1
|
Pereira LHS, Alves ADC, Lopes GFM, da Silva BF, Vieira MS, Lopes DDO, Ferreira JMS, Lara Dos Santos L. Soluble isoforms of the DC-SIGN receptor can increase the dengue virus infection in immature dendritic cells. Braz J Infect Dis 2024:103873. [PMID: 39341603 DOI: 10.1016/j.bjid.2024.103873] [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: 02/01/2024] [Revised: 08/01/2024] [Accepted: 09/08/2024] [Indexed: 10/01/2024] Open
Abstract
Dengue is a disease with a high-impact on public health worldwide. Many researches have focused on the cell receptors involved in its pathogenesis. The role of soluble isoforms of DC-SIGN (Dendritic Cell-Specific ICAM-3 Grabbing Non-integrin) receptor in the process of Dengue Virus (DENV) infection is not well understood. This work proposes to evaluate changes in the infection process of Immature Dendritic Cells (iDCs) by DENV in the presence of DC-SIGN recombinant soluble isoforms 8, 10, and 12. The recombinant isoforms were built by heterologous expression, the DENV-2 was multiplied in the Aedes albopictus C6/36 cells and quantified in BHK-21 cells, and the iDCs were produced from the THP-1 strain. Infection assays were performed in the presence of iDCs, DENV-2, and isoforms 8, 10, and 12 separately at 25, 50 and 100 ng/mL. The final viral load was estimated by qPCR and statistical analysis was performed by Kruskal-Wallis and ANOVA tests. The iDC profile was confirmed by increasing expression of CD11c, CD86, and CD209 surface markers and maintaining CD14 expression. Infection assays demonstrated a 23-fold increase in DENV viral load in the presence of isoforms 8 and 10 at 100 ng/mL compared to the viral control (p < 0.05), while isoform 12 did not alter the viral load. It was possible to conclude that at 100 ng/mL isoforms (8 and 10) can interact with DENV, increasing viral infection, and potentially acting as opsonins.
Collapse
Affiliation(s)
- Lailah Horácio Sales Pereira
- Universidade Federal de São João del-Rei (UFSJ), Laboratório de Biologia Molecular, Divinópolis, MG, Brazil; Universidade Federal de São João del-Rei (UFSJ), Laboratório de Microbiologia Médica, Divinópolis, MG, Brazil
| | - Amanda do Carmo Alves
- Universidade Federal de São João del-Rei (UFSJ), Laboratório de Biologia Molecular, Divinópolis, MG, Brazil
| | | | - Brenda Fernandes da Silva
- Universidade Federal de São João del-Rei (UFSJ), Laboratório de Biologia Molecular, Divinópolis, MG, Brazil
| | - Mariana Sousa Vieira
- Universidade Federal de Minas Gerais (UFMG), Laboratório de Imunoparasitologia, Belo Horizonte, MG, Brazil
| | - Débora de Oliveira Lopes
- Universidade Federal de São João del-Rei (UFSJ), Laboratório de Biologia Molecular, Divinópolis, MG, Brazil
| | | | - Luciana Lara Dos Santos
- Universidade Federal de São João del-Rei (UFSJ), Laboratório de Biologia Molecular, Divinópolis, MG, Brazil
| |
Collapse
|
2
|
Li C, Mao Y, Hu J, Su C, Li M, Tan H. Integrating machine learning and multi-omics analysis to develop an asparagine metabolism immunity index for improving clinical outcome and drug sensitivity in lung adenocarcinoma. Immunol Res 2024:10.1007/s12026-024-09544-y. [PMID: 39320693 DOI: 10.1007/s12026-024-09544-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Accepted: 09/13/2024] [Indexed: 09/26/2024]
Abstract
Lung adenocarcinoma (LUAD) is a malignancy affecting the respiratory system. Most patients are diagnosed with advanced or metastatic lung cancer due to the fact that most of their clinical symptoms are insidious, resulting in a bleak prognosis. Given that abnormal reprogramming of asparagine metabolism (AM) has emerged as an emerging therapeutic target for anti-tumor therapy. However, the clinical significance of abnormal reprogramming of AM in LUAD patients is unclear. In this study, we collected 864 asparagine metabolism-related genes (AMGs) and used a machine-learning computational framework to develop an asparagine metabolism immunity index (AMII) for LUAD patients. Through the utilization of median AMII scores, LUAD patients were segregated into either a low-AMII group or a high-AMII group. We observed outstanding performance of AMII in predicting survival prognosis in LUAD patients in the TCGA-LUAD cohort and in three externally independently validated GEO cohorts (GSE72094, GSE37745, and GSE30219), and poorer prognosis for LUAD patients in the high-AMII group. The results of univariate and multivariate analyses showed that AMII can be used as an independent risk factor for LUAD patients. In addition, the results of C-index analysis and decision analysis showed that AMII-based nomograms had a robust performance in terms of accuracy of prognostic prediction and net clinical benefit in patients with LUAD. Excitingly, LUAD patients in the low-AMII group were more sensitive to commonly used chemotherapeutic drugs. Consequently, AMII is expected to be a novel diagnostic tool for clinical classification, providing valuable insights for clinical decision-making and personalized management of LUAD patients.
Collapse
Affiliation(s)
- Chunhong Li
- Central Laboratory, The Second Affiliated Hospital of Guilin Medical University, Guilin , 541199, Guangxi, China.
- Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, Guangxi, China.
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, Guangxi, China.
| | - Yuhua Mao
- Department of Obstetrics, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, Guangxi, China
| | - Jiahua Hu
- Central Laboratory, The Second Affiliated Hospital of Guilin Medical University, Guilin , 541199, Guangxi, China
- Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, Guangxi, China
| | - Chunchun Su
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guilin Medical University, Guilin, 541199, Guangxi, China
| | - Mengqin Li
- College of Pharmacy, Guilin Medical University, Guilin, 541199, Guangxi, China
| | - Haiyin Tan
- School of Medical Laboratory Medicine, Guilin Medical University, Guilin, 541004, Guangxi, China
| |
Collapse
|
3
|
Corbin H, Yip L, Carty SE, Reyes-Múgica M, Seethala RR. Characterisation of Kürsteiner canals of parathyroid: imparting relevance to a one-and-a-quarter-century-old concept. Histopathology 2024. [PMID: 39315563 DOI: 10.1111/his.15326] [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: 07/13/2024] [Revised: 09/09/2024] [Accepted: 09/10/2024] [Indexed: 09/25/2024]
Abstract
AIMS Kürsteiner canals (KC) were described at least 125 years ago as pharyngeal pouch embryological remnants of parathyroid and thymic development. While considered precursors for a subset of parathyroid cysts and salivary heterotopias (SH), they remain enigmatic. We now define a comprehensive phenotype of KC remnants and investigate their role in a spectrum of parathyroid lesions. METHODS AND RESULTS `Sixty-two cystic and 22 non-cystic parathyroid lesions (73 patients) were retrieved from our institutional archive (2011-23) and evaluated for the presence of KC and prevalence of KC phenotype in parathyroid hormone (PTH)-positive and PTH-negative cysts. KC phenotype was defined as: cysts and tubules with surrounding sclerosis; bland, unilayered lining with frequent nuclear indentation of lumina; vesicular chromatin relative to chief cells; attenuated eosinophilic to 'hyper-cleared' cytoplasm; and staining pattern PTH-negative, SOX-10-positive, CK7-positive, GATA-3-positive and PAX-9 dim, a subset with oestrogen/progesterone receptor (ER/PR) positivity. Thirty PTH-negative cysts were identified in the neck/mediastinum; 14 of this group also showed SH. Thirty-two PTH-positive cysts included: 11 cystic parathyroid adenomas, 17 hyperplastic parathyroids, and four carcinomas. KC showed two distinct subtypes and were often found near PTH-negative cysts. PTH-negative cysts were associated with inferior parathyroids, SOX-10 positivity, fibrosclerosis, vesicular nuclei indenting cyst lumina and hyper-cleared or attenuated eosinophilic cytoplasm. CONCLUSIONS KC are common in parathyroids and show a distinct histological and immunohistochemical profile, with an inferior predilection favouring branchial cleft III distribution. Diagnostically, the high prevalence of this phenotype in PTH-negative cysts and salivary heterotopia supports derivation of non-functioning cysts from KC. Conversely, PTH-positive cysts are more compatible with cystic change within hyperfunctioning glands.
Collapse
Affiliation(s)
- Haley Corbin
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Linwah Yip
- Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Sally E Carty
- Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Miguel Reyes-Múgica
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Raja R Seethala
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| |
Collapse
|
4
|
Wang S, Zi H, Li M, Kong J, Fan C, Bai Y, Sun J, Wang T. Development and validation of a mitotic catastrophe-related genes prognostic model for breast cancer. PeerJ 2024; 12:e18075. [PMID: 39314848 PMCID: PMC11418815 DOI: 10.7717/peerj.18075] [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: 05/16/2024] [Accepted: 08/19/2024] [Indexed: 09/25/2024] Open
Abstract
Background Breast cancer has become the most common malignant tumor in women worldwide. Mitotic catastrophe (MC) is a way of cell death that plays an important role in the development of tumors. However, the exact relationship between MC-related genes (MCRGs) and the development of breast cancer is still unclear, and further research is needed to elucidate this complexity. Methods Transcriptome data and clinical data of breast cancer were downloaded from the Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) database. We identified differential expression of MCRGs by comparing tumor tissue with normal tissue. Subsequently, we used COX regression analysis and LASSO regression analysis to construct the prognosis risk model of MCRGs. Kaplan-Meier survival curve and receiver operating characteristic (ROC) curve were used to evaluate the predictive ability of prognostic model. Moreover, the clinical relevance, gene set enrichment analysis (GSEA), immune landscape, tumor mutation burden (TMB), and immunotherapy and drug sensitivity analysis between high-risk and low-risk groups were systematically investigated. Finally, we validated the expression levels of genes involved in constructing the prognostic model through real-time quantitative polymerase chain reaction (RT-qPCR) at the cellular and tissue levels. Results We identified 12 prognostic associated MCRGs, four of which were selected to construct prognostic model. The Kaplan-Meier analysis suggested that patients in the high-risk group had a shorter overall survival (OS). The Cox regression analysis and ROC analysis indicated that risk model had independent and excellent ability in predicting prognosis of breast cancer patients. Mechanistically, a remarkable difference was observed in clinical relevance, GSEA, immune landscape, TMB, immunotherapy response, and drug sensitivity analysis. RT-qPCR results showed that genes involved in constructing the prognostic model showed significant abnormal expressions and the expression change trends were consistent with the bioinformatics results. Conclusions We established a prognosis risk model based on four MCRGs that had the ability to predict clinical prognosis and immune landscape, proposing potential therapeutic targets for breast cancer.
Collapse
Affiliation(s)
- Shuai Wang
- The First Affiliated Hospital of Air Force Medical University, Department of Thyroid, Breast and Vascular Surgery, Xi’an, Shaanxi, China
| | - Haoyi Zi
- The First Affiliated Hospital of Air Force Medical University, Department of Thyroid, Breast and Vascular Surgery, Xi’an, Shaanxi, China
| | - Mengxuan Li
- The First Affiliated Hospital of Air Force Medical University, Department of Thyroid, Breast and Vascular Surgery, Xi’an, Shaanxi, China
| | - Jing Kong
- The First Affiliated Hospital of Air Force Medical University, Department of Thyroid, Breast and Vascular Surgery, Xi’an, Shaanxi, China
| | - Cong Fan
- The First Affiliated Hospital of Air Force Medical University, Department of Thyroid, Breast and Vascular Surgery, Xi’an, Shaanxi, China
| | - Yujie Bai
- The First Affiliated Hospital of Air Force Medical University, Department of Thyroid, Breast and Vascular Surgery, Xi’an, Shaanxi, China
| | - Jianing Sun
- The First Affiliated Hospital of Air Force Medical University, Department of Thyroid, Breast and Vascular Surgery, Xi’an, Shaanxi, China
| | - Ting Wang
- The First Affiliated Hospital of Air Force Medical University, Department of Thyroid, Breast and Vascular Surgery, Xi’an, Shaanxi, China
| |
Collapse
|
5
|
Gupta MK, Gouda G, Vadde R. Deciphering the role of FOXP4 in long COVID: exploring genetic associations, evolutionary conservation, and drug identification through bioinformatics analysis. Funct Integr Genomics 2024; 24:167. [PMID: 39298002 DOI: 10.1007/s10142-024-01451-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 09/02/2024] [Accepted: 09/09/2024] [Indexed: 09/21/2024]
Abstract
Long COVID (LC) refers to a condition characterized by a variety of lingering symptoms that persist for more than 4 to 12 weeks following the initial acute SARS-CoV-2 infection. Recent research has suggested that the FOXP4 gene could potentially be a significant factor contributing to LC. Owing to that, this study investigates FOXP4's role in LC by analyzing public datasets to understand its evolution and expression in diverse human populations and searching for drugs to reduce LC symptoms. Population genetic analysis of FOXP4 across human populations unmasks distinct genetic diversity patterns and positive selection signatures, suggesting potential population-specific susceptibilities to conditions like LC. Further, we also observed that FOXP4 experiences high expression during LC. To identify potential inhibitors, drug screening analysis identifies synthetic drugs like Glisoxepide, and natural compounds Kapurimycin A3 produced from Streptomyces sp, and Cucurbitacin B from Begonia nantoensis as promising candidates. Overall, our research contributes to understanding how FOXP4 may serve as a therapeutic target for mitigating the impact of LC.
Collapse
Affiliation(s)
- Manoj Kumar Gupta
- Department of Biotechnology and Bioinformatics, Yogi Vemana University, Kadapa, Andhra Pradesh, 516005, India.
| | - Gayatri Gouda
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753 006, India
| | - Ramakrishna Vadde
- Department of Biotechnology and Bioinformatics, Yogi Vemana University, Kadapa, Andhra Pradesh, 516005, India.
| |
Collapse
|
6
|
Beisl J, Jochum K, Chen Y, Varga E, Marko D. Combinatory Effects of Acrylamide and Deoxynivalenol on In Vitro Cell Viability and Cytochrome P450 Enzymes of Human HepaRG Cells. Toxins (Basel) 2024; 16:389. [PMID: 39330847 PMCID: PMC11436166 DOI: 10.3390/toxins16090389] [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: 08/05/2024] [Revised: 08/31/2024] [Accepted: 09/03/2024] [Indexed: 09/28/2024] Open
Abstract
Acrylamide (AA) can be formed during the thermal processing of carbohydrate-rich foods. Deoxynivalenol (DON), a mycotoxin produced by Fusarium spp., contaminates many cereal-based products. In addition to potential co-exposure through a mixed diet, co-occurrence of AA and DON in thermally processed cereal-based products is also likely, posing the question of combinatory toxicological effects. In the present study, the effects of AA (0.001-3 mM) and DON (0.1-30 µM) on the cytotoxicity, gene transcription, and expression of major cytochrome P450 (CYP) enzymes were investigated in differentiated human hepatic HepaRG cells. In the chosen ratios of AA-DON (10:1; 100:1), cytotoxicity was clearly driven by DON and no overadditive effects were observed. Using quantitative real-time PCR, about twofold enhanced transcript levels of CYP1A1 were observed at low DON concentrations (0.3 and 1 µM), reflected by an increase in CYP1A activity in the EROD assay. In contrast, CYP2E1 and CYP3A4 gene transcription decreased in a concentration-dependent manner after incubation with DON (0.01-0.3 µM). Nevertheless, confocal microscopy showed comparably constant protein levels. The present study provided no indication of an induction of CYP2E1 as a critical step in AA bioactivation by co-occurrence with DON. Taken together, the combination of AA and DON showed no clear physiologically relevant interaction in HepaRG cells.
Collapse
Affiliation(s)
- Julia Beisl
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Kristina Jochum
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
- German Federal Institute of Risk Assessment, Department of Pesticides Safety, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Yi Chen
- State Key Laboratory of Food Science and Technology, Nanchang University, 235 Nanjing East Road, Nanchang 330047, China
| | - Elisabeth Varga
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
- Unit Food Hygiene and Technology, Centre for Food Science and Veterinary Public Health, Clinical Department for Farm Animals and Food System Science, University of Veterinary Medicine, Veterinarplatz 1, 1210 Vienna, Austria
| | - Doris Marko
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| |
Collapse
|
7
|
Conforti JM, Ziegler AM, Worth CS, Nambiar AM, Bailey JT, Taube JH, Gallagher ES. Differences in Protein Capture by SP3 and SP4 Demonstrate Mechanistic Insights of Proteomics Cleanup Techniques. J Proteome Res 2024; 23:3877-3889. [PMID: 39161190 DOI: 10.1021/acs.jproteome.4c00206] [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: 08/21/2024]
Abstract
The goal of proteomics experiments is to identify proteins to observe changes in cellular processes and diseases. One challenge in proteomics is the removal of contaminants following protein extraction, which can limit protein identifications. Single-pot, solid-phase-enhanced sample preparation (SP3) is a cleanup technique in which proteins are captured on carboxylate-modified particles through a proposed hydrophilic-interaction-liquid-chromatography (HILIC)-like mechanism. Recent results have suggested that proteins are captured in SP3 due to a protein-aggregation mechanism. Solvent precipitation, single-pot, solid-phase-enhanced sample preparation (SP4) is a newer cleanup technique that employs protein aggregation to capture proteins without modified particles. We hypothesize that differences in capture mechanisms of SP3 and SP4 affect which proteins are identified by each cleanup technique. Herein, we assess the proteins identified and enriched using SP3 versus SP4 for MCF7 subcellular fractions and correlate protein capture in each method to protein hydrophobicity. Our results indicate that SP3 captures more hydrophilic proteins through a combination of HILIC-like and protein-aggregation mechanisms, while SP4 captures more hydrophobic proteins through a protein-aggregation mechanism. Ultimately, we demonstrate that protein-capture mechanisms are distinct, and the selection of a cleanup technique that yields high proteome coverage is dependent on protein-sample hydrophobicity. Data has been deposited into MassIVE (MSV000094130) and ProteomeXchange (PXD049965).
Collapse
Affiliation(s)
- Jessica M Conforti
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
| | - Amanda M Ziegler
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
| | - Charli S Worth
- Department of Biology, Baylor University, One Bear Place #97388, Waco, Texas 76798, United States
| | - Adhwaitha M Nambiar
- Department of Biology, Baylor University, One Bear Place #97388, Waco, Texas 76798, United States
| | - Jacob T Bailey
- Department of Biology, Baylor University, One Bear Place #97388, Waco, Texas 76798, United States
| | - Joseph H Taube
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
- Department of Biology, Baylor University, One Bear Place #97388, Waco, Texas 76798, United States
| | - Elyssia S Gallagher
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
| |
Collapse
|
8
|
Zhong H, Dong B, Zhu D, Fu Z, Liu J, Guan G, Jin Y. Schistosoma japonicumsja-let-7 Inhibits the Growth of Hepatocellular Carcinoma Cells via Cross-Species Regulation of Col1α2. Genes (Basel) 2024; 15:1165. [PMID: 39336756 PMCID: PMC11431810 DOI: 10.3390/genes15091165] [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: 08/14/2024] [Revised: 08/29/2024] [Accepted: 09/02/2024] [Indexed: 09/30/2024] Open
Abstract
Liver fibrosis, a critical precursor to hepatocellular carcinoma (HCC), results from chronic liver injury and significantly contributes to HCC progression. Schistosomiasis, a neglected tropical disease, is known to cause liver fibrosis; however, this process can be modulated by schistosome-derived miRNAs. Previous studies from our laboratory have demonstrated that Schistosoma japonicum extracellular vesicles (EVs) deliver sja-let-7 to hepatic stellate cells, leading to the inhibition of Col1α2 expression and alleviation of liver fibrosis. Given the well-documented antifibrotic and antiproliferative properties of the let-7 miRNA family, this study aims to preliminarily investigate the effects of the sja-let-7/Col1α2 axis on BALB/c mice and HCC cell line SNU387, providing a basis for the potential application of parasite-derived molecules in HCC therapy. In the present study, schistosome-induced fibrosis datasets were analyzed to identify the role of Col1α2 in extracellular matrix organization. Pan-cancer analysis revealed that Col1α2 is upregulated in various cancers, including HCC, with significant associations with immune cell infiltration and clinical parameters, highlighting its diagnostic importance. Functional assays demonstrated that transfection with sja-let-7 mimics significantly reduced Col1α2 expression, inhibited HCC cell proliferation, migration, and colony formation. These findings suggest that sja-let-7, by targeting Col1α2, has the potential to serve as a therapeutic agent in HCC treatment. This study indicates the pivotal role of Col1α2 in liver fibrosis and HCC, and the promising therapeutic application of helminth-derived miRNAs.
Collapse
Affiliation(s)
- Haoran Zhong
- National Reference Laboratory for Animal Schistosomiasis, Key Laboratory of Animal Parasitology of Ministry of Agriculture and Rural Affairs, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (H.Z.); (B.D.); (D.Z.); (Z.F.); (J.L.)
| | - Bowen Dong
- National Reference Laboratory for Animal Schistosomiasis, Key Laboratory of Animal Parasitology of Ministry of Agriculture and Rural Affairs, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (H.Z.); (B.D.); (D.Z.); (Z.F.); (J.L.)
| | - Danlin Zhu
- National Reference Laboratory for Animal Schistosomiasis, Key Laboratory of Animal Parasitology of Ministry of Agriculture and Rural Affairs, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (H.Z.); (B.D.); (D.Z.); (Z.F.); (J.L.)
| | - Zhiqiang Fu
- National Reference Laboratory for Animal Schistosomiasis, Key Laboratory of Animal Parasitology of Ministry of Agriculture and Rural Affairs, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (H.Z.); (B.D.); (D.Z.); (Z.F.); (J.L.)
| | - Jinming Liu
- National Reference Laboratory for Animal Schistosomiasis, Key Laboratory of Animal Parasitology of Ministry of Agriculture and Rural Affairs, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (H.Z.); (B.D.); (D.Z.); (Z.F.); (J.L.)
| | - Guiquan Guan
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou 730046, China;
| | - Yamei Jin
- National Reference Laboratory for Animal Schistosomiasis, Key Laboratory of Animal Parasitology of Ministry of Agriculture and Rural Affairs, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (H.Z.); (B.D.); (D.Z.); (Z.F.); (J.L.)
| |
Collapse
|
9
|
Gao AYL, Montagna DR, Hirst WD, Temkin PA. RIT2 regulates autophagy lysosomal pathway induction and protects against α-synuclein pathology in a cellular model of Parkinson's disease. Neurobiol Dis 2024; 199:106568. [PMID: 38885848 DOI: 10.1016/j.nbd.2024.106568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 06/12/2024] [Accepted: 06/12/2024] [Indexed: 06/20/2024] Open
Abstract
Substantial work has been devoted to better understand the contribution of the myriad of genes that may underly the development of Parkinson's disease (PD) and their role in disease etiology. The small GTPase Ras-like without CAAX2 (RIT2) is one such genetic risk factor, with one single nucleotide polymorphism in the RIT2 locus, rs12456492, having been associated with PD risk in multiple populations. While RIT2 has previously been shown to influence signaling pathways, dopamine transporter trafficking, and LRRK2 activity, its cellular function remains unclear. In the current study, we have situated RIT2 to be upstream of various diverse processes associated with PD. In cellular models, we have shown that RIT2 is necessary for activity-dependent changes in the expression of genes related to the autophagy-lysosomal pathway (ALP) by regulating the nuclear translocation of MiT/TFE3-family transcription factors. RIT2 is also associated with lysosomes and can regulate autophagic flux and clearance by regulating lysosomal hydrolase expression and activity. Interestingly, upregulation of RIT2 can augment ALP flux and protect against α-synuclein aggregation in cortical neurons. Taken together, the present study suggests that RIT2 can regulates gene expression upstream of ALP function and that enhancing RIT2 activity may provide therapeutic benefit in PD.
Collapse
Affiliation(s)
- Andy Y L Gao
- Neurodegeneration Research Unit, Biogen, 225 Binney St, Cambridge, MA 02142, USA; Biogen Postdoctoral Scientist Program, Biogen, 225 Binney St, Cambridge, MA 02142, USA
| | - Daniel R Montagna
- Neurodegeneration Research Unit, Biogen, 225 Binney St, Cambridge, MA 02142, USA
| | - Warren D Hirst
- Neurodegeneration Research Unit, Biogen, 225 Binney St, Cambridge, MA 02142, USA
| | - Paul A Temkin
- Neurodegeneration Research Unit, Biogen, 225 Binney St, Cambridge, MA 02142, USA.
| |
Collapse
|
10
|
Kabir AU, Zeng C, Subramanian M, Wu J, Kim M, Krchma K, Wang X, Halabi CM, Pan H, Wickline SA, Fremont DH, Artyomov MN, Choi K. ZBTB46 coordinates angiogenesis and immunity to control tumor outcome. Nat Immunol 2024; 25:1546-1554. [PMID: 39134750 DOI: 10.1038/s41590-024-01936-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 07/16/2024] [Indexed: 09/01/2024]
Abstract
Tumor angiogenesis and immunity show an inverse correlation in cancer progression and outcome1. Here, we report that ZBTB46, a repressive transcription factor and a widely accepted marker for classical dendritic cells (DCs)2,3, controls both tumor angiogenesis and immunity. Zbtb46 was downregulated in both DCs and endothelial cells by tumor-derived factors to facilitate robust tumor growth. Zbtb46 downregulation led to a hallmark pro-tumor microenvironment (TME), including dysfunctional vasculature and immunosuppressive conditions. Analysis of human cancer data revealed a similar association of low ZBTB46 expression with an immunosuppressive TME and a worse prognosis. In contrast, enforced Zbtb46 expression led to TME changes to restrict tumor growth. Mechanistically, Zbtb46-deficient endothelial cells were highly angiogenic, and Zbtb46-deficient bone marrow progenitors upregulated Cebpb and diverted the DC program to immunosuppressive myeloid lineage output, potentially explaining the myeloid lineage skewing phenomenon in cancer4. Conversely, enforced Zbtb46 expression normalized tumor vessels and, by suppressing Cebpb, skewed bone marrow precursors toward immunostimulatory myeloid lineage output, leading to an immune-hot TME. Remarkably, Zbtb46 mRNA treatment synergized with anti-PD1 immunotherapy to improve tumor management in preclinical models. These findings identify ZBTB46 as a critical factor for angiogenesis and for myeloid lineage skewing in cancer and suggest that maintaining its expression could have therapeutic benefits.
Collapse
Affiliation(s)
- Ashraf Ul Kabir
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Carisa Zeng
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Madhav Subramanian
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Jun Wu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Minseo Kim
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Karen Krchma
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Xiaoli Wang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Carmen M Halabi
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Hua Pan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Samuel A Wickline
- Health Heart Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Daved H Fremont
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kyunghee Choi
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
11
|
Medhavy A, Athanasopoulos V, Bassett K, He Y, Stanley M, Enosi Tuipulotu D, Cappello J, Brown GJ, Gonzalez-Figueroa P, Turnbull C, Shanmuganandam S, Tummala P, Hart G, Lea-Henry T, Wang H, Nambadan S, Shen Q, Roco JA, Burgio G, Wu P, Cho E, Andrews TD, Field MA, Wu X, Ding H, Guo Q, Shen N, Man SM, Jiang SH, Cook MC, Vinuesa CG. A TNIP1-driven systemic autoimmune disorder with elevated IgG4. Nat Immunol 2024; 25:1678-1691. [PMID: 39060650 PMCID: PMC11362012 DOI: 10.1038/s41590-024-01902-0] [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: 01/31/2023] [Accepted: 06/18/2024] [Indexed: 07/28/2024]
Abstract
Whole-exome sequencing of two unrelated kindreds with systemic autoimmune disease featuring antinuclear antibodies with IgG4 elevation uncovered an identical ultrarare heterozygous TNIP1Q333P variant segregating with disease. Mice with the orthologous Q346P variant developed antinuclear autoantibodies, salivary gland inflammation, elevated IgG2c, spontaneous germinal centers and expansion of age-associated B cells, plasma cells and follicular and extrafollicular helper T cells. B cell phenotypes were cell-autonomous and rescued by ablation of Toll-like receptor 7 (TLR7) or MyD88. The variant increased interferon-β without altering nuclear factor kappa-light-chain-enhancer of activated B cells signaling, and impaired MyD88 and IRAK1 recruitment to autophagosomes. Additionally, the Q333P variant impaired TNIP1 localization to damaged mitochondria and mitophagosome formation. Damaged mitochondria were abundant in the salivary epithelial cells of Tnip1Q346P mice. These findings suggest that TNIP1-mediated autoimmunity may be a consequence of increased TLR7 signaling due to impaired recruitment of downstream signaling molecules and damaged mitochondria to autophagosomes and may thus respond to TLR7-targeted therapeutics.
Collapse
Affiliation(s)
- Arti Medhavy
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Vicki Athanasopoulos
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Katharine Bassett
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Yuke He
- China Australia Center for Personalized Immunology, Shanghai Renji Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Maurice Stanley
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Daniel Enosi Tuipulotu
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Jean Cappello
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Grant J Brown
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Paula Gonzalez-Figueroa
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Cynthia Turnbull
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Somasundhari Shanmuganandam
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Padmaja Tummala
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Gemma Hart
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Tom Lea-Henry
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Hao Wang
- Francis Crick Institute, London, UK
| | - Sonia Nambadan
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | | | - Jonathan A Roco
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Gaetan Burgio
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Phil Wu
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Eun Cho
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - T Daniel Andrews
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Matt A Field
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- Center for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Queensland, Australia
| | - Xiaoqian Wu
- China Australia Center for Personalized Immunology, Shanghai Renji Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Huihua Ding
- Department of Rheumatology, Renji Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Qiang Guo
- Department of Rheumatology, Renji Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Nan Shen
- China Australia Center for Personalized Immunology, Shanghai Renji Hospital, Shanghai Jiaotong University, Shanghai, China
- Department of Rheumatology, Renji Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Si Ming Man
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Simon H Jiang
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Matthew C Cook
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Carola G Vinuesa
- Division of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia.
- China Australia Center for Personalized Immunology, Shanghai Renji Hospital, Shanghai Jiaotong University, Shanghai, China.
- Francis Crick Institute, London, UK.
| |
Collapse
|
12
|
Shen X, He L, Cai W. Role of Lipopolysaccharides in the Inflammation and Pyroptosis of Alveolar Epithelial Cells in Acute Lung Injury and Acute Respiratory Distress Syndrome. J Inflamm Res 2024; 17:5855-5869. [PMID: 39228678 PMCID: PMC11370780 DOI: 10.2147/jir.s479051] [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: 05/20/2024] [Accepted: 08/22/2024] [Indexed: 09/05/2024] Open
Abstract
Acute lung injury (ALI) and acute respiratory distress syndrome (ARDS) represent a spectrum of common critical respiratory conditions characterized by damage and death of alveolar epithelial cells (AECs). Pyroptosis is a form of programmed cell death with inflammatory characteristics, and activation of pyroptosis markers has been observed in AECs of patients with ALI/ARDS. Lipopolysaccharides (LPS) possess strong pro-inflammatory effects and are a crucial pathological factor leading to ALI in patients and animals. In LPS-induced ALI models, AECs undergo pyroptosis. However, physiologically and pathologically relevant concentrations of LPS lead to minor effects on AEC cell viability and minimal induction of cytokine release in vitro and do not induce classical pyroptosis. Nevertheless, LPS can enter the cytoplasm directly and induce non-classical pyroptosis in AECs when assisted by extracellular vesicles from bacteria, HMGB1, and pathogens. In this review, we have explored the effects of LPS on AECs concerning inflammation, cell viability, and pyroptosis, analyzing key factors that influence LPS actions. Notably, we highlight the intricate response of AECs to LPS within the framework of ALI and ARDS, emphasizing the variable induction of pyroptosis. Despite the minimal effects of LPS on AEC viability and cytokine release in vitro, LPS can induce non-classical pyroptosis under specific conditions, presenting potential pathways for therapeutic intervention. Collectively, understanding these mechanisms is crucial for the development of targeted treatments that mitigate the inflammatory responses in ALI/ARDS, thereby enhancing patient outcomes in these severe respiratory conditions.
Collapse
Affiliation(s)
- Xiao Shen
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310053, People’s Republic of China
| | - Linglin He
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, People’s Republic of China
| | - Wanru Cai
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, 310005, People’s Republic of China
| |
Collapse
|
13
|
Aqil A, Li Y, Wang Z, Islam S, Russell M, Kallak TK, Saitou M, Gokcumen O, Masuda N. Switch-like Gene Expression Modulates Disease Susceptibility. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.24.609537. [PMID: 39229158 PMCID: PMC11370615 DOI: 10.1101/2024.08.24.609537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
A fundamental challenge in biomedicine is understanding the mechanisms predisposing individuals to disease. While previous research has suggested that switch-like gene expression is crucial in driving biological variation and disease susceptibility, a systematic analysis across multiple tissues is still lacking. By analyzing transcriptomes from 943 individuals across 27 tissues, we identified 1,013 switch-like genes. We found that only 31 (3.1%) of these genes exhibit switch-like behavior across all tissues. These universally switch-like genes appear to be genetically driven, with large exonic genomic structural variants explaining five (~18%) of them. The remaining switch-like genes exhibit tissue-specific expression patterns. Notably, tissue-specific switch-like genes tend to be switched on or off in unison within individuals, likely under the influence of tissue-specific master regulators, including hormonal signals. Among our most significant findings, we identified hundreds of concordantly switched-off genes in the stomach and vagina that are linked to gastric cancer (41-fold, p<10-4) and vaginal atrophy (44-fold, p<10-4), respectively. Experimental analysis of vaginal tissues revealed that low systemic levels of estrogen lead to a significant reduction in both the epithelial thickness and the expression of the switch-like gene ALOX12. We propose a model wherein the switching off of driver genes in basal and parabasal epithelium suppresses cell proliferation therein, leading to epithelial thinning and, therefore, vaginal atrophy. Our findings underscore the significant biomedical implications of switch-like gene expression and lay the groundwork for potential diagnostic and therapeutic applications.
Collapse
Affiliation(s)
- Alber Aqil
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Yanyan Li
- Department of Mathematics, State University of New York at Buffalo, Buffalo, NY, USA
| | - Zhiliang Wang
- Department of Mathematics, State University of New York at Buffalo, Buffalo, NY, USA
| | - Saiful Islam
- Institute for Artificial Intelligence and Data Science, State University of New York at Buffalo, Buffalo, NY, USA
| | - Madison Russell
- Department of Mathematics, State University of New York at Buffalo, Buffalo, NY, USA
| | | | - Marie Saitou
- Faculty of Biosciences, Norwegian University of Life Sciences, Aas, Norway
| | - Omer Gokcumen
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Naoki Masuda
- Department of Mathematics, State University of New York at Buffalo, Buffalo, NY, USA
- Institute for Artificial Intelligence and Data Science, State University of New York at Buffalo, Buffalo, NY, USA
| |
Collapse
|
14
|
Ebrahim S, Ballesteros A, Zheng WS, Mukherjee S, Hu G, Weng WH, Montgomery JS, Agyemang Y, Cui R, Sun W, Krystofiak E, Foster MP, Sotomayor M, Kachar B. Transmembrane channel-like 4 and 5 proteins at microvillar tips are potential ion channels and lipid scramblases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.22.609173. [PMID: 39229161 PMCID: PMC11370596 DOI: 10.1101/2024.08.22.609173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Microvilli-membrane bound actin protrusions on the surface of epithelial cells-are sites of critical processes including absorption, secretion, and adhesion. Increasing evidence suggests microvilli are mechanosensitive, but underlying molecules and mechanisms remain unknown. Here, we localize transmembrane channel-like proteins 4 and 5 (TMC4 and 5) and calcium and integrin binding protein 3 (CIB3) to microvillar tips in intestinal epithelial cells, near glycocalyx insertion sites. We find that TMC5 colocalizes with CIB3 in cultured cells and that a TMC5 fragment forms a complex with CIB3 in vitro. Homology and AlphaFold2 models reveal a putative ion permeation pathway in TMC4 and 5, and molecular dynamics simulations predict both proteins can conduct ions and perform lipid scrambling. These findings raise the possibility that TMC4 and 5 interact with CIB3 at microvillar tips to form a mechanosensitive complex, akin to TMC1 and 2, and CIB2 and 3, within the mechanotransduction channel complex at the tips of inner ear stereocilia.
Collapse
Affiliation(s)
- Seham Ebrahim
- Center for Membrane and Cell Physiology, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
| | - Angela Ballesteros
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
- Section on Sensory Physiology and Biophysics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - W Sharon Zheng
- Center for Membrane and Cell Physiology, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
| | - Shounak Mukherjee
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Gaizun Hu
- Center for Membrane and Cell Physiology, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
| | - Wei-Hsiang Weng
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Biophysics Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Jonathan S Montgomery
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Yaw Agyemang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Runjia Cui
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Willy Sun
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Evan Krystofiak
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark P Foster
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Biophysics Program, The Ohio State University, Columbus, OH 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Marcos Sotomayor
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Biophysics Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Bechara Kachar
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
15
|
Vasan R, Ferrante AJ, Borensztejn A, Frick CL, Gaudreault N, Mogre SS, Morris B, Pires GG, Rafelski SM, Theriot JA, Viana MP. Interpretable representation learning for 3D multi-piece intracellular structures using point clouds. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.25.605164. [PMID: 39091871 PMCID: PMC11291148 DOI: 10.1101/2024.07.25.605164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
A key challenge in understanding subcellular organization is quantifying interpretable measurements of intracellular structures with complex multi-piece morphologies in an objective, robust and generalizable manner. Here we introduce a morphology-appropriate representation learning framework that uses 3D rotation invariant autoencoders and point clouds. This framework is used to learn representations of complex multi-piece morphologies that are independent of orientation, compact, and easy to interpret. We apply our framework to intracellular structures with punctate morphologies (e.g. DNA replication foci) and polymorphic morphologies (e.g. nucleoli). We systematically compare our framework to image-based autoencoders across several intracellular structure datasets, including a synthetic dataset with pre-defined rules of organization. We explore the trade-offs in the performance of different models by performing multi-metric benchmarking across efficiency, generative capability, and representation expressivity metrics. We find that our framework, which embraces the underlying morphology of multi-piece structures, facilitates the unsupervised discovery of sub-clusters for each structure. We show how our approach can also be applied to phenotypic profiling using a dataset of nucleolar images following drug perturbations. We implement and provide all representation learning models using CytoDL, a python package for flexible and configurable deep learning experiments.
Collapse
Affiliation(s)
- Ritvik Vasan
- Allen Institute for Cell Science, Seattle, WA, USA
| | | | | | | | | | | | | | | | | | - Julie A Theriot
- Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | | |
Collapse
|
16
|
Surana P, Dutta P, Davuluri RV. TransTEx: novel tissue-specificity scoring method for grouping human transcriptome into different expression groups. Bioinformatics 2024; 40:btae475. [PMID: 39120880 PMCID: PMC11319638 DOI: 10.1093/bioinformatics/btae475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/12/2024] [Accepted: 08/08/2024] [Indexed: 08/10/2024] Open
Abstract
MOTIVATION Although human tissues carry out common molecular processes, gene expression patterns can distinguish different tissues. Traditional informatics methods, primarily at the gene level, overlook the complexity of alternative transcript variants and protein isoforms produced by most genes, changes in which are linked to disease prognosis and drug resistance. RESULTS We developed TransTEx (Transcript-level Tissue Expression), a novel tissue-specificity scoring method, for grouping transcripts into four expression groups. TransTEx applies sequential cut-offs to tissue-wise transcript probability estimates, subsampling-based P-values and fold-change estimates. Application of TransTEx on GTEx mRNA-seq data divided 199 166 human transcripts into different groups as 17 999 tissue-specific (TSp), 7436 tissue-enhanced, 36 783 widely expressed (Wide), 79 191 lowly expressed (Low), and 57 757 no expression (Null) transcripts. Testis has the most (13 466) TSp isoforms followed by liver (890), brain (701), pituitary (435), and muscle (420). We found that the tissue specificity of alternative transcripts of a gene is predominantly influenced by alternate promoter usage. By overlapping brain-specific transcripts with the cell-type gene-markers in scBrainMap database, we found that 63% of the brain-specific transcripts were enriched in nonneuronal cell types, predominantly astrocytes followed by endothelial cells and oligodendrocytes. In addition, we found 61 brain cell-type marker genes encoding a total of 176 alternative transcripts as brain-specific and 22 alternative transcripts as testis-specific, highlighting the complex TSp and cell-type specific gene regulation and expression at isoform-level. TransTEx can be adopted to the analysis of bulk RNA-seq or scRNA-seq datasets to find tissue- and/or cell-type specific isoform-level gene markers. AVAILABILITY AND IMPLEMENTATION TransTEx database: https://bmi.cewit.stonybrook.edu/transtexdb/ and the R package is available via GitHub: https://github.com/pallavisurana1/TransTEx.
Collapse
Affiliation(s)
- Pallavi Surana
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Pratik Dutta
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Ramana V Davuluri
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY 11794, USA
| |
Collapse
|
17
|
Mótyán JA, Tőzsér J. The human retroviral-like aspartic protease 1 (ASPRV1): From in vitro studies to clinical correlations. J Biol Chem 2024; 300:107634. [PMID: 39098535 PMCID: PMC11402058 DOI: 10.1016/j.jbc.2024.107634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 07/25/2024] [Accepted: 07/27/2024] [Indexed: 08/06/2024] Open
Abstract
The human retroviral-like aspartic protease 1 (ASPRV1) is a retroviral-like protein that was first identified in the skin due to its expression in the stratum granulosum layer of the epidermis. Accordingly, it is also referred to as skin-specific aspartic protease. Similar to the retroviral polyproteins, the full-length ASPRV1 also undergoes self-proteolysis, the processing of the precursor is necessary for the autoactivation of the protease domain. ASPRV1's functions are well-established at the level of the skin: it is part of the epidermal proteolytic network and has a significant contribution to skin moisturization via the limited proteolysis of filaggrin; it is only natural protein substrate identified so far. Filaggrin and ASPRV1 are also specific for mammalians, these proteins provide unique features for the skins of these species, and the importance of filaggrin processing in hydration is proved by the fact that some ASPRV1 mutations are associated with skin diseases such as ichthyosis. ASPRV1 was also found to be expressed in macrophage-like neutrophil cells, indicating that its functions are not limited to the skin. In addition, differential expression of ASPRV1 was detected in many diseases, with yet unknown significance. The currently known enzymatic characteristics-that had been revealed mainly by in vitro studies-and correlations with pathogenic phenotypes imply potentially important functions in multiple cell types, which makes the protein a promising target of functional studies. In this review we describe the currently available knowledge and future perspective in regard to ASPRV1.
Collapse
Affiliation(s)
- János András Mótyán
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.
| | - József Tőzsér
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| |
Collapse
|
18
|
Xu Y, Yang T, Xu Q, Tang Y, Yang Q. Vesicle-associated membrane protein 8 knockdown exerts anti-proliferative, pro-apoptotic, anti-autophagic, and pro-ferroptotic effects on colorectal cancer cells by inhibition of the JAK/STAT3 pathway. J Bioenerg Biomembr 2024; 56:419-431. [PMID: 38720136 DOI: 10.1007/s10863-024-10019-w] [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: 03/14/2024] [Accepted: 04/20/2024] [Indexed: 07/03/2024]
Abstract
Vesicle-associated membrane protein 8 (VAMP8), a soluble n-ethylmaleimide-sensitive factor receptor protein, acts as an oncogenic gene in the progression of several malignancies. Nevertheless, the roles and mechanisms of VAMP8 in colorectal cancer (CRC) progression remain unknown. The expression and prognostic significance of VAMP8 in CRC samples were analyzed through bioinformatics analyses. Cell proliferation was detected using CCK-8 and EdU incorporation assays and apoptosis was evaluated via flow cytometry. Western blot analysis was conducted to examine the protein expression. Ferroptosis was evaluated by measurement of iron metabolism, lipid peroxidation, and glutathione (GSH) content. VAMP8 was increased in CRC samples relative to normal samples on the basis of GEPIA and HPA databases. CRC patients with high level of VAMP8 had a worse overall survival. VAMP8 depletion led to a suppression of proliferation and promotion of apoptosis in CRC cells. Additionally, VAMP8 knockdown suppressed beclin1 expression and LC3-II/LC3-I ratio, elevated p62 expression, increased Fe2+, labile iron pool, lipid reactive oxygen species, and malondialdehyde levels, and repressed GSH content and glutathione peroxidase activity. Moreover, VAMP8 knockdown inhibited the activation of janus kinase (JAK)/signal transducer and activator of transcription 3 (STAT3) pathway in CRC cells. Mechanistically, activation of the JAK/STAT3 pathway by JAK1 or JAK2 overexpression attenuated VAMP8 silencing-mediated anti-proliferative, pro-apoptotic, anti-autophagic, and pro-ferroptotic effects on CRC cells. In conclusion, VAMP8 knockdown affects the proliferation, apoptosis, autophagy, and ferroptosis by the JAK/STAT3 pathway in CRC cells.
Collapse
Affiliation(s)
- Yi Xu
- Department of General Surgery, Nanyang First People's Hospital, Nanyang, China
| | - Tianyao Yang
- Department of General Surgery, Tiantai People's Hospital of Zhejiang Province, Taizhou, China
| | - Qiu Xu
- Department of Thyroid and Breast Surgery, Nanyang First People's Hospital, Nanyang, China
- Nanyang Key Laboratory of Thyroid Tumor Prevention and Treatment, Nanyang First People's Hospital, Nanyang, China
| | - Yan Tang
- Department of General Surgery, Nanyang First People's Hospital, Nanyang, China
| | - Qiong Yang
- General Surgery, Cancer Center, Department of Breast Surgery, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China.
| |
Collapse
|
19
|
Khosroshahi EM, Maghsoudloo M, Fahimi H, Mokhtari K, Entezari M, Peymani M, Hashemi M, Wan R. Determining expression changes of ANO7 and SLC38A4 membrane transporters in colorectal cancer. Heliyon 2024; 10:e34464. [PMID: 39114022 PMCID: PMC11305260 DOI: 10.1016/j.heliyon.2024.e34464] [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: 04/03/2024] [Revised: 04/21/2024] [Accepted: 07/09/2024] [Indexed: 08/10/2024] Open
Abstract
Membrane transporters are proteins responsible for facilitating the movement of molecules within biological membranes. They play a vital role in maintaining cellular homeostasis by regulating the transport of nutrients, ions, and other molecules into and out of cells. Our aim is to identify biomarkers in colorectal cancer using membrane transporter proteins. We utilized COAD TCGA data for this purpose. Subsequently, we conducted differential gene analysis and feature selection using membrane transporter proteins. Furthermore, we identified two potential genes, including ANO7 and SLC38A4. To validate the expression profiles of ANO7 and SLC38A4, key genes in this context, RT-qPCR was employed on colorectal cancer samples and adjacent normal tissues. Additionally, utilizing GEPIA2, Kaplan-Meier survival analysis, and cBioPortal, we assessed the status of these genes in various cancers, examining their methylation and mutation patterns. In conclusion, we suggest that ANO7 and SLC38A4 serve as prognostic biomarkers in colorectal cancer.
Collapse
Affiliation(s)
- Elaheh Mohandesi Khosroshahi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical sciences, Islamic Azad University, Tehran, Iran
| | - Mazaher Maghsoudloo
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Hossein Fahimi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical sciences, Islamic Azad University, Tehran, Iran
| | - Khatere Mokhtari
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Maliheh Entezari
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical sciences, Islamic Azad University, Tehran, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Mehrdad Hashemi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical sciences, Islamic Azad University, Tehran, Iran
| | - Runlan Wan
- Department of Oncology, The Affiliated Hospital, Southwest Medical University, Luzhou 646000, China
- Key Laboratory of Medical Electrophysiology, Ministry of Education & Medical Electrophysiological Key Laboratory of Sichuan Province, (Collaborative Innovation Center for Prevention of Cardiovascular Diseases), Institute of Cardiovascular Research, Southwest Medical University, Luzhou 646000, China
| |
Collapse
|
20
|
Zhai S, Li Y, Yang Y, Lang W, Liu X, Liu K, Qu J, Zhu L. Scinderin is a potential prognostic biomarker and correlated with immunological regulation: from pan-cancer analysis to liver hepatocellular carcinoma. Front Immunol 2024; 15:1361657. [PMID: 39108273 PMCID: PMC11300247 DOI: 10.3389/fimmu.2024.1361657] [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: 12/26/2023] [Accepted: 07/05/2024] [Indexed: 09/17/2024] Open
Abstract
Aim This study aimed to systematically dissect the role of Scinderin (SCIN) in tumorigenesis. Methods Bioinformatics techniques were employed based on cancer data from TCGA, ENCORI, HPA, GEPIA2, UALCAN, Kaplan-Meier plotter, TIMER, TISIDB, cBioPortal, HCCDB, GeneMANIA and LinkedOmics database. Experiments in vitro and in vivo were conducted to dissect the role of SCIN in liver hepatocellular carcinoma (LIHC). Results Significantly differential expression of SCIN was found in nine types of cancers, including LIHC. Through pan-cancer analysis, the correlations between SCIN expression with prognosis and immune cell infiltration were proven, especially in LIHC, ovarian serous cystadenocarcinoma and lung adenocarcinoma. The highest frequency of alteration in SCIN (6.81%) was seen in patients with uterine corpus endometrial carcinoma, in which "mutation" was the predominant type, with a frequency of about 5.29%; meanwhile, S673F and S381Y were the two most frequent mutation sites. Furthermore, the abnormal expression of SCIN exhibited a strong relationship with immune cell subtypes, immune checkpoint genes, tumor mutation burden, microsatellite instability, neoantigen, molecular subtypes, mismatch repair signatures and DNA methyl-transferase in different cancer types. Through comparative analysis, we discovered that SCIN was dramatically up-regulated in LIHC, and associated with poor survival. Experiments in vitro and in vivo suggested the knockdown of SCIN could suppress tumor cell proliferation and improve the survival rate partly in animal models. Conclusion This study reveals SCIN may be a promising biomarker for prognosis and treatment in certain cancers, especially in LIHC.
Collapse
Affiliation(s)
- Shengyong Zhai
- Department of Gastrointestinal Surgery, Weifang People’s Hospital, The First Affiliated Hospital of Weifang Medical College, Weifang, Shandong, China
| | - Yuhua Li
- Department of Gastrointestinal Surgery, Weifang People’s Hospital, The First Affiliated Hospital of Weifang Medical College, Weifang, Shandong, China
| | - Yuanyuan Yang
- Department of Nuclear Medicine, Weifang People’s Hospital, The First Affiliated Hospital of Weifang Medical College, Weifang, Shandong, China
| | - Wei Lang
- Department of Gastrointestinal Surgery, Weifang People’s Hospital, The First Affiliated Hospital of Weifang Medical College, Weifang, Shandong, China
| | - Xiaoxia Liu
- Department of Anesthesiology, Weifang People’s Hospital, The First Affiliated Hospital of Weifang Medical College, Weifang, Shandong, China
| | - Kai Liu
- Department of Gastrointestinal Surgery, Weifang People’s Hospital, The First Affiliated Hospital of Weifang Medical College, Weifang, Shandong, China
| | - Jianjun Qu
- Department of Gastrointestinal Surgery, Weifang People’s Hospital, The First Affiliated Hospital of Weifang Medical College, Weifang, Shandong, China
| | - Lingyu Zhu
- Department of Gastroenterology, Weifang People’s Hospital, The First Affiliated Hospital of Weifang Medical College, Weifang, Shandong, China
| |
Collapse
|
21
|
Martín-Villanueva S, Galmozzi CV, Ruger-Herreros C, Kressler D, de la Cruz J. The Beak of Eukaryotic Ribosomes: Life, Work and Miracles. Biomolecules 2024; 14:882. [PMID: 39062596 PMCID: PMC11274626 DOI: 10.3390/biom14070882] [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: 06/19/2024] [Revised: 07/19/2024] [Accepted: 07/21/2024] [Indexed: 07/28/2024] Open
Abstract
Ribosomes are not totally globular machines. Instead, they comprise prominent structural protrusions and a myriad of tentacle-like projections, which are frequently made up of ribosomal RNA expansion segments and N- or C-terminal extensions of ribosomal proteins. This is more evident in higher eukaryotic ribosomes. One of the most characteristic protrusions, present in small ribosomal subunits in all three domains of life, is the so-called beak, which is relevant for the function and regulation of the ribosome's activities. During evolution, the beak has transitioned from an all ribosomal RNA structure (helix h33 in 16S rRNA) in bacteria, to an arrangement formed by three ribosomal proteins, eS10, eS12 and eS31, and a smaller h33 ribosomal RNA in eukaryotes. In this review, we describe the different structural and functional properties of the eukaryotic beak. We discuss the state-of-the-art concerning its composition and functional significance, including other processes apparently not related to translation, and the dynamics of its assembly in yeast and human cells. Moreover, we outline the current view about the relevance of the beak's components in human diseases, especially in ribosomopathies and cancer.
Collapse
Affiliation(s)
- Sara Martín-Villanueva
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013 Seville, Spain; (S.M.-V.); (C.V.G.); (C.R.-H.)
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, E-41012 Seville, Spain
| | - Carla V. Galmozzi
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013 Seville, Spain; (S.M.-V.); (C.V.G.); (C.R.-H.)
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, E-41012 Seville, Spain
| | - Carmen Ruger-Herreros
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013 Seville, Spain; (S.M.-V.); (C.V.G.); (C.R.-H.)
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, E-41012 Seville, Spain
| | - Dieter Kressler
- Department of Biology, University of Fribourg, CH-1700 Fribourg, Switzerland;
| | - Jesús de la Cruz
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013 Seville, Spain; (S.M.-V.); (C.V.G.); (C.R.-H.)
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, E-41012 Seville, Spain
| |
Collapse
|
22
|
Lin G, Liu X. Key extracellular proteins and TF-miRNA co-regulatory network in diabetic foot ulcer: Bioinformatics and experimental insights. PLoS One 2024; 19:e0307205. [PMID: 39037979 PMCID: PMC11262672 DOI: 10.1371/journal.pone.0307205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 07/02/2024] [Indexed: 07/24/2024] Open
Abstract
BACKGROUND Diabetic foot ulcers (DFUs), a serious complication of diabetes, are associated with abnormal extracellular protein (EP) metabolism. The identification of key EPs and their regulatory networks is crucial for the understanding of DFU formation and development of effective treatments. In this study, a large-scale bioinformatics analysis was conducted to identify potential therapeutic targets and experimental validation was performed to ensure the reliability and biological relevance of the findings. METHODS Due to the comprehensive profiling of DFU samples provided by the GSE80178 dataset, we initially selected it to derive differentially expressed genes (DEGs) associated with DFU. Subsequently, utilizing the UniProt database and annotated EP list from the Human Protein Atlas annotation database, we screened for extracellular protein-related differentially expressed genes (EP-DEGs) due to their crucial role in the pathogenesis and healing of DFU. We examined EP-DEG pathway enrichment and protein-protein interaction networks, analyzed paired full-thickness skin tissue samples from 24 patients with DFUs and healthy controls, and performed polymerase chain reaction (PCR) experiments to validate candidate genes. Ultimately, we constructed a transcription factor (TF)-microRNA (miRNA)-hub gene co-regulatory network to explore upstream and downstream regulatory connections based on validated DEGs. RESULTS Four crucial candidate genes (FMOD, LUM, VCAN, and S100A12) were identified and verified via PCR analysis. The TF-miRNA-hub EP-DEG regulatory network contained the pivotal TFs TRIM28 and STAT3 and the miRNAs hsa-mir-20a-5p, hsa-miR-21, and hsa-miR-203. CONCLUSION The findings of this study advance our understanding of the pathology of DFU by defining key roles of specific EPs and elucidating a comprehensive regulatory network. These insights pave the way for novel approaches to improve DFU treatment outcomes.
Collapse
Affiliation(s)
- Guanlin Lin
- Department of Orthopaedic Surgery, General Hospital of Central Theater Command, Wuhan, China
- College of Acupuncture and Orthopaedic, Hubei University of Chinese Medicine, Wuhan, China
- The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Ximing Liu
- Department of Orthopaedic Surgery, General Hospital of Central Theater Command, Wuhan, China
- College of Acupuncture and Orthopaedic, Hubei University of Chinese Medicine, Wuhan, China
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| |
Collapse
|
23
|
Ehrhardt B, Angstmann H, Höschler B, Kovacevic D, Hammer B, Roeder T, Rabe KF, Wagner C, Uliczka K, Krauss-Etschmann S. Airway specific deregulation of asthma-related serpins impairs tracheal architecture and oxygenation in D. melanogaster. Sci Rep 2024; 14:16567. [PMID: 39019933 PMCID: PMC11255251 DOI: 10.1038/s41598-024-66752-0] [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: 09/28/2023] [Accepted: 07/03/2024] [Indexed: 07/19/2024] Open
Abstract
Serine proteases are important regulators of airway epithelial homeostasis. Altered serum or cellular levels of two serpins, Scca1 and Spink5, have been described for airway diseases but their function beyond antiproteolytic activity is insufficiently understood. To close this gap, we generated fly lines with overexpression or knockdown for each gene in the airways. Overexpression of both fly homologues of Scca1 and Spink5 induced the growth of additional airway branches, with more variable results for the respective knockdowns. Dysregulation of Scca1 resulted in a general delay in fruit fly development, with increases in larval and pupal mortality following overexpression of this gene. In addition, the morphological changes in the airways were concomitant with lower tolerance to hypoxia. In conclusion, the observed structural changes of the airways evidently had a strong impact on the airway function in our model as they manifested in a lower physical fitness of the animals. We assume that this is due to insufficient tissue oxygenation. Future work will be directed at the identification of key molecular regulators following the airway-specific dysregulation of Scca1 and Spink5 expression.
Collapse
Affiliation(s)
- Birte Ehrhardt
- Division of Early Life Origins of Chronic Lung Diseases, Research Center Borstel, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Parkallee 1, 23845, Borstel, Germany
| | - Hanna Angstmann
- Division of Early Life Origins of Chronic Lung Diseases, Research Center Borstel, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Parkallee 1, 23845, Borstel, Germany
| | - Beate Höschler
- Division of Early Life Origins of Chronic Lung Diseases, Research Center Borstel, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Parkallee 1, 23845, Borstel, Germany
| | - Draginja Kovacevic
- Division of Early Life Origins of Chronic Lung Diseases, Research Center Borstel, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Parkallee 1, 23845, Borstel, Germany
- DZL Laboratory for Experimental Microbiome Research, Research Center Borstel, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Borstel, Germany
| | - Barbara Hammer
- Division of Early Life Origins of Chronic Lung Diseases, Research Center Borstel, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Parkallee 1, 23845, Borstel, Germany
- DZL Laboratory for Experimental Microbiome Research, Research Center Borstel, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Borstel, Germany
| | - Thomas Roeder
- Division of Molecular Physiology, Institute of Zoology, Christian-Albrechts University Kiel, Kiel, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Borstel, Germany
| | - Klaus F Rabe
- Department of Pneumology, LungenClinic, Grosshansdorf, Germany
- Department of Medicine, Christian Albrechts University, Kiel, Germany
| | - Christina Wagner
- Division of Invertebrate Models, Priority Research Area Asthma and Allergy, Research Center Borstel, Borstel, Germany
| | - Karin Uliczka
- Division of Early Life Origins of Chronic Lung Diseases, Research Center Borstel, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Parkallee 1, 23845, Borstel, Germany
- Division of Invertebrate Models, Priority Research Area Asthma and Allergy, Research Center Borstel, Borstel, Germany
| | - Susanne Krauss-Etschmann
- Division of Early Life Origins of Chronic Lung Diseases, Research Center Borstel, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Parkallee 1, 23845, Borstel, Germany.
- DZL Laboratory for Experimental Microbiome Research, Research Center Borstel, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Borstel, Germany.
- Institute of Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany.
| |
Collapse
|
24
|
Liu Y, Hou J, Zhao Y, Zhou J, Bai S, Ding Y. Comprehensive pan-cancer analysis of the C2ORF40 expression: Infiltration associations and prognostic implications. FASEB J 2024; 38:e23761. [PMID: 38941213 DOI: 10.1096/fj.202302386rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 05/28/2024] [Accepted: 06/13/2024] [Indexed: 06/30/2024]
Abstract
In recent years, C2ORF40 has been identified as a tumor suppressor gene with multiple functions, including roles in cell proliferation, migration, and senescence. To explore the role of the C2ORF40 gene in different tumors, we used multiple databases for analysis. Compared to adjacent normal tissues, C2ORF40 is downregulated in a variety of malignant tumors, including tumors such as breast cancer, colorectal cancer, bladder cancer, hepatocellular carcinoma and prostate cancer. Notably, low expression of the gene is significantly associated with poor overall survival and relapse-free survival rates. In specific cancers including colon cancer and prostate cancer, the expression of C2ORF40 is correlated with the infiltration of CAFs. C2ORF40 is also involved in biological processes such as cell apoptosis and regulation of protein stability. In conclusion, C2ORF40 can hold promise as a prognostic marker for pan-cancer analysis.
Collapse
Affiliation(s)
- Yuxi Liu
- School of Basic Medical Sciences, Shandong Second Medical University, Weifang, China
| | | | - Yunrong Zhao
- School of Basic Medical Sciences, Shandong Second Medical University, Weifang, China
| | - Jiangshan Zhou
- School of Basic Medical Sciences, Shandong Second Medical University, Weifang, China
| | - Shuhua Bai
- Department of Pharmaceutical and Administrative Sciences, College of Pharmacy and Health Sciences, Western New England University, Springfield, Massachusetts, USA
| | - Yi Ding
- School of Basic Medical Sciences, Shandong Second Medical University, Weifang, China
| |
Collapse
|
25
|
Ghosh G, Neely BA, Bland AM, Whitmer ER, Field CL, Duignan PJ, Janech MG. Identification of Candidate Protein Biomarkers Associated with Domoic Acid Toxicosis in Cerebrospinal Fluid of California Sea Lions ( Zalophus californianus). J Proteome Res 2024; 23:2419-2430. [PMID: 38807289 PMCID: PMC11232103 DOI: 10.1021/acs.jproteome.4c00103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 05/10/2024] [Accepted: 05/20/2024] [Indexed: 05/30/2024]
Abstract
Since 1998, California sea lion (Zalophus californianus) stranding events associated with domoic acid toxicosis (DAT) have consistently increased. Outside of direct measurement of domoic acid in bodily fluids at the time of stranding, there are no practical nonlethal clinical tests for the diagnosis of DAT that can be utilized in a rehabilitation facility. Proteomics analysis was conducted to discover candidate protein markers of DAT using cerebrospinal fluid from stranded California sea lions with acute DAT (n = 8), chronic DAT (n = 19), or without DAT (n = 13). A total of 2005 protein families were identified experiment-wide. A total of 83 proteins were significantly different in abundance across the three groups (adj. p < 0.05). MDH1, PLD3, ADAM22, YWHAG, VGF, and CLSTN1 could discriminate California sea lions with or without DAT (AuROC > 0.75). IGKV2D-28, PTRPF, KNG1, F2, and SNCB were able to discriminate acute DAT from chronic DAT (AuROC > 0.75). Proteins involved in alpha synuclein deposition were over-represented as classifiers of DAT, and many of these proteins have been implicated in a variety of neurodegenerative diseases. These proteins should be considered potential markers for DAT in California sea lions and should be prioritized for future validation studies as biomarkers.
Collapse
Affiliation(s)
- Gautam Ghosh
- Department of Biology, Grice Marine Laboratory, College of Charleston, Charleston, South Carolina 29412, United States
| | - Benjamin A Neely
- National Institute of Standards and Technology (NIST) Charleston, Charleston, South Carolina 29412, United States
| | - Alison M Bland
- Department of Biology, Grice Marine Laboratory, College of Charleston, Charleston, South Carolina 29412, United States
- Hollings Marine Laboratory, College of Charleston, Charleston, South Carolina 29412, United States
| | - Emily R Whitmer
- The Marine Mammal Center, 2000 Bunker Road, Sausalito, California 94965, United States
| | - Cara L Field
- The Marine Mammal Center, 2000 Bunker Road, Sausalito, California 94965, United States
| | - Pádraig J Duignan
- The Marine Mammal Center, 2000 Bunker Road, Sausalito, California 94965, United States
| | - Michael G Janech
- Department of Biology, Grice Marine Laboratory, College of Charleston, Charleston, South Carolina 29412, United States
- Hollings Marine Laboratory, College of Charleston, Charleston, South Carolina 29412, United States
| |
Collapse
|
26
|
Luís C, Fernandes R, Soares R. Exploring variations in glycolytic and gluconeogenic enzymes and isoforms across breast cancer cell lines and tissues. Carbohydr Res 2024; 541:109169. [PMID: 38838492 DOI: 10.1016/j.carres.2024.109169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 05/07/2024] [Accepted: 05/29/2024] [Indexed: 06/07/2024]
Abstract
It is well established that tumour cells undergo metabolic changes to acquire biological advantage over normal cells with activation of the glycolytic pathway, a process termed "Warburg effect". Enzyme isoforms are alternative enzymatic forms with the same function but with different biochemical or epigenetic features. Moreover, isoforms may have varying impacts on different metabolic pathways. We challenge ourselves to analyse the glycolytic and gluconeogenic enzymes and isoforms in breast cancer, a complex and heterogeneous pathology, associated with high incidence and mortality rates especially among women. We analysed epithelial and tumour cell lines by RT-PCR and compared values to a publicly available database for the expression profile of normal and tumour tissues (Gepia) of enzymes and enzymatic isoforms from glycolytic and gluconeogenic pathways. Additionally, GeneMANIA was used to evaluate interactions, pathways, and attributes of each glycolytic/gluconeogenic steps. The findings reveal that the enzymes and enzymatic isoforms expressed in cell culture were somewhat different from those in breast tissue. We propose that the tumor microenvironment plays a crucial role in the expression of glycolytic and gluconeogenic enzymes and isoforms in tumour cells. Nonetheless, they not only participate in glycolytic and gluconeogenic enzymatic activities but may also influence other pathways, such as the Pentose-Phosphate-Pathway, TCA cycle, as well as other carbohydrate, lipid, and amino acid metabolism.
Collapse
Affiliation(s)
- Carla Luís
- Biochemistry Unit, Department of Biomedicine, Faculty of Medicine, University of Porto (FMUP), Porto, Portugal; i3S - Instituto de Inovação e Investigação em Saúde, Universidade do Porto, Porto, Portugal.
| | - Rúben Fernandes
- Faculty of Health Sciences, University Fernando Pessoa, Fernando Pessoa Hospital School (FCS/HEFP/UFP), Porto, Portugal
| | - Raquel Soares
- Biochemistry Unit, Department of Biomedicine, Faculty of Medicine, University of Porto (FMUP), Porto, Portugal; i3S - Instituto de Inovação e Investigação em Saúde, Universidade do Porto, Porto, Portugal
| |
Collapse
|
27
|
He S, Chen H, Yi Y, Hou D, Fu X, Xie J, Zhang J, Liu C, Ru X, Wang J. A novel bioinformatics strategy to uncover the active ingredients and molecular mechanisms of Bai Shao in the treatment of non-alcoholic fatty liver disease. Front Pharmacol 2024; 15:1406188. [PMID: 39005933 PMCID: PMC11239447 DOI: 10.3389/fphar.2024.1406188] [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: 03/24/2024] [Accepted: 06/10/2024] [Indexed: 07/16/2024] Open
Abstract
Introduction: As a new discipline, network pharmacology has been widely used to disclose the material basis and mechanism of Traditional Chinese Medicine in recent years. However, numerous researches indicated that the material basis of TCMs identified based on network pharmacology was the mixtures of beneficial and harmful substances rather than the real material basis. In this work, taking the anti-NAFLD (non-alcoholic fatty liver disease) effect of Bai Shao (BS) as a case, we attempted to propose a novel bioinformatics strategy to uncover the material basis and mechanism of TCMs in a precise manner. Methods: In our previous studies, we have done a lot work to explore TCM-induced hepatoprotection. Here, by integrating our previous studies, we developed a novel computational pharmacology method to identify hepatoprotective ingredients from TCMs. Then the developed method was used to discover the material basis and mechanism of Bai Shao against Non-alcoholic fatty liver disease by combining with the techniques of molecular network, microarray data analysis, molecular docking, and molecular dynamics simulation. Finally, literature verification method was utilized to validate the findings. Results: A total of 12 ingredients were found to be associated with the anti-NAFLD effect of BS, including monoterpene glucosides, flavonoids, triterpenes, and phenolic acids. Further analysis found that IL1-β, IL6, and JUN would be the key targets. Interestingly, molecular docking and molecular dynamics simulation analysis showed that there indeed existed strong and stable binding affinity between the active ingredients and the key targets. In addition, a total of 23 NAFLD-related KEGG pathways were enriched. The major biological processes involved by these pathways including inflammation, apoptosis, lipid metabolism, and glucose metabolism. Of note, there was a great deal of evidence available in the literature to support the findings mentioned above, indicating that our method was reliable. Discussion: In summary, the contributions of this work can be summarized as two aspects as follows. Firstly, we systematically elucidated the material basis and mechanism of BS against NAFLD from multiple perspectives. These findings further enhanced the theoretical foundation of BS on NAFLD. Secondly, a novel computational pharmacology research strategy was proposed, which would assist network pharmacology to uncover the scientific connotation TCMs in a more precise manner.
Collapse
Affiliation(s)
- Shuaibing He
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, School of Medicine, Huzhou Central Hospital, Huzhou University, Huzhou, China
- Key Laboratory for Precise Prevention and Control of Major Chronic Diseases, Huzhou University, Huzhou, China
| | - Hantao Chen
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, School of Medicine, Huzhou Central Hospital, Huzhou University, Huzhou, China
- Key Laboratory for Precise Prevention and Control of Major Chronic Diseases, Huzhou University, Huzhou, China
| | - Yanfeng Yi
- Department of Life Sciences and Health, School of Science and Engineering, Huzhou College, Huzhou, China
| | - Diandong Hou
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, School of Medicine, Huzhou Central Hospital, Huzhou University, Huzhou, China
- Key Laboratory for Precise Prevention and Control of Major Chronic Diseases, Huzhou University, Huzhou, China
| | - Xuyan Fu
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, School of Medicine, Huzhou Central Hospital, Huzhou University, Huzhou, China
- Key Laboratory for Precise Prevention and Control of Major Chronic Diseases, Huzhou University, Huzhou, China
| | - Jinlu Xie
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, School of Medicine, Huzhou Central Hospital, Huzhou University, Huzhou, China
- Key Laboratory for Precise Prevention and Control of Major Chronic Diseases, Huzhou University, Huzhou, China
| | - Juan Zhang
- XinJiang Institute of Chinese Materia Medica and Ethnodrug, Urumqi, China
| | - Chongbin Liu
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, School of Medicine, Huzhou Central Hospital, Huzhou University, Huzhou, China
- Key Laboratory for Precise Prevention and Control of Major Chronic Diseases, Huzhou University, Huzhou, China
| | - Xiaochen Ru
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, School of Medicine, Huzhou Central Hospital, Huzhou University, Huzhou, China
- Key Laboratory for Precise Prevention and Control of Major Chronic Diseases, Huzhou University, Huzhou, China
| | - Juan Wang
- School of Traditional Chinese Medicine, Zhejiang Pharmaceutical University, Ningbo, China
| |
Collapse
|
28
|
Wang M, Ying Q, Ding R, Xing Y, Wang J, Pan Y, Pan B, Xiang G, Liu Z. Elucidating prognosis in cervical squamous cell carcinoma and endocervical adenocarcinoma: a novel anoikis-related gene signature model. Front Oncol 2024; 14:1352638. [PMID: 38988712 PMCID: PMC11234598 DOI: 10.3389/fonc.2024.1352638] [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: 12/08/2023] [Accepted: 06/10/2024] [Indexed: 07/12/2024] Open
Abstract
Background Cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) are among the most prevalent gynecologic malignancies globally. The prognosis is abysmal once cervical cancer progresses to lymphatic metastasis. Anoikis, a specialized form of apoptosis induced by loss of cell adhesion to the extracellular matrix, plays a critical role. The prediction model based on anoikis-related genes (ARGs) expression and clinical data could greatly aid clinical decision-making. However, the relationship between ARGs and CESC remains unclear. Methods ARGs curated from the GeneCards and Harmonizome portals were instrumental in delineating CESC subtypes and in developing a prognostic framework for patients afflicted with this condition. We further delved into the intricacies of the immune microenvironment and pathway enrichment across the identified subtypes. Finally, our efforts culminated in the creation of an innovative nomogram that integrates ARGs. The utility of this prognostic tool was underscored by Decision Curve Analysis (DCA), which illuminate its prospective benefits in guiding clinical interventions. Results In our study, We discerned a set of 17 survival-pertinent, anoikis-related differentially expressed genes (DEGs) in CESC, from which nine were meticulously selected for the construction of prognostic models. The derived prognostic risk score was subsequently validated as an autonomous prognostic determinant. Through comprehensive functional analyses, we observed distinct immune profiles and drug response patterns among divergent prognostic stratifications. Further, we integrated the risk scores with the clinicopathological characteristics of CESC to develop a robust nomogram. DCA corroborated the utility of our model, demonstrating its potential to enhance patient outcomes through tailored clinical treatment strategies. Conclusion The predictive signature, encompassing nine pivotal genes, alongside the meticulously constructed nomogram developed in this research, furnishes clinicians with a sophisticated tool for tailoring treatment strategies to individual patients diagnosed with CESC.
Collapse
Affiliation(s)
- Mingwei- Wang
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Qiaohui- Ying
- Institute of Oral Basic Research, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Ru Ding
- Department of Obstetrics and Gynecology, The First Hospital of Jilin University, Changchun, China
| | - Yuncan- Xing
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jue Wang
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Yiming- Pan
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Bo Pan
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Guifen- Xiang
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
- School of Public Health, Anhui Medical University, Hefei, China
| | - Zhong Liu
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| |
Collapse
|
29
|
Du X, Sun X, Li M. Knowledge Graph Convolutional Network with Heuristic Search for Drug Repositioning. J Chem Inf Model 2024; 64:4928-4937. [PMID: 38837744 DOI: 10.1021/acs.jcim.4c00737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Drug repositioning is a strategy of repurposing approved drugs for treating new indications, which can accelerate the drug discovery process, reduce development costs, and lower the safety risk. The advancement of biotechnology has significantly accelerated the speed and scale of biological data generation, offering significant potential for drug repositioning through biomedical knowledge graphs that integrate diverse entities and relations from various biomedical sources. To fully learn the semantic information and topological structure information from the biological knowledge graph, we propose a knowledge graph convolutional network with a heuristic search, named KGCNH, which can effectively utilize the diversity of entities and relationships in biological knowledge graphs, as well as topological structure information, to predict the associations between drugs and diseases. Specifically, we design a relation-aware attention mechanism to compute the attention scores for each neighboring entity of a given entity under different relations. To address the challenge of randomness of the initial attention scores potentially impacting model performance and to expand the search scope of the model, we designed a heuristic search module based on Gumbel-Softmax, which uses attention scores as heuristic information and introduces randomness to assist the model in exploring more optimal embeddings of drugs and diseases. Following this module, we derive the relation weights, obtain the embeddings of drugs and diseases through neighborhood aggregation, and then predict drug-disease associations. Additionally, we employ feature-based augmented views to enhance model robustness and mitigate overfitting issues. We have implemented our method and conducted experiments on two data sets. The results demonstrate that KGCNH outperforms competing methods. In particular, case studies on lithium and quetiapine confirm that KGCNH can retrieve more actual drug-disease associations in the top prediction results.
Collapse
Affiliation(s)
- Xiang Du
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, China
- School of Information Engineering, Jiangxi University of Science and Technology, Ganzhou, Jiangxi 341000, China
| | - Xinliang Sun
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, China
| | - Min Li
- School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, China
| |
Collapse
|
30
|
Rouse WB, Tompkins VS, O’Leary CA, Moss WN. The RNA secondary structure of androgen receptor-FL and V7 transcripts reveals novel regulatory regions. Nucleic Acids Res 2024; 52:6596-6613. [PMID: 38554103 PMCID: PMC11194067 DOI: 10.1093/nar/gkae220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/18/2024] [Indexed: 04/01/2024] Open
Abstract
The androgen receptor (AR) is a ligand-dependent nuclear transcription factor belonging to the steroid hormone nuclear receptor family. Due to its roles in regulating cell proliferation and differentiation, AR is tightly regulated to maintain proper levels of itself and the many genes it controls. AR dysregulation is a driver of many human diseases including prostate cancer. Though this dysregulation often occurs at the RNA level, there are many unknowns surrounding post-transcriptional regulation of AR mRNA, particularly the role that RNA secondary structure plays. Thus, a comprehensive analysis of AR transcript secondary structure is needed. We address this through the computational and experimental analyses of two key isoforms, full length (AR-FL) and truncated (AR-V7). Here, a combination of in-cell RNA secondary structure probing experiments (targeted DMS-MaPseq) and computational predictions were used to characterize the static structural landscape and conformational dynamics of both isoforms. Additionally, in-cell assays were used to identify functionally relevant structures in the 5' and 3' UTRs of AR-FL. A notable example is a conserved stem loop structure in the 5'UTR of AR-FL that can bind to Poly(RC) Binding Protein 2 (PCBP2). Taken together, our results reveal novel features that regulate AR expression.
Collapse
Affiliation(s)
- Warren B Rouse
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Van S Tompkins
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Collin A O’Leary
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
- Current Address: Departments of Biology and Chemistry, Cornell College, Mount Vernon, IA 52314, USA
| | - Walter N Moss
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| |
Collapse
|
31
|
Li J, Zhong J, Tang A, Yin J, Li S. PRAMEF12, a novel cancer/testis gene, regulates proliferation and apoptosis to promote progression of glioma. Biomark Med 2024; 18:385-397. [PMID: 38913622 PMCID: PMC11285353 DOI: 10.2217/bmm-2023-0219] [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: 04/09/2023] [Accepted: 11/17/2023] [Indexed: 06/26/2024] Open
Abstract
Aim: To evaluate whether PRAMEF12 can serve as a diagnostic biomarker for glioma. Methods: We examined PRAMEF12 expression in multiple normal and glioma tissues. The diagnostic value of PRAMEF12 was evaluated using receiver operating characteristic curve analysis. The effect of PRAMEF12 ablation on proliferation, cell cycle and apoptosis was investigated. Database analyses were utilized for functional enrichment analysis. Results: PRAMEF12 expression in normal tissue was restricted to the human testis. PRAMEF12 displayed significant diagnostic value in glioma. PRAMEF12 knockdown inhibited cell proliferation, induced apoptosis and resulted in induction of S-phase cell cycle arrest. Pathway enrichment analysis indicated that PRAMEF12 may participate in cancer. Conclusion: PRAMEF12, a novel cancer/testis gene, may be a potential new diagnostic biomarker for glioma.
Collapse
Affiliation(s)
- Jiaqiang Li
- Department of Pediatric Urology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, 518026, China
| | - Jianhua Zhong
- Department of Science & Education, The Second People’s Hospital of Shenzhen, The First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, 518035, China
| | - Aifa Tang
- Department of Science & Education, The Second People’s Hospital of Shenzhen, The First Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, 518035, China
| | - Jianchun Yin
- Department of Pediatric Urology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, 518026, China
| | - Shoulin Li
- Department of Pediatric Urology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, 518026, China
| |
Collapse
|
32
|
Soni RK. Frontiers in plasma proteome profiling platforms: innovations and applications. Clin Proteomics 2024; 21:43. [PMID: 38902643 PMCID: PMC11191172 DOI: 10.1186/s12014-024-09497-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024] Open
Abstract
Biomarkers play a crucial role in advancing precision medicine by enabling more targeted and individualized approaches to diagnosis and treatment. Various biofluids, including serum, plasma, cerebrospinal fluid (CSF), saliva, tears, pancreatic cyst fluids, and urine, have been identified as rich sources of potential for the early detection of disease biomarkers in conditions such as cancer, cardiovascular diseases, and neurodegenerative disorders. The analysis of plasma and serum in proteomics research encounters challenges due to their high complexity and the wide dynamic range of protein abundance. These factors impede the sensitivity, coverage, and precision of protein detection when employing mass spectrometry, a widely utilized technology in discovery proteomics. Conventional approaches such as Neat Plasma workflow are inefficient in accurately quantifying low-abundant proteins, including those associated with tissue leakage, immune response molecules, interleukins, cytokines, and interferons. Moreover, the manual nature of the workflow poses a significant hurdle in conducting large cohort studies. In this study, our focus is on comparing workflows for plasma proteomic profiling to establish a methodology that is not only sensitive and reproducible but also applicable for large cohort studies in biomarker discovery. Our investigation revealed that the Proteograph XT workflow outperforms other workflows in terms of plasma proteome depth, quantitative accuracy, and reproducibility while offering complete automation of sample preparation. Notably, Proteograph XT demonstrates versatility by applying it to various types of biofluids. Additionally, the proteins quantified widely cover secretory proteins in peripheral blood, and the pathway analysis enriched with relevant components such as interleukins, tissue necrosis factors, chemokines, and B and T cell receptors provides valuable insights. These proteins, often challenging to quantify in complex biological samples, hold potential as early detection markers for various diseases, thereby contributing to the improvement of patient care quality.
Collapse
Affiliation(s)
- Rajesh Kumar Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Columbia University Irving Medical Center, New York, USA.
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, USA.
| |
Collapse
|
33
|
Jariwala N, Ozols M, Eckersley A, Mambwe B, Watson REB, Zeef L, Gilmore A, Debelle L, Bell M, Bradley EJ, Doush Y, Keenan A, Courage C, Leroux R, Peschard O, Mondon P, Ringenbach C, Bernard L, Pitois A, Sherratt MJ. Prediction, screening and characterization of novel bioactive tetrapeptide matrikines for skin rejuvenation. Br J Dermatol 2024; 191:92-106. [PMID: 38375775 DOI: 10.1093/bjd/ljae061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 02/08/2024] [Accepted: 02/10/2024] [Indexed: 02/21/2024]
Abstract
BACKGROUND Extracellular matrices play a critical role in tissue structure and function and aberrant remodelling of these matrices is a hallmark of many age-related diseases. In skin, loss of dermal collagens and disorganization of elastic fibre components are key features of photoageing. Although the application of some small matrix-derived peptides to aged skin has been shown to beneficially affect in vitro cell behaviour and, in vivo, molecular architecture and clinical appearance, the discovery of new peptides has lacked a guiding hypothesis. OBJECTIVES To identify, using protease cleavage site prediction, novel putative matrikines with beneficial activities for skin composition and structure. METHODS Here, we present an in silico (peptide cleavage prediction) to in vitro (proteomic and transcriptomic activity testing in cultured human dermal fibroblasts) to in vivo (short-term patch test and longer-term split-face clinical study) discovery pipeline, which enables the identification and characterization of peptides with differential activities. RESULTS Using this pipeline we showed that cultured fibroblasts were responsive to all applied peptides, but their associated bioactivity was sequence-dependent. Based on bioactivity, toxicity and protein source, we further characterized a combination of two novel peptides, GPKG (glycine-proline-lysine-glycine) and LSVD (leucine-serine-valine-aspartate), that acted in vitro to enhance the transcription of matrix -organization and cell proliferation genes and in vivo (in a short-term patch test) to promote processes associated with epithelial and dermal maintenance and remodelling. Prolonged use of a formulation containing these peptides in a split-face clinical study led to significantly improved measures of crow's feet and firmness in a mixed population. CONCLUSIONS This approach to peptide discovery and testing can identify new synthetic matrikines, providing insights into biological mechanisms of tissue homeostasis and repair and new pathways to clinical intervention.
Collapse
Affiliation(s)
- Nathan Jariwala
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Science
| | - Matiss Ozols
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Science
- Department of Human Genetics, Wellcome Sanger Institute, Genome Campus, Hinxton, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
| | - Alexander Eckersley
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Science
- Division of Musculoskeletal and Dermatological Sciences
| | | | - Rachel E B Watson
- Division of Musculoskeletal and Dermatological Sciences
- A*STAR Skin Research Laboratory (A*SRL), Agency for Science, Technology and Research (A*STAR) and National Skin Centre, Skin Research Institute of Singapore, Republic of Singapore
| | | | - Andrew Gilmore
- Wellcome Centre for Cell Matrix Research, Division of Cancer Sciences; Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Laurent Debelle
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Science
- UMR CNRS 7369 MEDyC, Université de Reims Champagne Ardenne, UFR Sciences Exactes et Naturelles, SFR CAP Santé, Moulin de la Housse, Reims, France
| | - Mike Bell
- No7 Beauty Company, Walgreens Boots Alliance, Nottingham, UK
| | | | - Yegor Doush
- No7 Beauty Company, Walgreens Boots Alliance, Nottingham, UK
| | - Amy Keenan
- No7 Beauty Company, Walgreens Boots Alliance, Nottingham, UK
| | - Carole Courage
- No7 Beauty Company, Walgreens Boots Alliance, Nottingham, UK
| | | | | | | | | | | | | | - Michael J Sherratt
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Science
| |
Collapse
|
34
|
Guo Z, Cao B, Hu Z, Wu J, Zhou W, Zhang W, Shi Z. Immunotherapy, prognostic, and tumor biomarker based on pancancer analysis, SMARCD3. Aging (Albany NY) 2024; 16:10074-10107. [PMID: 38862250 PMCID: PMC11210247 DOI: 10.18632/aging.205921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/10/2024] [Indexed: 06/13/2024]
Abstract
BACKGROUND SMARCD3 has recently been shown to be an important gene affecting cancer, playing an important role in medulloblastoma and pancreatic ductal adenocarcinoma. Therefore, we conducted this research to investigate the potential involvement of SMARCD3 across cancers and to offer recommendations for future studies. METHODS Utilizing information on 33 malignancies in the UCSC Xena database, SMARCD3 expression and its prognostic value were assessed. The tumor microenvironment was evaluated with the "CIBERSORT" and "ESTIMATE" algorithms. SMARCD3 and immune-related genes were analyzed using the TISIDB website. The pathways related to the target genes were examined using GSEA. MSI (microsatellite instability), TMB (tumor mutational burden), and immunotherapy analysis were used to evaluate the impact of target genes on the response to immunotherapy. RESULTS There is heterogeneity in terms of the expression and prognostic value of SMARCD3 among various cancers, but it is a risk factor for many cancers including uterine corpus endometrial cancer (UCEC), renal clear cell carcinoma (KIRC), and gastric adenocarcinoma (STAD). GSEA revealed that SMARCD3 is related to chromatin remodeling and transcriptional activation, lipid metabolism, and the activities of various immune cells. The TMB and MSI analyses suggested that SMARCD3 affects the immune response efficiency of KIRC, LUAD and STAD. Immunotherapy analysis suggested that SMARCD3 may be a potential immunotherapy target. RT-qPCR demonstrated the variation in SMARCD3 expression in KIRC, LUAD, and STAD. CONCLUSION Our study revealed that SMARCD3 affects the prognosis and immunotherapy response of some tumors, providing a direction for further research on this gene.
Collapse
Affiliation(s)
- Zishun Guo
- Department of Thoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Bingji Cao
- Department of Thoracic Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, China
| | - Zhuozheng Hu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Jiajun Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Weijun Zhou
- Department of Thoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Wenxiong Zhang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Zhihua Shi
- Department of Thoracic Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, China
| |
Collapse
|
35
|
Tiberi S, Meili J, Cai P, Soneson C, He D, Sarkar H, Avalos-Pacheco A, Patro R, Robinson MD. DifferentialRegulation: a Bayesian hierarchical approach to identify differentially regulated genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.17.553679. [PMID: 37645841 PMCID: PMC10462127 DOI: 10.1101/2023.08.17.553679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Motivation Although transcriptomics data is typically used to analyse mature spliced mRNA, recent attention has focused on jointly investigating spliced and unspliced (or precursor-) mRNA, which can be used to study gene regulation and changes in gene expression production. Nonetheless, most methods for spliced/unspliced inference (such as RNA velocity tools) focus on individual samples, and rarely allow comparisons between groups of samples (e.g., healthy vs. diseased). Furthermore, this kind of inference is challenging, because spliced and unspliced mRNA abundance is characterized by a high degree of quantification uncertainty, due to the prevalence of multi-mapping reads, i.e., reads compatible with multiple transcripts (or genes), and/or with both their spliced and unspliced versions. Results Here, we present DifferentialRegulation, a Bayesian hierarchical method to discover changes between experimental conditions with respect to the relative abundance of unspliced mRNA (over the total mRNA). We model the quantification uncertainty via a latent variable approach, where reads are allocated to their gene/transcript of origin, and to the respective splice version. We designed several benchmarks where our approach shows good performance, in terms of sensitivity and error control, versus state-of-the-art competitors. Importantly, our tool is flexible, and works with both bulk and single-cell RNA-sequencing data. Availability and implementation DifferentialRegulation is distributed as a Bioconductor R package.
Collapse
Affiliation(s)
- Simone Tiberi
- Department of Statistical Sciences, University of Bologna, Bologna, Italy
- Department of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Joël Meili
- Department of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Peiying Cai
- Department of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Charlotte Soneson
- Computational Biology Platform, Friedrich Miescher Institute for Biomedical Research and SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Dongze He
- Department of Cell Biology and Molecular Genetics, University of Maryland, MD, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, MD, USA
| | - Hirak Sarkar
- Department of Computer Science, Princeton University, NJ, USA
| | - Alejandra Avalos-Pacheco
- Research Unit of Applied Statistics, TU Wien, Vienna, Austria
- Harvard-MIT Center for Regulatory Science, Harvard Medical School, Boston, MA, USA
| | - Rob Patro
- Department of Computer Science, University of Maryland, MD, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, MD, USA
| | - Mark D Robinson
- Department of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| |
Collapse
|
36
|
Budeus B, Álvaro-Benito M, Crivello P. HLA-DM and HLA-DO interplay for the peptide editing of HLA class II in healthy tissues and leukemia. Best Pract Res Clin Haematol 2024; 37:101561. [PMID: 39098801 DOI: 10.1016/j.beha.2024.101561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/13/2024] [Accepted: 06/27/2024] [Indexed: 08/06/2024]
Abstract
HLA class II antigen presentation is modulated by the activity of the peptide editor HLA-DM and its antagonist HLA-DO, with their interplay controlling the peptide repertoires presented by normal and malignant cells. The role of these molecules in allogeneic hematopoietic cell transplantation (alloHCT) is poorly investigated. Balanced expression of HLA-DM and HLA-DO can influence the presentation of leukemia-associated antigens and peptides targeted by alloreactive T cells, therefore affecting both anti-leukemia immunity and the potential onset of Graft versus Host Disease. We leveraged on a large collection of bulk and single cell RNA sequencing data, available at different repositories, to comprehensively review the level and distribution of HLA-DM and HLA-DO in different cell types and tissues of the human body. The resulting expression atlas will help future investigations aiming to dissect the dual role of HLA class II peptide editing in alloHCT, and their potential impact on its clinical outcome.
Collapse
Affiliation(s)
- Bettina Budeus
- Institute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg-Essen, Essen, Germany.
| | - Miguel Álvaro-Benito
- School of Medicine, Universidad Complutense de Madrid, 12 de Octubre Health Research Institute, Madrid, Spain; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.
| | - Pietro Crivello
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany.
| |
Collapse
|
37
|
Wang B, Sun D, Li H, Chen J. A bird's eye view of the potential role of NFKBIA in pan-cancer. Heliyon 2024; 10:e31204. [PMID: 38813139 PMCID: PMC11133827 DOI: 10.1016/j.heliyon.2024.e31204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/07/2024] [Accepted: 05/13/2024] [Indexed: 05/31/2024] Open
Abstract
In the 21st century, cancer remains a serious threat to people's health and has become a prominent public health problem. NFKBIA is involved in the pathological process of many diseases including cancer, but its specific role in pan-cancer has not yet been fully elucidated. This study aims to deepen the understanding of cancer pathology by analyzing the potential functions of NFKBIA in pan-cancer. We used TCGA data to analyze differences of expression of NFKBIA in pan-cancer. We explored the prognostic value, clinical relevance, immune relevance, potential biological function, and diagnosis and treatment value of NFKBIA in pan-cancer through bioinformatics analysis. This study found that in pan-cancer, NFKBIA exhibits differences in expression, which correlate with the prognosis, diagnosis, treatment value and clinical and immune parameters. We have identified that Aspirin, Astaxanthin and Bardoxolone methyl are expected to play a potential therapeutic role in pan-cancer. The results of this study will help to improve our understanding of the role and potential mechanism of NFKBIA in cancer pathology, which may provide guidance for cancer-related research and clinical diagnosis and treatment.
Collapse
Affiliation(s)
- Bin Wang
- Department of Sports Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Difang Sun
- Department of Ophthalmology, Qingdao Eye Hospital of Shandong First Medical University, State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, China
| | - Haifeng Li
- Department of Sports Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Jinli Chen
- Department of Sports Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| |
Collapse
|
38
|
Guo M, Liu J, Zhang Y, Gu J, Xin J, Du M, Chu H, Wang M, Liu H, Zhang Z. Genetic variants in C1GALT1 are associated with gastric cancer risk by influencing immune infiltration. J Biomed Res 2024; 38:348-357. [PMID: 38807485 PMCID: PMC11300523 DOI: 10.7555/jbr.37.20230161] [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: 07/12/2023] [Revised: 12/09/2023] [Accepted: 01/08/2024] [Indexed: 05/30/2024] Open
Abstract
Core 1 synthase glycoprotein-N-acetylgalactosamine 3-β-galactosyltransferase 1 (C1GALT1) is known to play a critical role in the development of gastric cancer, but few studies have elucidated associations between genetic variants in C1GALT1 and gastric cancer risk. By using the genome-wide association study data from the database of Genotype and Phenotype (dbGAP), we evaluated such associations with a multivariable logistic regression model and identified that the rs35999583 G>C in C1GALT1 was associated with gastric cancer risk (odds ratio, 0.83; 95% confidence interval [CI], 0.75-0.92; P = 3.95 × 10 -4). C1GALT1 mRNA expression levels were significantly higher in gastric tumor tissues than in normal tissues, and gastric cancer patients with higher C1GALT1 mRNA levels had worse overall survival rates (hazards ratio, 1.33; 95% CI, 1.05-1.68; P log-rank = 1.90 × 10 -2). Furthermore, we found that C1GALT1 copy number differed in various immune cells and that C1GALT1 mRNA expression levels were positively correlated with the infiltrating levels of CD4 + T cells and macrophages. These results suggest that genetic variants of C1GALT1 may play an important role in gastric cancer risk and provide a new insight for C1GALT1 into a promising predictor of gastric cancer susceptibility and immune status.
Collapse
Affiliation(s)
- Mengfan Guo
- Departments of Environmental Genomics and Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health; Institute of Clinical Research, the Affiliated Taizhou People's Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Jingyuan Liu
- Departments of Environmental Genomics and Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Yujuan Zhang
- Departments of Environmental Genomics and Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Jingjing Gu
- Departments of Environmental Genomics and Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Junyi Xin
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Mulong Du
- Departments of Environmental Genomics and Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Haiyan Chu
- Departments of Environmental Genomics and Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Meilin Wang
- Departments of Environmental Genomics and Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Hanting Liu
- Departments of Environmental Genomics and Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Zhengdong Zhang
- Departments of Environmental Genomics and Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health; Institute of Clinical Research, the Affiliated Taizhou People's Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| |
Collapse
|
39
|
Sarkarai Nadar V, Yoshinaga-Sakurai K, Rosen BP. Anticancer Effects of the Trivalent Organoarsenical 2-Amino-4-(dihydroxyarsinoyl) Butanoate. Organometallics 2024; 43:1137-1142. [PMID: 38817537 PMCID: PMC11134607 DOI: 10.1021/acs.organomet.4c00082] [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: 02/28/2024] [Revised: 04/17/2024] [Accepted: 04/22/2024] [Indexed: 06/01/2024]
Abstract
According to the National Cancer Institute, breast cancer is a leading cause of death in women. The lack of progesterone and estrogen receptors in triple-negative breast cancer (TNBC) cells results in a lack of response to hormonal, monoclonal, or tyrosine kinase inhibitor therapies. Despite intensive drug discovery, there is still no approved targeted treatment for TNBC. The metalloid arsenic has been used in herbal medicines, antibiotics, and chemotherapeutic drugs for centuries. This paper demonstrates that a trivalent arsenic-containing, nonproteogenic amino acid, R-AST-OH (2-amino-4-(dihydroxyarsinoyl) butanoate), inhibits kidney-type glutaminase (KGA), the enzyme that controls glutamine metabolism and is correlated with tumor malignancy. Cell-based assays using the TNBC MDA-MB-231 and HCC1569 cell lines showed that R-AST-OH kills TNBC cells and is not cytotoxic to a control cell line. The results of in silico molecular docking predictions indicate that R-AST-OH binds to the glutamine binding site and forms a covalent bond with an active site cysteine residue. We hypothesize that R-AST-OH is a single warhead for KGA that irreversibly binds to KGA through the formation of an As-S bond. We propose that R-AST-OH is a promising lead compound for the design of new drugs for the treatment of TNBC.
Collapse
Affiliation(s)
- Venkadesh Sarkarai Nadar
- Department of Cellular and Molecular
Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida 33199, United States
| | - Kunie Yoshinaga-Sakurai
- Department of Cellular and Molecular
Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida 33199, United States
| | - Barry P. Rosen
- Department of Cellular and Molecular
Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida 33199, United States
| |
Collapse
|
40
|
Serambeque B, Mestre C, Correia-Barros G, Teixo R, Marto CM, Gonçalves AC, Caramelo F, Silva I, Paiva A, Beck HC, Carvalho AS, Botelho MF, Carvalho MJ, Matthiesen R, Laranjo M. Influence of Aldehyde Dehydrogenase Inhibition on Stemness of Endometrial Cancer Stem Cells. Cancers (Basel) 2024; 16:2031. [PMID: 38893151 PMCID: PMC11171353 DOI: 10.3390/cancers16112031] [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: 05/07/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024] Open
Abstract
Endometrial cancer is one of the most common gynaecological malignancies. Although often diagnosed at an early stage, there is a subset of patients with recurrent and metastatic disease for whom current treatments are not effective. Cancer stem cells (CSCs) play a pivotal role in triggering tumorigenesis, disease progression, recurrence, and metastasis, as high aldehyde dehydrogenase (ALDH) activity is associated with invasiveness and chemotherapy resistance. Therefore, this study aimed to evaluate the effects of ALDH inhibition in endometrial CSCs. ECC-1 and RL95-2 cells were submitted to a sphere-forming protocol to obtain endometrial CSCs. ALDH inhibition was evaluated through ALDH activity and expression, sphere-forming capacity, self-renewal, projection area, and CD133, CD44, CD24, and P53 expression. A mass spectrometry-based proteomic study was performed to determine the proteomic profile of endometrial cancer cells upon N,N-diethylaminobenzaldehyde (DEAB). DEAB reduced ALDH activity and expression, along with a significant decrease in sphere-forming capacity and projection area, with increased CD133 expression. Additionally, DEAB modulated P53 expression. Endometrial cancer cells display a distinct proteomic profile upon DEAB, sharing 75 up-regulated and 30 down-regulated proteins. In conclusion, DEAB inhibits ALDH activity and expression, influencing endometrial CSC phenotype. Furthermore, ALDH18A1, SdhA, and UBAP2L should be explored as novel molecular targets for endometrial cancer.
Collapse
Affiliation(s)
- Beatriz Serambeque
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) Area of Environment Genetics and Oncobiology (CIMAGO), Institute of Biophysics, Faculty of Medicine, 3000-548 Coimbra, Portugal; (C.M.); (G.C.-B.); (R.T.); (C.M.M.); (M.F.B.); (M.J.C.)
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal; (A.C.G.); (F.C.); (A.P.)
| | - Catarina Mestre
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) Area of Environment Genetics and Oncobiology (CIMAGO), Institute of Biophysics, Faculty of Medicine, 3000-548 Coimbra, Portugal; (C.M.); (G.C.-B.); (R.T.); (C.M.M.); (M.F.B.); (M.J.C.)
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal; (A.C.G.); (F.C.); (A.P.)
| | - Gabriela Correia-Barros
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) Area of Environment Genetics and Oncobiology (CIMAGO), Institute of Biophysics, Faculty of Medicine, 3000-548 Coimbra, Portugal; (C.M.); (G.C.-B.); (R.T.); (C.M.M.); (M.F.B.); (M.J.C.)
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal; (A.C.G.); (F.C.); (A.P.)
| | - Ricardo Teixo
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) Area of Environment Genetics and Oncobiology (CIMAGO), Institute of Biophysics, Faculty of Medicine, 3000-548 Coimbra, Portugal; (C.M.); (G.C.-B.); (R.T.); (C.M.M.); (M.F.B.); (M.J.C.)
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal; (A.C.G.); (F.C.); (A.P.)
| | - Carlos Miguel Marto
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) Area of Environment Genetics and Oncobiology (CIMAGO), Institute of Biophysics, Faculty of Medicine, 3000-548 Coimbra, Portugal; (C.M.); (G.C.-B.); (R.T.); (C.M.M.); (M.F.B.); (M.J.C.)
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal; (A.C.G.); (F.C.); (A.P.)
- Univ Coimbra, Institute of Experimental Pathology, Faculty of Medicine, 3000-548 Coimbra, Portugal
- Clinical Academic Centre of Coimbra (CACC), 3004-561 Coimbra, Portugal
| | - Ana Cristina Gonçalves
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal; (A.C.G.); (F.C.); (A.P.)
- Clinical Academic Centre of Coimbra (CACC), 3004-561 Coimbra, Portugal
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) Area of Environment Genetics and Oncobiology (CIMAGO), Laboratory of Oncobiology and Hematology (LOH) and University Clinics of Hematology and Oncology, Faculty of Medicine, 3000-548 Coimbra, Portugal
| | - Francisco Caramelo
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal; (A.C.G.); (F.C.); (A.P.)
- Clinical Academic Centre of Coimbra (CACC), 3004-561 Coimbra, Portugal
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) Area of Environment Genetics and Oncobiology (CIMAGO) and Laboratory of Biostatistics and Medical Informatics (LBIM), Faculty of Medicine, 3004-531 Coimbra, Portugal
| | - Isabel Silva
- Cytometry Operational Management Unit, Clinical Pathology Department, Unidade de Saúde Local de Coimbra, 3004-561 Coimbra, Portugal;
| | - Artur Paiva
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal; (A.C.G.); (F.C.); (A.P.)
- Cytometry Operational Management Unit, Clinical Pathology Department, Unidade de Saúde Local de Coimbra, 3004-561 Coimbra, Portugal;
- Polytechnic Institute of Coimbra, Coimbra Health School, Laboratory Biomedical Sciences, 3045-043 Coimbra, Portugal
| | - Hans C. Beck
- Department of Clinical Biochemistry, Odense University Hospital, 5000 Odense, Denmark;
| | - Ana Sofia Carvalho
- iNOVA4Health, NOVA Medical School (NMS), Faculdade de Ciências Médicas (FCM), Universidade Nova de Lisboa, 1150-082 Lisboa, Portugal; (A.S.C.); (R.M.)
| | - Maria Filomena Botelho
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) Area of Environment Genetics and Oncobiology (CIMAGO), Institute of Biophysics, Faculty of Medicine, 3000-548 Coimbra, Portugal; (C.M.); (G.C.-B.); (R.T.); (C.M.M.); (M.F.B.); (M.J.C.)
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal; (A.C.G.); (F.C.); (A.P.)
- Univ Coimbra, Institute of Experimental Pathology, Faculty of Medicine, 3000-548 Coimbra, Portugal
- Clinical Academic Centre of Coimbra (CACC), 3004-561 Coimbra, Portugal
| | - Maria João Carvalho
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) Area of Environment Genetics and Oncobiology (CIMAGO), Institute of Biophysics, Faculty of Medicine, 3000-548 Coimbra, Portugal; (C.M.); (G.C.-B.); (R.T.); (C.M.M.); (M.F.B.); (M.J.C.)
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal; (A.C.G.); (F.C.); (A.P.)
- Clinical Academic Centre of Coimbra (CACC), 3004-561 Coimbra, Portugal
- Univ Coimbra, Universitary Clinic of Gynecology, Faculty of Medicine, 3004-561 Coimbra, Portugal
- Gynecology Service, Department of Gynecology, Obstetrics, Reproduction and Neonatology, Unidade Local de Saúde de Coimbra, 3004-561 Coimbra, Portugal
| | - Rune Matthiesen
- iNOVA4Health, NOVA Medical School (NMS), Faculdade de Ciências Médicas (FCM), Universidade Nova de Lisboa, 1150-082 Lisboa, Portugal; (A.S.C.); (R.M.)
| | - Mafalda Laranjo
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) Area of Environment Genetics and Oncobiology (CIMAGO), Institute of Biophysics, Faculty of Medicine, 3000-548 Coimbra, Portugal; (C.M.); (G.C.-B.); (R.T.); (C.M.M.); (M.F.B.); (M.J.C.)
- Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), 3000-548 Coimbra, Portugal; (A.C.G.); (F.C.); (A.P.)
- Clinical Academic Centre of Coimbra (CACC), 3004-561 Coimbra, Portugal
| |
Collapse
|
41
|
Xu H, Song Y. Analyzing the Functional Roles and Immunological Features of Chemokines in COAD. Int J Mol Sci 2024; 25:5410. [PMID: 38791448 PMCID: PMC11121388 DOI: 10.3390/ijms25105410] [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: 04/16/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Chemokines are key proteins that regulate cell migration and immune responses and are essential for modulating the tumor microenvironment. Despite their close association with colon cancer, the expression patterns, prognosis, immunity, and specific roles of chemokines in colon cancer are still not fully understood. In this study, we investigated the mutational features, differential expression, and immunological characteristics of chemokines in colon cancer (COAD) by analyzing the Tumor Genome Atlas (TCGA) database. We clarified the biological functions of these chemokines using Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. By univariate and multivariate COX regression analyses, we developed chemokine-based prognostic risk models. In addition, using Gene Set Enrichment Analysis (GSEA) and Gene Set Variant Analysis (GSVA), we analyzed the differences in immune responses and signaling pathways among different risk groups. The results showed that the mutation rate of chemokines was low in COAD, but 25 chemokines were significantly differentially expressed. These chemokines function in several immune-related biological processes and play key roles in signaling pathways including cytokine-cytokine receptor interactions, NF-kappa B, and IL-17. Prognostic risk models based on CCL22, CXCL1, CXCL8, CXCL9, and CXCL11 performed well. GSEA and GSVA analyses showed significant differences in immune responses and signaling pathways across risk groups. In conclusion, this study reveals the potential molecular mechanisms of chemokines in COAD and proposes a new prognostic risk model based on these insights.
Collapse
Affiliation(s)
- Houxi Xu
- School of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China;
| | - Yihua Song
- School of Artificial Intelligence and Information Technology, Nanjing University of Chinese Medicine, Nanjing 210023, China
| |
Collapse
|
42
|
Zhou H, Zhou X, Zhu R, Zhao Z, Yang K, Shen Z, Sun H. A ferroptosis-related signature predicts the clinical diagnosis and prognosis, and associates with the immune microenvironment of lung cancer. Discov Oncol 2024; 15:163. [PMID: 38743344 PMCID: PMC11093956 DOI: 10.1007/s12672-024-01032-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 05/10/2024] [Indexed: 05/16/2024] Open
Abstract
Targeting ferroptosis-related pathway is a potential strategy for treatment of lung cancer (LC). Consequently, exploration of ferroptosis-related markers is important for treating LC. We collected LC clinical data and mRNA expression profiles from TCGA and GEO database. Ferroptosis-related genes (FRGs) were obtained through FerrDB database. Expression analysis was performed to obtain differentially expressed FRGs. Diagnostic and prognostic models were constructed based on FRGs by LASSO regression, univariate, and multivariate Cox regression analysis, respectively. External verification cohorts GSE72094 and GSE157011 were used for validation. The interrelationship between prognostic risk scores based on FRGs and the tumor immune microenvironment was analyzed. Immunocytochemistry, Western blotting, and RT-qPCR detected the FRGs level. Eighteen FRGs were used for diagnostic models, 8 FRGs were used for prognostic models. The diagnostic model distinguished well between LC and normal samples in training and validation cohorts of TCGA. The prognostic models for TCGA, GSE72094, and GSE157011 cohorts significantly confirmed lower overall survival (OS) in high-risk group, which demonstrated excellent predictive properties of the survival model. Multivariate Cox regression analysis further confirmed risk score was an independent risk factor related with OS. Immunoassays revealed that in high-risk group, a significantly higher proportion of Macrophages_M0, Neutrophils, resting Natural killer cells and activated Mast cells and the level of B7H3, CD112, CD155, B7H5, and ICOSL were increased. In conclusion, diagnostic and prognostic models provided superior diagnostic and predictive power for LC and revealed a potential link between ferroptosis and TIME.
Collapse
Affiliation(s)
- Hua Zhou
- Department of Oncology Radiotherapy, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China
| | - Xiaoting Zhou
- Medical School, Kunming University of Science and Technology, Kunming, 650031, Yunnan, China
| | - Runying Zhu
- Department of Oncology Radiotherapy, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China
| | - Zhongquan Zhao
- Department of Oncology Radiotherapy, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China
| | - Kang Yang
- Department of Thoracic Surgery, First Affiliated Hospital of Kunming Medical University, No.295 Xichang Rd, Kunming, 650032, Yunnan, China
| | - Zhenghai Shen
- Department of Thoracic Surgery, Yunnan Cancer Hospital, Kunming, 650118, Yunnan, China
| | - Hongwen Sun
- Department of Thoracic Surgery, First Affiliated Hospital of Kunming Medical University, No.295 Xichang Rd, Kunming, 650032, Yunnan, China.
| |
Collapse
|
43
|
Shlapakova PS, Dobrynina LA, Kalashnikova LA, Gubanova MV, Danilova MS, Gnedovskaya EV, Grigorenko AP, Gusev FE, Manakhov AD, Rogaev EI. Peripheral Blood Gene Expression Profiling Reveals Molecular Pathways Associated with Cervical Artery Dissection. Int J Mol Sci 2024; 25:5205. [PMID: 38791244 PMCID: PMC11121660 DOI: 10.3390/ijms25105205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/01/2024] [Accepted: 05/05/2024] [Indexed: 05/26/2024] Open
Abstract
Cervical artery dissection (CeAD) is the primary cause of ischemic stroke in young adults. Monogenic heritable connective tissue diseases account for fewer than 5% of cases of CeAD. The remaining sporadic cases have known risk factors. The clinical, radiological, and histological characteristics of systemic vasculopathy and undifferentiated connective tissue dysplasia are present in up to 70% of individuals with sporadic CeAD. Genome-wide association studies identified CeAD-associated genetic variants in the non-coding genomic regions that may impact the gene transcription and RNA processing. However, global gene expression profile analysis has not yet been carried out for CeAD patients. We conducted bulk RNA sequencing and differential gene expression analysis to investigate the expression profile of protein-coding genes in the peripheral blood of 19 CeAD patients and 18 healthy volunteers. This was followed by functional annotation, heatmap clustering, reports on gene-disease associations and protein-protein interactions, as well as gene set enrichment analysis. We found potential correlations between CeAD and the dysregulation of genes linked to nucleolar stress, senescence-associated secretory phenotype, mitochondrial malfunction, and epithelial-mesenchymal plasticity.
Collapse
Affiliation(s)
- Polina S. Shlapakova
- Third Neurological Department, Research Center of Neurology, Moscow 125367, Russia; (P.S.S.); (L.A.K.); (M.V.G.); (E.V.G.)
| | - Larisa A. Dobrynina
- Third Neurological Department, Research Center of Neurology, Moscow 125367, Russia; (P.S.S.); (L.A.K.); (M.V.G.); (E.V.G.)
| | - Ludmila A. Kalashnikova
- Third Neurological Department, Research Center of Neurology, Moscow 125367, Russia; (P.S.S.); (L.A.K.); (M.V.G.); (E.V.G.)
| | - Mariia V. Gubanova
- Third Neurological Department, Research Center of Neurology, Moscow 125367, Russia; (P.S.S.); (L.A.K.); (M.V.G.); (E.V.G.)
| | - Maria S. Danilova
- Third Neurological Department, Research Center of Neurology, Moscow 125367, Russia; (P.S.S.); (L.A.K.); (M.V.G.); (E.V.G.)
| | - Elena V. Gnedovskaya
- Third Neurological Department, Research Center of Neurology, Moscow 125367, Russia; (P.S.S.); (L.A.K.); (M.V.G.); (E.V.G.)
| | - Anastasia P. Grigorenko
- Department of Genomics and Human Genetics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119333, Russia (F.E.G.)
| | - Fedor E. Gusev
- Department of Genomics and Human Genetics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119333, Russia (F.E.G.)
- Department of Genetics, Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi 354340, Russia; (A.D.M.)
| | - Andrey D. Manakhov
- Department of Genetics, Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi 354340, Russia; (A.D.M.)
- Center for Genetics and Genetic Technologies, Faculty of Biology, Lomonosov Moscow State University, Moscow 119192, Russia
| | - Evgeny I. Rogaev
- Department of Genetics, Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi 354340, Russia; (A.D.M.)
- Department of Psychiatry, UMass Chan Medical School, 222 Maple Ave, Reed-Rose-Gordon Building, Shrewsbury, MA 01545, USA
| |
Collapse
|
44
|
Lin Q, Serratore A, Perri J, Roy Chaudhuri T, Qu J, Ma WW, Kandel ES, Straubinger RM. Expression of fibroblast growth factor receptor 1 correlates inversely with the efficacy of single-agent fibroblast growth factor receptor-specific inhibitors in pancreatic cancer. Br J Pharmacol 2024; 181:1383-1403. [PMID: 37994108 DOI: 10.1111/bph.16289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 10/28/2023] [Accepted: 11/08/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND AND PURPOSE Elevated fibroblast growth factor receptor (FGFR) activity correlates with pancreatic adenocarcinoma (PDAC) progression and poor prognosis. However, its potential as a therapeutic target remains largely unexplored. EXPERIMENTAL APPROACH The mechanisms of action and therapeutic effects of selective pan-FGFR inhibitors (pan-FGFRi) were explored using in vitro and in vivo PDAC models ranging from gemcitabine-sensitive to highly gemcitabine-resistant (GemR). Gain-/loss-of-function investigations were employed to define the role of individual FGFRs in cell proliferation, migration, and treatment response and resistance. RESULTS The pan-FGFRi NVP-BGJ398 significantly inhibited cell proliferation, migration, and invasion, and downregulated key cell survival- and invasiveness markers in multiple PDAC cell lines. Gemcitabine is a standard-of-care for PDAC, but development of resistance to gemcitabine (GemR) compromises its efficacy. Acquired GemR was modelled experimentally by developing highly GemR cells using escalating gemcitabine exposure in vitro and in vivo. FGFRi treatment inhibited GemR cell proliferation, migration, GemR marker expression, and tumour progression. FGFR2 or FGFR3 loss-of-function by shRNA knockdown failed to decrease cell growth, whereas FGFR1 knockdown was lethal. FGFR1 overexpression promoted cell migration more than proliferation, and reduced FGFRi-mediated inhibition of proliferation and migration. Single-agent FGFRi suppressed the viability and growth of multiple patient-derived xenografts inversely with respect to FGFR1 expression, underscoring the influence of FGFR1-dependent tumour responses to FGFRi. Importantly, secondary data analysis showed that PDAC tumours expressed FGFR1 at lower levels than in normal pancreas tissue. CONCLUSIONS AND IMPLICATIONS Single-agent FGFR inhibitors mediate selective, molecularly-targeted suppression of PDAC proliferation, and their effects are greatest in PDAC tumours expressing low-to-moderate levels of FGFR1.
Collapse
Affiliation(s)
- Qingxiang Lin
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York, USA
- New York State Center of Excellence in Bioinformatics & Life Sciences, University at Buffalo, State University of New York, Buffalo, New York, USA
| | - Andrea Serratore
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York, USA
| | - Jonathan Perri
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York, USA
| | - Tista Roy Chaudhuri
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York, USA
- New York State Center of Excellence in Bioinformatics & Life Sciences, University at Buffalo, State University of New York, Buffalo, New York, USA
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York, USA
- New York State Center of Excellence in Bioinformatics & Life Sciences, University at Buffalo, State University of New York, Buffalo, New York, USA
| | - Wen Wee Ma
- Department of Hematology and Medical Oncology, Cleveland Clinic, Cleveland, Ohio, USA
| | - Eugene S Kandel
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Robert M Straubinger
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York, USA
- New York State Center of Excellence in Bioinformatics & Life Sciences, University at Buffalo, State University of New York, Buffalo, New York, USA
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| |
Collapse
|
45
|
Wen JW, Zhang HL, Du PF. Vislocas: Vision transformers for identifying protein subcellular mis-localization signatures of different cancer subtypes from immunohistochemistry images. Comput Biol Med 2024; 174:108392. [PMID: 38608321 DOI: 10.1016/j.compbiomed.2024.108392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/22/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024]
Abstract
Proteins must be sorted to specific subcellular compartments to perform their functions. Abnormal protein subcellular localizations are related to many diseases. Although many efforts have been made in predicting protein subcellular localization from various static information, including sequences, structures and interactions, such static information cannot predict protein mis-localization events in diseases. On the contrary, the IHC (immunohistochemistry) images, which have been widely applied in clinical diagnosis, contains information that can be used to find protein mis-localization events in disease states. In this study, we create the Vislocas method, which is capable of finding mis-localized proteins from IHC images as markers of cancer subtypes. By combining CNNs and vision transformer encoders, Vislocas can automatically extract image features at both global and local level. Vislocas can be trained with full-sized IHC images from scratch. It is the first attempt to create an end-to-end IHC image-based protein subcellular location predictor. Vislocas achieved comparable or better performances than state-of-the-art methods. We applied Vislocas to find significant protein mis-localization events in different subtypes of glioma, melanoma and skin cancer. The mis-localized proteins, which were found purely from IHC images by Vislocas, are in consistency with clinical or experimental results in literatures. All codes of Vislocas have been deposited in a Github repository (https://github.com/JingwenWen99/Vislocas). All datasets of Vislocas have been deposited in Zenodo (https://zenodo.org/records/10632698).
Collapse
Affiliation(s)
- Jing-Wen Wen
- College of Intelligence and Computing, Tianjin University, Tianjin, 300350, China.
| | - Han-Lin Zhang
- College of Intelligence and Computing, Tianjin University, Tianjin, 300350, China.
| | - Pu-Feng Du
- College of Intelligence and Computing, Tianjin University, Tianjin, 300350, China.
| |
Collapse
|
46
|
Jarosławska J, Kordas B, Miłowski T, Juranek JK. Mammalian Diaphanous1 signalling in neurovascular complications of diabetes. Eur J Neurosci 2024; 59:2628-2645. [PMID: 38491850 DOI: 10.1111/ejn.16310] [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: 12/20/2023] [Accepted: 02/18/2024] [Indexed: 03/18/2024]
Abstract
Over the past few decades, diabetes gradually has become one of the top non-communicable disorders, affecting 476.0 million in 2017 and is predicted to reach 570.9 million people in 2025. It is estimated that 70 to 100% of all diabetic patients will develop some if not all, diabetic complications over the course of the disease. Despite different symptoms, mechanisms underlying the development of diabetic complications are similar, likely stemming from deficits in both neuronal and vascular components supplying hyperglycaemia-susceptible tissues and organs. Diaph1, protein diaphanous homolog 1, although mainly known for its regulatory role in structural modification of actin and related cytoskeleton proteins, in recent years attracted research attention as a cytoplasmic partner of the receptor of advanced glycation end-products (RAGE) a signal transduction receptor, whose activation triggers an increase in proinflammatory molecules, oxidative stressors and cytokines in diabetes and its related complications. Both Diaph1 and RAGE are also a part of the RhoA signalling cascade, playing a significant role in the development of neurovascular disturbances underlying diabetes-related complications. In this review, based on the existing knowledge as well as compelling findings from our past and present studies, we address the role of Diaph1 signalling in metabolic stress and neurovascular degeneration in diabetic complications. In light of the most recent developments in biochemical, genomic and transcriptomic research, we describe current theories on the aetiology of diabetes complications, highlighting the function of the Diaph1 signalling system and its role in diabetes pathophysiology.
Collapse
Affiliation(s)
- Julia Jarosławska
- Department of Biological Functions of Food, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Bernard Kordas
- Department of Human Physiology and Pathophysiology, School of Medicine, University of Warmia and Mazury, Olsztyn, Poland
| | - Tadeusz Miłowski
- Department of Emergency Medicine, School of Public Health, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Judyta K Juranek
- Department of Human Physiology and Pathophysiology, School of Medicine, University of Warmia and Mazury, Olsztyn, Poland
| |
Collapse
|
47
|
Shen X, Yan Z, Huang Y, Zhu Q, Zhang G, Ci H, Wu Q, Wu L. ALDH2 as an immunological and prognostic biomarker: Insights from pan-cancer analysis. Medicine (Baltimore) 2024; 103:e37820. [PMID: 38640328 PMCID: PMC11030019 DOI: 10.1097/md.0000000000037820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/17/2024] [Accepted: 03/15/2024] [Indexed: 04/21/2024] Open
Abstract
Aldehyde dehydrogenase 2 (ALDH2) plays a critical role in safeguarding cells against acetaldehyde toxicity and is closely linked to human metabolism. Nevertheless, the involvement of ALDH2 in cancer remains enigmatic. This investigation seeks to comprehensively assess ALDH2's significance in pan-cancer. We conducted an all-encompassing analysis of pan-cancer utilizing multiple databases, including TCGA, linkedomicshs, UALCAN, and Kaplan-Meier plotter. We employed diverse algorithms such as EPIC, MCPCOUNTER, TIDTIMER, xCell, MCP-counter, CIBERSORT, quanTIseq, and EPIC to examine the connection between ALDH2 expression and immune cell infiltration. Single-cell sequencing analysis furnished insights into ALDH2's functional status in pan-cancer. Immunohistochemical staining was performed to validate ALDH2 expression in cancer tissues. In a comprehensive assessment, we observed that tumor tissues demonstrated diminished ALDH2 expression levels compared to normal tissues across 16 different cancer types. ALDH2 expression exhibited a significant positive correlation with the infiltration of immune cells, including CD4 + T cells, CD8 + T cells, neutrophils, B cells, and macrophages, in various tumor types. Moreover, this study explored the association between ALDH2 and patient survival, examined the methylation patterns of ALDH2 in normal and primary tumor tissues, and delved into genetic variations and mutations of ALDH2 in tumors. The findings suggest that ALDH2 could serve as a valuable prognostic biomarker in pan-cancer, closely linked to the tumor's immune microenvironment.
Collapse
Affiliation(s)
- Xiaorong Shen
- Department of Pathology, Bengbu Medical University, Bengbu, China
| | - Ziyi Yan
- Department of Pathology, Bengbu Medical University, Bengbu, China
| | - Yuanli Huang
- Department of Pathology, Bengbu Medical University, Bengbu, China
| | - Qing Zhu
- Department of Pathology, Bengbu Medical University, Bengbu, China
| | - Guanghui Zhang
- Department of Pathology, Bengbu Medical University, Bengbu, China
| | - Hongfei Ci
- Department of Pathology, Bengbu Medical University, Bengbu, China
| | - Qiong Wu
- Department of Pathology, Bengbu Medical University, Bengbu, China
| | - Ligao Wu
- Department of Pathology, Bengbu Medical University, Bengbu, China
| |
Collapse
|
48
|
An Y, Duan H. ALKBH5 modulates macrophages polarization in tumor microenvironment of ovarian cancer. J Ovarian Res 2024; 17:84. [PMID: 38637813 PMCID: PMC11025218 DOI: 10.1186/s13048-024-01394-4] [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: 06/07/2022] [Accepted: 03/14/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Macrophages play an essential role in regulating ovarian cancer immune microenvironment. Studies have shown that m6A methylation could influence immune microenvironment in cancer. In this study, we investigated the roles of m6A demethylase ALKBH5 and m6A recognition protein IGF2BP2 played in regulating macrophages polarization in ovarian cancer. METHODS In this study, we first explored the differentially expressed m6A methylation enzymes in M0 and M2 macrophages according to two independent GEO datasets. TIMER2.0 and GSCA database were used to explore the immune analysis of ALKBH5 and IGF2BP2 in ovarian cancer. K-M plotter and TIMER2.0 databases were used to evaluate the prognostic role of ALKBH5 and IGF2BP2 in ovarian cancer. For CNV mutation analysis of ALKBH5 and IGF2BP2, cBioPortal and GSCA databases were used. For single-cell analysis, sc-TIME and HPA softwares were used to analyze the roles of ALKBH5 and IGF2BP2 played in immune cells in ovarian cancer. To identify the role of ALKBH5 played in macrophage polarization, RT-PCR was used to verify the macrophage polarization related markers in vitro study. The function of ALKBH5 played in ovarian cancer was further analyzed through GO and KEGG analysis. FINDINGS In this study, we found that ALKBH5 and IGF2BP2 were up-regulated in M2 macrophages, which showed closely correlation with immune cells expressions in ovarian cancer, especially with macrophages. Ovarian cancer patients with higher expression of ALKBH5 and IGF2BP2 showed worse prognosis, possibly because of their close correlation with immune response. ALKBH5 also correlated with macrophage phenotypes in single-cell levels analysis. However, the expression level of IGF2BP2 in ovarian cancer immune microenvironment was very low. The results of RT-PCR indicated the potential role of ALKBH5 in M2 polarization of macrophages. INTERPRETATION ALKBH5 participated in regulating macrophage M2 polarization in ovarian cancer immune microenvironment.
Collapse
Affiliation(s)
- Yuanyuan An
- Gynecological Mini-Invasive Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, 17 Qihelou Street, Beijing, 100006, China
| | - Hua Duan
- Gynecological Mini-Invasive Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, 17 Qihelou Street, Beijing, 100006, China.
| |
Collapse
|
49
|
Zabransky DJ, Chhabra Y, Fane ME, Kartalia E, Leatherman JM, Hüser L, Zimmerman JW, Delitto D, Han S, Armstrong TD, Charmsaz S, Guinn S, Pramod S, Thompson ED, Hughes SJ, O'Connell J, Egan JM, Jaffee EM, Weeraratna AT. Fibroblasts in the Aged Pancreas Drive Pancreatic Cancer Progression. Cancer Res 2024; 84:1221-1236. [PMID: 38330147 DOI: 10.1158/0008-5472.can-24-0086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 02/10/2024]
Abstract
Pancreatic cancer is more prevalent in older individuals and often carries a poorer prognosis for them. The relationship between the microenvironment and pancreatic cancer is multifactorial, and age-related changes in nonmalignant cells in the tumor microenvironment may play a key role in promoting cancer aggressiveness. Because fibroblasts have profound impacts on pancreatic cancer progression, we investigated whether age-related changes in pancreatic fibroblasts influence cancer growth and metastasis. Proteomics analysis revealed that aged fibroblasts secrete different factors than young fibroblasts, including increased growth/differentiation factor 15 (GDF-15). Treating young mice with GDF-15 enhanced tumor growth, whereas aged GDF-15 knockout mice showed reduced tumor growth. GDF-15 activated AKT, rendering tumors sensitive to AKT inhibition in an aged but not young microenvironment. These data provide evidence for how aging alters pancreatic fibroblasts and promotes tumor progression, providing potential therapeutic targets and avenues for studying pancreatic cancer while accounting for the effects of aging. SIGNIFICANCE Aged pancreatic fibroblasts secrete GDF-15 and activate AKT signaling to promote pancreatic cancer growth, highlighting the critical role of aging-mediated changes in the pancreatic cancer microenvironment in driving tumor progression. See related commentary by Isaacson et al., p. 1185.
Collapse
Affiliation(s)
- Daniel J Zabransky
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Yash Chhabra
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Mitchell E Fane
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Fox Chase Cancer Center, Cancer Signaling and Microenvironment Program, Philadelphia, Pennsylvania
| | - Emma Kartalia
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - James M Leatherman
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Laura Hüser
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Mannheim, Germany
| | - Jacquelyn W Zimmerman
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Daniel Delitto
- Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, California
- Department of Surgery, Stanford University School of Medicine, Stanford, California
| | - Song Han
- Department of Surgery, University of Florida College of Medicine, Gainesville, Florida
| | - Todd D Armstrong
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Soren Charmsaz
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Samantha Guinn
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sneha Pramod
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Elizabeth D Thompson
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Steven J Hughes
- Department of Surgery, University of Florida College of Medicine, Gainesville, Florida
| | - Jennifer O'Connell
- Diabetes Section/Laboratory of Clinical Investigation, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - Josephine M Egan
- Diabetes Section/Laboratory of Clinical Investigation, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - Elizabeth M Jaffee
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Johns Hopkins Cancer Convergence Institute, Baltimore, Maryland
| | - Ashani T Weeraratna
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| |
Collapse
|
50
|
Gao Y, Yu Y, Wu H, Xiao Z, Li J. Mitochondrial ribosomal protein S24 is associated with immunosuppressive microenvironment and cold tumor in lung adenocarcinoma. Heliyon 2024; 10:e29171. [PMID: 38617968 PMCID: PMC11015142 DOI: 10.1016/j.heliyon.2024.e29171] [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: 01/09/2024] [Revised: 03/29/2024] [Accepted: 04/02/2024] [Indexed: 04/16/2024] Open
Abstract
Objective MRPS24 (Mitochondrial Ribosomal Protein S24) belongs to the mitochondrial ribosomal protein family, which participates in the protein synthesis of the mitochondrion. However, the relationship of MRPS24 with lung adenocarcinoma (LUAD) remained unknown. We aimed to identify its immunological and functional mechanisms in LUAD. Methods The analysis of MRPS24 expression, clinical features, diagnosis, prognosis, function analysis, genetic alteration, copy number variations, methylation, and tumor microenvironment was investigated by the TCGA, UCSC Xena, GEO, HPA, GEPIA, cBioPortal, MethSurv, TIMER, TIMER2.0, and TISIDB databases. Results MRPS24 was found to be more abundant in LUAD tumor tissue than in normal tissue. High levels of MRPS24 expression were found to be an independent prognostic factor by multivariate analysis. Functional analysis revealed that MRPS24 expression was associated with the immune, cell cycle and methylation. MRPS24 methylation level was inversely linked with its expression (p < 0.001). Patients with low MRPS24 methylation had a worse prognosis than those with high methylation (p < 0.05). In addition, the result revealed that the MRPS24 expression was inversely linked to the immune cell infiltration in LUAD. Finally, the validations of the expression level, prognosis, and immune cell infiltration of MRPS24 were in accordance with our previous results. Conclusions This study systematically explored that MRPS24 expression was significantly correlated with prognosis, tumorigenesis, genetic alteration, copy number variations, methylation, and immune cell infiltration in LUAD. MRPS24 might be a potential immune-related biomarker in the development and treatment of LUAD, thereby acting as a promising predictor of immunotherapy response in LUAD.
Collapse
Affiliation(s)
- Yanni Gao
- Department of Clinical Laboratory, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Yilin Yu
- Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Haixia Wu
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, China
| | - Zhenzhou Xiao
- Department of Clinical Laboratory, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| | - Jiancheng Li
- Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China
| |
Collapse
|