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Wu JJ, Zhang SY, Mu L, Dong ZG, Zhang YJ. Heyingwuzi formulation alleviates diabetic retinopathy by promoting mitophagy via the HIF-1α/BNIP3/NIX axis. World J Diabetes 2024; 15:1317-1339. [DOI: 10.4239/wjd.v15.i6.1317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/22/2024] [Accepted: 04/01/2024] [Indexed: 06/11/2024] Open
Abstract
BACKGROUND Diabetic retinopathy (DR) is the primary cause of visual problems in patients with diabetes. The Heyingwuzi formulation (HYWZF) is effective against DR.
AIM To determine the HYWZF prevention mechanisms, especially those underlying mitophagy.
METHODS Human retinal capillary endothelial cells (HRCECs) were treated with high glucose (hg), HYWZF serum, PX-478, or Mdivi-1 in vitro. Then, cell counting kit-8, transwell, and tube formation assays were used to evaluate HRCEC proliferation, invasion, and tube formation, respectively. Transmission electron microscopy was used to assess mitochondrial morphology, and Western blotting was used to determine the protein levels. Flow cytometry was used to assess cell apoptosis, reactive oxygen species (ROS) production, and mitochondrial membrane potential. Moreover, C57BL/6 mice were established in vivo using streptozotocin and treated with HYWZF for four weeks. Blood glucose levels and body weight were monitored continuously. Changes in retinal characteristics were evaluated using hematoxylin and eosin, tar violet, and periodic acid-Schiff staining. Protein levels in retinal tissues were determined via Western blotting, immunohistochemistry, and immunostaining.
RESULTS HYWZF inhibited excessive ROS production, apoptosis, tube formation, and invasion in hg-induced HRCECs via mitochondrial autophagy in vitro. It increased the mRNA expression levels of BCL2-interacting protein 3 (BNIP3), FUN14 domain-containing 1, BNIP3-like (BNIP3L, also known as NIX), PARKIN, PTEN-induced kinase 1, and hypoxia-inducible factor (HIF)-1α. Moreover, it downregulated the protein levels of vascular endothelial cell growth factor and increased the light chain 3-II/I ratio. However, PX-478 and Mdivi-1 reversed these effects. Additionally, PX-478 and Mdivi-1 rescued the effects of HYWZF by decreasing oxidative stress and apoptosis and increasing mitophagy. HYWZF intervention improved the symptoms of diabetes, tissue damage, number of acellular capillaries, and oxidative stress in vivo. Furthermore, in vivo experiments confirmed the results of in vitro experiments.
CONCLUSION HYWZF alleviated DR and associated damage by promoting mitophagy via the HIF-1α/BNIP3/NIX axis.
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Affiliation(s)
- Jia-Jun Wu
- Department of Ophthalmology, Longhua Hospital Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Shu-Yan Zhang
- Department of Ophthalmology, Longhua Hospital Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Lin Mu
- Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai 200031, China
| | - Zhi-Guo Dong
- Department of Ophthalmology, Longhua Hospital Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Yin-Jian Zhang
- Department of Ophthalmology, Longhua Hospital Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
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Raj-Kumar PK, Lin X, Liu T, Sturtz LA, Gritsenko MA, Petyuk VA, Sagendorf TJ, Deyarmin B, Liu J, Praveen-Kumar A, Wang G, McDermott JE, Shukla AK, Moore RJ, Monroe ME, Webb-Robertson BJM, Hooke JA, Fantacone-Campbell L, Mostoller B, Kvecher L, Kane J, Melley J, Somiari S, Soon-Shiong P, Smith RD, Mural RJ, Rodland KD, Shriver CD, Kovatich AJ, Hu H. Proteogenomic characterization of difficult-to-treat breast cancer with tumor cells enriched through laser microdissection. Breast Cancer Res 2024; 26:76. [PMID: 38745208 PMCID: PMC11094977 DOI: 10.1186/s13058-024-01835-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 05/05/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Breast cancer (BC) is the most commonly diagnosed cancer and the leading cause of cancer death among women globally. Despite advances, there is considerable variation in clinical outcomes for patients with non-luminal A tumors, classified as difficult-to-treat breast cancers (DTBC). This study aims to delineate the proteogenomic landscape of DTBC tumors compared to luminal A (LumA) tumors. METHODS We retrospectively collected a total of 117 untreated primary breast tumor specimens, focusing on DTBC subtypes. Breast tumors were processed by laser microdissection (LMD) to enrich tumor cells. DNA, RNA, and protein were simultaneously extracted from each tumor preparation, followed by whole genome sequencing, paired-end RNA sequencing, global proteomics and phosphoproteomics. Differential feature analysis, pathway analysis and survival analysis were performed to better understand DTBC and investigate biomarkers. RESULTS We observed distinct variations in gene mutations, structural variations, and chromosomal alterations between DTBC and LumA breast tumors. DTBC tumors predominantly had more mutations in TP53, PLXNB3, Zinc finger genes, and fewer mutations in SDC2, CDH1, PIK3CA, SVIL, and PTEN. Notably, Cytoband 1q21, which contains numerous cell proliferation-related genes, was significantly amplified in the DTBC tumors. LMD successfully minimized stromal components and increased RNA-protein concordance, as evidenced by stromal score comparisons and proteomic analysis. Distinct DTBC and LumA-enriched clusters were observed by proteomic and phosphoproteomic clustering analysis, some with survival differences. Phosphoproteomics identified two distinct phosphoproteomic profiles for high relapse-risk and low relapse-risk basal-like tumors, involving several genes known to be associated with breast cancer oncogenesis and progression, including KIAA1522, DCK, FOXO3, MYO9B, ARID1A, EPRS, ZC3HAV1, and RBM14. Lastly, an integrated pathway analysis of multi-omics data highlighted a robust enrichment of proliferation pathways in DTBC tumors. CONCLUSIONS This study provides an integrated proteogenomic characterization of DTBC vs LumA with tumor cells enriched through laser microdissection. We identified many common features of DTBC tumors and the phosphopeptides that could serve as potential biomarkers for high/low relapse-risk basal-like BC and possibly guide treatment selections.
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Affiliation(s)
- Praveen-Kumar Raj-Kumar
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Xiaoying Lin
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Tao Liu
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Lori A Sturtz
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | | | | | | | - Brenda Deyarmin
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | - Jianfang Liu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | | | - Guisong Wang
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | | | - Anil K Shukla
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ronald J Moore
- Pacific Northwest National Laboratory, Richland, WA, USA
| | | | | | - Jeffrey A Hooke
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Leigh Fantacone-Campbell
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Brad Mostoller
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | - Leonid Kvecher
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jennifer Kane
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | - Jennifer Melley
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | - Stella Somiari
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | | | | | - Richard J Mural
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | | | - Craig D Shriver
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
- Department of Surgery, Walter Reed National Military Medical Center, Bethesda, MD, USA.
| | - Albert J Kovatich
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Hai Hu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA.
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
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3
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Kim YA, Choi Y, Kim TG, Jeong J, Yu S, Kim T, Sheen K, Lee Y, Choi T, Park YH, Kang MS, Kim MS. Multi-System-Level Analysis with RNA-Seq on Pterygium Inflammation Discovers Association between Inflammatory Responses, Oxidative Stress, and Oxidative Phosphorylation. Int J Mol Sci 2024; 25:4789. [PMID: 38732006 PMCID: PMC11083828 DOI: 10.3390/ijms25094789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/18/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024] Open
Abstract
A pterygium is a common conjunctival degeneration and inflammatory condition. It grows onto the corneal surface or limbus, causing blurred vision and cosmetic issues. Ultraviolet is a well-known risk factor for the development of a pterygium, although its pathogenesis remains unclear, with only limited understanding of its hereditary basis. In this study, we collected RNA-seq from both pterygial tissues and conjunctival tissues (as controls) from six patients (a total of twelve biological samples) and retrieved publicly available data, including eight pterygium samples and eight controls. We investigated the intrinsic gene regulatory mechanisms closely linked to the inflammatory reactions of pterygiums and compared Asian (Korea) and the European (Germany) pterygiums using multiple analysis approaches from different perspectives. The increased expression of antioxidant genes in response to oxidative stress and DNA damage implies an association between these factors and pterygium development. Also, our comparative analysis revealed both similarities and differences between Asian and European pterygiums. The decrease in gene expressions involved in the three primary inflammatory signaling pathways-JAK/STAT, MAPK, and NF-kappa B signaling-suggests a connection between pathway dysfunction and pterygium development. We also observed relatively higher activity of autophagy and antioxidants in the Asian group, while the European group exhibited more pronounced stress responses against oxidative stress. These differences could potentially be necessitated by energy-associated pathways, specifically oxidative phosphorylation.
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Affiliation(s)
- Ye-Ah Kim
- Translational-Transdisciplinary Research Center, Clinical Research Institute, Kyung Hee University Hospital at Gangdong, Kyung Hee University College of Medicine, Seoul 05278, Republic of Korea; (Y.-A.K.); (Y.C.); (J.J.); (S.Y.); (T.K.); (K.S.); (Y.L.)
- Department of Biomedical Science and Technology, Graduate School, Kyung Hee University, Seoul 02453, Republic of Korea
| | - Yueun Choi
- Translational-Transdisciplinary Research Center, Clinical Research Institute, Kyung Hee University Hospital at Gangdong, Kyung Hee University College of Medicine, Seoul 05278, Republic of Korea; (Y.-A.K.); (Y.C.); (J.J.); (S.Y.); (T.K.); (K.S.); (Y.L.)
- Department of Biomedical Science and Technology, Graduate School, Kyung Hee University, Seoul 02453, Republic of Korea
| | - Tae Gi Kim
- Department of Ophthalmology, Kyung Hee University Hospital at Gangdong, Kyung Hee University College of Medicine, Seoul 05278, Republic of Korea;
| | - Jisu Jeong
- Translational-Transdisciplinary Research Center, Clinical Research Institute, Kyung Hee University Hospital at Gangdong, Kyung Hee University College of Medicine, Seoul 05278, Republic of Korea; (Y.-A.K.); (Y.C.); (J.J.); (S.Y.); (T.K.); (K.S.); (Y.L.)
- Department of Biomedical Science and Technology, Graduate School, Kyung Hee University, Seoul 02453, Republic of Korea
| | - Sanghyeon Yu
- Translational-Transdisciplinary Research Center, Clinical Research Institute, Kyung Hee University Hospital at Gangdong, Kyung Hee University College of Medicine, Seoul 05278, Republic of Korea; (Y.-A.K.); (Y.C.); (J.J.); (S.Y.); (T.K.); (K.S.); (Y.L.)
- Department of Biomedical Science and Technology, Graduate School, Kyung Hee University, Seoul 02453, Republic of Korea
| | - Taeyoon Kim
- Translational-Transdisciplinary Research Center, Clinical Research Institute, Kyung Hee University Hospital at Gangdong, Kyung Hee University College of Medicine, Seoul 05278, Republic of Korea; (Y.-A.K.); (Y.C.); (J.J.); (S.Y.); (T.K.); (K.S.); (Y.L.)
- Department of Biomedical Science and Technology, Graduate School, Kyung Hee University, Seoul 02453, Republic of Korea
| | - Kisung Sheen
- Translational-Transdisciplinary Research Center, Clinical Research Institute, Kyung Hee University Hospital at Gangdong, Kyung Hee University College of Medicine, Seoul 05278, Republic of Korea; (Y.-A.K.); (Y.C.); (J.J.); (S.Y.); (T.K.); (K.S.); (Y.L.)
- Department of Biomedical Science and Technology, Graduate School, Kyung Hee University, Seoul 02453, Republic of Korea
| | - Yoonsung Lee
- Translational-Transdisciplinary Research Center, Clinical Research Institute, Kyung Hee University Hospital at Gangdong, Kyung Hee University College of Medicine, Seoul 05278, Republic of Korea; (Y.-A.K.); (Y.C.); (J.J.); (S.Y.); (T.K.); (K.S.); (Y.L.)
| | - Taesoo Choi
- Department of Urology, School of Medicine, Kyung Hee University, Seoul 05278, Republic of Korea;
| | - Yong Hwan Park
- Department of Microbiology, Ajou University School of Medicine, Suwon 16499, Republic of Korea;
| | - Min Seok Kang
- Department of Ophthalmology, Kyung Hee University Hospital, Kyung Hee University College of Medicine, Seoul 02447, Republic of Korea
| | - Man S. Kim
- Translational-Transdisciplinary Research Center, Clinical Research Institute, Kyung Hee University Hospital at Gangdong, Kyung Hee University College of Medicine, Seoul 05278, Republic of Korea; (Y.-A.K.); (Y.C.); (J.J.); (S.Y.); (T.K.); (K.S.); (Y.L.)
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4
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Lin M, Zhong Y, Zhou D, Guan B, Hu B, Wang P, Liu F. Proximal tubule cells in blood and urine as potential biomarkers for kidney disease biopsy. PeerJ 2023; 11:e16499. [PMID: 38077419 PMCID: PMC10710128 DOI: 10.7717/peerj.16499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/31/2023] [Indexed: 12/18/2023] Open
Abstract
Early diagnosis and treatment are crucial for managing kidney disease, yet there remains a need to further explore pathological mechanisms and develop minimally invasive diagnostic methods. In this study, we employed single-cell RNA sequencing (scRNA-seq) to assess the cellular heterogeneity of kidney diseases. We analyzed gene expression profiles from renal tissue, peripheral blood mononuclear cells (PBMCs), and urine of four patients with nephritis. Our findings identified 12 distinct cell subsets in renal tissues and leukocytes. These subsets encompassed fibroblast cells, mesangial cells, epithelial cells, proximal tubule cells (PTCs), and six immune cell types: CD8+ T cells, macrophages, natural killer cells, dendritic cells, B cells, and neutrophils. Interestingly, PTCs were present in both PBMCs and urine samples but absent in healthy blood samples. Furthermore, several populations of fibroblast cells, mesangial cells, and PTCs exhibited pro-inflammatory or pro-apoptotic behaviors. Our gene expression analysis highlighted the critical role of inflammatory PTCs and fibroblasts in nephritis development and progression. These cells showed high expression of pro-inflammatory genes, which could have chemotactic and activating effect on neutrophils. This was substantiated by the widespread in these cells. Notably, the gene expression profiles of inflammatory PTCs in PBMCs, urine, and kidney tissues had high similarity. This suggests that PTCs in urine and PBMCs hold significant potential as alternative markers to invasive kidney biopsies.
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Affiliation(s)
- Minwa Lin
- Depament of Nephrology, The First People’s Hospital of Foshan, Foshan, China
| | - Yingxue Zhong
- Depament of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Dan Zhou
- Cancer Center, The First People’s Hospital of Foshan, Foshan, China
| | - Baozhang Guan
- Depament of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Bo Hu
- Depament of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Panpan Wang
- Department of Traditional Chinese Medicine, the First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Fanna Liu
- Depament of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou, China
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5
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Zhang Y, Xu J, Yu J, Si L, Chang L, Li T, Yan D. Identification of CCCH-type zinc finger antiviral protein 1 (ZAP) gene from Pacific white shrimp (Penaeus vannamei): Characterization and expression analysis in response to viral infection. FISH & SHELLFISH IMMUNOLOGY 2023; 140:108948. [PMID: 37453491 DOI: 10.1016/j.fsi.2023.108948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023]
Abstract
Zinc-finger proteins (ZFPs) are a huge family that exert multiple roles in the cells. ZFPs could be divided into nine types based on the numbers and positions of conserved Cys and His residues, in which CCCH-type ZFP was one of the most widely studied types. CCCH-type zinc finger antiviral protein 1 (ZAP), a CCCH-type ZFP that can inhibit the replication of certain RNA viruses and DNA viruses by mediating degradation of viral RNA and repressing mRNA translation, plays significant roles in the host innate immune defenses against viral infections. Presently, there have been numerous reports investigating the antiviral ability of ZAP, while no data is available about ZAP gene in the species of shrimps or even crustaceans. In this study, a novel protein containing CCCH-type zinc finger motifs (ZnF-CCCH), CCCH-type zinc finger antiviral protein 1 (ZAP) gene, was identified from Pacific white shrimp (Penaeus vannamei) and its role in antiviral immunity was further investigated. Similar to mammalian ZAPs, in addition to ZnF-CCCH, PvZAP also possesses central WWE domains and C-terminal PARP domain. Phylogenetic analysis showed that PvZAP was close to that of the crustacean Pacific oyster, separating from the cluster of vertebrate ZAP proteins. Upon in vivo infection by IHHNV, gene expression of PvZAP was strongly up-regulated in the hepatopancreas and gills of both adult and juvenile shrimps, where adult individuals showed higher fold changes of up-regulation than in juvenile individuals. These results suggested that PvZAP might play an important role in the innate immune defense of Pacific white shrimp against IHHNV infection. This allows us to gain new insights into the immunological function of ZAP in the innate immunity of shrimp species and even crustaceans.
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Affiliation(s)
- Yingying Zhang
- School of Agriculture, Ludong University, Yantai, 264025, PR China
| | - Jiahui Xu
- School of Agriculture, Ludong University, Yantai, 264025, PR China
| | - Jiyue Yu
- School of Agriculture, Ludong University, Yantai, 264025, PR China
| | - Lingjun Si
- School of Agriculture, Ludong University, Yantai, 264025, PR China
| | - Linrui Chang
- School of Agriculture, Ludong University, Yantai, 264025, PR China
| | - Ting Li
- School of Agriculture, Ludong University, Yantai, 264025, PR China.
| | - Dongchun Yan
- School of Agriculture, Ludong University, Yantai, 264025, PR China.
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6
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Zhou P, Yin C, Wang Y, Yin Z, Liu Y. Genomic Association Analysis of Growth and Backfat Traits in Large White Pigs. Genes (Basel) 2023; 14:1258. [PMID: 37372438 DOI: 10.3390/genes14061258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
The pig industry is significantly influenced by complex traits such as growth rate and fat deposition, which have substantial implications for economic returns. Over the years, remarkable genetic advancements have been achieved through intense artificial selection to enhance these traits in pigs. In this study, we aimed to investigate the genetic factors that contribute to growth efficiency and lean meat percentages in Large White pigs. Specifically, we focused on analyzing two key traits: age at 100 kg live weight (AGE100) and backfat thickness at 100 kg (BF100), in three distinct Large White pig populations-500 Canadian, 295 Danish, and 1500 American Large White pigs. By employing population genomic techniques, we observed significant population stratification among these pig populations. Utilizing imputed whole-genome sequencing data, we conducted single population genome-wide association studies (GWAS) as well as a combined meta-analysis across the three populations to identify genetic markers associated with the aforementioned traits. Our analyses highlighted several candidate genes, such as CNTN1-which has been linked to weight loss in mice and is potentially influential for AGE100-and MC4R, which is associated with obesity and appetite and may impact both traits. Additionally, we identified other genes-namely, PDZRN4, LIPM, and ANKRD22-which play a partial role in fat growth. Our findings provide valuable insights into the genetic basis of these important traits in Large White pigs, which may inform breeding strategies for improved production efficiency and meat quality.
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Affiliation(s)
- Peng Zhou
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Chang Yin
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuwei Wang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zongjun Yin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Yang Liu
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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7
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Mirzaei S, Paskeh MDA, Entezari M, Mirmazloomi SR, Hassanpoor A, Aboutalebi M, Rezaei S, Hejazi ES, Kakavand A, Heidari H, Salimimoghadam S, Taheriazam A, Hashemi M, Samarghandian S. SOX2 function in cancers: Association with growth, invasion, stemness and therapy response. Biomed Pharmacother 2022; 156:113860. [DOI: 10.1016/j.biopha.2022.113860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/30/2022] [Accepted: 10/08/2022] [Indexed: 11/29/2022] Open
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8
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Pu Z, Liu J, Liu Z, Peng F, Zhu Y, Wang X, He J, Yi P, Hu X, Fan X, Chen J. STING pathway contributes to the prognosis of hepatocellular carcinoma and identification of prognostic gene signatures correlated to tumor microenvironment. Cancer Cell Int 2022; 22:314. [PMID: 36224658 PMCID: PMC9554977 DOI: 10.1186/s12935-022-02734-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 09/26/2022] [Indexed: 11/10/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is one of the most malignant solid tumors worldwide. Recent evidence shows that the stimulator of interferon genes (STING) pathway is essential for anti-tumor immunity via inducing the production of downstream inflammatory cytokines. However, its impact on the prognosis and tumor microenvironment of HCC was still limited known. Methods We obtained gene expression profiles of HCC from GEO, TCGA, and ICGC databases, and immune-related genes (IRGs) from the ImmPort database. Multivariate Cox regression was performed to identify independent prognostic factors. Nomogram was established to predict survival probability for individual patients. Kaplan–Meier curve was used to evaluate the survival difference. Afterward, ESTIMATE, TISCH, and TIMER databases were combined to assess the immune cell infiltration. Furthermore, the qPCR, western blotting, and immunohistochemistry were done to evaluate gene expression, and in vitro cell models were built to determine cell migratory ability. Results We found that gene markers of NLRC3, STING1, TBK1, TRIM21, and XRCC6 within STING pathway were independent prognostic factors in HCC patients. Underlying the finding, a predictive nomogram was constructed in TCGA-training cohort and further validated in TCGA-all and ICGC datasets, showing credible performance. Experimentally, up-regulated TBK1 promotes the ability of HCC cell migration. Next, the survival-related immune-related co-expressed gene signatures (IRCGS) (VAV1, RHOA, and ZC3HAV1) were determined in HCC cohorts and their expression was verified in human HCC cells and clinical samples. Furthermore, survival-related IRCGS was associated with the infiltration of various immune cell subtypes in HCC, the transcriptional expression of prominent immune checkpoints, and immunotherapeutic response. Conclusion Collectively, we constructed a novel prognostic nomogram model for predicting the survival probability of individual HCC patients. Moreover, an immune-related prognostic gene signature was determined. Both might function as potential therapeutic targets for HCC treatment in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-022-02734-4.
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Affiliation(s)
- Zhangya Pu
- Department of Infectious Diseases, Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, No. 87, Xiangya Rd, Kaifu District, Changsha, 410008, Hunan Province, China.,Department of Infectious Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang Province, China
| | - Jinghua Liu
- Department of Hepatobiliary Surgery, Linyi People's Hospital, Linyi, Shandong, China
| | - Zelong Liu
- Division of Interventional Ultrasound, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Fang Peng
- Department of Infectious Diseases, Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, No. 87, Xiangya Rd, Kaifu District, Changsha, 410008, Hunan Province, China.,NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, 41800, Hunan Province, China
| | - Yuanyuan Zhu
- Department of Infectious Diseases, Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, No. 87, Xiangya Rd, Kaifu District, Changsha, 410008, Hunan Province, China.,NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, 41800, Hunan Province, China
| | - Xiaofang Wang
- Department of Infectious Diseases, Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, No. 87, Xiangya Rd, Kaifu District, Changsha, 410008, Hunan Province, China
| | - Jiayan He
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310000, Zhejiang Province, China
| | - Panpan Yi
- Department of Infectious Diseases, Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, No. 87, Xiangya Rd, Kaifu District, Changsha, 410008, Hunan Province, China
| | - Xingwang Hu
- Department of Infectious Diseases, Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, No. 87, Xiangya Rd, Kaifu District, Changsha, 410008, Hunan Province, China.
| | - Xuegong Fan
- Department of Infectious Diseases, Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, No. 87, Xiangya Rd, Kaifu District, Changsha, 410008, Hunan Province, China.
| | - Jiang Chen
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310000, Zhejiang Province, China.
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Zhang D, Lu W, Zhuo Z, Mei H, Wu X, Cui Y. Construction of a breast cancer prognosis model based on alternative splicing and immune infiltration. Discov Oncol 2022; 13:78. [PMID: 35988113 PMCID: PMC9393119 DOI: 10.1007/s12672-022-00506-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/24/2022] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Breast cancer (BC) is the most common malignancy among women in the world. Alternative splicing (AS) is an important mechanism for regulating gene expression and producing proteome diversity, which is closely related to tumorigenesis. Understanding the role of AS in BC may be helpful to reveal new therapeutic targets for clinical interventions. METHODS RNA-seq, clinical and AS data of TCGA-BRCA were downloaded from TCGA and TCGA SpliceSeq databases. AS events associated with prognosis were filtered by univariate Cox regression. The AS risk model of BC was built by Lasso regression, random forest and multivariate Cox regression. The accuracy of the AS risk model and clinicopathological factors were evaluated by time-dependent receiver operating characteristic (ROC) curves. The significant factors were used to construct the nomogram model. Tumor microenvironment analysis, immune infiltration and immune checkpoint analysis were performed to show the differences between the high and low AS risk groups. The expression differences of genes of AS events constituting the risk model in tumor tissues and normal tissues were analyzed, the genes with significant differences were screened, and their relationship with prognosis, tumor microenvironment, immune infiltration and immune checkpoint were analyzed. Finally, Pearson correlation analysis was used to calculate the correlation coefficient between splicing factors (SF) and prognostic AS events in TCGA-BRCA. The results were imported into Cytoscape, and the associated network was constructed. RESULTS A total of 21,232 genes had 45,421 AS events occurring in TCGA-BRCA, while 1604 AS events were found to be significantly correlated with survival. The BRCA risk model consisted of 5 AS events, (TTC39C|44853|AT*- 2.67) + (HSPBP1|52052|AP*- 4.28) + (MAZ|35942|ES*2.34) + (ANK3|11845|AP*1.18) + (ZC3HAV1|81940|AT*1.59), which were confirmed to be valuable for predicting BRCA prognosis to a certain degree, including ROC curve, survival analysis, tumor microenvironment analysis, immune infiltration and immune checkpoint analysis. Based on this, we constructed a nomogram prediction model composed of clinicopathological features and the AS risk signature. Furthermore, we found that MAZ was a core gene indicating the connection of tumor prognosis and AS events. Ultimately, a network of SF-AS regulation was established to reveal the relationship between them. CONCLUSIONS We constructed a nomogram model combined with clinicopathological features and AS risk score to predict the prognosis of BC. The detailed analysis of tumor microenvironment and immune infiltration in the AS risk model may further reveal the potential mechanisms of BC recurrence and development.
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Affiliation(s)
- Dongni Zhang
- Oncology Department, China Academy of Chinese Medical Sciences Guang'anmen Hospital, Beijing, China
| | - Wenping Lu
- Oncology Department, China Academy of Chinese Medical Sciences Guang'anmen Hospital, Beijing, China.
| | - Zhili Zhuo
- Oncology Department, China Academy of Chinese Medical Sciences Guang'anmen Hospital, Beijing, China
| | - Heting Mei
- Oncology Department, China Academy of Chinese Medical Sciences Guang'anmen Hospital, Beijing, China
| | - Xiaoqing Wu
- Oncology Department, China Academy of Chinese Medical Sciences Guang'anmen Hospital, Beijing, China
| | - Yongjia Cui
- Oncology Department, China Academy of Chinese Medical Sciences Guang'anmen Hospital, Beijing, China
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ZAP isoforms regulate unfolded protein response and epithelial- mesenchymal transition. Proc Natl Acad Sci U S A 2022; 119:e2121453119. [PMID: 35881805 PMCID: PMC9351355 DOI: 10.1073/pnas.2121453119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human ZAP inhibits many viruses, including HIV and coronaviruses, by binding to viral RNAs to promote their degradation and/or translation suppression. However, the regulatory role of ZAP in host mRNAs is largely unknown. Two major alternatively spliced ZAP isoforms, the constitutively expressed ZAPL and the infection-inducible ZAPS, play overlapping yet different antiviral and other roles that need further characterization. We found that the splicing factors hnRNPA1/A2, PTBP1/2, and U1-snRNP inhibit ZAPS production and demonstrated the feasibility to modulate the ZAPL/S balance by splice-switching antisense oligonucleotides in human cells. Transcriptomic analysis of ZAP-isoform-specific knockout cells revealed uncharacterized host mRNAs targeted by ZAPL/S with broad cellular functions such as unfolded protein response (UPR), epithelial-mesenchymal transition (EMT), and innate immunity. We established that endogenous ZAPL and ZAPS localize to membrane compartments and cytosol, respectively, and that the differential localization correlates with their target-RNA specificity. We showed that the ZAP isoforms regulated different UPR branches under resting and stress conditions and affected cell viability during ER stress. We also provided evidence for a different function of the ZAP isoforms in EMT-related cell migration, with effects that are cell-type dependent. Overall, this study demonstrates that the competition between splicing and IPA is a potential target for the modulation of the ZAPL/S balance, and reports new cellular transcripts and processes regulated by the ZAP isoforms.
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Wang Q, Zhong Y, Li Z, Zhu D, Lu H, Chen P, Li C, Peng X, Li Q, Zeng K. Multitranscriptome analyses of keloid fibroblasts reveal the role of the HIF-1α/HOXC6/ERK axis in keloid development. BURNS & TRAUMA 2022; 10:tkac013. [PMID: 35547861 PMCID: PMC9085412 DOI: 10.1093/burnst/tkac013] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/01/2022] [Indexed: 11/23/2022]
Abstract
Background A keloid is a disease of excessive fibrosis that is characterized by the aberrant proliferation of fibroblasts. However, the molecular mechanisms of fibroblasts during the development of keloids remain unclear. This study aims to identify new molecular targets that promote the proliferation and migration of keloid fibroblasts, providing new ideas for the prevention and treatment of keloids. Methods We utilized bioinformatics tools to analyze data from keloid fibroblasts (KFs) available in the Gene Expression Omnibus (GEO) database to identify the key genes involved in keloid development. Homeobox C6 (HOXC6) emerged as a hub gene in KFs from the GEO database was verified in keloid tissue samples and KFs using reverse transcription-quantitative polymerase chain reaction, western blot (WB) and immunohistochemistry. Subsequently, the effects of downregulated HOXC6 expression on the cellular behaviors of KFs were examined by performing Cell Counting Kit-8, flow cytometry, transwell migration and WB assays. Meanwhile, we performed transcriptome sequencing and gene set enrichment analysis (GSEA) to further explore HOXC6-related mechanisms and validated the signaling pathways by performing a series of experiments. Results HOXC6 was the top-ranking hub gene of KFs in microarray datasets from GEO and was upregulated in keloid tissue samples and KFs. Downregulation of HOXC6 inhibited proliferation, migration and extracellular matrix (ECM) accumulation and promoted KF apoptosis. GSEA predicted that the hypoxia signaling pathway was associated with HOXC6 in KFs. Transcriptome sequencing suggested that the extracellular regulated protein kinase (ERK) pathway was one of the downstream pathways of HOXC6 in KFs. Our experiments confirmed that hypoxia-inducible factor-1α (HIF-1α) upregulates HOXC6, contributing to KFs proliferation, migration, apoptosis inhibition and collagen accumulation through the ERK signaling pathway. Conclusions Our findings first revealed that HOXC6 acts as an oncogenic driver in the molecular mechanisms of fibroblasts in keloids. The HIF-1α/HOXC6/ERK axis promotes proliferation, migration and ECM production by KFs, contributing to the progression of keloids. Taken together, HOXC6 may serve as a promising novel therapeutic target and new focus for research designed to understand the pathogenesis of keloids.
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Affiliation(s)
- Qi Wang
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Yixiu Zhong
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Zhijia Li
- Molecular Diagnosis and Treatment Center for Infectious Diseases, Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Dingheng Zhu
- Department of Dermatologic Surgery, Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Hongyan Lu
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Pingjiao Chen
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Changxing Li
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Xuebiao Peng
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Qian Li
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Kang Zeng
- Department of Dermatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
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Gul Mohammad A, Li D, He R, Lei X, Mao L, Zhang B, Zhong X, Yin Z, Cao W, Zhang W, Hei R, Zheng Q, Zhang Y. Integrated analyses of an RNA binding protein-based signature related to tumor immune microenvironment and candidate drugs in osteosarcoma. Am J Transl Res 2022; 14:2501-2526. [PMID: 35559393 PMCID: PMC9091083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 03/24/2022] [Indexed: 06/15/2023]
Abstract
OBJECTIVE Osteosarcoma is the most frequent primary bone malignancy, associated with frequent recurrence and lung metastasis. RNA-binding proteins (RBPs) are pivotal in regulating several aspects of cancer biology. Nonetheless, interaction between RBPs and the osteosarcoma immune microenvironment is poorly understood. We investigated whether RBPs can predict prognosis and immunotherapy response in osteosarcoma patients. METHODS We constructed an RBP-related prognostic signature (RRPS) by univariate coupled with multivariate analyses and verified the independent prognostic efficacy of the signature. Single-sample Gene Set Enrichment Analysis (ssGSEA) along with ESTIMATE analysis were carried out to investigate the variations in immune characteristics between subgroups with various RRPS-scores. Furthermore, we investigatedpossible small molecule drugs using the connectivity map database and validated the expression of hub RBPs by qRT-PCR. RESULTS The RRPS, consisting of seven hub RBPs, was an independent prognostic factor compared to traditional clinical features. The RRPS could distinguish immune functions, immune score, stromal score, tumor purity and tumor infiltration by immune cells in different osteosarcoma subjects. Additionally, patients with high RRPS-scores had lower expression of immune checkpoint genes than patients with low RRPS-scores. We finally identified six small molecule drugs that may improve prognosis in osteosarcoma patients and substantiated notable differences in the contents of these RBPs. CONCLUSION We evaluated the prognostic value and clinical application of an RBPs-based prognostic signature and identified promising biomarkers to predict immune cell infiltration and immunotherapy response in osteosarcoma.
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Affiliation(s)
- Abdulraheem Gul Mohammad
- Department of Orthopedics, Affiliated Hospital of Jiangsu UniversityZhenjiang 212001, Jiangsu, China
| | - Dapeng Li
- Department of Orthopedics, Affiliated Hospital of Jiangsu UniversityZhenjiang 212001, Jiangsu, China
| | - Rong He
- Cancer Institute, The Affiliated People’s Hospital of Jiangsu UniversityZhenjiang 212000, Jiangsu, China
| | - Xuan Lei
- Department of Burn and Plastic Surgery, Affiliated Hospital of Jiangsu UniversityZhenjiang 212001, Jiangsu, China
| | - Lianghao Mao
- Department of Orthopedics, Affiliated Hospital of Jiangsu UniversityZhenjiang 212001, Jiangsu, China
| | - Bing Zhang
- Department of Orthopedics, Affiliated Hospital of Jiangsu UniversityZhenjiang 212001, Jiangsu, China
| | - Xinyu Zhong
- Department of Orthopedics, Affiliated Hospital of Jiangsu UniversityZhenjiang 212001, Jiangsu, China
| | - Zhengyu Yin
- Department of Orthopedics, Affiliated Hospital of Jiangsu UniversityZhenjiang 212001, Jiangsu, China
| | - Wenbing Cao
- Department of Orthopedics, Affiliated Hospital of Jiangsu UniversityZhenjiang 212001, Jiangsu, China
| | - Wenchao Zhang
- Department of Orthopedics, Affiliated Hospital of Jiangsu UniversityZhenjiang 212001, Jiangsu, China
| | - Ruoxuan Hei
- Department of Hematological Laboratory Science, Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu UniversityZhenjiang 212000, Jiangsu, China
| | - Qiping Zheng
- Department of Hematological Laboratory Science, Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu UniversityZhenjiang 212000, Jiangsu, China
- Shenzhen Academy of Peptide Targeting Technology at Pingshan, and Shenzhen Tyercan Bio-Pharm Co., Ltd.Shenzhen 518118, Guangdong, China
| | - Yiming Zhang
- Department of Orthopedics, Affiliated Hospital of Jiangsu UniversityZhenjiang 212001, Jiangsu, China
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