - Xixi Yu
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Xiaoqiang Ding
- Department of Nephrology, Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Shanghai, 200032, China.
- Shanghai Medical Center of Kidney Disease, No. 180 Fenglin Road, Shanghai, 200032, China.
- Shanghai Key Laboratory of Kidney and Blood Purification, No. 180 Fenglin Road, Shanghai, 200032, China.
- Shanghai Institute of Kidney and Dialysis, No. 180 Fenglin Road, Shanghai, 200032, China.
| | - Xiaoyan Zhang
- Department of Nephrology, Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Shanghai, 200032, China.
- Shanghai Medical Center of Kidney Disease, No. 180 Fenglin Road, Shanghai, 200032, China.
- Shanghai Key Laboratory of Kidney and Blood Purification, No. 180 Fenglin Road, Shanghai, 200032, China.
- Shanghai Institute of Kidney and Dialysis, No. 180 Fenglin Road, Shanghai, 200032, China.
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Zhang M, Guo M, Gao Y, Wu C, Pan X, Huang Z. Mechanisms and therapeutic targets of ferroptosis: Implications for nanomedicine design. J Pharm Anal 2024; 14:100960. [PMID: 39135963 PMCID: PMC11318476 DOI: 10.1016/j.jpha.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/27/2024] [Accepted: 03/04/2024] [Indexed: 08/15/2024] Open
Abstract
Ferroptosis is a nonapoptotic form of cell death and differs considerably from the well-known forms of cell death in terms of cell morphology, genetics, and biochemistry. The three primary pathways for cell ferroptosis are system Xc-/glutathione peroxidase 4 (GPX4), lipid metabolism, and ferric metabolism. Since the discovery of ferroptosis, mounting evidence has revealed its critical regulatory role in several diseases, especially as a novel potential target for cancer therapy, thereby attracting increasing attention in the fields of tumor biology and anti-tumor therapy. Accordingly, broad prospects exist for identifying ferroptosis as a potential therapeutic target. In this review, we aimed to systematically summarize the activation and defense mechanisms of ferroptosis, highlight the therapeutic targets, and discuss the design of nanomedicines for ferroptosis regulation. In addition, we opted to present the advantages and disadvantages of current ferroptosis research and provide an optimistic vision of future directions in related fields. Overall, we aim to provide new ideas for further ferroptosis research and inspire new strategies for disease diagnosis and treatment.
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Affiliation(s)
- Meihong Zhang
- College of Pharmacy, University of Jinan, Guangzhou, 510632, China
| | - Mengqin Guo
- College of Pharmacy, University of Jinan, Guangzhou, 510632, China
| | - Yue Gao
- College of Pharmacy, University of Jinan, Guangzhou, 510632, China
| | - Chuanbin Wu
- College of Pharmacy, University of Jinan, Guangzhou, 510632, China
| | - Xin Pan
- College of Pharmacy, University of Sun Yat-sen, Guangzhou, 510275, China
| | - Zhengwei Huang
- College of Pharmacy, University of Jinan, Guangzhou, 510632, China
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Zhao R, Chen Q, Qiao P, Lu Y, Chen X. A signature of four ferroptosis-related genes in laryngeal squamous cell carcinoma. Transl Cancer Res 2024; 13:2938-2949. [PMID: 38988911 PMCID: PMC11231803 DOI: 10.21037/tcr-23-2046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 04/06/2024] [Indexed: 07/12/2024]
Abstract
Background Laryngeal squamous cell carcinoma (LSCC) prognosis has not improved significantly in the past few decades, and more effective treatments are needed to be explored. Ferroptosis is a newly discovered kind of regulated cell death in recent years, which is related to tumor immunity and can used to treat tumors. Therefore, the prognostic value of ferroptosis-related genes in laryngeal cancer needs further clarification. Methods In this study, the mRNA expression profile data of LSCC were downloaded from the public database. After identifying ferroptosis-related differentially expressed genes (FDGs), we explored the role of these genes through functional enrichment analysis. FDGs with prognostic significance were identified by univariate Cox and least absolute shrinkage and selection operator (LASSO) regression analyses. By calculating the risk score, we constructed a prognostic model. Kaplan-Meier (K-M) analysis, the receiver operating characteristic (ROC) curves, and the nomogram were utilized to investigate this model. Public databases and quantitative real-time polymerase chain reaction (qRT-PCR) were performed to verify the expression of model genes. Results The model consisting of four FDGs was acknowledged to be a self-determining predictor of prognosis. The K-M survival curves and the ROC curves confirmed the model's predictive ability. The C index (0.805) indicates that the nomogram has a good predictive ability. In vitro studies have confirmed the differential expression of the four FDGs. Conclusions We identified a novel ferroptosis-related gene signature for predicting prognosis in LSCC.
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Affiliation(s)
- Runyu Zhao
- Postgraduate Training Base at Shanghai Gongli Hospital, Ningxia Medical University, Shanghai, China
| | - Qun Chen
- Department of Otolaryngology, Gongli Hospital of Shanghai Pudong New Area, Shanghai, China
| | - Peipei Qiao
- Postgraduate Training Base at Shanghai Gongli Hospital, Ningxia Medical University, Shanghai, China
| | - Yingying Lu
- School of Medicine, Shanghai University, Shanghai, China
| | - Xiaoping Chen
- Department of Otolaryngology, Gongli Hospital of Shanghai Pudong New Area, Shanghai, China
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Brignola C, Pecoraro A, Danisi C, Iaccarino N, Di Porzio A, Romano F, Carotenuto P, Russo G, Russo A. uL3 Regulates Redox Metabolism and Ferroptosis Sensitivity of p53-Deleted Colorectal Cancer Cells. Antioxidants (Basel) 2024; 13:757. [PMID: 39061826 PMCID: PMC11274089 DOI: 10.3390/antiox13070757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 06/15/2024] [Accepted: 06/18/2024] [Indexed: 07/28/2024] Open
Abstract
Despite advancements in therapeutic strategies, the development of drug resistance and metastasis remains a serious concern for the efficacy of chemotherapy against colorectal cancer (CRC). We have previously demonstrated that low expression of ribosomal protein uL3 positively correlates with chemoresistance in CRC patients. Here, we demonstrated that the loss of uL3 increased the metastatic capacity of CRC cells in chick embryos. Metabolomic analysis revealed large perturbations in amino acid and glutathione metabolism in resistant uL3-silenced CRC cells, indicating that uL3 silencing dramatically triggered redox metabolic reprogramming. RNA-Seq data revealed a notable dysregulation of 108 genes related to ferroptosis in CRC patients. Solute Carrier Family 7 Member 11 (SLC7A11) is one of the most dysregulated genes; its mRNA stability is negatively regulated by uL3, and its expression is inversely correlated with uL3 levels. Inhibition of SLC7A11 with erastin impaired resistant uL3-silenced CRC cell survival by inducing ferroptosis. Of interest, the combined treatment erastin plus uL3 enhanced the chemotherapeutic sensitivity of uL3-silenced CRC cells to erastin. The antimetastatic potential of the combined strategy was evaluated in chick embryos. Overall, our study sheds light on uL3-mediated chemoresistance and provides evidence of a novel therapeutic approach, erastin plus uL3, to induce ferroptosis, establishing individualized therapy by examining p53, uL3 and SLC7A11 profiles in tumors.
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Affiliation(s)
- Chiara Brignola
- Department of Pharmacy, University of Naples “Federico II”, Via Domenico Montesano, 49, 80131 Naples, Italy; (C.B.); (A.P.); (C.D.); (N.I.); (A.D.P.); (F.R.); (G.R.)
| | - Annalisa Pecoraro
- Department of Pharmacy, University of Naples “Federico II”, Via Domenico Montesano, 49, 80131 Naples, Italy; (C.B.); (A.P.); (C.D.); (N.I.); (A.D.P.); (F.R.); (G.R.)
| | - Camilla Danisi
- Department of Pharmacy, University of Naples “Federico II”, Via Domenico Montesano, 49, 80131 Naples, Italy; (C.B.); (A.P.); (C.D.); (N.I.); (A.D.P.); (F.R.); (G.R.)
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples “Federico II”, Via Domenico Montesano, 49, 80131 Naples, Italy; (C.B.); (A.P.); (C.D.); (N.I.); (A.D.P.); (F.R.); (G.R.)
| | - Anna Di Porzio
- Department of Pharmacy, University of Naples “Federico II”, Via Domenico Montesano, 49, 80131 Naples, Italy; (C.B.); (A.P.); (C.D.); (N.I.); (A.D.P.); (F.R.); (G.R.)
| | - Francesca Romano
- Department of Pharmacy, University of Naples “Federico II”, Via Domenico Montesano, 49, 80131 Naples, Italy; (C.B.); (A.P.); (C.D.); (N.I.); (A.D.P.); (F.R.); (G.R.)
| | - Pietro Carotenuto
- TIGEM, Telethon Institute of Genetics and Medicine, Via Campi Flegrei, 34, 80078 Naples, Italy;
- Medical Genetics, Department of Translational Medical Science, University of Naples “Federico II”, Corso Umberto I, 40, 80138 Naples, Italy
| | - Giulia Russo
- Department of Pharmacy, University of Naples “Federico II”, Via Domenico Montesano, 49, 80131 Naples, Italy; (C.B.); (A.P.); (C.D.); (N.I.); (A.D.P.); (F.R.); (G.R.)
| | - Annapina Russo
- Department of Pharmacy, University of Naples “Federico II”, Via Domenico Montesano, 49, 80131 Naples, Italy; (C.B.); (A.P.); (C.D.); (N.I.); (A.D.P.); (F.R.); (G.R.)
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Wang K, Yang C, Xie J, Zhang X, Wei T, Yan Z. Long non-coding RNAs in ferroptosis and cuproptosis impact on prognosis and treatment in hepatocellular carcinoma. Clin Exp Med 2024; 24:135. [PMID: 38907744 PMCID: PMC11193701 DOI: 10.1007/s10238-024-01397-x] [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: 04/18/2024] [Accepted: 06/08/2024] [Indexed: 06/24/2024]
Abstract
Ferroptosis and cuproptosis are recently discovered forms of cell death that have gained interest as potential cancer treatments, particularly for hepatocellular carcinoma. Long non-coding RNAs (lncRNAs) influence cancer cell activity by interacting with various nucleic acids and proteins. However, the role of ferroptosis and cuproptosis-related lncRNAs (FCRLs) in cancer remains underexplored. Ferroptosis and cuproptosis scores for each sample were assessed using Gene Set Variation Analysis (GSVA). Weighted correlation network analysis identified the FCRLs most relevant to our study. A risk model based on FCRLs was developed to categorize patients into high-risk and low-risk groups. We then compared overall survival (OS), tumor immune microenvironment, and clinical characteristics between these groups. The IPS score and ImmuCellAI webpage were used to predict the association between FCRL-related signatures and immunotherapy response. Finally, we validated the accuracy of FCRLs in hepatocellular carcinoma cell lines using induction agents (elesclomol and erastin). Patients in different risk subgroups showed significant differences in OS, immune cell infiltration, pathway activity, and clinical characteristics. Cellular assays revealed significant changes in the expression of AC019080.5, AC145207.5, MIR210HG, and LINC01063 in HCC cell lines following the addition of ferroptosis and cuproptosis inducers. We created a signature of four FCRLs that accurately predicted survival in HCC patients, laid the foundation for basic research related to ferroptosis and cuproptosis in hepatocellular carcinoma, and provided therapeutic recommendations for HCC patients.
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Affiliation(s)
- Kun Wang
- Department of Gastroenterology, The First People's Hospital of Lianyungang, Lianyungang, China
| | - Chunqian Yang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jingen Xie
- Department of General Medicine, Huai'an Cancer Hospital, Huai'an, China
| | - Xiao Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Ting Wei
- Department of Gastroenterology, The First People's Hospital of Lianyungang, Lianyungang, China.
| | - Zhu Yan
- Emergency Medicine Department, Huai'an Hospital Affiliated to Yangzhou University (The Fifth People's Hospital of Huai'an), Huaian, China.
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Hou HX, Pang L, Zhao L, Xing J. Ferroptosis-related gene MAPK3 is associated with the neurological outcome after cardiac arrest. PLoS One 2024; 19:e0301647. [PMID: 38885209 PMCID: PMC11182507 DOI: 10.1371/journal.pone.0301647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 03/19/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Neuronal ferroptosis is closely related to the disease of the nervous system, and the objective of the present study was to recognize and verify the potential ferroptosis-related genes to forecast the neurological outcome after cardiac arrest. METHODS Cardiac Arrest-related microarray datasets GSE29540 and GSE92696 were downloaded from GEO and batch normalization of the expression data was performed using "sva" of the R package. GSE29540 was analyzed to identify DEGs. Venn diagram was applied to recognize ferroptosis-related DEGs from the DEGs. Subsequently, The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed, and PPI network was applied to screen hub genes. Receiver operating characteristic (ROC) curves were adopted to determine the predictive value of the biomarkers, and the GSE92696 dataset was applied to further evaluate the diagnostic efficacy of the biomarkers. We explore transcription factors and miRNAs associated with hub genes. The "CIBERSORT" package of R was utilized to analyse the proportion infiltrating immune cells. Finally, validated by a series of experiments at the cellular level. RESULTS 112 overlapping ferroptosis-related DEGs were further obtained via intersecting these DEGs and ferroptosis-related genes. The GO and KEGG analysis demonstrate that ferroptosis-related DEGs are mainly involved in response to oxidative stress, ferroptosis, apoptosis, IL-17 signalling pathway, autophagy, toll-like receptor signalling pathway. The top 10 hub genes were selected, including HIF1A, MAPK3, PPARA, IL1B, PTGS2, RELA, TLR4, KEAP1, SREBF1, SIRT6. Only MAPK3 was upregulated in both GSE29540 and GAE92696. The AUC values of the MAPK3 are 0.654 and 0.850 in GSE29540 and GSE92696 respectively. The result of miRNAs associated with hub genes indicates that hsa-miR-214-3p and hsa-miR-483-5p can regulate the expression of MAPK3. MAPK3 was positively correlated with naive B cells, macrophages M0, activated dendritic cells and negatively correlated with activated CD4 memory T cells, CD8 T cells, and memory B cells. Compared to the OGD4/R24 group, the OGD4/R12 group had higher MAPK3 expression at both mRNA and protein levels and more severe ferroptosis. CONCLUSION In summary, the MAPK3 ferroptosis-related gene could be used as a biomarker to predict the neurological outcome after cardiac arrest. Potential biological pathways provide novel insights into the pathogenesis of cardiac arrest.
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Affiliation(s)
- Hong xiang Hou
- Department of Emergency, The First Hospital of Jilin University, Changchun, China
| | - Li Pang
- Department of Emergency, The First Hospital of Jilin University, Changchun, China
| | - Liang Zhao
- Rehabilitation Department, The First Hospital of Jilin University, Changchun, China
| | - Jihong Xing
- Department of Emergency, The First Hospital of Jilin University, Changchun, China
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Wang L, Wang Y, Xu H, Li W. Effect of dapagliflozin on ferroptosis through the gut microbiota metabolite TMAO during myocardial ischemia-reperfusion injury in diabetes mellitus rats. Sci Rep 2024; 14:13851. [PMID: 38879701 PMCID: PMC11180094 DOI: 10.1038/s41598-024-64909-5] [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: 12/28/2023] [Accepted: 06/14/2024] [Indexed: 06/19/2024] Open
Abstract
Dapagliflozin (DAPA) demonstrates promise in the management of diabetic mellitus (DM) and cardiomyopathy. Trimethylamine N-oxide (TMAO) is synthesized by the gut microbiota through the metabolic conversion of choline and phosphatidylcholine. Ferroptosis may offer novel therapeutic avenues for the management of diabetes and myocardial ischemia-reperfusion injury (IRI). However, the precise mechanism underlying ferroptosis in cardiomyocytes and the specific role of TMAO generated by gut microbiota in the therapeutic approach for DM and myocardial IRI utilizing DAPA need to be further explored. Nine male SD rats with specific pathogen-free (SPF) status were randomly divided equally into the normal group, the DM + IRI (DIR) group, and the DAPA group. The diversity of the gut microbiota was analyzed using 16S rRNA gene sequencing. Additionally, the Wekell technique was employed to measure the levels of TMAO in the three groups. Application of network pharmacology to search for intersection targets of DAPA, DIR, and ferroptosis, and RT-PCR experimental verification. Ultimately, the overlapping targets that were acquired were subjected to molecular docking analysis with TMAO. The changes of Bacteroidetes and Firmicutes in the gut microbiota of DIR rats were most significantly affected by DAPA. Escherichia-Shigella and Prevotella_9 within the phylum Bacteroidetes could be identified as the primary effects of DAPA on DIR. Compared with the normal group, the TMAO content in the DIR group was significantly increased, while the TMAO content in the DAPA group was decreased compared to the DIR group. For the network pharmacology analysis, DAPA and DIR generated 43 intersecting target genes, and then further intersected with ferroptosis-related genes, resulting in 11 overlapping target genes. The mRNA expression of ALB, HMOX1, PPARG, CBS, LCN2, and PPARA decreased in the DIR group through reverse transcription polymerase chain reaction (RT-PCR) validation, while the opposite trend was observed in the DAPA group. The docking score between TMAO and DPP4 was - 5.44, and the MM-GBSA result of - 22.02 kcal/mol. It epitomizes the finest docking performance among all the target genes with the lowest score. DAPA could reduce the levels of metabolite TMAO produced by gut microbiota, thereby regulating related target genes to decrease ferroptosis in DIR cardiomyocytes.
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Affiliation(s)
- Lian Wang
- Department of Infectious Diseases, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China
- College of Medicine, Wuhan University of Science and Technology, Wuhan, 430070, Hubei, China
| | - Yao Wang
- Department of Infectious Diseases, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China
| | - Heng Xu
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China
| | - Wenyuan Li
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China.
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Guo X, Feng X, Yang Y, An W, Bai L. Machine learning-based identification and immune characterization of ferroptosis-related molecular clusters in osteoarthritis and validation. Aging (Albany NY) 2024; 16:9437-9459. [PMID: 38814177 PMCID: PMC11210262 DOI: 10.18632/aging.205875] [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: 01/15/2024] [Accepted: 04/18/2024] [Indexed: 05/31/2024]
Abstract
Osteoarthritis (OA), a degenerative joint disease, involves synovial inflammation, subchondral bone erosion, and cartilage degeneration. Ferroptosis, a regulated non-apoptotic programmed cell death, is associated with various diseases. This study investigates ferroptosis-related molecular subtypes in OA to comprehend underlying mechanisms. The Gene Expression Omnibus datasets GSE206848, GSE55457, GSE55235, GSE77298 and GSE82107 were used utilized. Unsupervised clustering identified the ferroptosis-related gene (FRG) subtypes, and their immune characteristics were assessed. FRG signatures were derived using LASSO and SVM-RFE algorithms, forming models to evaluate OA's ferroptosis-related immune features. Three FRG clusters were found to be immunologically heterogeneous, with cluster 1 displaying robust immune response. Models identified nine key signature genes via algorithms, demonstrating strong diagnostic and prognostic performance. Finally, qRT-PCR and Western blot validated these genes, offering consistent results. In addition, some of these genes may have implications as new therapeutic targets and can be used to guide clinical applications.
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Affiliation(s)
- Xiaocheng Guo
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xinyuan Feng
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yue Yang
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Wenying An
- Department of Cadre Wards, Liaoning University of Traditional Chinese Medicine Affiliated Orthopedic Hospital, Shenyang, China
| | - Lunhao Bai
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, China
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Liu X, Li D, Gao W, Chen P, Liu H, Zhao Y, Zhao W, Dong G. Molecular characterization, clinical value, and cancer-immune interactions of genes related to disulfidptosis and ferroptosis in colorectal cancer. Discov Oncol 2024; 15:183. [PMID: 38787520 PMCID: PMC11126553 DOI: 10.1007/s12672-024-01031-y] [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: 03/20/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND This research strived to construct a new signature utilizing disulfidptosis-related ferroptosis (SRF) genes to anticipate response to immunotherapy, prognosis, and drug sensitivity in individuals with colorectal cancer (CRC). METHODS The data for RNA sequencing as well as corresponding clinical information of individuals with CRC, were extracted from The Cancer Genome Atlas (TCGA) dataset. SRF were constructed with the help of the random forest (RF), least absolute shrinkage and selection operator (LASSO), and stepwise regression algorithms. To validate the SRF model, we applied it to an external cohort, GSE38832. Prognosis, immunotherapy response, drug sensitivity, molecular functions of genes, and somatic mutations of genes were compared across the high- and low-risk groups (categories). Following this, all statistical analyses were conducted with the aid of the R (version 4.23) software and various packages of the Cytoscape (version 3.8.0) tool. RESULTS SRF was developed based on five genes (ATG7, USP7, MMD, PLIN4, and THDC2). Both univariate and multivariate Cox regression analyses established SRF as an independent, prognosis-related risk factor. Individuals from the high-risk category had a more unfavorable prognosis, elevated tumor mutational burden (TMB), and significant immunosuppressive status. Hence, they might have better outcomes post-immunotherapy and might benefit from the administration of pazopanib, lapatinib, and sunitinib. CONCLUSION In conclusion, SRF can act as a new biomarker for prognosis assessment. Moreover, it is also a good predictor of drug sensitivity and immunotherapy response in CRC but should undergo optimization before implementation in clinical settings.
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Affiliation(s)
- Xianqiang Liu
- Medical School of Chinese PLA, Beijing, 100853, China
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Dingchang Li
- Medical School of Chinese PLA, Beijing, 100853, China
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Wenxing Gao
- Medical School of Chinese PLA, Beijing, 100853, China
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Peng Chen
- Medical School of Chinese PLA, Beijing, 100853, China
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Hao Liu
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Yingjie Zhao
- Medical School of Chinese PLA, Beijing, 100853, China
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Wen Zhao
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China.
- School of Medicine, Nankai University, Tianjin, 300071, China.
| | - Guanglong Dong
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China.
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Chen H, Nie P, Li J, Wu Y, Yao B, Yang Y, Lash GE, Li P. Cyclophosphamide induces ovarian granulosa cell ferroptosis via a mechanism associated with HO-1 and ROS-mediated mitochondrial dysfunction. J Ovarian Res 2024; 17:107. [PMID: 38762721 PMCID: PMC11102268 DOI: 10.1186/s13048-024-01434-z] [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: 09/04/2023] [Accepted: 05/07/2024] [Indexed: 05/20/2024] Open
Abstract
Abnormal granulosa cell (GC) death contributes to cyclophosphamide (CTX) induced primary ovarian insufficiency (POI). To investigate the contribution of GCs to POI, gene profiles of GCs exposed to CTX were assessed using RNA-Seq and bioinformatics analysis. The results showed the differentially expressed genes (DEGs) were enriched in the ferroptosis-related pathway, which is correlated with upregulated heme oxygenase 1 (HO-1) and downregulated glutathione peroxidase-4 (GPX4). Using CTX-induced cell culture (COV434 and KGN cells), the levels of iron, reactive oxygen species (ROS), lipid peroxide, mitochondrial superoxide, mitochondrial morphology and mitochondrial membrane potential (MMP) were detected by DCFDA, MitoSOX, C11-BODIPY, MitoTracker, Nonylacridine Orange (NAO), JC-1 and transmission electron microscopy respectively. The results showed iron overload and disrupted ROS, including cytoROS, mtROS and lipROS homeostasis, were associated with upregulation of HO-1 and could induce ferroptosis via mitochondrial dysfunction in CTX-induced GCs. Moreover, HO-1 inhibition could suppress ferroptosis induced GPX4 depletion. This implies a role for ROS in CTX-induced ferroptosis and highlights the effect of HO-1 modulators in improving CTX-induced ovarian damage, which may provide a theoretical basis for preventing or restoring GC and ovarian function in patients with POI.
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Affiliation(s)
- Hui Chen
- Department of Pathology, Jinan University School of Medicine, Guangzhou, 510632, China
| | - Ping Nie
- Department of Pathology, Jinan University School of Medicine, Guangzhou, 510632, China
| | - Jingling Li
- Department of Pathology, Jinan University School of Medicine, Guangzhou, 510632, China
| | - Yongqi Wu
- Department of Pathology, Jinan University School of Medicine, Guangzhou, 510632, China
| | - Bo Yao
- Department of Pathology, Jinan University School of Medicine, Guangzhou, 510632, China
| | - Yabing Yang
- Guangdong Second Provincial General Hospital, Postdoctoral Research Station of Basic Medicine, Jinan University School of Medicine, Guangzhou, 510317, China
| | - Gendie E Lash
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Ping Li
- Department of Pathology, Jinan University School of Medicine, Guangzhou, 510632, China.
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Yu J, Li H, Huang C, Chen H. Identification and characterization of ferroptosis-related genes in therapy-resistant gastric cancer. Medicine (Baltimore) 2024; 103:e38193. [PMID: 38758860 PMCID: PMC11098190 DOI: 10.1097/md.0000000000038193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/18/2024] [Indexed: 05/19/2024] Open
Abstract
Therapy resistance in gastric cancer poses ongoing challenges, necessitating the identification of ferroptosis-related genes linked to overall survival for potential therapeutic insights. The purpose of the study was to identify ferroptosis-related genes contributing to therapy resistance in gastric cancer and explore their associations with overall survival. Differentially expressed ferroptosis-related genes were identified in therapy-resistant versus therapy-responsive gastric cancer patients. Hub genes were selected from these genes. Enrichment analysis focused on oxidative stress and ROS metabolism. Validation was conducted in a TCGA stomach adenocarcinoma dataset. A hub gene-based risk model (DUSP1/TNF/NOX4/LONP1) was constructed and assessed for overall survival prediction. Associations with the tumor immune microenvironment were examined using the ESTIMATE algorithm and correlation analysis. Ten hub genes were identified, enriched in oxidative stress and ROS metabolism. Validation confirmed their aberrant expressions in the TCGA dataset. The hub gene-based risk model effectively predicted overall survival. High G6PD/TNF expression and low NOX4/SREBF1/MAPK3/DUSP1/KRAS/SIRT3/LONP1 expression correlated with stromal and immune scores. KRAS/TNF/MAPK3 expression positively correlated with immune-related SREBF1/NOX4 expression. DUSP1/NOX4/SREBF1/TNF/KRAS expression was associated with immune cell infiltration. The hub gene-based risk model (DUSP1/TNF/NOX4/LONP1) shows promise as an overall survival predictor in gastric cancer. Ferroptosis-related hub genes represent potential therapeutic targets for overcoming therapy resistance in gastric cancer treatment.
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Affiliation(s)
- Jieli Yu
- Department of Geriatric Oncology, Jiangxi Cancer Hospital, Nanchang, China
| | - Hua Li
- Department of Oncology, Pengze County People’s Hospital, Jiujiang, China
| | - Can Huang
- Department of Geriatric Oncology, Jiangxi Cancer Hospital, Nanchang, China
| | - Huoguo Chen
- Department of Geriatric Oncology, Jiangxi Cancer Hospital, Nanchang, China
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28
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Hou CY, Lv P, Yuan HF, Zhao LN, Wang YF, Zhang HH, Yang G, Zhang XD. Bevacizumab induces ferroptosis and enhances CD8 + T cell immune activity in liver cancer via modulating HAT1 and increasing IL-9. Acta Pharmacol Sin 2024:10.1038/s41401-024-01299-4. [PMID: 38760543 DOI: 10.1038/s41401-024-01299-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/24/2024] [Accepted: 04/24/2024] [Indexed: 05/19/2024] Open
Abstract
Bevacizumab is a recombinant humanized monoclonal immunoglobulin (Ig) G1 antibody of VEGF, and inhibits angiogenesis and tumor growth in hepatocellular carcinoma (HCC). Ferroptosis, a new form of regulated cell death function independently of the apoptotic machinery, has been accepted as an attractive target for pharmacological intervention; the ferroptosis pathway can enhance cell immune activity of anti-PD1 immunotherapy in HCC. In this study we investigated whether and how bevacizumab regulated ferroptosis and immune activity in liver cancer. Firstly, we performed RNA-sequencing in bevacizumab-treated human liver cancer cell line HepG2 cells, and found that bevacizumab significantly altered the expression of a number of genes including VEGF, PI3K, HAT1, SLC7A11 and IL-9 in liver cancer, bevacizumab upregulated 37 ferroptosis-related drivers, and downregulated 17 ferroptosis-related suppressors in particular. We demonstrated that bevacizumab triggered ferroptosis in liver cancer cells by driving VEGF/PI3K/HAT1/SLC7A11 axis. Clinical data confirmed that the expression levels of VEGF were positively associated with those of PI3K, HAT1 and SLC7A11 in HCC tissues. Meanwhile, we found that bevacizumab enhanced immune cell activity in tumor immune-microenvironment. We identified that HAT1 up-regulated miR-143 targeting IL-9 mRNA 3'UTR in liver cancer cells; bevacizumab treatment resulted in the increase of IL-9 levels and its secretion via VEGF/PI3K/HAT1/miR-143/IL-9 axis, which led to the inhibition of tumor growth in vivo through increasing the release of IL-2 and Granzyme B from activated CD8+ T cells. We conclude that in addition to inhibiting angiogenesis, bevacizumab induces ferroptosis and enhances CD8+ T cell immune activity in liver cancer. This study provides new insight into the mechanisms by which bevacizumab synergistically modulates ferroptosis and CD8+ T cell immune activity in liver cancer.
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Affiliation(s)
- Chun-Yu Hou
- National Key Laboratory of Draggability Evaluation and Systematic Translational Medicine, Tianjin's Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, Department of Gastrointestinal Cancer Biology, Tianjin Cancer Institute, Liver Cancer Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Pan Lv
- National Key Laboratory of Draggability Evaluation and Systematic Translational Medicine, Tianjin's Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, Department of Gastrointestinal Cancer Biology, Tianjin Cancer Institute, Liver Cancer Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Hong-Feng Yuan
- National Key Laboratory of Draggability Evaluation and Systematic Translational Medicine, Tianjin's Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, Department of Gastrointestinal Cancer Biology, Tianjin Cancer Institute, Liver Cancer Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Li-Na Zhao
- National Key Laboratory of Draggability Evaluation and Systematic Translational Medicine, Tianjin's Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, Department of Gastrointestinal Cancer Biology, Tianjin Cancer Institute, Liver Cancer Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Yu-Fei Wang
- National Key Laboratory of Draggability Evaluation and Systematic Translational Medicine, Tianjin's Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, Department of Gastrointestinal Cancer Biology, Tianjin Cancer Institute, Liver Cancer Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Hui-Hui Zhang
- National Key Laboratory of Draggability Evaluation and Systematic Translational Medicine, Tianjin's Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, Department of Gastrointestinal Cancer Biology, Tianjin Cancer Institute, Liver Cancer Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Guang Yang
- National Key Laboratory of Draggability Evaluation and Systematic Translational Medicine, Tianjin's Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, Department of Gastrointestinal Cancer Biology, Tianjin Cancer Institute, Liver Cancer Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China.
| | - Xiao-Dong Zhang
- National Key Laboratory of Draggability Evaluation and Systematic Translational Medicine, Tianjin's Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, Department of Gastrointestinal Cancer Biology, Tianjin Cancer Institute, Liver Cancer Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China.
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29
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Li Y, Wang W, Kong C, Chen X, Li C, Lu S. Identifying the miRNA-gene networks contributes to exploring paravertebral muscle degeneration's underlying pathogenesis and therapy strategy. Heliyon 2024; 10:e30517. [PMID: 38765163 PMCID: PMC11098802 DOI: 10.1016/j.heliyon.2024.e30517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/24/2024] [Accepted: 04/29/2024] [Indexed: 05/21/2024] Open
Abstract
Low back pain (LBP) is a worldwide problem with public health. Paravertebral muscle degeneration (PMD) is believed to be associated with LBP. Increasing evidence has demonstrated that microRNA (miRNA)-mRNA signaling networks have been implicated in the pathophysiology of diseases. Research suggests that cell death, oxidative stress, inflammatory and immune response, and extracellular matrix (ECM) metabolism are the pathogenesis of PMD; however, the miRNA-mRNA mediated the pathological process of PMD remains elusive. RNA sequencing (RNA-seq) and single cell RNA-seq (scRNA-seq) are invaluable tools for uncovering the functional biology underlying these miRNA and gene expression changes. Using scRNA-seq, we show that multiple immunocytes are presented during PMD, revealing that they may have been implicated with PMD. Additionally, using RNA-seq, we identified 76 differentially expressed genes (DEGs) and 106 differentially expressed miRNAs (DEMs), among which IL-24 and CCDC63 were the top upregulated and downregulated genes in PMD. Comprehensive bioinformatics analyses, including Venn diagrams, differential expression, functional enrichment, and protein-protein interaction analysis, were then conducted to identify six ferroptosis-related DEGs, two oxidative stress-related DEGs, eleven immunity-related DEGs, five ECM-related DEGs, among which AKR1C2/AKR1C3/SIRT1/ALB/IL-24 belong to inflammatory genes. Furthermore, 67 DEMs were predicted to be upstream miRNAs of 25 key DEGs by merging RNA-seq, TargetScan, and mirDIP databases. Finally, a miRNA-gene network was constructed using Cytoscape software and an alluvial plot. ROC curve analysis unveiled multiple key DEGs with the high clinical diagnostic value, providing novel approaches for diagnosing and treating PMD diseases.
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Affiliation(s)
- Yongjin Li
- Department of Orthopedics, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing, China
- Spine Center, Department of Orthopaedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, No.17, Lujiang Road, Hefei, Anhui, 230001, China
| | - Wei Wang
- Department of Orthopedics, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing, China
| | - Chao Kong
- Department of Orthopedics, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing, China
| | - Xiaolong Chen
- Department of Orthopedics, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing, China
| | - Chaoyi Li
- Department of Joint Surgery, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570311, China
| | - Shibao Lu
- Department of Orthopedics, Xuanwu Hospital, Capital Medical University, No. 45 Changchun Street, Xicheng District, Beijing, China
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30
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Zhang Y, Gu X, Li Y, Li X, Huang Y, Ju S. Transfer RNA-derived fragment tRF-23-Q99P9P9NDD promotes progression of gastric cancer by targeting ACADSB. J Zhejiang Univ Sci B 2024; 25:438-450. [PMID: 38725342 PMCID: PMC11087185 DOI: 10.1631/jzus.b2300215] [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: 04/06/2023] [Accepted: 08/07/2023] [Indexed: 05/13/2024]
Abstract
Gastric cancer (GC) is one of the most common gastrointestinal tumors. As a newly discovered type of non-coding RNAs, transfer RNA (tRNA)-derived small RNAs (tsRNAs) play a dual biological role in cancer. Our previous studies have demonstrated the potential of tRF-23-Q99P9P9NDD as a diagnostic and prognostic biomarker for GC. In this work, we confirmed for the first time that tRF-23-Q99P9P9NDD can promote the proliferation, migration, and invasion of GC cells in vitro. The dual luciferase reporter gene assay confirmed that tRF-23-Q99P9P9NDD could bind to the 3' untranslated region (UTR) site of acyl-coenzyme A dehydrogenase short/branched chain (ACADSB). In addition, ACADSB could rescue the effect of tRF-23-Q99P9P9NDD on GC cells. Next, we used Gene Ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) to find that downregulated ACADSB in GC may promote lipid accumulation by inhibiting fatty acid catabolism and ferroptosis. Finally, we verified the correlation between ACADSB and 12 ferroptosis genes at the transcriptional level, as well as the changes in reactive oxygen species (ROS) levels by flow cytometry. In summary, this study proposes that tRF-23-Q99P9P9NDD may affect GC lipid metabolism and ferroptosis by targeting ACADSB, thereby promoting GC progression. It provides a theoretical basis for the diagnostic and prognostic monitoring value of GC and opens up new possibilities for treatment.
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Affiliation(s)
- Yu Zhang
- Medical School of Nantong University, Nantong University, Nantong 226001, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Xinliang Gu
- Medical School of Nantong University, Nantong University, Nantong 226001, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Yang Li
- Medical School of Nantong University, Nantong University, Nantong 226001, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Xun Li
- Medical School of Nantong University, Nantong University, Nantong 226001, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Yuejiao Huang
- Medical School of Nantong University, Nantong University, Nantong 226001, China.
- Department of Medical Oncology, Affiliated Hospital of Nantong University, Nantong 226001, China.
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong 226001, China. ,
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31
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Wang L, Gong WH. Predictive model using four ferroptosis-related genes accurately predicts gastric cancer prognosis. World J Gastrointest Oncol 2024; 16:2018-2037. [PMID: 38764813 PMCID: PMC11099433 DOI: 10.4251/wjgo.v16.i5.2018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 01/31/2024] [Accepted: 03/08/2024] [Indexed: 05/09/2024] Open
Abstract
BACKGROUND Gastric cancer (GC) is a common malignancy of the digestive system. According to global 2018 cancer data, GC has the fifth-highest incidence and the third-highest fatality rate among malignant tumors. More than 60% of GC are linked to infection with Helicobacter pylori (H. pylori), a gram-negative, active, microaerophilic, and helical bacterium. This parasite induces GC by producing toxic factors, such as cytotoxin-related gene A, vacuolar cytotoxin A, and outer membrane proteins. Ferroptosis, or iron-dependent programmed cell death, has been linked to GC, although there has been little research on the link between H. pylori infection-related GC and ferroptosis. AIM To identify coregulated differentially expressed genes among ferroptosis-related genes (FRGs) in GC patients and develop a ferroptosis-related prognostic model with discrimination ability. METHODS Gene expression profiles of GC patients and those with H. pylori-associated GC were obtained from The Cancer Genome Atlas and Gene Expression Omnibus (GEO) databases. The FRGs were acquired from the FerrDb database. A ferroptosis-related gene prognostic index (FRGPI) was created using least absolute shrinkage and selection operator-Cox regression. The predictive ability of the FRGPI was validated in the GEO cohort. Finally, we verified the expression of the hub genes and the activity of the ferroptosis inducer FIN56 in GC cell lines and tissues. RESULTS Four hub genes were identified (NOX4, MTCH1, GABARAPL2, and SLC2A3) and shown to accurately predict GC and H. pylori-associated GC. The FRGPI based on the hub genes could independently predict GC patient survival; GC patients in the high-risk group had considerably worse overall survival than did those in the low-risk group. The FRGPI was a significant predictor of GC prognosis and was strongly correlated with disease progression. Moreover, the gene expression levels of common immune checkpoint proteins dramatically increased in the high-risk subgroup of the FRGPI cohort. The hub genes were also confirmed to be highly overexpressed in GC cell lines and tissues and were found to be primarily localized at the cell membrane. The ferroptosis inducer FIN56 inhibited GC cell proliferation in a dose-dependent manner. CONCLUSION In this study, we developed a predictive model based on four FRGs that can accurately predict the prognosis of GC patients and the efficacy of immunotherapy in this population.
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Affiliation(s)
- Li Wang
- Department of Emergency, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310000, Zhejiang Province, China
| | - Wei-Hua Gong
- Department of Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou 310052, Zhejiang Province, China
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32
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Zhou H, Zhou X, Zhu R, Zhao Z, Yang K, Shen Z, Sun H. A ferroptosis-related signature predicts the clinical diagnosis and prognosis, and associates with the immune microenvironment of lung cancer. Discov Oncol 2024; 15:163. [PMID: 38743344 PMCID: PMC11093956 DOI: 10.1007/s12672-024-01032-x] [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: 10/20/2023] [Accepted: 05/10/2024] [Indexed: 05/16/2024] Open
Abstract
Targeting ferroptosis-related pathway is a potential strategy for treatment of lung cancer (LC). Consequently, exploration of ferroptosis-related markers is important for treating LC. We collected LC clinical data and mRNA expression profiles from TCGA and GEO database. Ferroptosis-related genes (FRGs) were obtained through FerrDB database. Expression analysis was performed to obtain differentially expressed FRGs. Diagnostic and prognostic models were constructed based on FRGs by LASSO regression, univariate, and multivariate Cox regression analysis, respectively. External verification cohorts GSE72094 and GSE157011 were used for validation. The interrelationship between prognostic risk scores based on FRGs and the tumor immune microenvironment was analyzed. Immunocytochemistry, Western blotting, and RT-qPCR detected the FRGs level. Eighteen FRGs were used for diagnostic models, 8 FRGs were used for prognostic models. The diagnostic model distinguished well between LC and normal samples in training and validation cohorts of TCGA. The prognostic models for TCGA, GSE72094, and GSE157011 cohorts significantly confirmed lower overall survival (OS) in high-risk group, which demonstrated excellent predictive properties of the survival model. Multivariate Cox regression analysis further confirmed risk score was an independent risk factor related with OS. Immunoassays revealed that in high-risk group, a significantly higher proportion of Macrophages_M0, Neutrophils, resting Natural killer cells and activated Mast cells and the level of B7H3, CD112, CD155, B7H5, and ICOSL were increased. In conclusion, diagnostic and prognostic models provided superior diagnostic and predictive power for LC and revealed a potential link between ferroptosis and TIME.
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Affiliation(s)
- Hua Zhou
- Department of Oncology Radiotherapy, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China
| | - Xiaoting Zhou
- Medical School, Kunming University of Science and Technology, Kunming, 650031, Yunnan, China
| | - Runying Zhu
- Department of Oncology Radiotherapy, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China
| | - Zhongquan Zhao
- Department of Oncology Radiotherapy, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China
| | - Kang Yang
- Department of Thoracic Surgery, First Affiliated Hospital of Kunming Medical University, No.295 Xichang Rd, Kunming, 650032, Yunnan, China
| | - Zhenghai Shen
- Department of Thoracic Surgery, Yunnan Cancer Hospital, Kunming, 650118, Yunnan, China
| | - Hongwen Sun
- Department of Thoracic Surgery, First Affiliated Hospital of Kunming Medical University, No.295 Xichang Rd, Kunming, 650032, Yunnan, China.
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Lu J, Li H, Yu Z, Cao C, Xu Z, Peng L, Zhang JH, Chen G. Cathepsin B as a key regulator of ferroptosis in microglia following intracerebral hemorrhage. Neurobiol Dis 2024; 194:106468. [PMID: 38460801 DOI: 10.1016/j.nbd.2024.106468] [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: 11/01/2023] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024] Open
Abstract
Intracerebral hemorrhage (ICH) is a subtype of stroke marked by elevated mortality and disability rates. Recently, mounting evidence suggests a significant role of ferroptosis in the pathogenesis of ICH. Through a combination of bioinformatics analysis and basic experiments, our goal is to identify the primary cell types and key molecules implicated in ferroptosis post-ICH. This aims to propel the advancement of ferroptosis research, offering potential therapeutic targets for ICH treatment. Our study reveals pronounced ferroptosis in microglia and identifies the target gene, cathepsin B (Ctsb), by analyzing differentially expressed genes following ICH. Ctsb, a cysteine protease primarily located in lysosomes, becomes a focal point in our investigation. Utilizing in vitro and in vivo models, we explore the correlation between Ctsb and ferroptosis in microglia post-ICH. Results demonstrate that ICH and hemin-induced ferroptosis in microglia coincide with elevated levels and activity of Ctsb protein. Effective alleviation of ferroptosis in microglia after ICH is achieved through the inhibition of Ctsb protease activity and protein levels using inhibitors and shRNA. Additionally, a notable increase in m6A methylation levels of Ctsb mRNA post-ICH is observed, suggesting a pivotal role of m6A methylation in regulating Ctsb translation. These research insights deepen our comprehension of the molecular pathways involved in ferroptosis after ICH, underscoring the potential of Ctsb as a promising target for mitigating brain damage resulting from ICH.
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Affiliation(s)
- Jinxin Lu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215006, China; Institute of Stroke Research, Soochow University, Suzhou 215006, China
| | - Haiying Li
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215006, China; Institute of Stroke Research, Soochow University, Suzhou 215006, China
| | - Zhengquan Yu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215006, China; Institute of Stroke Research, Soochow University, Suzhou 215006, China.
| | - Chang Cao
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215006, China; Institute of Stroke Research, Soochow University, Suzhou 215006, China
| | - Zhongmou Xu
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215006, China; Institute of Stroke Research, Soochow University, Suzhou 215006, China
| | - Lu Peng
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215006, China; Institute of Stroke Research, Soochow University, Suzhou 215006, China
| | - John H Zhang
- Departments of Neurosurgery, Anesthesiology, Physiology and Pharmacology, Pathology and Human Anatomy, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Gang Chen
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215006, China; Institute of Stroke Research, Soochow University, Suzhou 215006, China.
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Zhao ST, Qiu ZC, Zeng RY, Zou HX, Qiu RB, Peng HZ, Zhou LF, Xu ZQ, Lai SQ, Wan L. Exploring the molecular biology of ischemic cardiomyopathy based on ferroptosis‑related genes. Exp Ther Med 2024; 27:221. [PMID: 38590563 PMCID: PMC11000445 DOI: 10.3892/etm.2024.12509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 02/21/2024] [Indexed: 04/10/2024] Open
Abstract
Ischemic cardiomyopathy (ICM) is a serious cardiac disease with a very high mortality rate worldwide, which causes myocardial ischemia and hypoxia as the main damage. Further understanding of the underlying pathological processes of cardiomyocyte injury is key to the development of cardioprotective strategies. Ferroptosis is an iron-dependent form of regulated cell death characterized by the accumulation of lipid hydroperoxides to lethal levels, resulting in oxidative damage to the cell membrane. The current understanding of the role and regulation of ferroptosis in ICM is still limited, especially in the absence of evidence from large-scale transcriptomic data. Through comprehensive bioinformatics analysis of human ICM transcriptome data obtained from the Gene Expression Omnibus database, the present study identified differentially expressed ferroptosis-related genes (DEFRGs) in ICM. Subsequently, their potential biological mechanisms and cross-talk were analyzed, and hub genes were identified by constructing protein-protein interaction networks. Ferroptosis features such as reactive oxygen species generation, changes in ferroptosis marker proteins, iron ion aggregation and lipid oxidation, were identified in the H9c2 anoxic reoxygenation injury model. Finally, the diagnostic ability of Gap junction alpha-1 (GJA1), Solute carrier family 40 member 1 (SLC40A1), Alpha-synuclein (SNCA) were identified through receiver operating characteristic curves and the expression of DEFRGs was verified in an in vitro model. Furthermore, potential drugs (retinoic acid) that could regulate ICM ferroptosis were predicted based on key DEFRGs. The present article presents new insights into the role of ferroptosis in ICM, investigating the regulatory role of ferroptosis in the pathological process of ICM and advocating for ferroptosis as a potential novel therapeutic target for ICM based on evidence from the ICM transcriptome.
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Affiliation(s)
- Shi-Tao Zhao
- Department of Cardiovascular Surgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
- Institute of Cardiovascular Surgical Diseases, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Zhi-Cong Qiu
- Department of Cardiovascular Surgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
- Institute of Cardiovascular Surgical Diseases, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Rui-Yuan Zeng
- Department of Cardiovascular Surgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
- Institute of Cardiovascular Surgical Diseases, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Hua-Xi Zou
- Department of Cardiovascular Surgery, The Second Affiliated Hospita, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330200, P.R. China
| | - Rong-Bin Qiu
- Department of Cardiovascular Surgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
- Institute of Cardiovascular Surgical Diseases, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Han-Zhi Peng
- Department of Cardiovascular Surgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
- Institute of Cardiovascular Surgical Diseases, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Lian-Fen Zhou
- Department of Cardiovascular Surgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
- Institute of Cardiovascular Surgical Diseases, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Zhi-Qiang Xu
- Department of Cardiovascular Surgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
- Institute of Cardiovascular Surgical Diseases, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Song-Qing Lai
- Department of Cardiovascular Surgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
- Institute of Cardiovascular Surgical Diseases, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Li Wan
- Department of Cardiovascular Surgery, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
- Institute of Cardiovascular Surgical Diseases, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
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Qiu L, Ji H, Wang K, Liu W, Huang Q, Pan X, Ye H, Li Z, Chen G, Xing X, Dong X, Tang R, Xu H, Liu J, Cai Z, Liu X. TLR3 activation enhances abscopal effect of radiotherapy in HCC by promoting tumor ferroptosis. EMBO Mol Med 2024; 16:1193-1219. [PMID: 38671318 PMCID: PMC11098818 DOI: 10.1038/s44321-024-00068-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 04/03/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Radiotherapy (RT) has been reported to induce abscopal effect in advanced hepatocellular carcinoma (HCC), but such phenomenon was only observed in sporadic cases. Here, we demonstrated that subcutaneous administration of Toll-like receptor 3 (TLR3) agonist poly(I:C) could strengthen the abscopal effect during RT through activating tumor cell ferroptosis signals in bilateral HCC subcutaneous tumor mouse models, which could be significantly abolished by TLR3 knock-out or ferroptosis inhibitor ferrostatin-1. Moreover, poly(I:C) could promote the presentation of tumor neoantigens by dendritic cells to enhance the recruitment of activated CD8+ T cells into distant tumor tissues for inducing tumor cell ferroptosis during RT treatment. Finally, the safety and feasibility of combining poly(I:C) with RT for treating advanced HCC patients were further verified in a prospective clinical trial. Thus, enhancing TLR3 signaling activation during RT could provide a novel strategy for strengthening abscopal effect to improve the clinical benefits of advanced HCC patients.
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Affiliation(s)
- Liman Qiu
- College of Chemical Engineering, Fuzhou University, Fuzhou, P. R. China
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, P. R. China
- Mengchao Med-X Center, Fuzhou University, Fuzhou, P. R. China
| | - Hongbing Ji
- Radiotherapy Department, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China
| | - Kai Wang
- Radiotherapy Department, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China
| | - Wenhan Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China
| | - Qizhen Huang
- Radiotherapy Department, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China
| | - Xinting Pan
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, P. R. China
- Mengchao Med-X Center, Fuzhou University, Fuzhou, P. R. China
| | - Honghao Ye
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China
| | - Zhenli Li
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, P. R. China
- Mengchao Med-X Center, Fuzhou University, Fuzhou, P. R. China
| | - Geng Chen
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, P. R. China
- Mengchao Med-X Center, Fuzhou University, Fuzhou, P. R. China
| | - Xiaohua Xing
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, P. R. China
- Mengchao Med-X Center, Fuzhou University, Fuzhou, P. R. China
| | - Xiuqing Dong
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, P. R. China
- Mengchao Med-X Center, Fuzhou University, Fuzhou, P. R. China
| | - Ruijing Tang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, P. R. China
- Mengchao Med-X Center, Fuzhou University, Fuzhou, P. R. China
| | - Haipo Xu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, P. R. China
- Mengchao Med-X Center, Fuzhou University, Fuzhou, P. R. China
| | - Jingfeng Liu
- College of Chemical Engineering, Fuzhou University, Fuzhou, P. R. China
| | - Zhixiong Cai
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China.
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, P. R. China.
- Mengchao Med-X Center, Fuzhou University, Fuzhou, P. R. China.
| | - Xiaolong Liu
- College of Chemical Engineering, Fuzhou University, Fuzhou, P. R. China.
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, P. R. China.
- The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, P. R. China.
- Mengchao Med-X Center, Fuzhou University, Fuzhou, P. R. China.
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Chen Z, Wei S, Yuan Z, Chang R, Chen X, Fu Y, Wu W. Machine learning reveals ferroptosis features and a novel ferroptosis classifier in patients with sepsis. Immun Inflamm Dis 2024; 12:e1279. [PMID: 38780016 PMCID: PMC11112629 DOI: 10.1002/iid3.1279] [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: 11/06/2023] [Revised: 04/24/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
OBJECTIVE Sepsis is an organ malfunction disease that may become fatal and is commonly accompanied by severe complications such as multiorgan dysfunction. Patients who are already hospitalized have a high risk of death due to sepsis. Even though early diagnosis is very important, the technology and clinical approaches that are now available are inadequate. Hence, there is an immediate necessity to investigate biological markers that are sensitive, specific, and reliable for the prompt detection of sepsis to reduce mortality and improve patient prognosis. Mounting research data indicate that ferroptosis contributes to the occurrence, development, and prevention of sepsis. However, the specific regulatory mechanism of ferroptosis remains to be elucidated. This research evaluated the expression profiles of ferroptosis-related genes (FRGs) and the diagnostic significance of the ferroptosis-related classifiers in sepsis. METHODS AND RESULTS We collected three peripheral blood data sets from septic patients, integrated the clinical examination data and mRNA expression profile of these patients, and identified 13 FRGs in sepsis through a co-expression network and differential analysis. Then, an optimal classifier tool for sepsis was constructed by integrating a variety of machine learning algorithms. Two key genes, ATG16L1 and SRC, were shown to be shared between the algorithms, and thus were identified as the FRG signature of classifier. The tool exhibited satisfactory diagnostic efficiency in the training data set (AUC = 0.711) and two external verification data sets (AUC = 0.961; AUC = 0.913). In the rat cecal ligation puncture sepsis model, in vivo experiments verified the involvement of ATG16L1 and SRC in the early sepsis process. CONCLUSION These findings confirm that FRGs may participate in the development of sepsis, the ferroptosis related classifiers can provide a basis for the development of new strategies for the early diagnosis of sepsis and the discovery of new potential therapeutic targets for life-threatening infections.
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Affiliation(s)
- Zhigang Chen
- Department of Anesthesiology, Shanghai Pulmonary Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Shiyou Wei
- Department of Anesthesiology, Shanghai Pulmonary Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Zhize Yuan
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Rui Chang
- Medical Department, Shanghai Pulmonary Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Xue Chen
- Department of Anesthesiology, Shanghai Pulmonary Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Yu Fu
- Department of Anesthesiology, Shanghai Pulmonary Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Wei Wu
- Department of Anesthesiology, Shanghai Pulmonary Hospital, School of MedicineTongji UniversityShanghaiChina
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Vinik Y, Maimon A, Dubey V, Raj H, Abramovitch I, Malitsky S, Itkin M, Ma'ayan A, Westermann F, Gottlieb E, Ruppin E, Lev S. Programming a Ferroptosis-to-Apoptosis Transition Landscape Revealed Ferroptosis Biomarkers and Repressors for Cancer Therapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307263. [PMID: 38441406 PMCID: PMC11077643 DOI: 10.1002/advs.202307263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 02/11/2024] [Indexed: 05/09/2024]
Abstract
Ferroptosis and apoptosis are key cell-death pathways implicated in several human diseases including cancer. Ferroptosis is driven by iron-dependent lipid peroxidation and currently has no characteristic biomarkers or gene signatures. Here a continuous phenotypic gradient between ferroptosis and apoptosis coupled to transcriptomic and metabolomic landscapes is established. The gradual ferroptosis-to-apoptosis transcriptomic landscape is used to generate a unique, unbiased transcriptomic predictor, the Gradient Gene Set (GGS), which classified ferroptosis and apoptosis with high accuracy. Further GGS optimization using multiple ferroptotic and apoptotic datasets revealed highly specific ferroptosis biomarkers, which are robustly validated in vitro and in vivo. A subset of the GGS is associated with poor prognosis in breast cancer patients and PDXs and contains different ferroptosis repressors. Depletion of one representative, PDGFA-assaociated protein 1(PDAP1), is found to suppress basal-like breast tumor growth in a mouse model. Omics and mechanistic studies revealed that ferroptosis is associated with enhanced lysosomal function, glutaminolysis, and the tricarboxylic acid (TCA) cycle, while its transition into apoptosis is attributed to enhanced endoplasmic reticulum(ER)-stress and phosphatidylethanolamine (PE)-to-phosphatidylcholine (PC) metabolic shift. Collectively, this study highlights molecular mechanisms underlying ferroptosis execution, identified a highly predictive ferroptosis gene signature with prognostic value, ferroptosis versus apoptosis biomarkers, and ferroptosis repressors for breast cancer therapy.
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Affiliation(s)
- Yaron Vinik
- Molecular Cell Biology DepartmentWeizmann Institute of ScienceRehovot76100Israel
| | - Avi Maimon
- Molecular Cell Biology DepartmentWeizmann Institute of ScienceRehovot76100Israel
| | - Vinay Dubey
- Molecular Cell Biology DepartmentWeizmann Institute of ScienceRehovot76100Israel
| | - Harsha Raj
- Molecular Cell Biology DepartmentWeizmann Institute of ScienceRehovot76100Israel
| | - Ifat Abramovitch
- The Ruth and Bruce RappaportFaculty of MedicineTechnion–Israel Institute of TechnologyHaifa3525433Israel
| | - Sergey Malitsky
- Metabolic Profiling UnitWeizmann Institute of ScienceRehovot76100Israel
| | - Maxim Itkin
- Metabolic Profiling UnitWeizmann Institute of ScienceRehovot76100Israel
| | - Avi Ma'ayan
- Department of Pharmacological SciencesMount Sinai Center for BioinformaticsIcahn School of Medicine at Mount SinaiNew YorkNY10029USA
| | - Frank Westermann
- Neuroblastoma GenomicsGerman Cancer Research Center (DKFZ)69120HeidelbergGermany
| | - Eyal Gottlieb
- The Ruth and Bruce RappaportFaculty of MedicineTechnion–Israel Institute of TechnologyHaifa3525433Israel
| | - Eytan Ruppin
- Cancer Data Science LaboratoryNational Cancer InstituteNational Institutes of HealthBethesdaMD20892USA
| | - Sima Lev
- Molecular Cell Biology DepartmentWeizmann Institute of ScienceRehovot76100Israel
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Zhu L, Zhou J, Yu C, Gu L, Wang Q, Xu H, Zhu Y, Guo M, Hu M, Peng W, Fang H, Wang H. Unraveling the Molecular Regulation of Ferroptosis in Respiratory Diseases. J Inflamm Res 2024; 17:2531-2546. [PMID: 38689798 PMCID: PMC11059637 DOI: 10.2147/jir.s457092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 04/06/2024] [Indexed: 05/02/2024] Open
Abstract
Ferroptosis, a type of programmed cell death that relies on iron, is distinct in terms of its morphological, biochemical and genetic features. Unlike other forms of cell death, such as autophagy, apoptosis, necrosis, and pyroptosis, ferroptosis is primarily caused by lipid peroxidation. Cells that die due to iron can potentially trigger an immune response which intensifies inflammation and causes severe inflammatory reactions that eventually lead to multiple organ failure. In recent years, ferroptosis has been identified in an increasing number of medical fields, including neurological pathologies, chronic liver diseases and sepsis. Ferroptosis has the potential to cause an inflammatory tempest, with many of the catalysts and pathological indications of respiratory ailments being linked to inflammatory reactions. The growing investigation into ferroptosis in respiratory disorders has also garnered significant interest to better understand the mechanism of ferroptosis in these diseases. In this review, the recent progress in understanding the molecular control of ferroptosis and its mechanism in different respiratory disorders is examined. In addition, this review discusses current challenges and prospects for understanding the link between respiratory diseases and ferroptosis.
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Affiliation(s)
- Lujian Zhu
- Department of Infectious Diseases, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, People’s Republic of China
| | - Jing Zhou
- Department of Infectious Diseases, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, People’s Republic of China
| | - Chen Yu
- Department of Respiratory and Critical Care Medicine, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, People’s Republic of China
| | - Lei Gu
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Soochow University, Suzhou, People’s Republic of China
| | - Qin Wang
- Department of Infectious Diseases, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, People’s Republic of China
| | - Hanglu Xu
- Department of Infectious Diseases, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, People’s Republic of China
| | - Yin Zhu
- Department of Infectious Diseases, Taizhou Enze Medical Center (Group), Enze Hospital, Taizhou, People’s Republic of China
| | - Maodong Guo
- Department of Gastroenterology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, People’s Republic of China
| | - Minli Hu
- Department of Gastroenterology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, People’s Republic of China
| | - Wei Peng
- Department of Intensive Care Unit, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, People’s Republic of China
| | - Hao Fang
- Department of Trauma Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, People’s Republic of China
| | - Haizhen Wang
- Department of Health Management Center, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, People’s Republic of China
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Wang Y, Xu X, Shui X, Ren R, Liu Y. Molecular subtype identification of cerebral ischemic stroke based on ferroptosis-related genes. Sci Rep 2024; 14:9350. [PMID: 38653998 PMCID: PMC11039763 DOI: 10.1038/s41598-024-53327-2] [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: 07/18/2023] [Accepted: 01/31/2024] [Indexed: 04/25/2024] Open
Abstract
Cerebral ischemic stroke (CIS) has the characteristics of a high incidence, disability, and mortality rate. Here, we aimed to explore the potential pathogenic mechanisms of ferroptosis-related genes (FRGs) in CIS. Three microarray datasets from the Gene Expression Omnibus (GEO) database were utilized to analyze differentially expressed genes (DEGs) between CIS and normal controls. FRGs were obtained from a literature report and the FerrDb database. Weighted gene co-expression network analysis (WGCNA) and protein-protein interaction (PPI) network were used to screen hub genes. The receiver operating characteristic (ROC) curve was adopted to evaluate the diagnostic value of key genes in CIS, followed by analysis of immune microenvironment, transcription factor (TF) regulatory network, drug prediction, and molecular docking. In total, 128 CIS samples were divided into 2 subgroups after clustering analysis. Compared with cluster A, 1560 DEGs were identified in cluster B. After the construction of the WGCNA and PPI network, 5 hub genes, including MAPK3, WAS, DNAJC5, PRKCD, and GRB2, were identified for CIS. Interestingly, MAPK3 was a FRG that differentially expressed between cluster A and cluster B. The expression levels of 5 hub genes were all specifically highly in cluster A subtype. It is noted that neutrophils were the most positively correlated with all 5 real hub genes. PRKCD was one of the target genes of FASUDIL. In conclusion, five real hub genes were identified as potential diagnostic markers, which can distinguish the two subtypes well.
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Affiliation(s)
- Yufeng Wang
- Department of Neurosurgery, Shanxi Cardiovascular Hospital, No.18, Yifen Street, Taiyuan City, 030024, Shanxi Province, China.
| | - Xinjuan Xu
- Department of Neurosurgery, Shanxi Cardiovascular Hospital, No.18, Yifen Street, Taiyuan City, 030024, Shanxi Province, China
| | - Xinjun Shui
- Department of Neurosurgery, Shanxi Cardiovascular Hospital, No.18, Yifen Street, Taiyuan City, 030024, Shanxi Province, China
| | - Ruilin Ren
- Department of Neurosurgery, Shanxi Cardiovascular Hospital, No.18, Yifen Street, Taiyuan City, 030024, Shanxi Province, China
| | - Yu Liu
- Department of Surgical, Peking University First Hospital Taiyuan, Taiyuan, China
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Zong K, Lin C, Luo K, Deng Y, Wang H, Hu J, Chen S, Li R. Ferroptosis-related lncRNA NRAV affects the prognosis of hepatocellular carcinoma via the miR-375-3P/SLC7A11 axis. BMC Cancer 2024; 24:496. [PMID: 38637761 PMCID: PMC11027313 DOI: 10.1186/s12885-024-12265-y] [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: 08/16/2023] [Accepted: 04/15/2024] [Indexed: 04/20/2024] Open
Abstract
Ferroptosis has important value in cancer treatment. It is significant to explore the new ferroptosis-related lncRNAs prediction model in Hepatocellular carcinoma (HCC) and the potential molecular mechanism of ferroptosis-related lncRNAs. We constructed a prognostic multi-lncRNA signature based on ferroptosis-related differentially expressed lncRNAs in HCC. qRT-PCR was applied to determine the expression of lncRNA in HCC cells. The biological roles of NRAV in vitro and in vivo were determined by performing a series of functional experiments. Furthermore, dual-luciferase reporter and RNA immunoprecipitation (RIP) assays were used to confirm the interaction of NRAV with miR-375-3P. We identified 6 differently expressed lncRNAs associated with the prognosis of HCC. Kaplan-Meier analyses revealed the high-risk lncRNAs signature associated with poor prognosis of HCC. Moreover, the AUC of the lncRNAs signature showed utility in predicting HCC prognosis. Further functional experiments show that the high expression of NRAV can strengthen the viciousness of HCC. Interestingly, we found that NRAV can enhance iron export and ferroptosis resistance. Further study showed that NRAV competitively binds to miR-375-3P and attenuates the inhibitory effect of miR-375-3P on SLC7A11, affecting the prognosis of patients with HCC. In conclusion, We developed a novel ferroptosis-related lncRNAs prognostic model with important predictive value for the prognosis of HCC. NRAV is important in ferroptosis induction through the miR-375-3P/SLC7A11 axis.
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Affiliation(s)
- Ke Zong
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Caifeng Lin
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, No. 134, East Street, Fuzhou, Fujian Province, 350001, PR China
- Department of Hepatopancreatobiliary Surgery, Fujian Provincial Hospital, No. 134, East Street, Fuzhou, Fujian Province, 350001, PR China
| | - Kai Luo
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Yilei Deng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Hongfei Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Jianfei Hu
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, No. 134, East Street, Fuzhou, Fujian Province, 350001, PR China
- Department of Hepatopancreatobiliary Surgery, Fujian Provincial Hospital, No. 134, East Street, Fuzhou, Fujian Province, 350001, PR China
| | - Shi Chen
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, No. 134, East Street, Fuzhou, Fujian Province, 350001, PR China.
- Department of Hepatopancreatobiliary Surgery, Fujian Provincial Hospital, No. 134, East Street, Fuzhou, Fujian Province, 350001, PR China.
| | - Renfeng Li
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China.
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Zhao Z, Xing N, Guo H, Li J, Sun G. Identification of Lower Grade Glioma Antigens Based on Ferroptosis Status for mRNA Vaccine Development. Pharmgenomics Pers Med 2024; 17:105-123. [PMID: 38623558 PMCID: PMC11018127 DOI: 10.2147/pgpm.s449230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 03/16/2024] [Indexed: 04/17/2024] Open
Abstract
Purpose mRNA vaccines represent a promising and innovative strategy within the realm of cancer immunotherapy. However, their efficacy in treating lower-grade glioma (LGG) requires evaluation. Ferroptosis exhibits close associations with the initiation, evolution, and suppression of cancer. In this study, we explored the landscape of the ferroptosis-associated tumor microenvironment to facilitate the development of mRNA vaccines for LGG patients. Patients and Methods Genomic and clinical data of the LGG patients was obtained from the Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) databases. Ferroptosis-related tumor antigens were identified based on differential expression, mutation status, correlation with antigen-presenting cells, and prognosis, relevance to immunogenic cell death (ICD). Antigen expression levels in LGG specimens and cell lines were validated using real time-polymerase chain reaction (RT-PCR). Consensus clustering was employed for patient classification. The immune landscapes of ferroptosis subtypes were further characterized, including immune responses, prognostic ability, tumor microenvironment, and tumor-related signatures. Results Five tumor antigens, namely, HOTAIR, IDO1, KIF20A, NR5A2, and RRM2 were identified in LGG. RT-PCR demonstrated higher expression of these genes in LGG compared to the control. Twelve gene modules and four ferroptosis subtypes (FS1-FS4) of LGG were defined. FS2 and FS4, characterized as "cold" tumors due to their decreased tumor mutation burden (TMB) and immune checkpoint proteins (ICPs), were deemed appropriate candidates for the mRNA vaccine. Conclusion HOTAIR, IDO1, KIF20A, NR5A2, and RRM2 were identified as promising candidate antigens for the development of an LGG mRNA vaccine, particularly offering potential benefits to FS2 and FS4 patients.
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Affiliation(s)
- Zhenxiang Zhao
- Department of Neurosurgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, 050000, People’s Republic of China
| | - Na Xing
- Department of Endocrinology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, 050000, People’s Republic of China
| | - Hao Guo
- Department of Hepatobiliary Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, 050000, People’s Republic of China
| | - Jianfeng Li
- Department of Neurosurgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, 050000, People’s Republic of China
| | - Guozhu Sun
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, People’s Republic of China
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Prosz A, Sahgal P, Huffman BM, Sztupinszki Z, Morris CX, Chen D, Börcsök J, Diossy M, Tisza V, Spisak S, Likasitwatanakul P, Rusz O, Csabai I, Cecchini M, Baca Y, Elliott A, Enzinger P, Singh H, Ubellaker J, Lazaro JB, Cleary JM, Szallasi Z, Sethi NS. Mutational signature-based identification of DNA repair deficient gastroesophageal adenocarcinomas for therapeutic targeting. NPJ Precis Oncol 2024; 8:87. [PMID: 38589664 PMCID: PMC11001913 DOI: 10.1038/s41698-024-00561-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/22/2024] [Indexed: 04/10/2024] Open
Abstract
Homologous recombination (HR) and nucleotide excision repair (NER) are the two most frequently disabled DNA repair pathways in cancer. HR-deficient breast, ovarian, pancreatic and prostate cancers respond well to platinum chemotherapy and PARP inhibitors. However, the frequency of HR deficiency in gastric and esophageal adenocarcinoma (GEA) still lacks diagnostic and functional validation. Using whole exome and genome sequencing data, we found that a significant subset of GEA, but very few colorectal adenocarcinomas, show evidence of HR deficiency by mutational signature analysis (HRD score). High HRD gastric cancer cell lines demonstrated functional HR deficiency by RAD51 foci assay and increased sensitivity to platinum chemotherapy and PARP inhibitors. Of clinical relevance, analysis of three different GEA patient cohorts demonstrated that platinum treated HR deficient cancers had better outcomes. A gastric cancer cell line with strong sensitivity to cisplatin showed HR proficiency but exhibited NER deficiency by two photoproduct repair assays. Single-cell RNA-sequencing revealed that, in addition to inducing apoptosis, cisplatin treatment triggered ferroptosis in a NER-deficient gastric cancer, validated by intracellular GSH assay. Overall, our study provides preclinical evidence that a subset of GEAs harbor genomic features of HR and NER deficiency and may therefore benefit from platinum chemotherapy and PARP inhibitors.
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Affiliation(s)
- Aurel Prosz
- Danish Cancer Institute, Copenhagen, Denmark
| | - Pranshu Sahgal
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Brandon M Huffman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Gastrointestinal Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zsofia Sztupinszki
- Danish Cancer Institute, Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Clare X Morris
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David Chen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | | | - Miklos Diossy
- Danish Cancer Institute, Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Viktoria Tisza
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Sandor Spisak
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Pornlada Likasitwatanakul
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Orsolya Rusz
- 2nd Department of Pathology, SE NAP, Brain Metastasis Research Group, Semmelweis University, Budapest, Hungary
| | - Istvan Csabai
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
| | - Michael Cecchini
- Department of Medical Oncology, Center for Gastrointestinal Cancers, Yale Medical Center, New Haven, CT, USA
| | | | | | - Peter Enzinger
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastrointestinal Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Harshabad Singh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastrointestinal Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jessalyn Ubellaker
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jean-Bernard Lazaro
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for DNA Damage and Repair (CDDR), Dana-Farber Cancer Institute, Boston, MA, USA
| | - James M Cleary
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastrointestinal Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zoltan Szallasi
- Danish Cancer Institute, Copenhagen, Denmark.
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA.
- Department of Bioinformatics and Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary.
| | - Nilay S Sethi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA.
- Division of Gastrointestinal Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
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Li Y, Fu Q, Fang J, Xu Z, Zhang C, Tan L, Liao X, Wu Y. Analysis of ceRNA Network and Identification of Potential Treatment Target and Biomarkers of Endothelial Cell Injury in Sepsis. Genet Test Mol Biomarkers 2024; 28:133-143. [PMID: 38501698 DOI: 10.1089/gtmb.2023.0143] [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] [Indexed: 03/20/2024] Open
Abstract
Background: Sepsis is a complex clinical syndrome caused by a dysregulated host immune response to infection. This study aimed to identify a competing endogenous RNA (ceRNA) network that can greatly contribute to understanding the pathophysiological process of sepsis and determining sepsis biomarkers. Methods: The GSE100159, GSE65682, GSE167363, and GSE94717 datasets were obtained from the Gene Expression Omnibus (GEO) database. Weighted gene coexpression network analysis was performed to find modules possibly involved in sepsis. A long noncoding RNA-microRNA-messenger RNA (lncRNA-miRNA-mRNA) network was constructed based on the findings. Single-cell analysis was performed. Human umbilical vein endothelial cells were treated with lipopolysaccharide (LPS) to create an in vitro model of sepsis for network verification. Reverse transcription-polymerase chain reaction, fluorescence in situ hybridization, and luciferase reporter genes were used to verify the bioinformatic analysis. Result: By integrating data from three GEO datasets, we successfully constructed a ceRNA network containing 18 lncRNAs, 7 miRNAs, and 94 mRNAs based on the ceRNA hypothesis. The lncRNA ZFAS1 was found to be highly expressed in LPS-stimulated endothelial cells and may thus play a role in endothelial cell injury. Univariate and multivariate Cox analyses showed that only SLC26A6 was an independent predictor of prognosis in sepsis. Overall, our findings indicated that the ZFAS1/hsa-miR-449c-5p/SLC26A6 ceRNA regulatory axis may play a role in the progression of sepsis. Conclusion: The sepsis ceRNA network, especially the ZFAS1/hsa-miR-449c-5p/SLC26A6 regulatory axis, is expected to reveal potential biomarkers and therapeutic targets for sepsis management.
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Affiliation(s)
- Yulin Li
- The Department of Emergency, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Qinghui Fu
- The Department of SICU, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Junjun Fang
- The Department of SICU, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Zhipeng Xu
- The Department of SICU, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Chunhu Zhang
- The Department of SICU, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Longwei Tan
- The Department of SICU, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Xin Liao
- The Department of SICU, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Yao Wu
- The Department of SICU, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
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Akiyama H, Zhao R, Ostermann LB, Li Z, Tcheng M, Yazdani SJ, Moayed A, Pryor ML, Slngh S, Baran N, Ayoub E, Nishida Y, Mak PY, Ruvolo VR, Carter BZ, Schimmer AD, Andreeff M, Ishizawa J. Mitochondrial regulation of GPX4 inhibition-mediated ferroptosis in acute myeloid leukemia. Leukemia 2024; 38:729-740. [PMID: 38148395 PMCID: PMC11082873 DOI: 10.1038/s41375-023-02117-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 12/02/2023] [Accepted: 12/08/2023] [Indexed: 12/28/2023]
Abstract
Resistance to apoptosis in acute myeloid leukemia (AML) cells causes refractory or relapsed disease, associated with dismal clinical outcomes. Ferroptosis, a mode of non-apoptotic cell death triggered by iron-dependent lipid peroxidation, has been investigated as potential therapeutic modality against therapy-resistant cancers, but our knowledge of its role in AML is limited. We investigated ferroptosis in AML cells and identified its mitochondrial regulation as a therapeutic vulnerability. GPX4 knockdown induced ferroptosis in AML cells, accompanied with characteristic mitochondrial lipid peroxidation, exerting anti-AML effects in vitro and in vivo. Electron transport chains (ETC) are primary sources of coenzyme Q10 (CoQ) recycling for its function of anti-lipid peroxidation in mitochondria. We found that the mitochondria-specific CoQ potently inhibited GPX4 inhibition-mediated ferroptosis, suggesting that mitochondrial lipid redox regulates ferroptosis in AML cells. Consistently, Rho0 cells, which lack functional ETC, were more sensitive to GPX4 inhibition-mediated mitochondrial lipid peroxidation and ferroptosis than control cells. Furthermore, degradation of ETC through hyperactivation of a mitochondrial protease, caseinolytic protease P (ClpP), synergistically enhanced the anti-AML effects of GPX4 inhibition. Collectively, our findings indicate that in AML cells, GPX4 inhibition induces ferroptosis, which is regulated by mitochondrial lipid redox and ETC.
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Affiliation(s)
- Hiroki Akiyama
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ran Zhao
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lauren B Ostermann
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ziyi Li
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Matthew Tcheng
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Samar J Yazdani
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Arman Moayed
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Malcolm L Pryor
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sandeep Slngh
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Natalia Baran
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Edward Ayoub
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yuki Nishida
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Po Yee Mak
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vivian R Ruvolo
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bing Z Carter
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Aaron D Schimmer
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Michael Andreeff
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jo Ishizawa
- Section of Molecular Hematology and Therapy, Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Xiao W, Lai Y, Yang H, Que H. Predictive Role of a Novel Ferroptosis-Related lncRNA Pairs Model in the Prognosis of Papillary Thyroid Carcinoma. Biochem Genet 2024; 62:775-797. [PMID: 37436560 DOI: 10.1007/s10528-023-10447-0] [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: 02/27/2023] [Accepted: 06/29/2023] [Indexed: 07/13/2023]
Abstract
This study aimed to evaluate the potential prognostic value of ferroptosis-related long non-coding RNAs (lncRNAs) in papillary thyroid carcinoma (PTC). Based on The TCGA database, lncRNAs and ferroptosis-related genes with differential expression levels in PTC tumors vs. normal tissues were screened. After the co-expression network construction, ferroptosis-related lncRNAs (FRLs) were screened. Kaplan-Meier analysis was conducted to compare the survival performance of patients with PTC in the high- and low-risk groups. Furthermore, a nomogram was created to enhance PTC prognosis. CIBERSORT was used to investigate the infiltration of various immune cells in high- and low-risk groups. In total, 10 lncRNA pairs with differential expression levels were obtained. There were significant differences in the histological subtype and pathological stage between the high- and low-risk groups, and age (P = 7.39E-13) and FRLM model status (P = 1.09E-04) were identified as independent prognostic factors. Subsequently, the nomogram survival model showed that the predicted one-, three-, and five-year survival rates were similar to the actual one- (c-index = 0.8475), three- (c-index = 0.7964), and five-year (c-index = 0.7555) survival rates. Subjects in the low-risk group had significantly more CD4 + memory T cells and resting myeloid dendritic cells, and subjects in the high-risk group had more plasma B cells and monocytes. The risk assessment model constructed using FRLs showed good predictive value for the prognosis of patients with PTC.
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Affiliation(s)
- Wen Xiao
- Department of Traditional Chinese Surgery, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Yi Lai
- Department of Head and Neck Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200127, China
| | - Haojie Yang
- Department of Coloproctology, Yueyang Hospital of Integrated Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, No.1200, Cailun Road, Shanghai, 200032, China.
| | - Huafa Que
- Department of Traditional Chinese Surgery, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China.
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Zhou Y, Chen Z, Yang M, Chen F, Yin J, Zhang Y, Zhou X, Sun X, Ni Z, Chen L, Lv Q, Zhu F, Liu S. FERREG: ferroptosis-based regulation of disease occurrence, progression and therapeutic response. Brief Bioinform 2024; 25:bbae223. [PMID: 38742521 PMCID: PMC11091744 DOI: 10.1093/bib/bbae223] [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: 10/17/2023] [Revised: 03/25/2024] [Accepted: 04/21/2024] [Indexed: 05/16/2024] Open
Abstract
Ferroptosis is a non-apoptotic, iron-dependent regulatory form of cell death characterized by the accumulation of intracellular reactive oxygen species. In recent years, a large and growing body of literature has investigated ferroptosis. Since ferroptosis is associated with various physiological activities and regulated by a variety of cellular metabolism and mitochondrial activity, ferroptosis has been closely related to the occurrence and development of many diseases, including cancer, aging, neurodegenerative diseases, ischemia-reperfusion injury and other pathological cell death. The regulation of ferroptosis mainly focuses on three pathways: system Xc-/GPX4 axis, lipid peroxidation and iron metabolism. The genes involved in these processes were divided into driver, suppressor and marker. Importantly, small molecules or drugs that mediate the expression of these genes are often good treatments in the clinic. Herein, a newly developed database, named 'FERREG', is documented to (i) providing the data of ferroptosis-related regulation of diseases occurrence, progression and drug response; (ii) explicitly describing the molecular mechanisms underlying each regulation; and (iii) fully referencing the collected data by cross-linking them to available databases. Collectively, FERREG contains 51 targets, 718 regulators, 445 ferroptosis-related drugs and 158 ferroptosis-related disease responses. FERREG can be accessed at https://idrblab.org/ferreg/.
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Affiliation(s)
- Yuan Zhou
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, School of Pharmacy, and Department of Respiratory Medicine of Affiliated Hospital, Hangzhou Normal University, Hangzhou, 311121, China
| | - Zhen Chen
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Mengjie Yang
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, School of Pharmacy, and Department of Respiratory Medicine of Affiliated Hospital, Hangzhou Normal University, Hangzhou, 311121, China
| | - Fengyun Chen
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, School of Pharmacy, and Department of Respiratory Medicine of Affiliated Hospital, Hangzhou Normal University, Hangzhou, 311121, China
| | - Jiayi Yin
- Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine
| | - Yintao Zhang
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Xuheng Zhou
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Xiuna Sun
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Ziheng Ni
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, School of Pharmacy, and Department of Respiratory Medicine of Affiliated Hospital, Hangzhou Normal University, Hangzhou, 311121, China
| | - Lu Chen
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, School of Pharmacy, and Department of Respiratory Medicine of Affiliated Hospital, Hangzhou Normal University, Hangzhou, 311121, China
| | - Qun Lv
- Department of Respiratory, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, 311121, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, 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
| | - Shuiping Liu
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, School of Pharmacy, and Department of Respiratory Medicine of Affiliated Hospital, Hangzhou Normal University, Hangzhou, 311121, China
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47
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Xiang S, Yan W, Ren X, Feng J, Zu X. Role of ferroptosis and ferroptosis-related long non'coding RNA in breast cancer. Cell Mol Biol Lett 2024; 29:40. [PMID: 38528461 DOI: 10.1186/s11658-024-00560-2] [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: 12/18/2023] [Accepted: 03/15/2024] [Indexed: 03/27/2024] Open
Abstract
Ferroptosis, a therapeutic strategy for tumours, is a regulated cell death characterised by the increased accumulation of iron-dependent lipid peroxides (LPO). Tumour-associated long non-coding RNAs (lncRNAs), when combined with traditional anti-cancer medicines or radiotherapy, can improve efficacy and decrease mortality in cancer. Investigating the role of ferroptosis-related lncRNAs may help strategise new therapeutic options for breast cancer (BC). Herein, we briefly discuss the genes and pathways of ferroptosis involved in iron and reactive oxygen species (ROS) metabolism, including the XC-/GSH/GPX4 system, ACSL4/LPCAT3/15-LOX and FSP1/CoQ10/NAD(P)H pathways, and investigate the correlation between ferroptosis and LncRNA in BC to determine possible biomarkers related to ferroptosis.
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Affiliation(s)
- Shasha Xiang
- Cancer Research Institute, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Wen Yan
- Cancer Research Institute, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Xing Ren
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Jianbo Feng
- Cancer Research Institute, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China.
| | - Xuyu Zu
- Cancer Research Institute, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China.
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48
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Qi YC, Bai H, Hu SL, Li SJ, Li QZ. Coregulatory effects of multiple histone modifications in key ferroptosis-related genes for lung adenocarcinoma. Epigenomics 2024; 16:609-633. [PMID: 38511238 PMCID: PMC11160448 DOI: 10.2217/epi-2023-0403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 02/22/2024] [Indexed: 03/22/2024] Open
Abstract
Aim: The present study was designed to investigate the coregulatory effects of multiple histone modifications (HMs) on gene expression in lung adenocarcinoma (LUAD). Materials & methods: Ten histones for LUAD were analyzed using ChIP-seq and RNA-seq data. An innovative computational method is proposed to quantify the coregulatory effects of multiple HMs on gene expression to identify strong coregulatory genes and regions. This method was applied to explore the coregulatory mechanisms of key ferroptosis-related genes in LUAD. Results: Nine strong coregulatory regions were identified for six ferroptosis-related genes with diverse coregulatory patterns (CA9, PGD, CDKN2A, PML, OTUB1 and NFE2L2). Conclusion: This quantitative method could be used to identify important HM coregulatory genes and regions that may be epigenetic regulatory targets in cancers.
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Affiliation(s)
- Ye-Chen Qi
- Laboratory of Theoretical Biophysics, School of Physical Science & Technology, Inner Mongolia University, Hohhot, 010021, China
| | - Hui Bai
- Laboratory of Theoretical Biophysics, School of Physical Science & Technology, Inner Mongolia University, Hohhot, 010021, China
| | - Si-Le Hu
- Laboratory of Theoretical Biophysics, School of Physical Science & Technology, Inner Mongolia University, Hohhot, 010021, China
| | - Shu-Juan Li
- Laboratory of Theoretical Biophysics, School of Physical Science & Technology, Inner Mongolia University, Hohhot, 010021, China
| | - Qian-Zhong Li
- Laboratory of Theoretical Biophysics, School of Physical Science & Technology, Inner Mongolia University, Hohhot, 010021, China
- The State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010070, China
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49
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Wang H, Li Y, Liu X, Wu Y. Identification and validation of ferroptosis-related gene SLC2A1 as a novel prognostic biomarker in AKI. Aging (Albany NY) 2024; 16:5634-5650. [PMID: 38517368 PMCID: PMC11006501 DOI: 10.18632/aging.205669] [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: 09/04/2023] [Accepted: 02/27/2024] [Indexed: 03/23/2024]
Abstract
BACKGROUND Emerging evidence reveals the key role of ferroptosis in the pathophysiological process of acute kidney injury (AKI). Our study aimed to investigate the potential ferroptosis-related gene in AKI through bioinformatics and experimental validation. METHODS The AKI single-cell sequencing dataset was retrieved from the GEO database and ferroptosis-related genes were extracted from the GENECARD website. The potential differentially expressed ferroptosis-related genes of AKI were selected. Functional enrichment analysis was performed. Machine learning algorithms were used to identify key ferroptosis-related genes associated with AKI. A multi-factor Cox regression analysis was used to construct a risk score model. The accuracy of the risk score model was validated using receiver operating characteristic (ROC) curve analysis. We extensively explored the immune landscape of AKI using CIBERSORT tool. Finally, expressions of ferroptosis DEGs were validated in vivo and in vitro by Western blot, ICH and transfection experiments. RESULTS Three hub genes (BAP1, MDM4, SLC2A1) were identified and validated by constructing drug regulatory network and subsequent screening using experimentally determined interactions. The risk mode showed the low-risk group had significantly better prognosis compared to high-risk group. The risk score was independently associated with overall survival. The ROC curve analysis showed that the prognosis model had good predictive ability. Additionally, CIBERSORT immune infiltration analysis suggest that the hub gene may influence cell recruitment and infiltration in AKI. Validation experiments revealed that SLC2A1 functions by regulating ferroptosis. CONCLUSIONS In summary, our study not only identifies SLC2A1 as diagnostic biomarker for AKI, but also sheds light on the role of it in AKI progression, providing novel insights for the clinical diagnosis and treatment of AKI.
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Affiliation(s)
- Huaying Wang
- Department of Nephrology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, PR China
| | - Yuanyuan Li
- Department of Nephrology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, PR China
| | - Xinran Liu
- Department of Nephrology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, PR China
| | - Yonggui Wu
- Department of Nephrology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, PR China
- Center for Scientific Research of Anhui Medical University, Hefei, Anhui 230022, PR China
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50
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Cao Y, Zhao W, Zhong Y, Jiang X, Mei H, Chang Y, Wu D, Dou J, Vasquez E, Shi X, Yang J, Jia Z, Tan X, Li Q, Dong Y, Xie R, Gao J, Wu Y, Liu Y. Effects of chronic low-level lead (Pb) exposure on cognitive function and hippocampal neuronal ferroptosis: An integrative approach using bioinformatics analysis, machine learning, and experimental validation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170317. [PMID: 38301787 DOI: 10.1016/j.scitotenv.2024.170317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 02/03/2024]
Abstract
Lead (Pb), a pervasive and ancient toxic heavy metal, continues to pose significant neurological health risks, particularly in regions such as Southeast Asia. While previous research has primarily focused on the adverse effects of acute, high-level lead exposure on neurological systems, studies on the impacts of chronic, low-level exposure are less extensive, especially regarding the precise mechanisms linking ferroptosis - a novel type of neuron cell death - with cognitive impairment. This study aims to explore the potential effects of chronic low-level lead exposure on cognitive function and hippocampal neuronal ferroptosis. This research represents the first comprehensive investigation into the impact of chronic low-level lead exposure on hippocampal neuronal ferroptosis, spanning clinical settings, bioinformatic analyses, and experimental validation. Our findings reveal significant alterations in the expression of genes associated with iron metabolism and Nrf2-dependent ferroptosis following lead exposure, as evidenced by comparing gene expression in the peripheral blood of lead-acid battery workers and workers without lead exposure. Furthermore, our in vitro and in vivo experimental results strongly suggest that lead exposure may precipitate cognitive dysfunction and induce hippocampal neuronal ferroptosis. In conclusion, our study indicates that chronic low-level lead exposure may activate microglia, leading to the promotion of ferroptosis in hippocampal neurons.
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Affiliation(s)
- Yingsi Cao
- Department of Pediatrics, Affiliated Hospital of Jiangnan University, Wuxi, China; Lab of Modern Environmental Toxicology, Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Wenjing Zhao
- Yangzhou Key Laboratory of Anesthesiology, Northern Jiangsu People's Hospital Affiliated to Yangzhou University, Yangzhou, China
| | - Yanqi Zhong
- Department of Radiology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Xiaofan Jiang
- Department of Pediatrics, Affiliated Hospital of Jiangnan University, Wuxi, China; Lab of Modern Environmental Toxicology, Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Huiya Mei
- Department of Pediatrics, Affiliated Hospital of Jiangnan University, Wuxi, China; Lab of Modern Environmental Toxicology, Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Yuanjin Chang
- Department of Pediatrics, Affiliated Hospital of Jiangnan University, Wuxi, China; Lab of Modern Environmental Toxicology, Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Dongqin Wu
- Department of Pediatrics, Affiliated Hospital of Jiangnan University, Wuxi, China; Lab of Modern Environmental Toxicology, Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - JianRui Dou
- Center for Disease Control and Prevention of Yangzhou, Yangzhou, China
| | - Emely Vasquez
- School of Medicine, The City University of New York School of Medicine, New York, USA
| | - Xian Shi
- Lab of Modern Environmental Toxicology, Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China; Environment and Health Research Division, Public Health Research Center, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Jiatao Yang
- Lab of Modern Environmental Toxicology, Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China; Environment and Health Research Division, Public Health Research Center, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Zhongtang Jia
- Lab of Modern Environmental Toxicology, Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China; Environment and Health Research Division, Public Health Research Center, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Xiaochao Tan
- Lab of Modern Environmental Toxicology, Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China; Environment and Health Research Division, Public Health Research Center, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Qian Li
- Lab of Modern Environmental Toxicology, Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China; Environment and Health Research Division, Public Health Research Center, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Yuying Dong
- Center for Disease Control and Prevention of Yangzhou, Yangzhou, China
| | - Ruijin Xie
- Department of Pediatrics, Affiliated Hospital of Jiangnan University, Wuxi, China; Lab of Modern Environmental Toxicology, Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Ju Gao
- Yangzhou Key Laboratory of Anesthesiology, Northern Jiangsu People's Hospital Affiliated to Yangzhou University, Yangzhou, China.
| | - Yu Wu
- Lab of Modern Environmental Toxicology, Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China; Environment and Health Research Division, Public Health Research Center, Wuxi School of Medicine, Jiangnan University, Wuxi, China; The Key Laboratory of Modern Toxicology of Ministry of Education, Nanjing Medical University, Nanjing, China.
| | - Yueying Liu
- Department of Pediatrics, Affiliated Hospital of Jiangnan University, Wuxi, China.
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