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Zhao W, Hu X, Chen Z, Li X. Major Facilitator Superfamily Domain Containing 12 Is Overexpressed in Lung Cancer and Exhibits an Oncogenic Role in Lung Adenocarcinoma Cells. DNA Cell Biol 2024; 43:331-340. [PMID: 38687351 DOI: 10.1089/dna.2023.0378] [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: 05/02/2024] Open
Abstract
Major facilitator superfamily domain containing 12 (MFSD12) regulates lysosomal cysteine import and promotes the proliferation and survival of melanoma cells. However, the expression and function of MFSD12 in other cancers, particularly in lung cancer, remain unclear. The expression of MFSD12 across various types of cancers and corresponding control tissues was examined using TIMER. MFSD12 expression in lung adenocarcinoma (LUAD) and its correlation with distinct clinicopathological features of LUAD patients were analyzed with UALCAN. The correlation between MFSD12 expression and survival of LUAD patients was assessed using the R package, survival, and the relationship between MFSD12 expression and immune infiltration status in LUAD was investigated using CIBERSORT. In addition, MFSD12 expression was knocked down in PC9 LUAD cells and their proliferation, capacity for expansion, cell cycle, apoptosis, and migration/invasion were evaluated through CCK-8 assays, colony formation assays, 7-AAD staining, Annexin V/PI staining, and Transwell assays, respectively. The stemness of these PC9 cells was determined through Western blotting, flow cytometry, and tumor sphere formation assays. MFSD12 mRNA levels were significantly elevated in multiple types of cancers, including LUAD. MFSD12 expression was also positively correlated with cancer stage, nodal metastasis, and infiltration of various immune cells in LUAD, and high MFSD12 levels predicted poor survival among LUAD patients. Knockdown of MFSD12 in PC9 cells resulted in decreased proliferation, attenuated colony formation capacity, cell cycle arrest, elevated apoptosis, impaired migration/invasion, and reduced stemness in PC9 cells. MFSD12 is an oncogene in LUAD.
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Affiliation(s)
- Weijun Zhao
- Department of Thoracic Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Xilin Hu
- Department of Thoracic Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Zixuan Chen
- Department of Thoracic Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Xinjian Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, China
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2
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Ding L. The emerging role and clinicopathological significance of MFSD12 in cancer and lysosomal storage diseases. Front Pharmacol 2024; 15:1398320. [PMID: 38903991 PMCID: PMC11187322 DOI: 10.3389/fphar.2024.1398320] [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: 03/09/2024] [Accepted: 05/22/2024] [Indexed: 06/22/2024] Open
Abstract
MFSD12 protein has recently risen as a key factor in malignancy and plays a potential role in a variety of complex oncogenic signaling cascades. Current studies suggest that MFSD12 has a positive complex role in the growth and progression of tumors such as melanoma, breast cancer, and lung cancer. At the same time, as a transporter of cysteine, MFSD12 is also involved in the development of lysosomal storage diseases. Therefore, MFSD12 may be an effective target to inhibit tumor development, block metastasis, and expand the therapeutic effect. This article reviews the molecular mechanisms of MFSD12 in a variety of cancers and lysosomal storage diseases.
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Affiliation(s)
- Liqiong Ding
- Department of Pharmaceutics, School of Pharmacy, Hubei University of Science and Technology, Xianning, China
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3
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Bondue T, Khodaparast L, Khodaparast L, Cairoli S, Goffredo BM, Gijsbers R, van den Heuvel L, Levtchenko E. MFSD12 depletion reduces cystine accumulation without improvement in proximal tubular function in experimental models for cystinosis. Am J Physiol Renal Physiol 2024; 326:F981-F987. [PMID: 38545650 DOI: 10.1152/ajprenal.00014.2024] [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: 01/11/2024] [Revised: 03/20/2024] [Accepted: 03/20/2024] [Indexed: 05/24/2024] Open
Abstract
Cystinosis is an autosomal recessive lysosomal storage disorder, caused by mutations in the CTNS gene, resulting in an absent or altered cystinosin (CTNS) protein. Cystinosin exports cystine out of the lysosome, with a malfunction resulting in cystine accumulation and a defect in other cystinosin-mediated pathways. Cystinosis is a systemic disease, but the kidneys are the first and most severely affected organs. In the kidney, the disease initially manifests as a generalized dysfunction in the proximal tubules (also called renal Fanconi syndrome). MFSD12 is a lysosomal cysteine importer that directly affects the cystine levels in melanoma cells, HEK293T cells, and cystinosis patient-derived fibroblasts. In this study, we aimed to evaluate MFSD12 mRNA levels in cystinosis patient-derived proximal tubular epithelial cells (ciPTECs) and to study the effect of MFSD12 knockout on cystine levels. We showed similar MFSD12 mRNA expression in patient-derived ciPTECs in comparison with the control cells. CRISPR MFSD12 knockout in a patient-derived ciPTEC (CTNSΔ57kb) resulted in significantly reduced cystine levels. Furthermore, we evaluated proximal tubular reabsorption after injection of mfsd12a translation-blocking morpholino (TB MO) in a ctns-/- zebrafish model. This resulted in decreased cystine levels but caused a concentration-dependent increase in embryo dysmorphism. Furthermore, the mfsd12a TB MO injection did not improve proximal tubular reabsorption or megalin expression. In conclusion, MFSD12 mRNA depletion reduced cystine levels in both tested models without improvement of the proximal tubular function in the ctns-/- zebrafish embryo. In addition, the apparent toxicity of higher mfsd12a TB MO concentrations on the zebrafish development warrants further evaluation.NEW & NOTEWORTHY In this study, we show that MFSD12 depletion with either CRISPR/Cas9-mediated gene editing or a translation-blocking morpholino significantly reduced cystine levels in cystinosis ciPTECs and ctns-/- zebrafish embryos, respectively. However, we observed no improvement in the proximal tubular reabsorption of dextran in the ctns-/- zebrafish embryos injected with mfsd12a translation-blocking morpholino. Furthermore, a negative effect of the mfsd12a morpholino on the zebrafish development warrants further investigation.
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Affiliation(s)
- Tjessa Bondue
- Laboratory of Pediatric Nephrology, Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Laleh Khodaparast
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Ladan Khodaparast
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Sara Cairoli
- Laboratory of Metabolic Biochemistry, Department of Pediatric Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Bianca Maria Goffredo
- Laboratory of Metabolic Biochemistry, Department of Pediatric Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Rik Gijsbers
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
- Leuven Viral Vector Core, KU Leuven, Leuven, Belgium
| | - Lambertus van den Heuvel
- Laboratory of Pediatric Nephrology, Department of Development and Regeneration, KU Leuven, Leuven, Belgium
- Department of Pediatric Nephrology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Elena Levtchenko
- Laboratory of Pediatric Nephrology, Department of Development and Regeneration, KU Leuven, Leuven, Belgium
- Department of Pediatric Nephrology, Emma Children's Hospital, Amsterdam UMC, Amsterdam, The Netherlands
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Zhuang W, Liu C, Hong Y, Zheng Y, Huang M, Tang H, Zhao L, Huang Z, Tu M, Yu L, Chen J, Zhang Y, Chen X, Lin F, Gao Q, Yu C, Huang Y. Tumor-suppressive miR-4732-3p is sorted into fucosylated exosome by hnRNPK to avoid the inhibition of lung cancer progression. J Exp Clin Cancer Res 2024; 43:123. [PMID: 38654325 PMCID: PMC11036635 DOI: 10.1186/s13046-024-03048-1] [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: 12/19/2023] [Accepted: 04/16/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Aberrant fucosylation observed in cancer cells contributes to an augmented release of fucosylated exosomes into the bloodstream, where miRNAs including miR-4732-3p hold promise as potential tumor biomarkers in our pilot study. However, the mechanisms underlying the sorting of miR-4732-3p into fucosylated exosomes during lung cancer progression remain poorly understood. METHODS A fucose-captured strategy based on lentil lectin-magnetic beads was utilized to isolate fucosylated exosomes and evaluate the efficiency for capturing tumor-derived exosomes using nanoparticle tracking analysis (NTA). Fluorescence in situ hybridization (FISH) and qRT-PCR were performed to determine the levels of miR-4732-3p in non-small cell lung cancer (NSCLC) tissue samples. A co-culture system was established to assess the release of miRNA via exosomes from NSCLC cells. RNA immunoprecipitation (RIP) and miRNA pull-down were applied to validate the interaction between miR-4732-3p and heterogeneous nuclear ribonucleoprotein K (hnRNPK) protein. Cell functional assays, cell derived xenograft, dual-luciferase reporter experiments, and western blot were applied to examine the effects of miR-4732-3p on MFSD12 and its downstream signaling pathways, and the impact of hnRNPK in NSCLC. RESULTS We enriched exosomes derived from NSCLC cells using the fucose-captured strategy and detected a significant upregulation of miR-4732-3p in fucosylated exosomes present in the serum, while its expression declined in NSCLC tissues. miR-4732-3p functioned as a tumor suppressor in NSCLC by targeting 3'UTR of MFSD12, thereby inhibiting AKT/p21 signaling pathway to induce cell cycle arrest in G2/M phase. NSCLC cells preferentially released miR-4732-3p via exosomes instead of retaining them intracellularly, which was facilitated by the interaction of miR-4732-3p with hnRNPK protein for selective sorting into fucosylated exosomes. Moreover, knockdown of hnRNPK suppressed NSCLC cell proliferation, with the elevated levels of miR-4732-3p in NSCLC tissues but the decreased expression in serum fucosylated exosomes. CONCLUSIONS NSCLC cells escape suppressive effects of miR-4732-3p through hnRNPK-mediated sorting of them into fucosylated exosomes, thus supporting cell malignant properties and promoting NSCLC progression. Our study provides a promising biomarker for NSCLC and opens a novel avenue for NSCLC therapy by targeting hnRNPK to prevent the "exosome escape" of tumor-suppressive miR-4732-3p from NSCLC cells.
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Affiliation(s)
- Wanzhen Zhuang
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, 350001, China
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fuzhou, 350001, China
| | - Chengxiu Liu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, 361102, China
- Institute of Future Technology, Beijing Hotgen Biotech Co., Ltd, Beijing, 102600, China
| | - Yilin Hong
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Yue Zheng
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, 350001, China
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fuzhou, 350001, China
| | - Minjian Huang
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, 350001, China
- Center for Experimental Research in Clinical Medicine, Fujian Provincial Hospital, Fuzhou, 350001, China
| | - Haijun Tang
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, 350001, China
- Center for Experimental Research in Clinical Medicine, Fujian Provincial Hospital, Fuzhou, 350001, China
| | - Lilan Zhao
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, 350001, China
- Department of Thoracic Surgery, Fujian Provincial Hospital, Fuzhou, 350001, China
| | - Zhixin Huang
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fuzhou, 350001, China
- Integrated Chinese and Western Medicine College, Fujian University of Traditional Chinese Medicine, Fuzhou, 350108, China
| | - Mingshu Tu
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, 350001, China
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fuzhou, 350001, China
| | - Lili Yu
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, 350001, China
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fuzhou, 350001, China
| | - Jianlin Chen
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, 350001, China
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fuzhou, 350001, China
| | - Yi Zhang
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, 350001, China
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fuzhou, 350001, China
| | - Xiongfeng Chen
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, 350001, China
- Department of Scientific Research, Fujian Provincial Hospital, Fuzhou, 350001, China
| | - Fan Lin
- Department of Geriatric Medicine, Fujian Provincial Hospital, Fuzhou, 350001, China
- Fujian Provincial Center for Geriatrics, Fujian Provincial Hospital, Fuzhou, 350001, China
| | - Qi Gao
- Institute of Future Technology, Beijing Hotgen Biotech Co., Ltd, Beijing, 102600, China
| | - Chundong Yu
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, 350001, China.
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, 361102, China.
- Center for Experimental Research in Clinical Medicine, Fujian Provincial Hospital, Fuzhou, 350001, China.
| | - Yi Huang
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, 350001, China.
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fuzhou, 350001, China.
- Center for Experimental Research in Clinical Medicine, Fujian Provincial Hospital, Fuzhou, 350001, China.
- Fujian Provincial Center for Geriatrics, Fujian Provincial Hospital, Fuzhou, 350001, China.
- Central Laboratory, Fujian Provincial Hospital, Fuzhou, 350001, China.
- Fujian Provincial Key Laboratory of Critical Care Medicine, Fujian Provincial Key Laboratory of Cardiovascular Disease, Fuzhou, 350001, China.
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Yang Y, Li J, Wei C, Wang L, Gao Z, Shen K, Li Y, Ren M, Zhu Y, Ding Y, Wei C, Zhang T, Zheng S, Lu N, Gu J. Circular RNA circFCHO2(hsa_circ_0002490) promotes the proliferation of melanoma by directly binding to DND1. Cell Biol Toxicol 2024; 40:9. [PMID: 38311675 PMCID: PMC10838848 DOI: 10.1007/s10565-024-09851-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: 09/22/2023] [Accepted: 01/26/2024] [Indexed: 02/06/2024]
Abstract
Circular RNAs (circRNAs) have been documented to play crucial roles in the biology of various cancers. However, their investigation in melanoma is still at an early stage, particularly as a broader mechanism beyond acting as miRNA sponges needs to be explored. We report here that circFCHO2(hsa_circ_0002490), a circRNA encompassing exons 19 and 20 of the FCHO2 gene, exhibited a consistent overexpression in melanoma tissues. Furthermore, elevated circFCHO2 levels demonstrated a positive correlation with the malignant phenotype and poor prognosis among the 158 melanoma patients studied. Besides, we observed that heightened levels of circFCHO2 promoted melanoma cell proliferation, migration, and invasion in vitro, along with contributing to tumor growth in vivo. Furthermore, we found differences in the secondary structure of circFCHO2 compared to most other circular RNA structures. It has fewer miRNA binding sites, while it has more RNA binding protein binding sites. We therefore speculate that circFCHO2 may have a function of interacting with RNA binding proteins. Mechanistically, it was confirmed by fluorescence in situ hybridization (FISH), RNA-pull down, RNA immunoprecipitation (RIP), and western blotting assays that circFCHO2 interacts with dead end protein homolog 1 (DND1) and reverses the inhibition of the PI3K/AKT signaling pathway by binding to DND1. Our findings reveal that circFCHO2 drives melanoma progression by regulating the PI3K/AKT signaling pathway through direct binding to DND1 and may serve as a potential diagnostic biomarker and therapeutic target for the treatment of melanoma.
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Affiliation(s)
- Yang Yang
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, No. 180 Feng Lin Road, Shanghai, 200032, China
| | - Jianrui Li
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, No. 180 Feng Lin Road, Shanghai, 200032, China
| | - Chuanyuan Wei
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, No. 180 Feng Lin Road, Shanghai, 200032, China
| | - Lu Wang
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, No. 180 Feng Lin Road, Shanghai, 200032, China
| | - Zixu Gao
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, No. 180 Feng Lin Road, Shanghai, 200032, China
| | - Kangjie Shen
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, No. 180 Feng Lin Road, Shanghai, 200032, China
| | - Yinlam Li
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, No. 180 Feng Lin Road, Shanghai, 200032, China
| | - Ming Ren
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, No. 180 Feng Lin Road, Shanghai, 200032, China
| | - Yu Zhu
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, No. 180 Feng Lin Road, Shanghai, 200032, China
| | - Yiteng Ding
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, No. 180 Feng Lin Road, Shanghai, 200032, China
| | - Chenlu Wei
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, No. 180 Feng Lin Road, Shanghai, 200032, China
| | - Tianyi Zhang
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, No. 180 Feng Lin Road, Shanghai, 200032, China
| | - Shaoluan Zheng
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital (Xiamen), Fudan University, Xiamen Clinical Research Center for Cancer Therapy, Xiamen, 361015, China
| | - Nanhang Lu
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, No. 180 Feng Lin Road, Shanghai, 200032, China.
| | - Jianying Gu
- Department of Plastic and Reconstructive Surgery, Zhongshan Hospital, Fudan University, No. 180 Feng Lin Road, Shanghai, 200032, China.
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He L, Chen J, Deng P, Huang S, Liu P, Wang C, Huang X, Li Y, Chen B, Shi D, Xiao Y, Chen X, Ouyang Y, Song L, Lin C. Lysosomal cyst(e)ine storage potentiates tolerance to oxidative stress in cancer cells. Mol Cell 2023; 83:3502-3519.e11. [PMID: 37751742 DOI: 10.1016/j.molcel.2023.08.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 07/17/2023] [Accepted: 08/30/2023] [Indexed: 09/28/2023]
Abstract
Cyst(e)ine is a key precursor for the synthesis of glutathione (GSH), which protects cancer cells from oxidative stress. Cyst(e)ine is stored in lysosomes, but its role in redox regulation is unclear. Here, we show that breast cancer cells upregulate major facilitator superfamily domain containing 12 (MFSD12) to increase lysosomal cyst(e)ine storage, which is released by cystinosin (CTNS) to maintain GSH levels and buffer oxidative stress. We find that mTORC1 regulates MFSD12 by directly phosphorylating residue T254, while mTORC1 inhibition enhances lysosome acidification that activates CTNS. This switch modulates lysosomal cyst(e)ine levels in response to oxidative stress, fine-tuning redox homeostasis to enhance cell fitness. MFSD12-T254A mutant inhibits MFSD12 function and suppresses tumor progression. Moreover, MFSD12 overexpression correlates with poor neoadjuvant chemotherapy response and prognosis in breast cancer patients. Our findings reveal the critical role of lysosomal cyst(e)ine storage in adaptive redox homeostasis and suggest that MFSD12 is a potential therapeutic target.
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Affiliation(s)
- Lixin He
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Jinxin Chen
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Pinwei Deng
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Shumei Huang
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Pian Liu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Chanjuan Wang
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Xinjian Huang
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Yue Li
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Boyu Chen
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Dongni Shi
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Yunyun Xiao
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Xiangfu Chen
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Ying Ouyang
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Libing Song
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Institute of Oncology, Tumor Hospital, Guangzhou Medical University, Guangzhou 510080, China
| | - Chuyong Lin
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China; Guangdong Esophageal Cancer Institute, Guangzhou 510060, China.
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Fan K, Dong Y, Li T, Li Y. Cuproptosis-associated CDKN2A is targeted by plicamycin to regulate the microenvironment in patients with head and neck squamous cell carcinoma. Front Genet 2023; 13:1036408. [PMID: 36699463 PMCID: PMC9868476 DOI: 10.3389/fgene.2022.1036408] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 12/12/2022] [Indexed: 01/11/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC), the most common malignancy of the head and neck, has an overall 5-year survival rate of <50%. Genes associated with cuproptosis, a newly identified copper-dependent form of cell death, are aberrantly expressed in various tumours. However, their role in HNSCC remains unknown. In this study, bioinformatic analysis revealed that the cuproptosis-related gene CDKN2A was correlated with the malignant behaviour of HNSCC. Kaplan-Meier (KM) curves showed that patients with high CDKN2A expression had a better prognosis. Multiomic analysis revealed that CDKN2A may be associated with cell cycle and immune cell infiltration in the tumour microenvironment and is important for maintaining systemic homeostasis in the body. Furthermore, molecular docking and molecular dynamics simulations suggested strong binding between plicamycin and CDKN2A. And plicamycin inhibits the progression of HNSCC in cellular assays. In conclusion, this study elucidated a potential mechanism of action of the cuproptosis-associated gene CDKN2A in HNSCC and revealed that plicamycin targets CDKN2A to improve the prognosis of patients.
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8
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Ping S, Gong R, Lei K, Qing G, Zhang G, Chen J. Development and validation of a ferroptosis-related lncRNAs signature to predict prognosis and microenvironment for melanoma. Discov Oncol 2022; 13:125. [PMID: 36371574 PMCID: PMC9653531 DOI: 10.1007/s12672-022-00581-3] [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: 09/05/2022] [Accepted: 10/25/2022] [Indexed: 11/13/2022] Open
Abstract
Ferroptosis plays an important role in cancer. However, studies about ferroptosis-related lncRNAs (FRLs) in skin cutaneous melanoma (SKCM) are scarce. Moreover, the relationship between prognostic FRLs and tumor microenvironment (TME) in melanoma remains unclear. This study investigates the potential prognostic value of FRLs and their association with TME in SKCM. The RNA-sequencing data of SKCM were downloaded from The Cancer Genome Atlas (TCGA) database. Melanoma patients were randomly divided into training and testing groups in a 1:1 ratio. A signature composed of 19 FRLs was developed by the least absolute shrinkage and selection operator (LASSO) regression analysis to divide patients into a low-risk group with a better prognosis and a high-risk group with a poor prognosis. Multivariate Cox regression analysis suggested that the risk score was an independent prognostic factor. The Area Under Curve (AUC) value of the risk score reached 0.768 in the training group and 0.770 in the testing group. Subsequent analysis proved that immune-related signaling pathways were significantly enriched in the low-risk group. The tumor immune cell infiltration analysis demonstrated that melanoma in the high-risk group tended to be immunologically "cold". We identified a novel FRLs signature which could accurately predict the prognosis of patients with melanoma.
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Affiliation(s)
- Shuai Ping
- Department of Gastroenterology, Tumor Immunology and Cytotherapy, Medical Research Center, The Affiliated Hospital of Qingdao University, No. 1677 Wutaishan Road, Huangdao District, Qingdao, 266000 China
| | - Ruining Gong
- Department of Gastroenterology, Tumor Immunology and Cytotherapy, Medical Research Center, The Affiliated Hospital of Qingdao University, No. 1677 Wutaishan Road, Huangdao District, Qingdao, 266000 China
| | - Ke Lei
- Tumor Immunology and Cytotherapy, Medical Research Center, The Affiliated Hospital of Qingdao University, No. 1677 Wutaishan Road, Huangdao District, Qingdao, 266000 China
| | - Gong Qing
- Department of Gastroenterology, Tumor Immunology and Cytotherapy, Medical Research Center, The Affiliated Hospital of Qingdao University, No. 1677 Wutaishan Road, Huangdao District, Qingdao, 266000 China
| | - Guangheng Zhang
- Department of Orthopaedics, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430077 China
| | - Jianghai Chen
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 Hubei China
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Markiewicz E, Idowu OC. Evaluation of Personalized Skincare Through in-silico Gene Interactive Networks and Cellular Responses to UVR and Oxidative Stress. Clin Cosmet Investig Dermatol 2022; 15:2221-2243. [PMID: 36284733 PMCID: PMC9588296 DOI: 10.2147/ccid.s383790] [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: 07/26/2022] [Accepted: 10/13/2022] [Indexed: 11/07/2022]
Abstract
Purpose Personalized approaches in dermatology are designed to match the specific requirements based on the individual genetic makeup. One major factor accounting for the differences in skin phenotypes is single nucleotide polymorphism (SNP) within several genes with diverse roles that extend beyond skin tone and pigmentation. Therefore, the cellular sensitivities to the environmental stress and damage linked to extrinsic aging could also underlie the individual characteristics of the skin and dictate the unique skin care requirements. This study aimed to identify the likely biomarkers and molecular signatures expressed in skin cells of different ethnic backgrounds, which could aid further the design of personalized skin products based on specific demands. Methods Using data mining and in-silico modeling, the association of SNP-affected genes with three major skin types of European, Asian and African origin was analyzed and compared within the structure-function gene interaction networks. Cultured dermal fibroblasts were subsequently subjected to ultraviolet radiation and oxidative stress and analyzed for DNA damage and senescent markers. The protective applications of two cosmetic ingredients, Resveratrol and Quercetin, were validated in both cellular and in-silico models. Results Each skin type was characterized by the presence of SNPs in the genes controlling facultative and constitutive pigmentation, which could also underlie the major differences in responses to photodamage, such as oxidative stress, inflammation, and barrier homeostasis. Skin-type-specific dermal fibroblasts cultured in-vitro demonstrated distinctive sensitivities to ultraviolet radiation and oxidative stress, which could be modulated further by the bioactive compounds with the predicted capacities to interact with some of the genes in the in-silico models. Conclusion Evaluation of the SNP-affected gene networks and likely sensitivities of skin cells, defined as low threshold levels to extrinsic stress factors, can provide a valuable tool for the design and formulation of personalized skin products that match more accurately diverse ethnic backgrounds.
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Affiliation(s)
- Ewa Markiewicz
- Hexis Lab, The Catalyst, Newcastle Helix, Newcastle upon Tyne, UK
| | - Olusola C Idowu
- Hexis Lab, The Catalyst, Newcastle Helix, Newcastle upon Tyne, UK,Correspondence: Olusola C Idowu, HexisLab Limited, The Catalyst, Newcastle Helix, Newcastle upon Tyne, NE4 5TG, UK, Tel +44 1394 825487, Email
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10
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TRIP13/FLNA Complex Promotes Tumor Progression and Is Associated with Unfavorable Outcomes in Melanoma. JOURNAL OF ONCOLOGY 2022; 2022:1419179. [PMID: 36268276 PMCID: PMC9578791 DOI: 10.1155/2022/1419179] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/30/2022] [Indexed: 11/30/2022]
Abstract
Cutaneous melanoma is a high-grade malignant tumor originating from skin melanocytes with high risk of recurrence and metastasis. Further study on the mechanism of melanoma development is urgently needed. Here, we performed a bioinformatic analysis to identify critical genes in melanoma using public datasets in the Gene Expression Omnibus database. Among these differentially expressed genes, thyroid hormone receptor interactor 13 (TRIP13) has been reported to exert an important role in the development of various tumors, while its role in melanoma remains unclear. We selected TRIP13 as a candidate gene for further study. TRIP13 expression in clinical specimens was evaluated by immunohistochemistry, and its association with patient prognosis was analyzed by the Kaplan-Meier method and log-rank test. MV3 and A2058 melanoma cells were transfected with lentiviral vector to overexpress or knockdown TRIP13 expression level, and then, its biological function was studied using a series of in vitro and in vivo assays. RNA sequencing, co-immunoprecipitation, and mass spectrometry were used to identify the underlying mechanism of TRIP13. The results of this study exhibited that TRIP13 expression was upregulated in melanoma tissue compared with normal tissues, and high levels of TRIP13 were closely correlated with poor prognoses of melanoma patients. Elevated TRIP13 promoted the invasion and migration of melanoma cells in vitro and enhanced lung metastasis in vivo, without an influence on tumor growth. Importantly, elevated TRIP13 promoted the epithelial-mesenchymal transition (EMT) of melanoma cells, indicating a higher metastatic potential of these cells. Mechanically, TRIP13 physically interacted with filamin A (FLNA) and then activated the PI3K/AKT pathway to transcriptional activation of EMT-related genes. The present study revealed that TRIP13 is a novel prognostic biomarker and potential therapeutic target for melanoma treatment.
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11
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Mengyan X, Kun D, Xinming J, Yutian W, Yongqian S. Identification and verification of hub genes associated with the progression of non-small cell lung cancer by integrated analysis. Front Pharmacol 2022; 13:997842. [PMID: 36176446 PMCID: PMC9513139 DOI: 10.3389/fphar.2022.997842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Objectives: Lung cancer is one of the most common cancers worldwide and it is the leading cause of cancer-related mortality. Despite the treatment of patients with non-small cell lung carcinoma (NSCLC) have improved, the molecular mechanisms of NSCLC are still to be further explored. Materials and Methods: Microarray datasets from the Gene Expression Omnibus (GEO) database were selected to identify the candidate genes associated with tumorigenesis and progression of non-small cell lung carcinoma. The differentially expressed genes (DEGs) were identified by GEO2R. Protein-protein interaction network (PPI) were used to screen out hub genes. The expression levels of hub genes were verified by GEPIA, Oncomine and The Human Protein Atlas (HPA) databases. Survival analysis and receiver operating characteristic (ROC) curve analysis were performed to value the importance of hub genes in NSCLC diagnosis and prognosis. ENCODE and cBioPortal were used to explore the upstream regulatory mechanisms of hub genes. Analysis on CancerSEA Tool, CCK8 assay and colony formation assay revealed the functions of hub genes in NSCLC. Results: A total of 426 DEGs were identified, including 93 up-regulated genes and 333 down-regulated genes. And nine hub genes (CDC6, KIAA0101, CDC20, BUB1B, CCNA2, NCAPG, KIF11, BUB1 and CDK1) were found to increase with the tumorigenesis, progression and cisplatin resistance of NSCLC, especially EGFR- or KRAS-mutation driven NSCLC. Hub genes were valuable biomarkers for NSCLC, and the overexpression of hub genes led to poor survival of NSCLC patients. Function analysis showed that hub genes played roles in cell cycle and proliferation, and knockdown of hub genes significantly inhibited A549 and SPCA1 cell growth. Further exploration demonstrated that copy number alterations (CNAs) and transcription activation may account for the up-regulation of hub genes. Conclusion: Hub genes identified in this study provided better understanding of molecular mechanisms within tumorigenesis and progression of NSCLC, and provided potential targets for NSCLC treatment as well.
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Affiliation(s)
- Xie Mengyan
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ding Kun
- Department of Molecular Cell Biology and Toxicology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Jing Xinming
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wei Yutian
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shu Yongqian
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
- *Correspondence: Shu Yongqian,
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12
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Gao Z, Wang L, Song Z, Ren M, Yang Y, Li J, Shen K, Li Y, Ding Y, Yang Y, Zhou Y, Wei C, Gu J. Intratumoral CD73: An immune checkpoint shaping an inhibitory tumor microenvironment and implicating poor prognosis in Chinese melanoma cohorts. Front Immunol 2022; 13:954039. [PMID: 36131912 PMCID: PMC9483101 DOI: 10.3389/fimmu.2022.954039] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundAs a novel immune checkpoint, CD73 has been reported to play prominent roles in several malignancies. However, the significance of CD73 in melanoma remains ambiguous. This study sought to reveal the impact of CD73 on the tumor microenvironment (TME) and patients’ prognosis, and to investigate whether CD73 could be a therapeutic target in Chinese melanomas, which were dominated by acral and mucosal subtypes.MethodsTwo independent Chinese cohorts of 194 patients with melanoma were enrolled. CD73 and PD-L1 expression as well as CD8+ and CD56+ cell infiltrations were evaluated by immunohistochemistry in 194 resected melanoma samples. Clinical outcomes of patients were assessed utilizing the Kaplan-Meier plotter and Cox proportional hazard analysis. RNA-seq data was obtained from TCGA database. Gene set functional annotations were performed based on GO, KEGG and GSEA analysis. CIBERSORT, ssGSEA and TIMER were used to explore the association between CD73 and immune infiltration. These findings were validated by establishing tumor xenograft model, and functions of tumor-infiltrating immune cells were examined by flow cytometry and immunofluorescence.ResultsHigh CD73 expression showed poorer clinical outcomes and was identified as an independent prognostic indicator for survival in two cohorts. Expression of CD73 was more prevalent than PD-L1 in Chinese melanoma cohorts (54.6% vs 23.2%). Co-expression of both immune checkpoints was infrequent (12.9%) in melanoma, and 54.4% of PD-L1 negative cases showed elevated expression of CD73. CD73high tumors showed a microenvironment with fewer CD8+ T cells and CD56+ NK cells infiltration, which displayed a dysfunctional phenotype. With the treatment of CD73 inhibitor APCP, the amount of CD8+ T cells and CD56+ NK cells infiltrated in tumors was elevated and the immunosuppressive effect of CD73 was eliminated.ConclusionsHigh CD73 expression was associated with an inhibitory TME and adverse clinical outcomes of melanoma. In comparison to PD-L1, CD73 was more prevalent and possessed more definite prognostic significance. Therefore, it may serve as a prognostic indicator and immunotherapeutic target next to PD-L1 in melanoma for Chinese population.
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Affiliation(s)
- Zixu Gao
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lu Wang
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhengqing Song
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ming Ren
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yang Yang
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jianrui Li
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Kangjie Shen
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yinlam Li
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yiteng Ding
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yanwen Yang
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yuhong Zhou
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chuanyuan Wei
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- *Correspondence: Jianying Gu, ; Chuanyuan Wei,
| | - Jianying Gu
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- *Correspondence: Jianying Gu, ; Chuanyuan Wei,
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13
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Yepes S, Tucker MA, Koka H, Xiao Y, Zhang T, Jones K, Vogt A, Burdette L, Luo W, Zhu B, Hutchinson A, Yeager M, Hicks B, Brown KM, Freedman ND, Chanock SJ, Goldstein AM, Yang XR. Integrated Analysis of Coexpression and Exome Sequencing to Prioritize Susceptibility Genes for Familial Cutaneous Melanoma. J Invest Dermatol 2022; 142:2464-2475.e5. [PMID: 35181301 PMCID: PMC9378750 DOI: 10.1016/j.jid.2022.01.029] [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: 08/02/2021] [Revised: 01/05/2022] [Accepted: 01/05/2022] [Indexed: 11/17/2022]
Abstract
The application of whole-exome sequencing has led to the identification of high- and moderate-risk variants that contribute to cutaneous melanoma susceptibility. However, confirming disease-causing variants remains challenging. We applied a gene coexpression network analysis to prioritize the candidate genes identified from whole-exome sequencing of 34 melanoma-prone families, with at least three affected members sequenced per family (N = 119 cases). A coexpression network was constructed from genotype-tissue expression project, skin melanoma from the cancer genome atlas, and primary melanocyte cultures. We performed module-specific enrichment and focused on modules associated with pigmentation processes because they are the best-studied and most well-known risk factors for melanoma susceptibility. We found that pigmentation-associated modules across the four expression datasets examined were enriched for well-known melanoma susceptibility genes plus genes associated with pigmentation. We also used network properties to prioritize genes within pigmentation modules as candidate susceptibility genes. Integrating information from coexpression network analysis and variant prioritization, we identified 36 genes (such as DCT, TPCN2, TRPM1, ATP10A, and EPHA5) as potential melanoma risk genes in the families. Our approach also allowed us to link families with private gene mutations on the basis of gene coexpression patterns and thereby may provide an innovative perspective in gene identification in high-risk families.
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Affiliation(s)
- Sally Yepes
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.
| | - Margaret A Tucker
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Hela Koka
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Yanzi Xiao
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kristine Jones
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, Maryland, USA
| | - Aurelie Vogt
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, Maryland, USA
| | - Laurie Burdette
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, Maryland, USA
| | - Wen Luo
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, Maryland, USA
| | - Bin Zhu
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, Maryland, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, Maryland, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, Maryland, USA
| | - Belynda Hicks
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, Maryland, USA
| | - Kevin M Brown
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Alisa M Goldstein
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Xiaohong R Yang
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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14
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A novel inflammatory response-related signature predicts the prognosis of cutaneous melanoma and the effect of antitumor drugs. World J Surg Oncol 2022; 20:263. [PMID: 35982458 PMCID: PMC9389732 DOI: 10.1186/s12957-022-02726-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 08/06/2022] [Indexed: 11/10/2022] Open
Abstract
Cutaneous melanoma (CM) is a skin cancer that is highly metastatic and aggressive, with a dismal prognosis. This is the first study to use inflammatory response-related genes to build a model and evaluate their predictive significance in CM. This study used public databases to download CM patients' mRNA expression profiles and clinical data to create multigene prognostic markers in the UCSC cohort. We compared overall survival (OS) between high- and low-risk groups using the Kaplan-Meier curve and determined independent predictors using Cox analysis. We also used enrichment analysis to assess immune cell infiltration fraction and immune pathway-related activity using KEGG enrichment analysis. Furthermore, we detected prognostic genes' mRNA and protein expression in CM and normal skin tissues using qRT-PCR and immunohistochemistry. Finally, we developed a 5-gene predictive model that showed that patients in the high-risk group had a considerably shorter OS than those in the low-risk group. The analysis of the receiver operating characteristic (ROC) curve proved the model's predictive ability. We also conducted a drug sensitivity analysis and discovered that the expression levels of prognostic genes were substantially linked with cancer cell sensitivity to antitumor medicines. The findings show that the model we developed, which consists of five inflammatory response-related genes, can be used to forecast the prognosis and immunological state of CM, giving personalized and precision medicine a new goal and direction.
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15
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Ju D, Hui D, Hammond DA, Wonkam A, Tishkoff SA. Importance of Including Non-European Populations in Large Human Genetic Studies to Enhance Precision Medicine. Annu Rev Biomed Data Sci 2022; 5:321-339. [PMID: 35576557 PMCID: PMC9904154 DOI: 10.1146/annurev-biodatasci-122220-112550] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
One goal of genomic medicine is to uncover an individual's genetic risk for disease, which generally requires data connecting genotype to phenotype, as done in genome-wide association studies (GWAS). While there may be clinical promise to employing prediction tools such as polygenic risk scores (PRS), it currently stands that individuals of non-European ancestry may not reap the benefits of genomic medicine because of underrepresentation in large-scale genetics studies. Here, we discuss why this inequity poses a problem for genomic medicine and the reasons for the low transferability of PRS across populations. We also survey the ancestry representation of published GWAS and investigate how estimates of ancestry diversity in GWASparticipants might be biased. We highlight the importance of expanding genetic research in Africa, one of the most underrepresented regions in human genomics research, and discuss issues of ethics, resources, and technology for equitable advancement of genomic medicine.
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Affiliation(s)
- Dan Ju
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
| | - Daniel Hui
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
- Graduate Program in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Dorothy A Hammond
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
- Penn Center for Global Genomics & Health Equity, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ambroise Wonkam
- Division of Human Genetics, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA;
| | - Sarah A Tishkoff
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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16
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Feng S, Lou K, Zou X, Zou J, Zhang G. The Potential Role of Exosomal Proteins in Prostate Cancer. Front Oncol 2022; 12:873296. [PMID: 35747825 PMCID: PMC9209716 DOI: 10.3389/fonc.2022.873296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/16/2022] [Indexed: 01/10/2023] Open
Abstract
Prostate cancer is the most prevalent malignant tumor in men across developed countries. Traditional diagnostic and therapeutic methods for this tumor have become increasingly difficult to adapt to today’s medical philosophy, thus compromising early detection, diagnosis, and treatment. Prospecting for new diagnostic markers and therapeutic targets has become a hot topic in today’s research. Notably, exosomes, small vesicles characterized by a phospholipid bilayer structure released by cells that is capable of delivering different types of cargo that target specific cells to regulate biological properties, have been extensively studied. Exosomes composition, coupled with their interactions with cells make them multifaceted regulators in cancer development. Numerous studies have described the role of prostate cancer-derived exosomal proteins in diagnosis and treatment of prostate cancer. However, so far, there is no relevant literature to systematically summarize its role in tumors, which brings obstacles to the later research of related proteins. In this review, we summarize exosomal proteins derived from prostate cancer from different sources and summarize their roles in tumor development and drug resistance.
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Affiliation(s)
- Shangzhi Feng
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated hospital of Gannan Medical University, Ganzhou, China
| | - Kecheng Lou
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated hospital of Gannan Medical University, Ganzhou, China
| | - Xiaofeng Zou
- Department of Urology, The First Affiliated hospital of Gannan Medical University, Ganzhou, China
- Institute of Urology, The First Affiliated Hospital of Ganna Medical University, Ganzhou, China
- Department of Jiangxi Engineering Technology Research Center of Calculi Prevention, Gannan Medical University, Ganzhou, Jiangxi, China
| | - Junrong Zou
- Department of Urology, The First Affiliated hospital of Gannan Medical University, Ganzhou, China
- Institute of Urology, The First Affiliated Hospital of Ganna Medical University, Ganzhou, China
- Department of Jiangxi Engineering Technology Research Center of Calculi Prevention, Gannan Medical University, Ganzhou, Jiangxi, China
- *Correspondence: Junrong Zou, ; Guoxi Zhang,
| | - Guoxi Zhang
- Department of Urology, The First Affiliated hospital of Gannan Medical University, Ganzhou, China
- Institute of Urology, The First Affiliated Hospital of Ganna Medical University, Ganzhou, China
- Department of Jiangxi Engineering Technology Research Center of Calculi Prevention, Gannan Medical University, Ganzhou, Jiangxi, China
- *Correspondence: Junrong Zou, ; Guoxi Zhang,
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Yue Y, Wang S, Shi J, Xie Q, Li N, Guan J, Evivie SE, Liu F, Li B, Huo G. Effects of Lactobacillus acidophilus KLDS1.0901 on Proliferation and Apoptosis of Colon Cancer Cells. Front Microbiol 2022; 12:788040. [PMID: 35250903 PMCID: PMC8895954 DOI: 10.3389/fmicb.2021.788040] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/22/2021] [Indexed: 12/20/2022] Open
Abstract
Colon cancer is the most common type of malignant tumor. The cytotoxicity effect of lactic acid bacteria may be active by inhibiting cancer cell proliferation, producing anticancer compounds, and inducing apoptosis in cancer cells, but the mechanism is unclear. Our previous study revealed that Lactobacillus acidophilus KLDS1.0901 has good probiotic properties. In this study, We screened out the highest inhibition rate of L. acidophilus KLDS1.0901 and assessed the effects on the proliferation of HT-29, Caco-2, and IEC-6 cells. Then, the apoptosis mechanism of HT-29 cells was studied when treated with L. acidophilus KLDS1.0901. Results showed that L. acidophilus KLDS1.0901 inhibited the proliferation of HT-29 and Caco-2 cells in a dose-dependent manner and reached the maximum under the condition of multiplicity of infection (MOI) = 100 (rate of Lactobacillus to cells) at 48 h. With the increase in time and MOI, reactive oxygen species in HT-29 cells, the apoptosis rates of HT-29 cells were increased, and the amount of blue fluorescence of the cells was also increased after Hoechst 33258 staining. Furthermore, L. acidophilus KLDS1.0901 reduced the mitochondrial membrane potential of HT-29 cells. Notably, 1,133 differentially expressed genes were screened by transcriptomics research, including 531 up-regulated genes and 602 down-regulated genes. These genes were involved in the nuclear factor κB and PI3K-AKT signaling pathways related to the apoptosis of HT-29 cells. These findings suggested that L. acidophilus KLDS1.0901 has the potential to be used in the development of a new type of functional foods for adjuvant treatment of colon cancer.
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Affiliation(s)
- Yingxue Yue
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin, China
- Food College, Northeast Agricultural University, Harbin, China
| | - Song Wang
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin, China
- Food College, Northeast Agricultural University, Harbin, China
| | - Jialu Shi
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin, China
- Food College, Northeast Agricultural University, Harbin, China
| | - Qinggang Xie
- Heilongjiang Feihe Dairy Co., Ltd., Qiqihaer, China
| | - Na Li
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin, China
- Food College, Northeast Agricultural University, Harbin, China
| | - Jiaqi Guan
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin, China
- Food College, Northeast Agricultural University, Harbin, China
| | - Smith Etareri Evivie
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin, China
- Department of Animal Science, Faculty of Agriculture, University of Benin, Benin City, Nigeria
- Department of Food Science and Human Nutrition, Faculty of Agriculture, University of Benin, Benin City, Nigeria
| | - Fei Liu
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin, China
- Food College, Northeast Agricultural University, Harbin, China
| | - Bailiang Li
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin, China
- Food College, Northeast Agricultural University, Harbin, China
| | - Guicheng Huo
- Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin, China
- Food College, Northeast Agricultural University, Harbin, China
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Xuan X, Wang Y, Sun Y, Huang C. Identification of Genes Potentially Associated with Melanoma Tumorigenesis Through Co-Expression Network Analysis. Int J Gen Med 2021; 14:8495-8508. [PMID: 34824546 PMCID: PMC8610383 DOI: 10.2147/ijgm.s336295] [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: 08/26/2021] [Accepted: 11/02/2021] [Indexed: 12/24/2022] Open
Abstract
Background Melanoma is one of the most malignant and aggressive skin tumors, and its incidence is increasing worldwide. However, few studies have investigated the process of tumorigenesis from normal skin to melanoma. Methods Several bioinformatics analyses, including GEO databases, Oncomine database, TCGA database, STRING, MCODE and cytoHubba plug-ins, GEPIA, TIMER and TRRUST and DGIdb, were performed to disclose the hub genes and immunology implicated in primary melanoma tumorigenesis. Finally, immunohistochemistry (IHC) and quantitative real-time PCR (qPCR) were used to validate the results of bioinformatics analysis in vitro. Results A total of 295 overlapping DEGs (ODEGs) (157 upregulated and 138 downregulated) and 9 hub genes were identified between primary melanoma and normal skin tissues. Functional analysis of these 9 hub genes indicated that the genes were primarily enriched in cell chemotaxis, the chemokine-mediated signaling pathway, the extracellular region, the extracellular space, chemokine activity and CXCR3 chemokine receptor binding. KEGG pathway enrichment showed that these genes were primarily involved in the chemokine signaling pathway, cytokine–cytokine receptor interaction, the toll-like receptor signaling pathway, the cytosolic DNA-sensing pathway and the TNF signaling pathway. Upregulated CCL5, CCL4, CXCL9 and CXCL10 demonstrated good overall survival (OS), and most of them have a higher expression in stage 0 and 1 of melanoma. Moreover, immune infiltration analysis showed that the above hub genes showed a strong positive correlation between their expression and infiltration of the six immune cell subsets. Transcription factor regulation network suggested that RELA and NFKB1 are the transcription factors of CCL4, CCL5, CXCL10 and CXCL2, while IRF7, IRF3 and IRF1 are the transcription factors of CCL5 and CXCL10. Drug–gene interaction analysis identified 46 drug–gene interactions. In vitro data demonstrated that the level of CCL4, CCL5, CXCL9 and CXCL10 is higher in melanoma than that in normal skin tissues, either at tissue or cell lines level. Conclusion In summary, we identified 4 key chemokine members related to tumorigenesis and progression in primary melanoma, and these results may help to elucidate melanoma tumorigenesis and facilitate its treatment.
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Affiliation(s)
- Xiuyun Xuan
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, People's Republic of China
| | - Yuqi Wang
- Department of Radiology, Municipal Hospital Affiliated to Xuzhou Medical University, Xuzhou, Jiangsu, 221002, People's Republic of China
| | - Yanhong Sun
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, People's Republic of China
| | - Changzheng Huang
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, People's Republic of China
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Zeng N, Ma L, Cheng Y, Xia Q, Li Y, Chen Y, Lu Z, Lu Q, Jiang F, Luo D. Construction of a Ferroptosis-Related Gene Signature for Predicting Survival and Immune Microenvironment in Melanoma Patients. Int J Gen Med 2021; 14:6423-6438. [PMID: 34675611 PMCID: PMC8502037 DOI: 10.2147/ijgm.s327348] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/14/2021] [Indexed: 12/25/2022] Open
Abstract
Objective In this research, we studied the genes associated with ferroptosis to develop a prognostic model and find out an association with tumor immune microenvironment in skin cutaneous melanoma (SKCM) patients. Methods To find SKCM-related ferroptosis genes, we used Cox regression and LASSO approach on 60 genes related to ferroptosis and SKCM-related RNA-seq. Following that, a ferroptosis-related gene signature was created. Time-dependent ROC curve and Kaplan–Meier analysis were calculated to determine its capability of prediction. Besides, several assessments were used to evaluate overall survival (OS), accompanied by the creation of a nomogram for the clinicopathologic factors and the ferroptosis-related gene signature we established. We also investigated the relationship between ferroptosis-related gene signature with three immune checkpoints and immune cell infiltration. Results Our prognostic model included two genes (ALOX5, CHAC1). In both TCGA and GEO cohorts, OS was lower in high-risk category. Using our gene signature, we can reliably predict OS. Additionally, our gene signature can predict immune cell infiltration and SKCM immunotherapy response. Conclusion Our gene signature has shown to be a reliable predictor of OS, reflect the immune microenvironment, and predict the effectiveness of immunotherapy for SKCM patients.
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Affiliation(s)
- Ni Zeng
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, People's Republic of China.,Department of Dermatology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, People's Republic of China
| | - Liwen Ma
- Department of Dermatology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Yuxin Cheng
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Qingyue Xia
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Yueyue Li
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Yihe Chen
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Zhiyu Lu
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Qian Lu
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Feng Jiang
- Department of Neonatology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, 200011, People's Republic of China
| | - Dan Luo
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, People's Republic of China
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Lin J, Xu Z, Xie J, Deng X, Jiang L, Chen H, Peng C, Li H, Zhang J, Shen B. Oncogene APOL1 promotes proliferation and inhibits apoptosis via activating NOTCH1 signaling pathway in pancreatic cancer. Cell Death Dis 2021; 12:760. [PMID: 34341330 PMCID: PMC8329288 DOI: 10.1038/s41419-021-03985-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/22/2021] [Accepted: 06/22/2021] [Indexed: 12/11/2022]
Abstract
APOL1 encodes a secreted high-density lipoprotein, which has been considered as an aberrantly expressed gene in multiple cancers. Nevertheless, the role of APOL1 in the regulatory mechanisms of pancreatic cancer remains unknown and should be explored. We identified APOL1 was abnormally elevated in human pancreatic cancer tissues compared with that in adjacent tissues and was associated with poor prognosis. The effects of APOL1 in PC cell proliferation, cell cycle, and apoptosis was verified via functional in vitro and in vivo experiments. The results showed that knockdown of APOL1 significantly inhibited the proliferation and promoted apoptosis of pancreatic cancer. In addition, we identified APOL1 could be a regulator of NOTCH1 signaling pathway using bioinformatics tools, qRT-PCR, dual-luciferase reporter assay, and western blotting. In summary, APOL1 could function as an oncogene to promote proliferation and inhibit apoptosis through activating NOTCH1 signaling pathway expression in pancreatic cancer; therefore, it may act as a novel therapeutic target for pancreatic cancer.
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Affiliation(s)
- Jiewei Lin
- Pancreatic Disease Center, Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai, China.,Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhiwei Xu
- Pancreatic Disease Center, Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai, China.,Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Junjie Xie
- Pancreatic Disease Center, Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai, China.,Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaxing Deng
- Pancreatic Disease Center, Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai, China.,Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lingxi Jiang
- Pancreatic Disease Center, Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai, China.,Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hao Chen
- Pancreatic Disease Center, Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai, China.,Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chenghong Peng
- Pancreatic Disease Center, Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai, China.,Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hongwei Li
- Pancreatic Disease Center, Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai, China.,Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiaqiang Zhang
- Pancreatic Disease Center, Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China. .,Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China. .,State Key Laboratory of Oncogenes and Related Genes, Shanghai, China. .,Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Baiyong Shen
- Pancreatic Disease Center, Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China. .,Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China. .,State Key Laboratory of Oncogenes and Related Genes, Shanghai, China. .,Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China.
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21
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Dong C, Rao N, Du W, Gao F, Lv X, Wang G, Zhang J. mRBioM: An Algorithm for the Identification of Potential mRNA Biomarkers From Complete Transcriptomic Profiles of Gastric Adenocarcinoma. Front Genet 2021; 12:679612. [PMID: 34386038 PMCID: PMC8354214 DOI: 10.3389/fgene.2021.679612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/06/2021] [Indexed: 12/09/2022] Open
Abstract
Purpose In this work, an algorithm named mRBioM was developed for the identification of potential mRNA biomarkers (PmBs) from complete transcriptomic RNA profiles of gastric adenocarcinoma (GA). Methods mRBioM initially extracts differentially expressed (DE) RNAs (mRNAs, miRNAs, and lncRNAs). Next, mRBioM calculates the total information amount of each DE mRNA based on the coexpression network, including three types of RNAs and the protein-protein interaction network encoded by DE mRNAs. Finally, PmBs were identified according to the variation trend of total information amount of all DE mRNAs. Four PmB-based classifiers without learning and with learning were designed to discriminate the sample types to confirm the reliability of PmBs identified by mRBioM. PmB-based survival analysis was performed. Finally, three other cancer datasets were used to confirm the generalization ability of mRBioM. Results mRBioM identified 55 PmBs (41 upregulated and 14 downregulated) related to GA. The list included thirteen PmBs that have been verified as biomarkers or potential therapeutic targets of gastric cancer, and some PmBs were newly identified. Most PmBs were primarily enriched in the pathways closely related to the occurrence and development of gastric cancer. Cancer-related factors without learning achieved sensitivity, specificity, and accuracy of 0.90, 1, and 0.90, respectively, in the classification of the GA and control samples. Average accuracy, sensitivity, and specificity of the three classifiers with machine learning ranged within 0.94–0.98, 0.94–0.97, and 0.97–1, respectively. The prognostic risk score model constructed by 4 PmBs was able to correctly and significantly (∗∗∗p < 0.001) classify 269 GA patients into the high-risk (n = 134) and low-risk (n = 135) groups. GA equivalent classification performance was achieved using the complete transcriptomic RNA profiles of colon adenocarcinoma, lung adenocarcinoma, and hepatocellular carcinoma using PmBs identified by mRBioM. Conclusions GA-related PmBs have high specificity and sensitivity and strong prognostic risk prediction. MRBioM has also good generalization. These PmBs may have good application prospects for early diagnosis of GA and may help to elucidate the mechanism governing the occurrence and development of GA. Additionally, mRBioM is expected to be applied for the identification of other cancer-related biomarkers.
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Affiliation(s)
- Changlong Dong
- Center for Informational Biology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China
| | - Nini Rao
- Center for Informational Biology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China
| | - Wenju Du
- Center for Informational Biology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China
| | - Fenglin Gao
- Center for Informational Biology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiaoqin Lv
- Center for Informational Biology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China
| | - Guangbin Wang
- Center for Informational Biology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China
| | - Junpeng Zhang
- Center for Informational Biology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, China.,Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China
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22
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A Novel Autophagy-Related lncRNA Gene Signature to Improve the Prognosis of Patients with Melanoma. BIOMED RESEARCH INTERNATIONAL 2021; 2021:8848227. [PMID: 34250091 PMCID: PMC8238568 DOI: 10.1155/2021/8848227] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 05/20/2021] [Indexed: 01/04/2023]
Abstract
Objective Autophagy and long noncoding RNAs (lncRNAs) have been the focus of research on the pathogenesis of melanoma. However, the autophagy network of lncRNAs in melanoma has not been reported. The purpose of this study was to investigate the lncRNA prognostic markers related to melanoma autophagy and predict the prognosis of patients with melanoma. Methods We downloaded RNA sequencing data and clinical information of melanoma from the Cancer Genome Atlas. The coexpression of autophagy-related genes (ARGs) and lncRNAs was analyzed. The risk model of autophagy-related lncRNAs was established by univariate and multivariate Cox regression analyses, and the best prognostic index was evaluated combined with clinical data. Finally, gene set enrichment analysis was performed on patients in the high- and low-risk groups. Results According to the results of the univariate Cox analysis, only the overexpression of LINC00520 was associated with poor overall survival, unlike HLA-DQB1-AS1, USP30-AS1, AL645929, AL365361, LINC00324, and AC055822. The results of the multivariate Cox analysis showed that the overall survival of patients in the high-risk group was shorter than that recorded in the low-risk group (p < 0.001). Moreover, in the receiver operating characteristic curve of the risk model we constructed, the area under the curve (AUC) was 0.734, while the AUC of T and N was 0.707 and 0.658, respectively. The Gene Ontology was mainly enriched with the positive regulation of autophagy and the activation of the immune system. The results of the Kyoto Encyclopedia of Genes and Genomes enrichment were mostly related to autophagy, immunity, and melanin metabolism. Conclusion The positive regulation of autophagy may slow the transition from low-risk patients to high-risk patients in melanoma. Furthermore, compared with clinical information, the autophagy-related lncRNA risk model may better predict the prognosis of patients with melanoma and provide new treatment ideas.
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Zhang C, Cao C, Liu XL, Jun T, Liu P. Cul4b Promotes Progression of Malignant Cutaneous Melanoma Patients by Regulating CDKN2A. TOHOKU J EXP MED 2021; 254:33-39. [PMID: 34011786 DOI: 10.1620/tjem.254.33] [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: 12/24/2022]
Abstract
Although several molecular targeted therapy and immunotherapy have been developed, cutaneous melanoma prognosis is still not satisfying. Cul4b promotes the progression of several malignant tumors by regulating cell proliferation. However, its prognostic role in malignant cutaneous melanoma has not been evaluated. In this study, immunohistochemistry was performed to assess the expression of Cul4b in a consecutive patient cohort. The prognostic role of Cul4b was estimated with univariate and multivariate analysis. Cul4b was knocked down in melanoma cell line to evaluate its role in promoting cell proliferation. The results revealed that Cul4b was highly expressed in some of the cutaneous malignant melanoma patients and high expression of Cul4b was associated with poor melanoma-specific overall survival and poor disease-free survival. Cul4b expression was associated with Breslow categories, Clark level, and Ki67 expression. Univariate and multivariate analysis revealed that Cul4b is an independent prognosis risk factor of cutaneous melanoma. Downregulation of Cul4b inhibited the proliferation ability of melanoma cells and downregulated the expression of CDKN2A. These results suggest that Cul4b plays an essential role in cutaneous melanoma progression and may serve as a promising treatment target.
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Affiliation(s)
- Chao Zhang
- Department of Dermatology, The Second Affiliated Hospital of Shandong First Medical University
| | - Can Cao
- Department of Dermatology, The Second Affiliated Hospital of Shandong First Medical University
| | - Xiu-Li Liu
- Department of Neonatal, Gaotang People's Hospital
| | - Tan Jun
- Department of Dermatology, Shaanxi Provincial People's Hospital
| | - Pei Liu
- Department of Burn and Plastic Surgery, Qilu Hospital of Shandong University
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24
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Xian H, Huang W, Sun T, Yang S, Zhang C, Wang J, Zhang Y, Cui J. Unanchored ubiquitin chain sustains RIG-I-induced interferon-I activation and controls selective gene expression. Sci Bull (Beijing) 2021; 66:794-802. [PMID: 36654136 DOI: 10.1016/j.scib.2020.11.003] [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: 08/26/2020] [Revised: 09/21/2020] [Accepted: 10/23/2020] [Indexed: 01/20/2023]
Abstract
Ubiquitination plays a crucial role in retinoic acid-inducible gene I (RIG-I)-induced antiviral responses. However, the precise regulatory mechanisms of RIG-I activity mediated by conjugated and unanchored ubiquitin chains remain to be determined. In this study, we discovered that T55 of RIG-I was required for its binding ability for the unanchored ubiquitin chains. Experimental and mathematical analysis showed that unanchored ubiquitin chains associated with RIG-I were essential for sustained activation of type I interferon (IFN) signaling. Transcriptomics study revealed that the binding of RIG-I with unanchored ubiquitin chains additionally regulated the expression of a subset of metabolic and cell fate decision genes. Moreover, we found that ubiquitin-specific peptidase 21 (USP21) and USP3 deubiquitinate conjugated and unanchored ubiquitin chains on RIG-I respectively. Taken together, characterization of the regulation mode and functions of conjugated ubiquitination and the unconjugated ubiquitin chain-binding of RIG-I may provide means to fine-tune RIG-I-mediated type I IFN signaling.
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Affiliation(s)
- Huifang Xian
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; Department of Gastroenterology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Wanming Huang
- Department of Gastroenterology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Tingzhe Sun
- School of Life Sciences, Anqing Normal University, Anqing 246133, China
| | - Shuai Yang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Chuanxia Zhang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jun Wang
- Department of Gastroenterology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Yuxia Zhang
- Department of Gastroenterology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Jun Cui
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
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25
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Feng Y, McQuillan MA, Tishkoff SA. Evolutionary genetics of skin pigmentation in African populations. Hum Mol Genet 2021; 30:R88-R97. [PMID: 33438000 PMCID: PMC8117430 DOI: 10.1093/hmg/ddab007] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/07/2021] [Accepted: 01/07/2021] [Indexed: 12/14/2022] Open
Abstract
Skin color is a highly heritable human trait, and global variation in skin pigmentation has been shaped by natural selection, migration and admixture. Ethnically diverse African populations harbor extremely high levels of genetic and phenotypic diversity, and skin pigmentation varies widely across Africa. Recent genome-wide genetic studies of skin pigmentation in African populations have advanced our understanding of pigmentation biology and human evolutionary history. For example, novel roles in skin pigmentation for loci near MFSD12 and DDB1 have recently been identified in African populations. However, due to an underrepresentation of Africans in human genetic studies, there is still much to learn about the evolutionary genetics of skin pigmentation. Here, we summarize recent progress in skin pigmentation genetics in Africans and discuss the importance of including more ethnically diverse African populations in future genetic studies. In addition, we discuss methods for functional validation of adaptive variants related to skin pigmentation.
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Affiliation(s)
- Yuanqing Feng
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael A McQuillan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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26
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Ding Y, Li M, Tayier T, Zhang M, Chen L, Feng S. Bioinformatics analysis of lncRNA‑associated ceRNA network in melanoma. J Cancer 2021; 12:2921-2932. [PMID: 33854593 PMCID: PMC8040875 DOI: 10.7150/jca.51851] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 02/15/2021] [Indexed: 01/06/2023] Open
Abstract
Melanoma is an extremely malignant tumor with early metastasis and high mortality. Little is known about the process of by which melanoma occurs, as its mechanism is very complex and only limited data are available on its long non-coding RNA (lncRNA)-associated competing endogenous RNAs (ceRNAs). The purpose of this study was to screen out potential prognostic molecules and identify a ceRNA network related to the occurrence of melanoma. We screened 169 differentially expressed mRNAs (DEmRNAs) from E-MTAB-1862 and GSE3189; gene ontology (GO) enrichment analysis showed that these genes were closely related to the development of skin. In the protein-protein interaction network, we screened out a total of 19 hub genes. Furthermore, we predicted the microRNAs (miRNAs) that regulate hub genes using the miRWalk database and then intersected these with GSE35579, resulting in nine DEmiRNAs. We also predicted the lncRNAs that regulate the miRNAs using the LncBasev.2 database. According to the ceRNA hypothesis, and based on the intersection of the DElncRNAs with merged GTEx and TCGA data, we obtained 20 DElncRNAs. A total of four DEmRNAs, nine DEmiRNAs, and 20 DElncRNAs were included in the ceRNA network. Based on Cox stepwise regression and survival analysis, we identified five biomarkers, ZSCAN16-AS1, LINC00520, XIST, DTL, and let-7a-5p, and obtained risk scores. The results showed that most of the differentially expressed genes were related to epithelial-mesenchymal transition (EMT) in melanoma. Finally, we obtained a LINC00520/let-7a-5p/DTL molecular regulatory network. These results suggest that ceRNA networks have an important role in evaluating the prognosis of patients with melanoma and provide a new experimental basis for exploring the EMT process in the development of melanoma.
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Affiliation(s)
- Yi Ding
- Department of Histology and Embryology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Min Li
- Department of Histology and Embryology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Tuersong Tayier
- Department of Pharmacology, Pharmacy College, Xinjiang Medical University, Urumqi, China
| | - MeiLin Zhang
- Xinjiang Urumqi City Center Blood Station, Urumqi, China
| | - Long Chen
- Department of Histology and Embryology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, Xinjiang, China
| | - ShuMei Feng
- Department of Histology and Embryology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, Xinjiang, China
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Dai H, Guo L, Lin M, Cheng Z, Li J, Tang J, Huan X, Huang Y, Xu K. Comprehensive analysis and identification of key genes and signaling pathways in the occurrence and metastasis of cutaneous melanoma. PeerJ 2020; 8:e10265. [PMID: 33240619 PMCID: PMC7680623 DOI: 10.7717/peerj.10265] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/07/2020] [Indexed: 01/02/2023] Open
Abstract
Background Melanoma is a malignant tumor of melanocytes, and the incidence has increased faster than any other cancer over the past half century. Most primary melanoma can be cured by local excision, but metastatic melanoma has a poor prognosis. Cutaneous melanoma (CM) is prone to metastasis, so the research on the mechanism of melanoma occurrence and metastasis will be beneficial to diagnose early, improve treatment, and prolong life survival. In this study, we compared the gene expression of normal skin (N), primary cutaneous melanoma (PM) and metastatic cutaneous melanoma (MM) in the Gene Expression Omnibus (GEO) database. Then we identified the key genes and molecular pathways that may be involved in the development and metastasis of cutaneous melanoma, thus to discover potential markers or therapeutic targets. Methods Three gene expression profiles (GSE7553, GSE15605 and GSE46517) were downloaded from the GEO database, which contained 225 tissue samples. R software identified the differentially expressed genes (DEGs) between pairs of N, PM and MM samples in the three sets of data. Subsequently, we analyzed the gene ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway of the DEGs, and constructed a protein-protein interaction (PPI) network. MCODE was used to seek the most important modules in PPI network, and then the GO function and KEGG pathway of them were analyzed. Finally, the hub genes were calculated by the cytoHubba in Cytoscape software. The Cancer Genome Atlas (TCGA) data were analyzed using UALCAN and GEPIA to validate the hub genes and analyze the prognosis of patients. Results A total of 134, 317 and 147 DEGs were identified between N, PM and MM in pair. GO functions and KEGG pathways analysis results showed that the upregulated DEGs mainly concentrated in cell division, spindle microtubule, protein kinase activity and the pathway of transcriptional misregulation in cancer. The downregulated DEGs occurred in epidermis development, extracellular exosome, structural molecule activity, metabolic pathways and p53 signaling pathway. The PPI network obtained the most important module, whose GO function and KEGG pathway were enriched in oxidoreductase activity, cell division, cell exosomes, protein binding, structural molecule activity, and metabolic pathways. 14, 18 and 18 DEGs were identified respectively as the hub genes between N, PM and MM, and TCGA data confirmed the expression differences of hub genes. In addition, the overall survival curve of hub genes showed that the differences in these genes may lead to a significant decrease in overall survival of melanoma patients. Conclusions In this study, several hub genes were found from normal skin, primary melanoma and metastatic melanoma samples. These hub genes may play an important role in the production, invasion, recurrence or death of CM, and may provide new ideas and potential targets for its diagnosis or treatment.
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Affiliation(s)
- Hanying Dai
- Department of Laboratory Medicine, the Third Xiangya Hospital, Central South University, ChangSha, HuNan, People's Republic of China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, ChangSha, HuNan, People's Republic of China
| | - Lihuang Guo
- Department of Laboratory Medicine, the Third Xiangya Hospital, Central South University, ChangSha, HuNan, People's Republic of China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, ChangSha, HuNan, People's Republic of China
| | - Mingyue Lin
- Department of Laboratory Medicine, the Third Xiangya Hospital, Central South University, ChangSha, HuNan, People's Republic of China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, ChangSha, HuNan, People's Republic of China
| | - Zhenbo Cheng
- Department of Laboratory Medicine, the Third Xiangya Hospital, Central South University, ChangSha, HuNan, People's Republic of China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, ChangSha, HuNan, People's Republic of China
| | - Jiancheng Li
- Department of Laboratory Medicine, the Third Xiangya Hospital, Central South University, ChangSha, HuNan, People's Republic of China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, ChangSha, HuNan, People's Republic of China
| | - Jinxia Tang
- Department of Laboratory Medicine, the Third Xiangya Hospital, Central South University, ChangSha, HuNan, People's Republic of China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, ChangSha, HuNan, People's Republic of China
| | - Xisha Huan
- Department of Laboratory Medicine, the Third Xiangya Hospital, Central South University, ChangSha, HuNan, People's Republic of China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, ChangSha, HuNan, People's Republic of China
| | - Yue Huang
- Department of Laboratory Medicine, the Third Xiangya Hospital, Central South University, ChangSha, HuNan, People's Republic of China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, ChangSha, HuNan, People's Republic of China
| | - Keqian Xu
- Department of Laboratory Medicine, the Third Xiangya Hospital, Central South University, ChangSha, HuNan, People's Republic of China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, ChangSha, HuNan, People's Republic of China
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Xiang C, Cong S, Liang B, Cong S. Bioinformatic gene analysis for potential therapeutic targets of Huntington's disease in pre-symptomatic and symptomatic stage. J Transl Med 2020; 18:388. [PMID: 33054835 PMCID: PMC7559361 DOI: 10.1186/s12967-020-02549-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 09/27/2020] [Indexed: 01/18/2023] Open
Abstract
Background Huntington’s disease (HD) is a neurodegenerative disorder characterized by psychiatric symptoms, serious motor and cognitive deficits. Certain pathological changes can already be observed in pre-symptomatic HD (pre-HD) patients; however, the underlying molecular pathogenesis is still uncertain and no effective treatments are available until now. Here, we reanalyzed HD-related differentially expressed genes from the GEO database between symptomatic HD patients, pre-HD individuals, and healthy controls using bioinformatics analysis, hoping to get more insight in the pathogenesis of both pre-HD and HD, and shed a light in the potential therapeutic targets of the disease. Methods Pre-HD and symptomatic HD differentially expressed genes (DEGs) were screened by bioinformatics analysis Gene Expression Omnibus (GEO) dataset GSE1751. A protein–protein interaction (PPI) network was used to select hub genes. Subsequently, Gene Ontology (GO) enrichment analysis of DEGs and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of hub genes were applied. Dataset GSE24250 was downloaded to verify our hub genes by the Kaplan–Meier method using Graphpad Prism 5.0. Finally, target miRNAs of intersected hub genes involved in pre-HD and symptomatic HD were predicted. Results A total of 37 and 985 DEGs were identified in pre-HD and symptomatic HD, respectively. The hub genes, SIRT1, SUZ12, and PSMC6, may be implicated in pre-HD, and the hub genes, FIS1, SIRT1, CCNH, SUZ12, and 10 others, may be implicated in symptomatic HD. The intersected hub genes, SIRT1 and SUZ12, and their predicted target miRNAs, in particular miR-22-3p and miR-19b, may be significantly associated with pre-HD. Conclusion The PSMC6, SIRT1, and SUZ12 genes and their related ubiquitin-mediated proteolysis, transcriptional dysregulation, and histone metabolism are significantly associated with pre-HD. FIS1, CCNH, and their related mitochondrial disruption and transcriptional dysregulation processes are related to symptomatic HD, which might shed a light on the elucidation of potential therapeutic targets in HD.
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Affiliation(s)
- Chunchen Xiang
- Department of Neurology, Shengjing Hospital of China Medical University, 36 Sanhao Street, Heping District, Shenyang, 110004, Liaoning, People's Republic of China
| | - Shengri Cong
- Department of Neurology, Shengjing Hospital of China Medical University, 36 Sanhao Street, Heping District, Shenyang, 110004, Liaoning, People's Republic of China
| | - Bin Liang
- Bioinformatics of Department, School of Life Sciences, China Medical University, Shenyang, China
| | - Shuyan Cong
- Department of Neurology, Shengjing Hospital of China Medical University, 36 Sanhao Street, Heping District, Shenyang, 110004, Liaoning, People's Republic of China.
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29
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Xia Y, Xie J, Zhao J, Lou Y, Cao D. Screening and Identification of Key Biomarkers in Melanoma: Evidence from Bioinformatic Analyses. J Comput Biol 2020; 28:317-329. [PMID: 32985909 DOI: 10.1089/cmb.2019.0400] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Melanoma is an extremely malignant and occult tumor. To identify candidate genes related to melanoma carcinogenesis and progression, the microarray data sets GSE83583, GSE130244, and GSE31879 were retrieved from the Gene Expression Omnibus (GEO) database using the GEO2R analytical tool provided by the National Center for Biotechnology Information (NCBI). Gene expression analysis was carried out using the DAVID database for Gene Ontology and Kyoto Encyclopedia of Genes and Genomes functional enrichment analyses of differentially expressed genes. A protein-protein interaction network was constructed with the STRING database, the interaction data were imported into Cytoscape software, and the network topology was analyzed to identify key genes. Hub gene expression was verified in the Gene Expression Profiling Interactive Analysis and Human Protein Atlas databases. In addition, Kaplan-Meier survival analysis was performed on hub genes. A total of 142 differentially expressed genes were identified in melanoma tissues, including 50 upregulated genes and 92 downregulated genes. Five central genes (CCNA2, EBP, GABBR2, TRIM32, and ADAM10) were found based on the degree of the nodes. These genes are mainly enriched in protein serine/threonine kinase activity and apoptosis pathways. Survival analysis showed CCNA2 to be related to the overall survival (OS) of patients, and increased expression of TRIM32 led to increased OS and disease-free survival risk. Bioinformatics methods can be used to effectively select key genes in melanoma, and CCNA2 and TRIM32 may be new targets for treatment of this disease.
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Affiliation(s)
- Yijun Xia
- Department of Plastic and Reconstructive Surgery, Anhui Medical University, The Second Affiliated Hospital, Hefei, Anhui, China
| | - Juan Xie
- Department of Plastic and Reconstructive Surgery, Anhui Medical University, The Second Affiliated Hospital, Hefei, Anhui, China
| | - Jun Zhao
- Department of Plastic and Reconstructive Surgery, Anhui Medical University, The Second Affiliated Hospital, Hefei, Anhui, China
| | - Yin Lou
- Department of Plastic and Reconstructive Surgery, Anhui Medical University, The Second Affiliated Hospital, Hefei, Anhui, China
| | - Dongsheng Cao
- Department of Plastic and Reconstructive Surgery, Anhui Medical University, The Second Affiliated Hospital, Hefei, Anhui, China
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30
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Shou Y, Yang L, Yang Y, Zhu X, Li F, Xu J. Identification of Signatures of Prognosis Prediction for Melanoma Using a Hypoxia Score. Front Genet 2020; 11:570530. [PMID: 33133157 PMCID: PMC7550673 DOI: 10.3389/fgene.2020.570530] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/08/2020] [Indexed: 01/16/2023] Open
Abstract
Melanoma is one of the most aggressive cancers. Hypoxic microenvironment affects multiple cellular pathways and contributes to tumor progression. The purpose of the research was to investigate the association between hypoxia and melanoma, and identify the prognostic value of hypoxia-related genes. Based on the GSVA algorithm, gene expression profile collected from The Cancer Genome Atlas (TCGA) was used for calculating the hypoxia score. The Kaplan–Meier plot suggested that a high hypoxia score was correlated with the inferior survival of melanoma patients. Using differential gene expression analysis and WGCNA, a total of 337 overlapping genes associated with hypoxia were determined. Protein-protein interaction network and functional enrichment analysis were conducted, and Lasso Cox regression was performed to establish the prognostic gene signature. Lasso regression showed that seven genes displayed the best features. A novel seven-gene signature (including ABCA12, PTK6, FERMT1, GSDMC, KRT2, CSTA, and SPRR2F) was constructed for prognosis prediction. The ROC curve inferred good performance in both the TCGA cohort and validation cohorts. Therefore, our study determined the prognostic implication of the hypoxia score in melanoma and showed a novel seven-gene signature to predict prognosis, which may provide insights into the prognosis evaluation and clinical decision making.
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Affiliation(s)
- Yanhong Shou
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Lu Yang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yongsheng Yang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiaohua Zhu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Feng Li
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jinhua Xu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China.,Institute of Dermatology, Shanghai, China
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31
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Deng G, Zeng F, Su J, Zhao S, Hu R, Zhu W, Hu S, Chen X, Yin M. BET inhibitor suppresses melanoma progression via the noncanonical NF-κB/SPP1 pathway. Am J Cancer Res 2020; 10:11428-11443. [PMID: 33052224 PMCID: PMC7546000 DOI: 10.7150/thno.47432] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 08/30/2020] [Indexed: 12/12/2022] Open
Abstract
Background: Bromodomain and extra-terminal domain (BET) inhibitors have shown profound efficacy against hematologic malignancies and solid tumors in preclinical studies. However, the underlying molecular mechanism in melanoma is not well understood. Here we identified secreted phosphoprotein 1 (SPP1) as a melanoma driver and a crucial target of BET inhibitors in melanoma. Methods: Bioinformatics analysis and meta-analysis were used to evaluate the SPP1 expression in normal tissues, primary melanoma, and metastatic melanoma. Real-time PCR (RT-PCR) and Western blotting were employed to quantify SPP1 expression in melanoma cells and tissues. Cell proliferation, wound healing, and Transwell assays were carried out to evaluate the effects of SPP1 and BET inhibitors in melanoma cells in vitro. A xenograft mouse model was used to investigate the effect of SPP1 and BET inhibitors on melanoma in vivo. Chromatin immunoprecipitation (ChIP) assay was performed to evaluate the regulatory mechanism of BET inhibitors on SPP1. Results: SPP1 was identified as a melanoma driver by bioinformatics analysis, and meta-analysis determined it to be a diagnostic and prognostic biomarker for melanoma. SPP1 overexpression was associated with poor melanoma prognosis, and silencing SPP1 suppressed melanoma cell proliferation, migration, and invasion. Through a pilot drug screen, we identified BET inhibitors as ideal therapeutic agents that suppressed SPP1 expression. Also, SPP1 overexpression could partially reverse the suppressive effect of BET inhibitors on melanoma. We further demonstrated that bromodomain-containing 4 (BRD4) regulated SPP1 expression. Notably, BRD4 did not bind directly to the SPP1 promoter but regulated SPP1 expression through NFKB2. Silencing of NFKB2 resembled the phenotype of BET inhibitors treatment and SPP1 silencing in melanoma. Conclusion: Our findings highlight SPP1 as an essential target of BET inhibitors and provide a novel mechanism by which BET inhibitors suppress melanoma progression via the noncanonical NF-κB/SPP1 pathway.
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32
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Zheng X, Weigert A, Reu S, Guenther S, Mansouri S, Bassaly B, Gattenlöhner S, Grimminger F, Pullamsetti S, Seeger W, Winter H, Savai R. Spatial Density and Distribution of Tumor-Associated Macrophages Predict Survival in Non-Small Cell Lung Carcinoma. Cancer Res 2020; 80:4414-4425. [PMID: 32699134 DOI: 10.1158/0008-5472.can-20-0069] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 06/05/2020] [Accepted: 07/14/2020] [Indexed: 11/16/2022]
Abstract
The respective antitumoral and protumoral roles of M1 and M2 tumor-associated macrophages (TAM) typify the complexity of macrophage function in cancer. In lung cancer, density and topology of distinct TAM phenotypes at the tumor center (TC) versus the invasive margin (IM) are largely unknown. Here, we investigated TAM subtype density and distribution between TC and IM in human lung cancer and TAM associations with overall survival. Macrophages isolated from adjacent nontumor tissue (NM), the TC (TC-TAM), and the IM (IM-TAM) were analyzed with RNA-sequencing (RNA-seq). Lung tumor tissue microarrays from 104 patient samples were constructed. M1 and M2 TAMs were identified using multiplex immunofluorescence staining and a tumor cell-TAM proximity analysis was performed. RNA-seq identified marked differences among NM, TC-TAM, and IM-TAM. On the basis of a panel of five selected markers (CD68, IL12, CCR7, CD163, and ALOX15), M2 predominance over M1 and M2 proximity to tumor cells was observed, especially at IM. Tumor cell proximity to TAM was linked with tumor cell survival and hypoxia was associated with accumulation of M2 TAM. Notably, lower density of M1 TC-TAM and higher proximity of tumor cells to M2 IM-TAM or lower proximity to M1 IM-TAM were linked with poor survival. In addition, three novel molecules (UBXN4, MFSD12, and ACTR6) from RNA-seq served as potential prognostic markers for lung cancer, and M2 predominance and juxtaposition of M2 TAM near tumor cells were associated with poor survival. Together, our results reveal the marked heterogeneity of TAM populations in different tumor regions, with M2 TAM predominance, particularly at IM. SIGNIFICANCE: This study underlines the significance of the density, spatial distribution, and gene expression of TAM phenotypes as prognostic factors for overall survival in lung cancer. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/20/4414/F1.large.jpg.
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Affiliation(s)
- Xiang Zheng
- Max Planck Institute for Heart and Lung Research, German Center for Lung Research (DZL), Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
| | - Andreas Weigert
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Simone Reu
- Institute of Pathology, University of Würzburg, Würzburg, Germany
| | - Stefan Guenther
- Max Planck Institute for Heart and Lung Research, German Center for Lung Research (DZL), Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
| | - Siavash Mansouri
- Max Planck Institute for Heart and Lung Research, German Center for Lung Research (DZL), Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
| | - Birgit Bassaly
- Department of Pathology, Justus Liebig University, Giessen, Germany
| | | | - Friedrich Grimminger
- Department of Internal Medicine, German Center for Lung Research (DZL), Cardio-Pulmonary Institute (CPI), Justus Liebig University, Giessen, Germany
| | - Soni Pullamsetti
- Max Planck Institute for Heart and Lung Research, German Center for Lung Research (DZL), Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany.,Department of Internal Medicine, German Center for Lung Research (DZL), Cardio-Pulmonary Institute (CPI), Justus Liebig University, Giessen, Germany
| | - Werner Seeger
- Max Planck Institute for Heart and Lung Research, German Center for Lung Research (DZL), Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany.,Department of Internal Medicine, German Center for Lung Research (DZL), Cardio-Pulmonary Institute (CPI), Justus Liebig University, Giessen, Germany.,Institute for Lung Health (ILH), Justus Liebig University, Giessen, Germany
| | - Hauke Winter
- Department of Thoracic Surgery, Translational Lung Research Center (TLRC) Thoraxklinik at the University Hospital Heidelberg, German Center for Lung Research (DZL), Heidelberg, Germany
| | - Rajkumar Savai
- Max Planck Institute for Heart and Lung Research, German Center for Lung Research (DZL), Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany. .,Department of Internal Medicine, German Center for Lung Research (DZL), Cardio-Pulmonary Institute (CPI), Justus Liebig University, Giessen, Germany.,Institute for Lung Health (ILH), Justus Liebig University, Giessen, Germany.,Frankfurt Cancer Institute (FCI), Goethe University, Frankfurt am Main, Germany
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Wei CY, Zhu MX, Lu NH, Liu JQ, Yang YW, Zhang Y, Shi YD, Feng ZH, Li JX, Qi FZ, Gu JY. Circular RNA circ_0020710 drives tumor progression and immune evasion by regulating the miR-370-3p/CXCL12 axis in melanoma. Mol Cancer 2020; 19:84. [PMID: 32381016 PMCID: PMC7204052 DOI: 10.1186/s12943-020-01191-9] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/24/2020] [Indexed: 02/26/2023] Open
Abstract
Background Circular RNAs (circRNAs) have been reported to have critical regulatory roles in tumor biology. However, their contribution to melanoma remains largely unknown. Methods CircRNAs derived from oncogene CD151 were detected and verified by analyzing a large number of melanoma samples through quantitative real-time polymerase chain reaction (qRT-PCR). Melanoma cells were stably transfected with lentiviruses using circ_0020710 interference or overexpression plasmid, and then CCK-8, colony formation, wound healing, transwell invasion assays, and mouse xenograft models were employed to assess the potential role of circ_0020710. RNA immunoprecipitation, luciferase reporter assay and fluorescence in situ hybridization were used to evaluate the underlying mechanism of circ_0020710. Results Our findings indicated that circ_0020710 was generally overexpressed in melanoma tissues, and high level of circ_0020710 was positively correlated with malignant phenotype and poor prognosis of melanoma patients. Elevated circ_0020710 promoted melanoma cell proliferation, migration and invasion in vitro as well as tumor growth in vivo. Mechanistically, we found that high level of circ_0020710 could upregulate the CXCL12 expression via sponging miR-370-3p. CXCL12 downregulation could reverse the malignant behavior of melanoma cells conferred by circ_0020710 over expression. Moreover, we also found that elevated circ_0020710 was correlated with cytotoxic lymphocyte exhaustion, and a combination of AMD3100 (the CXCL12/CXCR4 axis inhibitor) and anti-PD-1 significantly attenuated tumor growth. Conclusions Elevated circ_0020710 drives tumor progression via the miR-370-3p/CXCL12 axis, and circ_0020710 is a potential target for melanoma treatment.
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Affiliation(s)
- Chuan-Yuan Wei
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, P. R. China
| | - Meng-Xuan Zhu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, P. R. China
| | - Nan-Hang Lu
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, P. R. China
| | - Jia-Qi Liu
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, P. R. China
| | - Yan-Wen Yang
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, P. R. China
| | - Yong Zhang
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, P. R. China
| | - Yue-Dong Shi
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, P. R. China
| | - Zi-Hao Feng
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, P. R. China
| | - Jia-Xia Li
- Department of Neurology, Hefei Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230000, P. R. China
| | - Fa-Zhi Qi
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, P. R. China.
| | - Jian-Ying Gu
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, P. R. China.
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Zhu MX, Wei CY, Zhang PF, Gao DM, Chen J, Zhao Y, Dong SS, Liu BB. Elevated TRIP13 drives the AKT/mTOR pathway to induce the progression of hepatocellular carcinoma via interacting with ACTN4. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:409. [PMID: 31533816 PMCID: PMC6749659 DOI: 10.1186/s13046-019-1401-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 08/29/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND ATPase associated with a variety of cellular activities (AAA ATPase) family members are closely linked to tumor formation and progression. However, their roles in hepatocellular carcinoma (HCC) largely remain unclear. METHODS Bioinformatic analyses of public databases were used to excavate the potential AAA ATPases that may contribute to HCC, and thyroid hormone receptor interactor 13 (TRIP13) was selected to following researches because of its most prominently differential expression. Western blot, qRT-PCR and immunohistochemistry were used to detect the expression of TRIP13 in HCC tissues, and then the relationship between TRIP13 expression and clinicopathological parameters were evaluated. Finally, its functions and potential mechanisms were investigated through a series gain- and loss-of-function strategies both in vitro and in vivo. RESULTS TRIP13 was significantly overexpressed in HCC tissues and high level of TRIP13 was closely correlated with a worse clinical outcome. Functionally, elevated TRIP13 facilitated cell proliferation, migration, invasion, and promoted cellular epithelial-mesenchymal transition (EMT) in vitro, while promote tumor growth and lung metastasis in vivo. Mechanistically, TRIP13 interacted with ACTN4 and positively regulated its expression, thus activating the AKT/mTOR pathway to drive tumor progression. Moreover, miR-192-5p served as an upstream regulator of TRIP13 by directly binding to TRIP13 mRNA 3' UTR, which may partially explain the high expression of TRIP13 in HCC. CONCLUSION Our findings identified TRIP13 as a promising candidate oncogene in HCC, and TRIP13 induced cell migration, invasion and metastasis of HCC through the AKT/mTOR signaling via interacting with ACTN4.
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Affiliation(s)
- Meng-Xuan Zhu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, 180 Fenglin Road, Shanghai, 200032, China
| | - Chuan-Yuan Wei
- Liver Cancer Institute, Zhongshan Hospital, Fudan University and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, 180 Fenglin Road, Shanghai, 200032, China.,Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, 180 FengLin Road, Shanghai, 200032, China
| | - Peng-Fei Zhang
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, 180 FengLin Road, Shanghai, 200032, China
| | - Dong-Mei Gao
- Liver Cancer Institute, Zhongshan Hospital, Fudan University and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, 180 Fenglin Road, Shanghai, 200032, China
| | - Jie Chen
- Liver Cancer Institute, Zhongshan Hospital, Fudan University and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, 180 Fenglin Road, Shanghai, 200032, China
| | - Yan Zhao
- Liver Cancer Institute, Zhongshan Hospital, Fudan University and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, 180 Fenglin Road, Shanghai, 200032, China
| | - Shuang-Shuang Dong
- Liver Cancer Institute, Zhongshan Hospital, Fudan University and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, 180 Fenglin Road, Shanghai, 200032, China
| | - Bin-Bin Liu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, 180 Fenglin Road, Shanghai, 200032, China.
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Wei CY, Zhu MX, Zhang PF, Yang X, Wang L, Ying JH, Luan WJ, Chen C, Liu JQ, Zhu M, Yang YW, Feng ZH, Qi FZ, Gu JY. Elevated kindlin-2 promotes tumour progression and angiogenesis through the mTOR/VEGFA pathway in melanoma. Aging (Albany NY) 2019; 11:6273-6285. [PMID: 31427543 PMCID: PMC6738412 DOI: 10.18632/aging.102187] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 08/10/2019] [Indexed: 02/06/2023]
Abstract
Background: In our previous study, kindlin-2 promoted skin wound healing and decreased the permeability of neovascularization during angiogenesis. Herein, we explored the biological function and underlying mechanism of kindlin-2 in cutaneous melanoma. Methods and Results: Through a series of in vitro assays, we found that high levels of kindlin-2 promoted migration and invasion of melanoma cells without influencing cell proliferation. Quantitative real-time polymerase chain reaction (qRT-PCR) and western blot analyses showed that upregulated kindlin-2 promoted the cellular epithelial-mesenchymal transition (EMT). Importantly, we found that melanoma cells overexpressing kindlin-2 promoted angiogenesis and VEGFA secretion in vitro and facilitated tumour growth and lung metastasis in vivo. To unveil the underlying mechanism, we conducted Next-generation sequencing (NGS) and differential expression analyses. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that overlapping differentially expressed genes (DEGs) were primarily enriched in the TGF-β, mTOR and VEGF signalling pathways. Then, we confirmed that the mTOR/VEGFA pathway was activated during the process of kindlin-2-induced melanoma progression and angiogenesis. Moreover, we demonstrated that kindlin-2 was significantly overexpressed in clinical melanoma samples and that a high level of kindlin-2 predicted a poor prognosis. Conclusions: Taken together, these findings showed that kindlin-2 promotes angiogenesis and tumour progression via the mTOR/VEGFA pathway.
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Affiliation(s)
- Chuan-Yuan Wei
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China.,Department of Liver Surgery and Transplantation, Liver Cancer Institute and Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, P.R. China
| | - Meng-Xuan Zhu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai 200032, P.R. China
| | - Peng-Fei Zhang
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200032, P.R. China
| | - Xuan Yang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute and Zhongshan Hospital, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, Shanghai 200032, P.R. China
| | - Lu Wang
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Jiang-Hui Ying
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Wen-Jie Luan
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Cheng Chen
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Jia-Qi Liu
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Ming Zhu
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Yan-Wen Yang
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Zi-Hao Feng
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Fa-Zhi Qi
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Jian-Ying Gu
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
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Wei CY, Wang L, Zhu MX, Deng XY, Wang DH, Zhang SM, Ying JH, Yuan X, Wang Q, Xuan TF, He AQ, Qi FZ, Gu JY. TRIM44 activates the AKT/mTOR signal pathway to induce melanoma progression by stabilizing TLR4. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:137. [PMID: 30922374 PMCID: PMC6437891 DOI: 10.1186/s13046-019-1138-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 03/13/2019] [Indexed: 01/07/2023]
Abstract
Background There is growing evidence that tripartite motif-containing protein 44 (TRIM44) plays crucial role in tumor development. However, the underlying mechanism of this deubiquitinating enzyme remains unclear. Methods Large clinical samples were used to detect TRIM44 expression and its associations with clinicopathological features and prognosis. Gain- and loss-of-function experiments in cell lines and mouse xenograft models were performed to elucidate the function and underlying mechanisms of TRIM44 induced tumor progression. Co-immunoprecipitation (Co-IP) assays and mass spectrometric analyses were applied to verify the interacting proteins of TRIM44. Results We found that TRIM44 was commonly amplified in melanoma tissues compared with paratumoral tissues. TRIM44 expression also positively correlated with more aggressive clinicopathological features, such as Breslow depth (p = 0.025), distant metastasis (p = 0.012), and TNM stage (p = 0.002). Importantly, we found that TRIM44 was an independent indicator of prognosis for melanoma patients. Functionally, overexpression of TRIM44 facilitated cell invasion, migration, apoptosis resistance and proliferation in vitro, and promoted lung metastasis and tumorigenic ability in vivo. Importantly, high level of TRIM44 induced melanoma cell epithelial-mesenchymal transition (EMT), which is one of the most important mechanisms for the promotion of tumor metastasis. Mechanistically, high levels of TRIM44 increased the levels of p-AKT (T308) and p-mTOR (S2448), and a specific AKT inhibitor inhibited TRIM44-induced tumor progression. Co-IP assays and mass spectrometric analyses indicated that TRIM44 overexpression induces cell EMT through activating AKT/mTOR pathway via directly binding and stabilizing TOLL-like receptor 4 (TLR4), and TLR4 interference impeded TRIM44 induced tumor progression. Moreover, we demonstrated that TRIM44 is the target of miR-26b-5p, which is significantly downregulated in melanoma tissues and may be responsible for the overexpression of TRIM44. Conclusions TRIM44, regulated by miR-26b-5p, promotes melanoma progression by stabilizing TLR4, which then activates the AKT/mTOR pathway. TRIM44 shows promise as a prognostic predictor and a therapeutic target for melanoma patients. Electronic supplementary material The online version of this article (10.1186/s13046-019-1138-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chuan-Yuan Wei
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, People's Republic of China.,Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Fudan University, Shanghai, 200032, People's Republic of China
| | - Lu Wang
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, People's Republic of China
| | - Meng-Xuan Zhu
- Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Fudan University, Shanghai, 200032, People's Republic of China
| | - Xin-Yi Deng
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, People's Republic of China
| | - Dao-He Wang
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, People's Republic of China
| | - Si-Min Zhang
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, People's Republic of China
| | - Jiang-Hui Ying
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, People's Republic of China
| | - Xin Yuan
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, People's Republic of China
| | - Qiang Wang
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, People's Republic of China
| | - Tian-Fan Xuan
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, People's Republic of China
| | - An-Qi He
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, People's Republic of China
| | - Fa-Zhi Qi
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, People's Republic of China
| | - Jian-Ying Gu
- Department of Plastic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, People's Republic of China.
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