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Shi H, Yuan X, Yang X, Huang R, Fan W, Liu G. A novel diabetic foot ulcer diagnostic model: identification and analysis of genes related to glutamine metabolism and immune infiltration. BMC Genomics 2024; 25:125. [PMID: 38287255 PMCID: PMC10826017 DOI: 10.1186/s12864-024-10038-2] [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: 11/07/2023] [Accepted: 01/22/2024] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND Diabetic foot ulcer (DFU) is one of the most common and severe complications of diabetes, with vascular changes, neuropathy, and infections being the primary pathological mechanisms. Glutamine (Gln) metabolism has been found to play a crucial role in diabetes complications. This study aims to identify and validate potential Gln metabolism biomarkers associated with DFU through bioinformatics and machine learning analysis. METHODS We downloaded two microarray datasets related to DFU patients from the Gene Expression Omnibus (GEO) database, namely GSE134431, GSE68183, and GSE80178. From the GSE134431 dataset, we obtained differentially expressed Gln-metabolism related genes (deGlnMRGs) between DFU and normal controls. We analyzed the correlation between deGlnMRGs and immune cell infiltration status. We also explored the relationship between GlnMRGs molecular clusters and immune cell infiltration status. Notably, WGCNA to identify differentially expressed genes (DEGs) within specific clusters. Additionally, we conducted GSVA to annotate enriched genes. Subsequently, we constructed and screened the best machine learning model. Finally, we validated the predictions' accuracy using a nomogram, calibration curves, decision curve analysis (DCA), and the GSE134431, GSE68183, and GSE80178 dataset. RESULTS In both the DFU and normal control groups, we confirmed the presence of deGlnMRGs and an activated immune response. From the GSE134431 dataset, we obtained 20 deGlnMRGs, including CTPS1, NAGS, SLC7A11, GGT1, GCLM, RIMKLA, ARG2, ASL, ASNS, ASNSD1, PPAT, GLS2, GLUD1, MECP2, ASS1, PRODH, CTPS2, ALDH5A1, DGLUCY, and SLC25A12. Furthermore, two clusters were identified in DFU. Immune infiltration analysis indicated the presence of immune heterogeneity in these two clusters. Additionally, we established a Support Vector Machine (SVM) model based on 5 genes (R3HCC1, ZNF562, MFN1, DRAM1, and PTGDS), which exhibited excellent performance on the external validation datasetGSE134431, GSE68183, and GSE80178 (AUC = 0.929). CONCLUSION This study has identified five Gln metabolism genes associated with DFU, revealing potential novel biomarkers and therapeutic targets for DFU. Additionally, the infiltration of immune-inflammatory cells plays a crucial role in the progression of DFU.
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Affiliation(s)
- Hongshuo Shi
- Department of Peripheral Vascular Surgery, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xin Yuan
- Department of Peripheral Vascular Surgery, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiao Yang
- Department of Peripheral Vascular Surgery, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Renyan Huang
- Department of Peripheral Vascular Surgery, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.
| | - Weijing Fan
- Department of Peripheral Vascular Surgery, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.
| | - Guobin Liu
- Department of Peripheral Vascular Surgery, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.
- Guangming Traditional Chinese Medicine Hospital Pudong New Area, Shanghai, China.
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Cheng Y, Qu Z, Jiang Q, Xu T, Zheng H, Ye P, He M, Tong Y, Ma Y, Bao A. Functional Materials for Subcellular Targeting Strategies in Cancer Therapy: Progress and Prospects. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023:e2305095. [PMID: 37665594 DOI: 10.1002/adma.202305095] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/26/2023] [Indexed: 09/05/2023]
Abstract
Neoadjuvant and adjuvant therapies have made significant progress in cancer treatment. However, tumor adjuvant therapy still faces challenges due to the intrinsic heterogeneity of cancer, genomic instability, and the formation of an immunosuppressive tumor microenvironment. Functional materials possess unique biological properties such as long circulation times, tumor-specific targeting, and immunomodulation. The combination of functional materials with natural substances and nanotechnology has led to the development of smart biomaterials with multiple functions, high biocompatibilities, and negligible immunogenicities, which can be used for precise cancer treatment. Recently, subcellular structure-targeting functional materials have received particular attention in various biomedical applications including the diagnosis, sensing, and imaging of tumors and drug delivery. Subcellular organelle-targeting materials can precisely accumulate therapeutic agents in organelles, considerably reduce the threshold dosages of therapeutic agents, and minimize drug-related side effects. This review provides a systematic and comprehensive overview of the research progress in subcellular organelle-targeted cancer therapy based on functional nanomaterials. Moreover, it explains the challenges and prospects of subcellular organelle-targeting functional materials in precision oncology. The review will serve as an excellent cutting-edge guide for researchers in the field of subcellular organelle-targeted cancer therapy.
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Affiliation(s)
- Yanxiang Cheng
- Department of Gynecology, Renmin Hospital, Wuhan University, No.238 Jiefang Road, Wuchang, Wuhan, 430060, P. R. China
| | - Zhen Qu
- Department of Blood Transfusion Research, Wuhan Blood Center (WHBC), HUST-WHBC United Hematology Optical Imaging Center, No.8 Baofeng 1st Road, Wuhan, Hubei, 430030, P. R. China
| | - Qian Jiang
- Department of Blood Transfusion Research, Wuhan Blood Center (WHBC), HUST-WHBC United Hematology Optical Imaging Center, No.8 Baofeng 1st Road, Wuhan, Hubei, 430030, P. R. China
| | - Tingting Xu
- Department of Clinical Laboratory, Wuhan Blood Center (WHBC), No.8 Baofeng 1st Road, Wuhan, Hubei, 430030, P. R. China
| | - Hongyun Zheng
- Department of Clinical Laboratory, Renmin Hospital, Wuhan University, No.238 Jiefang Road, Wuchang, Wuhan, 430060, P. R. China
| | - Peng Ye
- Department of Pharmacy, Renmin Hospital, Wuhan University, No.238 Jiefang Road, Wuchang, Wuhan, 430060, P. R. China
| | - Mingdi He
- Department of Blood Transfusion Research, Wuhan Blood Center (WHBC), HUST-WHBC United Hematology Optical Imaging Center, No.8 Baofeng 1st Road, Wuhan, Hubei, 430030, P. R. China
| | - Yongqing Tong
- Department of Clinical Laboratory, Renmin Hospital, Wuhan University, No.238 Jiefang Road, Wuchang, Wuhan, 430060, P. R. China
| | - Yan Ma
- Department of Blood Transfusion Research, Wuhan Blood Center (WHBC), HUST-WHBC United Hematology Optical Imaging Center, No.8 Baofeng 1st Road, Wuhan, Hubei, 430030, P. R. China
| | - Anyu Bao
- Department of Clinical Laboratory, Renmin Hospital, Wuhan University, No.238 Jiefang Road, Wuchang, Wuhan, 430060, P. R. China
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Tan J, Zhang J, Wang M, Wang Y, Dong M, Ma X, Sun B, Liu S, Zhao Z, Chen L, Jin W, Liu K, Xin Y, Zhuang L. DRAM1 increases the secretion of PKM2-enriched EVs from hepatocytes to promote macrophage activation and disease progression in ALD. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:375-389. [PMID: 35036051 PMCID: PMC8728309 DOI: 10.1016/j.omtn.2021.12.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/09/2021] [Indexed: 11/24/2022]
Abstract
DNA damage-regulated autophagy modulator 1 (DRAM1) could play important roles in inflammation and hepatic apoptosis, while its roles in alcohol-related liver disease (ALD), which is characterized by hepatic inflammation and apoptosis, are still unclear. In this study, we explored the expression, role, and mechanism of DRAM1 in ALD. Firstly, our results showed that DRAM1 was significantly increased in liver tissues of mice at the early stage of alcohol treatment. In addition, DRAM1 knockout reduced, and liver-specific overexpression of DRAM1 aggravated, alcohol-induced hepatic steatosis, injury, and expressions of M1 macrophage markers in mice. Furthermore, ethanol-induced DRAM1 of hepatic cells increased pyruvate kinase M2 (PKM2)-enriched extracellular vesicles (EVs), and ectosomes derived from hepatic cells with DRAM1 overexpression promoted macrophage activation. Mechanistic investigations showed that DRAM1 interacted with PKM2 and increased the PKM2 level in plasma membrane. At last, DRAM1 was significantly increased in liver tissues of ALD patients, and it was positively correlated with M1 macrophage markers. Taken together, this study revealed that ethanol-induced DRAM1 of hepatic cells could increase the PKM2-enriched EVs, promote macrophage activation, and aggravate the disease progression of ALD. These findings suggested that DRAM1 might be a potentially promising target for the therapy of ALD.
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Affiliation(s)
- Jie Tan
- Department of Infectious Diseases, Qingdao Municipal Hospital, Qingdao University, Qingdao 266011, China
| | - Jie Zhang
- Department of Infectious Diseases, Qingdao Municipal Hospital, Qingdao University, Qingdao 266011, China
| | - Mengke Wang
- Department of Infectious Diseases, Qingdao Municipal Hospital, Qingdao University, Qingdao 266011, China
| | - Yifen Wang
- Department of Infectious Diseases, Qingdao Municipal Hospital, Qingdao University, Qingdao 266011, China
| | - Mengzhen Dong
- Department of Infectious Diseases, Qingdao Municipal Hospital, Qingdao University, Qingdao 266011, China
| | - Xuefeng Ma
- Department of Infectious Diseases, Qingdao Municipal Hospital, Qingdao University, Qingdao 266011, China
| | - Baokai Sun
- Department of Infectious Diseases, Qingdao Municipal Hospital, Qingdao University, Qingdao 266011, China
| | - Shousheng Liu
- Clinical Research Center, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
| | - Zhenzhen Zhao
- Clinical Research Center, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
| | - Lizhen Chen
- Department of Infectious Diseases, Qingdao Municipal Hospital, Qingdao University, Qingdao 266011, China
| | - Wenwen Jin
- Department of Infectious Diseases, Qingdao Municipal Hospital, Qingdao University, Qingdao 266011, China
| | - Kai Liu
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Yongning Xin
- Department of Infectious Diseases, Qingdao Municipal Hospital, Qingdao University, Qingdao 266011, China
| | - Likun Zhuang
- Clinical Research Center, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
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Qiao X, Zhang Y, Sun L, Ma Q, Yang J, Ai L, Xue J, Chen G, Zhang H, Ji C, Gu X, Lei H, Yang Y, Liu C. Association of human breast cancer CD44 -/CD24 - cells with delayed distant metastasis. eLife 2021; 10:65418. [PMID: 34318746 PMCID: PMC8346282 DOI: 10.7554/elife.65418] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 07/25/2021] [Indexed: 12/09/2022] Open
Abstract
Tumor metastasis remains the main cause of breast cancer-related deaths, especially delayed breast cancer distant metastasis. The current study assessed the frequency of CD44-/CD24- breast cancer cells in 576 tissue specimens for associations with clinicopathological features and metastasis and investigated the underlying molecular mechanisms. The results indicated that higher frequency (≥19.5%) of CD44-/CD24- cells was associated with delayed postoperative breast cancer metastasis. Furthermore, CD44-/CD24-triple negative breast cancer (TNBC) cells spontaneously converted into CD44+/CD24-cancer stem cells (CSCs) with properties similar to CD44+/CD24-CSCs from primary human breast cancer cells and parental TNBC cells in terms of stemness marker expression, self-renewal, differentiation, tumorigenicity, and lung metastasis in vitro and in NOD/SCID mice. RNA sequencing identified several differentially expressed genes (DEGs) in newly converted CSCs and RHBDL2, one of the DEGs, expression was upregulated. More importantly, RHBDL2 silencing inhibited the YAP1/USP31/NF-κB signaling and attenuated spontaneous CD44-/CD24- cell conversion into CSCs and their mammosphere formation. These findings suggest that the frequency of CD44-/CD24- tumor cells and RHBDL2 may be valuable for prognosis of delayed breast cancer metastasis, particularly for TNBC.
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Affiliation(s)
- Xinbo Qiao
- Department of Oncology, Shengjing Hospital, China Medical University, Shenyang, China
| | - Yixiao Zhang
- Department of Oncology, Shengjing Hospital, China Medical University, Shenyang, China.,Dapartment of Urology, Shengjing Hospital, China Medical University, Shenyang, China
| | - Lisha Sun
- Department of Oncology, Shengjing Hospital, China Medical University, Shenyang, China
| | - Qingtian Ma
- Department of Oncology, Shengjing Hospital, China Medical University, Shenyang, China
| | - Jie Yang
- Department of Oncology, Shengjing Hospital, China Medical University, Shenyang, China
| | - Liping Ai
- Department of Oncology, Shengjing Hospital, China Medical University, Shenyang, China
| | - Jinqi Xue
- Department of Oncology, Shengjing Hospital, China Medical University, Shenyang, China
| | - Guanglei Chen
- Department of Oncology, Shengjing Hospital, China Medical University, Shenyang, China
| | - Hao Zhang
- Department of Oncology, Shengjing Hospital, China Medical University, Shenyang, China.,Department of Breast Surgery, Liaoning Cancer Hospital and Institute, Cancer Hospital of China Medical University, Shenyang, China
| | - Ce Ji
- Department of Oncology, Shengjing Hospital, China Medical University, Shenyang, China.,Department of General Surgery, Shengjing Hospital, China Medical University, Shenyang, China
| | - Xi Gu
- Department of Oncology, Shengjing Hospital, China Medical University, Shenyang, China
| | - Haixin Lei
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Yongliang Yang
- Center for Molecular Medicine, School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Caigang Liu
- Department of Oncology, Shengjing Hospital, China Medical University, Shenyang, China
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Geng J, Zhang R, Yuan X, Xu H, Zhu Z, Wang X, Wang Y, Xu G, Guo W, Wu J, Qin ZH. DRAM1 plays a tumor suppressor role in NSCLC cells by promoting lysosomal degradation of EGFR. Cell Death Dis 2020; 11:768. [PMID: 32943616 PMCID: PMC7498585 DOI: 10.1038/s41419-020-02979-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 09/03/2020] [Indexed: 02/07/2023]
Abstract
Lung cancer is the leading cause of cancer-associated mortality worldwide. DNA damage-regulated autophagy modulator 1 (DRAM1) plays an important roles in autophagy and tumor progression. However, the mechanisms by which DRAM1 inhibits tumor growth are not fully understood. Here, we report that DRAM1 was decreased in nonsmall-cell lung carcinoma (NSCLC) and was associated with poor prognosis. We confirmed that DRAM1 inhibited the growth, migration, and invasion of NSCLC cells in vitro. Furthermore, overexpression of DRAM1 suppressed xenografted NSCLC tumors in vivo. DRAM1 increased EGFR endocytosis and lysosomal degradation, downregulating EGFR signaling pathway. On one side, DRAM1 interacted with EPS15 to promote EGFR endocytosis, as evidence by the results of proximity labeling followed by proteomics; on the other, DRAM1 recruited V-ATP6V1 subunit to lysosomes, thereby increasing the assemble of the V-ATPase complex, resulting in decreased lysosomal pH and increased activation of lysosomal proteases. These two actions of DRAM1 results in acceleration of EGFR degradation. In summary, these in vitro and in vivo studies uncover a novel mechanism through which DRAM1 suppresses oncogenic properties of NSCLC by regulating EGFR trafficking and degradation and highlights the potential value of DRAM1 as a prognostic biomarker in lung cancers.
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Affiliation(s)
- Ji Geng
- Department of Pharmacology and Laboratory of Aging and Nervous Diseases, Jiangsu Key Laboratory of Neuropsychiatric Diseases, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rong Zhang
- Department of Pharmacology and Laboratory of Aging and Nervous Diseases, Jiangsu Key Laboratory of Neuropsychiatric Diseases, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Xiao Yuan
- Pathology Department, The First Affiliated Hospital of Soochow University, Suzhou, 215123, PR China
| | - Haidong Xu
- Department of Pharmacology and Laboratory of Aging and Nervous Diseases, Jiangsu Key Laboratory of Neuropsychiatric Diseases, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Zhou Zhu
- Mr. and Mrs. Ko Chi Ming Centre for Parkinson's Disease Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, SAR, China
| | - Xinxin Wang
- Department of Pharmacology and Laboratory of Aging and Nervous Diseases, Jiangsu Key Laboratory of Neuropsychiatric Diseases, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Yan Wang
- Department of Pharmacology and Laboratory of Aging and Nervous Diseases, Jiangsu Key Laboratory of Neuropsychiatric Diseases, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Guoqiang Xu
- Department of Pharmacology and Laboratory of Aging and Nervous Diseases, Jiangsu Key Laboratory of Neuropsychiatric Diseases, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Wenjie Guo
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210093, PR China
| | - Junchao Wu
- Department of Pharmacology and Laboratory of Aging and Nervous Diseases, Jiangsu Key Laboratory of Neuropsychiatric Diseases, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China.
| | - Zheng-Hong Qin
- Department of Pharmacology and Laboratory of Aging and Nervous Diseases, Jiangsu Key Laboratory of Neuropsychiatric Diseases, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China.
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