1
|
Zhou L, Liu Q, Fang Z, Li QL, Wong HM. Targeted antimicrobial self-assembly peptide hydrogel with in situ bio-mimic remineralization for caries management. Bioact Mater 2025; 44:428-446. [PMID: 39534787 PMCID: PMC11555604 DOI: 10.1016/j.bioactmat.2024.10.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2024] [Revised: 10/01/2024] [Accepted: 10/20/2024] [Indexed: 11/16/2024] Open
Abstract
The single-function agents with wide-spectrum activity which tend to disturb the ecological balance of oral cavity cannot satisfy dental treatment need. A multi-functional agent with specifically targeted killing property and in situ remineralization is warranted for caries management. A novel multi-functional agent (8DSS-C8-P-113) consisting of three domains, i.e., a non-specific antimicrobial peptide (AMP) (P-113), a competence stimulating peptide (C8), and an enhancing remineralization domain (8DSS), is fabricated and evaluated in this study. The findings demonstrates that 2 μM mL-1 of 8DSS-C8-P-113 eliminates planktonic Streptococcus mutans (S. mutans) without disrupting the oral normal flora. At a concentration of 8 μM mL-1, it exhibits the ability to prevent S. mutans' adhesion. Furthermore, 8DSS-C8-P-113 self-assembles a hydrogel state at the higher concentration of 16 μM mL-1. This hydrogel self-adheres on the tooth surface, resisting acid attack, eradicating S. mutans' biofilm, and inducing mineralization in order to facilitate the repair of demineralized dental hard tissue. Its significant effectiveness in reducing the severity of dental caries is also demonstrated in vivo in a rat model. This study suggests that the multi-functional bioactive AMP 8DSS-C8-P-113 is a promising agent to specifically target pathogen, prevent tooth demineralization, and effectively induce in situ bio-mimic remineralization for the management of dental caries.
Collapse
Affiliation(s)
- Li Zhou
- Faculty of Dentistry, The University of Hong Kong, Pokfulam Road, Hong Kong, 999077, China
| | - Qing Liu
- Faculty of Dentistry, The University of Hong Kong, Pokfulam Road, Hong Kong, 999077, China
| | - Zehui Fang
- Faculty of Dentistry, The University of Hong Kong, Pokfulam Road, Hong Kong, 999077, China
| | - Quan Li Li
- Institute of Oral Science, Department of Stomatology, Longgang Otorhinolaryngology Hospital, No. 3004L Longgang Avenue, Shenzhen, 518172, China
- Key Lab. of Oral Diseases Research of Anhui Province, College and Hospital of Stomatology, Anhui Medical University, Meishan Road, Hefei, 230000, China
| | - Hai Ming Wong
- Faculty of Dentistry, The University of Hong Kong, Pokfulam Road, Hong Kong, 999077, China
| |
Collapse
|
2
|
Ciucci G, Braga L, Zacchigna S. Discovery platforms for RNA therapeutics. Br J Pharmacol 2025; 182:281-295. [PMID: 38760893 DOI: 10.1111/bph.16424] [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: 11/29/2023] [Revised: 04/14/2024] [Accepted: 04/19/2024] [Indexed: 05/20/2024] Open
Abstract
RNA therapeutics are emerging as a unique opportunity to drug currently "undruggable" molecules and diseases. While their advantages over conventional, small molecule drugs, their therapeutic implications and the tools for their effective in vivo delivery have been extensively reviewed, little attention has been so far paid to the technological platforms exploited for the discovery of RNA therapeutics. Here, we provide an overview of the existing platforms and ex vivo assays for RNA discovery, their advantages and disadvantages, as well as their main fields of application, with specific focus on RNA therapies that have reached either phase 3 or market approval. LINKED ARTICLES: This article is part of a themed issue Non-coding RNA Therapeutics. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v182.2/issuetoc.
Collapse
Affiliation(s)
- Giulio Ciucci
- Cardiovascular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Luca Braga
- Functional Cell Biology Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Serena Zacchigna
- Cardiovascular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| |
Collapse
|
3
|
Huang G, Liu Y, Li L, Li B, Jiang T, Cao Y, Yang X, Liu X, Qu H, Li S, Zheng X. Integration analysis of microRNAs as potential biomarkers in early-stage lung adenocarcinoma: the diagnostic and therapeutic significance of miR-183-3p. Front Oncol 2024; 14:1508715. [PMID: 39759146 PMCID: PMC11697600 DOI: 10.3389/fonc.2024.1508715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2024] [Accepted: 12/03/2024] [Indexed: 01/07/2025] Open
Abstract
Introduction Lung adenocarcinoma (LUAD) poses a significant therapeutic challenge, primarily due to delayed diagnosis and the limited efficacy of existing treatments. Methods To understand the pathogenesis and identify diagnostic biomarkers for LUAD in the early stage, we investigated differential miRNA expression in 33 stage I LUAD patients between tumor and matched paracancerous tissues by Illumina Sequencing. Target genes of differentially expressed miRNAs were predicted using TargetScan and miRDB databases and further analyzed by GO and KEGG pathway enrichment analysis. The miRNAs expression results were verified using qRT-PCR. Additionally, we evaluated the clinical significance of miRNAs by the TCGA database. miR-183-3p was chosen for subsequent biological functional studies by cell proliferation assays, cell migration and cell invasion assays, cell apoptosis and cell cycle assays in LUAD cells. The clinical relevance target genes of miR-183-3p were predicted by TargetScan databases and bioinformatics assays. Gene-specific experimental validation was performed using qRT-PCR, western blotting and luciferase reporter assays. Results We identified 36 differentially expressed miRNAs between LUAD tissues and matched paracancerous tissues. Target genes for these miRNAs revealed associations with processes and pathways such as RNA biosynthesis, intracellular signaling, protein transport, and the Ras, MAPK, and PI3K-AKT pathways. The qRT-PCR results were in alignment with the sequencing data for 19 out of these 21 miRNAs which not yet implicated in LUAD, 13 were up-regulated, 6 were down-regulated. The clinical relevance assays showed that 5 up-regulated miRNAs have diagnostic value for LUAD. miR-183-3p showed significant advantages in the result of sequencing, qRT-PCR, and clinical relevance assay. Biological functional assays showed that miR-183-3p emerged as a key regulator, promoting LUAD cell proliferation, decreasing apoptosis, and augmenting migration and invasion capabilities. The clinical relevance assays and experimental validation showed SESN1 as a clinical significance target of miR-183-3p. Discussion Our study lays the foundation for investigating miRNAs with diagnostic significance in early-stage LUAD, pointing out that inhibition of miR-183-3p may serve as a novel therapeutic in LUAD.
Collapse
Affiliation(s)
- Guodong Huang
- Central Laboratory, Qingdao Hiser Hospital Affiliated of Qingdao University (Qingdao Hospital of Traditional Chinese Medicine), Qingdao, Shandong, China
| | - Yuxia Liu
- Department of Respiration, Second Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Lisha Li
- Department of Respiration, Qingdao Hiser Hospital Affiliated of Qingdao University (Qingdao Hospital of Traditional Chinese Medicine), Qingdao, Shandong, China
| | - Bing Li
- Central Laboratory, Qingdao Hiser Hospital Affiliated of Qingdao University (Qingdao Hospital of Traditional Chinese Medicine), Qingdao, Shandong, China
| | - Ting Jiang
- Central Laboratory, Qingdao Hiser Hospital Affiliated of Qingdao University (Qingdao Hospital of Traditional Chinese Medicine), Qingdao, Shandong, China
| | - Yufeng Cao
- Cancer Center, Qingdao Hiser Hospital Affiliated of Qingdao University (Qingdao Hospital of Traditional Chinese Medicine), Qingdao, Shandong, China
| | - Xiaoping Yang
- Department of Respiration, Qingdao Hiser Hospital Affiliated of Qingdao University (Qingdao Hospital of Traditional Chinese Medicine), Qingdao, Shandong, China
| | - Xinning Liu
- Central Laboratory, Qingdao Hiser Hospital Affiliated of Qingdao University (Qingdao Hospital of Traditional Chinese Medicine), Qingdao, Shandong, China
| | - Honglin Qu
- Central Laboratory, Qingdao Hiser Hospital Affiliated of Qingdao University (Qingdao Hospital of Traditional Chinese Medicine), Qingdao, Shandong, China
| | - Shitao Li
- Department of Respiration, Second Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Xin Zheng
- Central Laboratory, Qingdao Hiser Hospital Affiliated of Qingdao University (Qingdao Hospital of Traditional Chinese Medicine), Qingdao, Shandong, China
| |
Collapse
|
4
|
Meier MJ, Caiment F, Corton JC, Frötschl R, Fujita Y, Jennen D, Mezencev R, Yauk C. Outcome of IWGT workshop on transcriptomic biomarkers for genotoxicity: Key considerations for bioinformatics. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2024. [PMID: 39676751 DOI: 10.1002/em.22644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Revised: 11/23/2024] [Accepted: 11/26/2024] [Indexed: 12/17/2024]
Abstract
As a part of the International Workshop on Genotoxicity Testing (IWGT) in 2022, a workgroup was formed to evaluate the level of validation and regulatory acceptance of transcriptomic biomarkers that identify genotoxic substances. Several such biomarkers have been developed using various molecular techniques and computational approaches. Within the IWGT workgroup on transcriptomic biomarkers, bioinformatics was a central topic of discussion, focusing on the current approaches used to process the underlying molecular data to distill a reliable predictive signal; that is, a gene set that is indicative of genotoxicity and can then be used in later studies to predict potential DNA damaging properties for uncharacterized chemicals. While early studies used microarray data, a technological shift occurred in the past decade to incorporate modern transcriptome measuring techniques such as high-throughput transcriptomics, which in turn is based on high-throughput sequencing. Herein, we present the workgroup's review of the current bioinformatic approaches to identify genes comprising transcriptomic biomarkers. Within the context of regulatory toxicology, the reproducibility of a given analysis is critical. Therefore, the workgroup provides consensus recommendations on how to facilitate sufficient reporting of experimental parameters for the analytical procedures used in a transcriptomic biomarker study, including the recommendation to develop a biomarker-specific reporting module within the OECD Omics Reporting Framework.
Collapse
Affiliation(s)
- Matthew J Meier
- Environmental Health, Science and Research Bureau, Health Canada, Ottawa, Ontario, Canada
| | - Florian Caiment
- Department of Translational Genomics, GROW Research Institute for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - J Christopher Corton
- Center for Computational Toxicology and Exposure, US-EPA, Research Triangle Park, North Carolina, USA
| | - Roland Frötschl
- BfArM-Bundesinstitut für Arzneimittel und Medizinprodukte, Federal Institute for Drugs and Medical Devices, Bonn, Germany
| | - Yurika Fujita
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Danyel Jennen
- Department of Translational Genomics, GROW Research Institute for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Roman Mezencev
- Center for Public Health and Environmental Assessment, Office of Research and Development, US EPA, Washington, DC, USA
| | - Carole Yauk
- Department of Biology, Faculty of Science, University of Ottawa, Ottawa, Ontario, Canada
| |
Collapse
|
5
|
Mansoor S, Hamid S, Tuan TT, Park JE, Chung YS. Advance computational tools for multiomics data learning. Biotechnol Adv 2024; 77:108447. [PMID: 39251098 DOI: 10.1016/j.biotechadv.2024.108447] [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: 05/19/2024] [Revised: 09/01/2024] [Accepted: 09/05/2024] [Indexed: 09/11/2024]
Abstract
The burgeoning field of bioinformatics has seen a surge in computational tools tailored for omics data analysis driven by the heterogeneous and high-dimensional nature of omics data. In biomedical and plant science research multi-omics data has become pivotal for predictive analytics in the era of big data necessitating sophisticated computational methodologies. This review explores a diverse array of computational approaches which play crucial role in processing, normalizing, integrating, and analyzing omics data. Notable methods such similarity-based methods, network-based approaches, correlation-based methods, Bayesian methods, fusion-based methods and multivariate techniques among others are discussed in detail, each offering unique functionalities to address the complexities of multi-omics data. Furthermore, this review underscores the significance of computational tools in advancing our understanding of data and their transformative impact on research.
Collapse
Affiliation(s)
- Sheikh Mansoor
- Department of Plant Resources and Environment, Jeju National University, 63243, Republic of Korea
| | - Saira Hamid
- Watson Crick Centre for Molecular Medicine, Islamic University of Science and Technology, Awantipora, Pulwama, J&K, India
| | - Thai Thanh Tuan
- Department of Plant Resources and Environment, Jeju National University, 63243, Republic of Korea; Multimedia Communications Laboratory, University of Information Technology, Ho Chi Minh city 70000, Vietnam; Multimedia Communications Laboratory, Vietnam National University, Ho Chi Minh city 70000, Vietnam
| | - Jong-Eun Park
- Department of Animal Biotechnology, College of Applied Life Science, Jeju National University, Jeju, Jeju-do, Republic of Korea.
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, 63243, Republic of Korea.
| |
Collapse
|
6
|
Yari AH, Aghbash PS, Bayat M, Lahouti S, Jalilzadeh N, Zadeh LN, Yari AM, Tabrizi-Nezhadi P, Nahand JS, MotieGhader H, Baghi HB. Novel bioinformatic approaches show the role of driver genes in the progression of cervical cancer: An in-silico study. Heliyon 2024; 10:e40179. [PMID: 39634417 PMCID: PMC11616557 DOI: 10.1016/j.heliyon.2024.e40179] [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: 02/12/2024] [Revised: 10/31/2024] [Accepted: 11/05/2024] [Indexed: 12/07/2024] Open
Abstract
Background The goal of this bioinformatics research is to get a comprehensive understanding of the driver genes and their function in the development, progression, and treatment of cervical cancer. This study constitutes a pioneering attempt, adding to our knowledge of genetic diversity and its ramifications. Material and methods In this project, we use bioinformatics and systems biology methods to identify candidate transcription factors and the genes they regulate in order to identify microRNAs and LncRNAs that regulate these transcription factors and lead to the discovery of new medicines for the treatment of cervical cancer. From the differentially expressed genes available via GEO's GSE63514 accession, we use driver genes to choose these candidates. We then used the WGCNA tool in R to rebuild the co-expression network and its modules. The hub genes of each module were determined using CytoHubba, a Cystoscope plugin. The biomarker potential of hub genes was analyzed using the UCSC Xena browser and the GraphPad prism program. The TRRUST database is used to locate the TFs that regulate the expression of these genes. In order to learn how drugs, MicroRNAs, and LncRNAs interact with transcription factors, we consulted the Drug Target Information Database (DGIDB), the miRWalk database, and the LncHub database. Finally, the online database Enrichr is utilized to analyze the enrichment of Gene Ontology and KEGG pathways. Results By combining the mRNA expression levels of 2041 driver genes from 14 early-stage Cervical cancer and 24 control samples, a co-expression network was built. The cluster analysis shows that the collection of shared genes may be broken down into seven distinct groups, or "modules." According to the average linkage hierarchical clustering and Summary smaller than 2, we found five modules (represented by the colors blue, brown, red, green, and grey) in our research. Then, we identify 5 high-degree genes from these modules that may serve as diagnostic biomarkers (ZBBX, PLCH1, TTC7B, DNAH7, and ZMYND10). In addition, we identify four transcription factors (SRF, RELA, NFKB1, and SP1) that regulate the expression of genes in the co-expression module. Drugs, microRNAs, and long noncoding RNAs are then shown to cooperate with transcription factors. At last, the KEGG database's pathways were mined for information on how the co-expression module fits within them. More clinical trials are required for more trustworthy outcomes, and we collected this data using bioinformatics methods. Conclusion The major goal of this research was to identify diagnostic and therapeutic targets for cervical cancer by learning more about the involvement of driver genes in cancer's earliest stages.
Collapse
Affiliation(s)
- Amir Hossein Yari
- Department of Biology, Tabriz Branch, Islamic Azad University, Tabriz, Iran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Parisa Shiri Aghbash
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mobina Bayat
- Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Shiva Lahouti
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nazila Jalilzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Leila Nariman Zadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amir Mohammad Yari
- Department of Biology, Tabriz Branch, Islamic Azad University, Tabriz, Iran
| | | | - Javid Sadri Nahand
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Habib MotieGhader
- Department of Biology, Tabriz Branch, Islamic Azad University, Tabriz, Iran
- Department of Software Engineering, Engineering Faculty, Istanbul Topkapi University, Istanbul, Turkey
| | - Hossein Bannazadeh Baghi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| |
Collapse
|
7
|
Chakraborty C, Bhattacharya M, Alshammari A, Albekairi NA, Lee SS. Mapping the Potential Genes and Associated Pathways Involved in Long COVID-Associated Brain Fog Using Integrative Bioinformatics and Systems Biology Strategy. Mol Biotechnol 2024:10.1007/s12033-024-01324-1. [PMID: 39604720 DOI: 10.1007/s12033-024-01324-1] [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: 07/05/2024] [Accepted: 11/06/2024] [Indexed: 11/29/2024]
Abstract
One of the recent emerging global health issues is long COVID. Among long COVID patients, long COVID-associated brain fog is an important area. We noted an immense gap in understanding the genes and associated pathways involved in long COVID-associated brain fog. Therefore, the study has been selected to understand the genes and pathways involved in patients with long COVID-associated brain fog. A GEO dataset, which was developed through the RNA-seq, was used for the analysis. The dataset encompasses 22 human samples of PBMC. The dataset (human samples of PBMC) was grouped into four cohorts for this study: healthy cohort, COVID convalescent, long COVID, and long COVID brain fog. Therefore, the selection criteria for the 22 PBMC samples were based on the individual infection type (COVID convalescent, long COVID, and long COVID brain fog) and the healthy cohort. Using DEG profile evaluation, we revealed 250 top-ranked DEGs with P values, Padj, baseMean, etc. From the top-ranked DEGs, we listed 24 significant DEGs and some significant DEGs are SMAD3 (P value = 6.34e-07), PF4 (P value = 1.88e-05), TNFAIP3 (P value = 3.70e-06), CXCL5 (P value = 1.22e-08), etc. Among the top-ranked DEGs, we found some genes linked with different biological functions, such as inflammatory cytokine secretion, inflammation, microclot formation, and BBB disruption. From our investigation, we found some genes that are associated with this condition, namely PF4, SMAD3, CXCL5, TNFAIP3, etc. From the literature survey and functional pathway enrichment analysis, we noted the function of the genes such as PF4, SMAD3, and CXCL5. We found that PF4 assists in clot formation, and SMAD3 is associated with neuroinflammation. Similarly, CXCL5 is an inflammatory marker associated with neuroinflammation and BBB damage. At the same time, the study with functional pathway enrichment analysis reflects that DEGs of long COVID-related brain fog might be associated with several biological pathways and processes, cell signatures, and gene-disease associations. It reflects that the disease is a highly complex one. Our study will provide an understanding of the genes and associated pathways in long COVID-related brain fog, which will assist in the next-generation biomarker discovery and therapeutics for these patients.
Collapse
Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal, 700126, India.
| | - Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore, Odisha, 756020, India
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, 11451, Riyadh, Saudi Arabia
| | - Norah A Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, 11451, Riyadh, Saudi Arabia
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-Si, Gangwon-Do, 24252, Republic of Korea
| |
Collapse
|
8
|
Chen W, Guo P, Su L, Guo X, Shi M, Geng J, Zong Y, Zhao Y, Du R, He Z. Combining Network Pharmacology and Transcriptomic Strategies to Explore the Pharmacological Mechanism of Total Ginsenoside Ginseng Root and Its Impact on Antidepressant Effects. Int J Mol Sci 2024; 25:12606. [PMID: 39684318 DOI: 10.3390/ijms252312606] [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: 11/05/2024] [Revised: 11/20/2024] [Accepted: 11/21/2024] [Indexed: 12/18/2024] Open
Abstract
Depression is one of the most common neurological diseases, which imposes a substantial social and economic burden on modern society. The purpose of this study was to explore the mechanism of total ginsenoside ginseng root (TGGR) in the treatment of depression through a comprehensive strategy combining network pharmacology, transcriptomics, and in vivo experimental validation. The Traditional Chinese Medicine Systematic Pharmacology (TCMSP) database and literature were used to collect the main components and targets of TGGR. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were applied to explore the underlying mechanisms. In addition, the chronic unpredictable mild stress (CUMS)-induced C57BL/6 mouse model was used to evaluate the antidepressant activity of TGGR. The results showed that TGGR improved depression-like behavior in mice and increased the decrease in serum 5-hydroxytryptamine (5-HT) and brain-derived neurotrophic factor (BDNF) levels caused by CUMS. Combined network pharmacology and transcriptomic analysis showed that the AMP-activated kinase (AMPK) signaling pathway mainly enriched the core target. Immunohistochemistry, Western blotting, and reverse transcription quantitative polymerase chain reaction (RT-qPCR) were used to confirm whether TGGR exerts antidepressant effects by regulating this pathway. The results showed that TGGR has a regulatory impact on related proteins in the AMPK pathway, and the regulatory effect of TGGR on proteins was inhibited after the administration of related pathway inhibitors. In summary, total ginsenosides may regulate the AMPK signaling pathway and activate the sirtuin 1 (SIRT1) peroxisome proliferator-activated receptor-gamma coactivator 1-alpha (PGC-1α) pathway to have therapeutic effects on depression.
Collapse
Affiliation(s)
- Weijia Chen
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun 130118, China
- Jilin Provincial Engineering Research Center for Efficient Breeding and Product Development of Sika Deer, Changchun 130118, China
- Key Laboratory of Animal Production and Product Quality and Security, Ministry of Education, Ministry of National Education, Changchun 130118, China
| | - Pengli Guo
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun 130118, China
| | - Lili Su
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun 130118, China
| | - Xiangjuan Guo
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun 130118, China
| | - Meiling Shi
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun 130118, China
| | - Jianan Geng
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun 130118, China
- Jilin Provincial Engineering Research Center for Efficient Breeding and Product Development of Sika Deer, Changchun 130118, China
- Key Laboratory of Animal Production and Product Quality and Security, Ministry of Education, Ministry of National Education, Changchun 130118, China
| | - Ying Zong
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun 130118, China
- Jilin Provincial Engineering Research Center for Efficient Breeding and Product Development of Sika Deer, Changchun 130118, China
- Key Laboratory of Animal Production and Product Quality and Security, Ministry of Education, Ministry of National Education, Changchun 130118, China
| | - Yan Zhao
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun 130118, China
- Jilin Provincial Engineering Research Center for Efficient Breeding and Product Development of Sika Deer, Changchun 130118, China
- Key Laboratory of Animal Production and Product Quality and Security, Ministry of Education, Ministry of National Education, Changchun 130118, China
| | - Rui Du
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun 130118, China
- Jilin Provincial Engineering Research Center for Efficient Breeding and Product Development of Sika Deer, Changchun 130118, China
- Key Laboratory of Animal Production and Product Quality and Security, Ministry of Education, Ministry of National Education, Changchun 130118, China
| | - Zhongmei He
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun 130118, China
- Jilin Provincial Engineering Research Center for Efficient Breeding and Product Development of Sika Deer, Changchun 130118, China
- Key Laboratory of Animal Production and Product Quality and Security, Ministry of Education, Ministry of National Education, Changchun 130118, China
| |
Collapse
|
9
|
Shu X, Gao J, Xu H, Li Q, Gong Y, Li J. The Effects of Dexamethasone on Human Lens Epithelial Cells and the Analysis of Related Pathways with Transcriptome Sequencing. FRONT BIOSCI-LANDMRK 2024; 29:391. [PMID: 39614453 DOI: 10.31083/j.fbl2911391] [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: 08/06/2024] [Revised: 10/16/2024] [Accepted: 10/28/2024] [Indexed: 12/01/2024]
Abstract
BACKGROUND The goal of this study was to investigate the effects of dexamethasone on human lens epithelial cells (HLECs) and the potential mechanisms. METHODS HLECs (HLE-B3) were cultured in vitro to assess the effects of dexamethasone on cell size at different concentrations. Immunofluorescence staining was used to detect specific protein expression in HLE-B3 cells. The cell size was observed using phase-contrast microscopy, and the length and area were quantitatively measured with ImageJ software for statistical analysis. Flow cytometry was used to verify these outcomes. The means of three groups were statistically analyzed using one-way analysis of variance, whereas the means of two groups were statistically analyzed with the parametric Student's t-test. Additionally, high-throughput transcriptome sequencing was performed to compare messenger RNA (mRNA) expression levels between different concentrations of dexamethasone treatment groups and the control group, to identify potential signaling pathways. Subsequently, we performed quantitative Polymerase Chain Reaction (qPCR), immunofluorescence staining, and molecular docking experiments on the key differentially expressed genes. RESULTS Dexamethasone affected the size of HLE-B3 cells. Both 0.25 and 0.5 μmol/L dexamethasone increased cell length and area, exhibiting no significant difference between the two treatment groups. Flow cytometry showed that dexamethasone increased cell size and granularity, with 0.25 μmol/L dexamethasone leading to larger cell areas and higher intracellular granularity. High-throughput transcriptome sequencing revealed significant upregulation of lysophosphatidic acid receptor 1 (LPAR1) and the pathways related to the glucocorticoid (GC) receptor. CONCLUSIONS Certain concentrations of dexamethasone impact the morphology and biological functions of HLECs. As a subtype of G protein-coupled receptors, LPAR1 on the cell membrane may interact with dexamethasone, affecting cell size and inhibiting autophagy via the phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT)/mammalian target of rapamycin (mTOR) pathway. These discoveries offer crucial biological insights into how dexamethasone influences the morphology and function of HLECs and the pathogenesis of GC-induced cataracts, offering potential molecular targets for future therapeutic strategies.
Collapse
Affiliation(s)
- Xinjie Shu
- Department of Ophthalmology, University-Town Hospital of Chongqing Medical University, 401331 Chongqing, China
| | - Jiamin Gao
- Department of Ophthalmology, University-Town Hospital of Chongqing Medical University, 401331 Chongqing, China
- Department of Ophthalmology and Optometry, Chongqing Medical University, 401331 Chongqing, China
| | - Han Xu
- Department of Ophthalmology, University-Town Hospital of Chongqing Medical University, 401331 Chongqing, China
- Department of Ophthalmology and Optometry, Chongqing Medical University, 401331 Chongqing, China
| | - Qiyou Li
- Department of Ophthalmology, Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), 400038 Chongqing, China
| | - Yu Gong
- Department of Ophthalmology, University-Town Hospital of Chongqing Medical University, 401331 Chongqing, China
| | - Jiawen Li
- Department of Ophthalmology, University-Town Hospital of Chongqing Medical University, 401331 Chongqing, China
- Department of Ophthalmology and Optometry, Chongqing Medical University, 401331 Chongqing, China
| |
Collapse
|
10
|
Lacinski RA, Dziadowicz SA, Roth CA, Ma L, Melemai VK, Fitzpatrick B, Chaharbakhshi E, Heim T, Lohse I, Schoedel KE, Hu G, Llosa NJ, Weiss KR, Lindsey BA. Proteomic and transcriptomic analyses identify apo-transcobalamin-II as a biomarker of overall survival in osteosarcoma. Front Oncol 2024; 14:1417459. [PMID: 39493449 PMCID: PMC11527601 DOI: 10.3389/fonc.2024.1417459] [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: 04/15/2024] [Accepted: 09/17/2024] [Indexed: 11/05/2024] Open
Abstract
Background The large-scale proteomic platform known as the SomaScan® assay is capable of simultaneously measuring thousands of proteins in patient specimens through next-generation aptamer-based multiplexed technology. While previous studies have utilized patient peripheral blood to suggest serum biomarkers of prognostic or diagnostic value in osteosarcoma (OSA), the most common primary pediatric bone cancer, they have ultimately been limited in the robustness of their analyses. We propose utilizing this aptamer-based technology to describe the systemic proteomic milieu in patients diagnosed with this disease. Methods To determine novel biomarkers associated with overall survival in OSA, we deployed the SomaLogic SomaScan® 7k assay to investigate the plasma proteomic profile of naive primary, recurrent, and metastatic OSA patients. Following identification of differentially expressed proteins (DEPs) between 2-year deceased and survivor cohorts, publicly available databases including Survival Genie, TIGER, and KM Plotter Immunotherapy, among others, were utilized to investigate the significance of our proteomic findings. Results Apo-transcobalamin-II (APO-TCN2) was identified as the most DEP between 2-year deceased and survivor cohorts (Log2 fold change = 6.8, P-value = 0.0017). Survival analysis using the Survival Genie web-based platform indicated that increased intratumoral TCN2 expression was associated with better overall survival in both OSA (TARGET-OS) and sarcoma (TCGA-SARC) datasets. Cell-cell communication analysis using the TIGER database suggested that TCN2+ Myeloid cells likely interact with marginal zone and immunoglobin-producing B lymphocytes expressing the TCN2 receptor (CD320) to promote their proliferation and survival in both non-small cell lung cancer and melanoma tumors. Analysis of publicly available OSA scRNA-sequencing datasets identified similar populations in naive primary tumors. Furthermore, circulating APO-TCN2 levels in OSA were then associated with a plasma proteomic profile likely necessary for robust B lymphocyte proliferation, infiltration, and formation of intratumoral tertiary lymphoid structures for improved anti-tumor immunity. Conclusions Overall, APO-TCN2, a circulatory protein previously described in various lymphoproliferative disorders, was associated with 2-year survival status in patients diagnosed with OSA. The relevance of this protein and apparent immunological function (anti-tumor B lymphocyte responses) was suggested using publicly available solid tumor RNA-sequencing datasets. Further studies characterizing the biological function of APO-TCN2 and its relevance in these diseases is warranted.
Collapse
Affiliation(s)
- Ryan A. Lacinski
- Department of Orthopaedics, West Virginia University School of Medicine, Morgantown, WV, United States
- West Virginia University Cancer Institute, West Virginia University School of Medicine, Morgantown, WV, United States
| | - Sebastian A. Dziadowicz
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University School of Medicine, Morgantown, WV, United States
- Bioinformatics Core, West Virginia University School of Medicine, Morgantown, WV, United States
| | - Clark A. Roth
- Department of Orthopaedic Surgery, University of Pittsburgh, Pittsburgh, PA, United States
| | - Li Ma
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University School of Medicine, Morgantown, WV, United States
- Bioinformatics Core, West Virginia University School of Medicine, Morgantown, WV, United States
| | - Vincent K. Melemai
- Department of Orthopaedics, West Virginia University School of Medicine, Morgantown, WV, United States
| | - Brody Fitzpatrick
- Department of Orthopaedics, West Virginia University School of Medicine, Morgantown, WV, United States
| | - Edwin Chaharbakhshi
- Department of Orthopaedics, West Virginia University School of Medicine, Morgantown, WV, United States
| | - Tanya Heim
- Department of Orthopaedic Surgery, University of Pittsburgh, Pittsburgh, PA, United States
| | - Ines Lohse
- Department of Orthopaedic Surgery, University of Pittsburgh, Pittsburgh, PA, United States
| | - Karen E. Schoedel
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Gangqing Hu
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University School of Medicine, Morgantown, WV, United States
- Bioinformatics Core, West Virginia University School of Medicine, Morgantown, WV, United States
| | - Nicolas J. Llosa
- Department of Orthopaedic Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Kurt R. Weiss
- Department of Orthopaedic Surgery, University of Pittsburgh, Pittsburgh, PA, United States
| | - Brock A. Lindsey
- Department of Orthopaedic Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| |
Collapse
|
11
|
Kim J, Kang JH, Noh MG, Lee B, Choi YD, Kim OJ, Kim Y. New potential diagnostic markers for verrucous hyperplasia and verrucous carcinoma based on RNA-sequencing data. Mol Cell Probes 2024; 77:101980. [PMID: 39127310 DOI: 10.1016/j.mcp.2024.101980] [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: 05/31/2024] [Revised: 08/08/2024] [Accepted: 08/08/2024] [Indexed: 08/12/2024]
Abstract
Verrucous carcinoma (VC) is a rare subtype of squamous cell carcinoma (SCC) characterized by its histological presentation as a low-grade tumor with no potential for metastasis, setting it apart from invasive SCC. However, distinguishing VC from its benign counterpart, verrucous hyperplasia (VH), is challenging due to their clinical and morphological similarities. Despite the importance of accurate diagnosis for determining treatment strategies, diagnosis of VH and VC relied only on lesion recurrence after resection. To address this challenge, we generated RNA profiling data from tissue samples of VH and VC patients to identify novel diagnostic markers. We analyzed differentially expressed (DE) mRNA and long non-coding RNA (lncRNA) in tissue samples from VH and VC patients. Additionally, ChIP-X Enrichment Analysis 3 (ChEA3) was conducted to identify the top five transcription factors potentially regulating the expression of DE mRNAs in VH and VC. Our analysis of mRNA and lncRNA expression profiles in VH and VC provides insights into the underlying molecular characteristics of these diseases and offers potential new diagnostic markers. The identification of specific DE genes and lncRNAs may enable clinicians to more accurately differentiate between VH and VC, leading to better treatment choices.
Collapse
Affiliation(s)
- Janghyun Kim
- Department of Oral Pathology, School of Dentistry, Chonnam National University, Gwangju, 61186, Republic of Korea; Hard-Tissue Biointerface Research Center, School of Dentistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jee-Hye Kang
- Deparment of Dental Science, Graduate School, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Myung-Giun Noh
- Department of Pathology, School of Medicine, Ajou University, Gyeonggi-do, 16499, Republic of Korea
| | - Bora Lee
- Department of Biochemistry, Chonnam National University Medical School, Jeollanam-do, Hwasun 58128, Republic of Korea
| | - Yoo-Duk Choi
- Department of Pathology, Chonnam National University Medical School, Gwangju, 61469, Republic of Korea
| | - Ok Joon Kim
- Department of Oral Pathology, School of Dentistry, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Young Kim
- Department of Oral Pathology, School of Dentistry, Chonnam National University, Gwangju, 61186, Republic of Korea; Hard-Tissue Biointerface Research Center, School of Dentistry, Chonnam National University, Gwangju 61186, Republic of Korea.
| |
Collapse
|
12
|
Fan Y, Pavani KC, Bogado Pascottini O, Smits K, Van Soom A, Peelman L. Selection and application of small non-coding RNAs for normalizing RT-qPCR data of bovine preimplantation embryo conditioned medium. Theriogenology 2024; 226:87-94. [PMID: 38870583 DOI: 10.1016/j.theriogenology.2024.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/24/2024] [Accepted: 06/07/2024] [Indexed: 06/15/2024]
Abstract
Small non-coding RNAs (sncRNAs) present in the conditioned medium (CM) of bovine preimplantation embryos are potential noninvasive biomarkers for assessing embryo quality. Accurate quantification of sncRNA levels in the spent CM is of utmost importance in this regard. RT-qPCR is considered as the gold standard for quantifying RNA. In order to standardize RT-qPCR data in the sample type under investigation, the use of suitable stable sncRNAs is essential. Here, we selected 10 sncRNAs from small RNA sequencing of CM samples derived from both bovine blastocysts and degenerate embryos, and evaluated their expression stability together with that of cel-miR-39 as a spike and the often-used U6 small nuclear RNA at different embryo developmental stages. In CM of 2-cell embryos, rsRNA-1044 showed the most stable expression, while tDR-1:32-Gly-CCC-1 was the most stable expressed sncRNA in CM of the stages beyond the 2-cell stage. Next, tDR-1:32-Gly-CCC-1 was used for normalizing the RT-qPCR data from the CM of blastocysts and degenerate embryos. Bta-miR-155 and tDR-39:75-Arg-CCG-2 were found to be significantly up-regulated in the CM of blastocysts compared to that of the degenerated embryos (P = 0.028 and P = 0.017, respectively), suggesting their expression levels are related to embryo development stage. In conclusion, tDR-1:32-Gly-CCC-1 can serve as a suitable reference sncRNA for normalization of RT-qPCR data of the CM from bovine blastocysts.
Collapse
Affiliation(s)
- Yuan Fan
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, 9820, Merelbeke, Belgium
| | - Krishna Chaitanya Pavani
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, 9820, Merelbeke, Belgium; Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Osvaldo Bogado Pascottini
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, 9820, Merelbeke, Belgium
| | - Katrien Smits
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, 9820, Merelbeke, Belgium
| | - Ann Van Soom
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, 9820, Merelbeke, Belgium
| | - Luc Peelman
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, 9820, Merelbeke, Belgium.
| |
Collapse
|
13
|
Khaw SC, Martins da Silva S. From Bench to Babies - Drug Development for Male Subfertility. REPRODUCTION AND FERTILITY 2024; 5:RAF-24-0022. [PMID: 39226216 PMCID: PMC11466258 DOI: 10.1530/raf-24-0022] [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: 03/21/2024] [Accepted: 09/03/2024] [Indexed: 09/05/2024] Open
Abstract
Infertility is estimated to affect more than 50 million couples around the world, with male factor accounting for half of these cases, yet there is a notable absence of effective treatment options for men, other than in-vitro fertilisation (IVF) or intracytoplasmic sperm injection (ICSI). This review considers unlicensed and empirical treatments used for male subfertility, including hormonal therapy, phosphodiesterase inhibitors, and antioxidants. Compounds generally demonstrate variable improvements in sperm function but benefits for fertility are less clear. There is a pressing need for effective treatment options for subfertile men, however, our knowledge of sperm function is limited, restricting the identification of precise treatment targets. The traditional drug discovery pathway is also notorious for its extensive resource and time requirements, often extending over decades and demanding significant financial investment. Unfortunately, a substantial number of potential therapies fail before reaching the marketplace. Furthermore, reliance on mammalian models is not possible in the drug development process for male subfertility, due to significant variability between animals and man. We review recent breakthroughs and highlight novel methods aimed at improving the effectiveness and efficiency of drug discovery for male subfertility. High-throughput screening, combinatorial chemistry, and the repurposing of established medications have great potential. These strategies offer the promise of accelerating the pace of drug development, curbing the extensive demand for resources, and, in the case of drug repurposing, diminish the demand for comprehensive pharmacokinetic and pharmacodynamic studies. As these innovative approaches are adopted, the feasibility of addressing male subfertility through scientific advancements appears to be increasingly attainable.
Collapse
Affiliation(s)
- Shen Chuen Khaw
- S Khaw, Reproductive Medicine Research Group, University of Dundee, Dundee, United Kingdom of Great Britain and Northern Ireland
| | - Sarah Martins da Silva
- S Martins da Silva, Reproductive Medicine Research Group, University of Dundee, Dundee, DD1 9SY, United Kingdom of Great Britain and Northern Ireland
| |
Collapse
|
14
|
Haghayegh F, Norouziazad A, Haghani E, Feygin AA, Rahimi RH, Ghavamabadi HA, Sadighbayan D, Madhoun F, Papagelis M, Felfeli T, Salahandish R. Revolutionary Point-of-Care Wearable Diagnostics for Early Disease Detection and Biomarker Discovery through Intelligent Technologies. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400595. [PMID: 38958517 PMCID: PMC11423253 DOI: 10.1002/advs.202400595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 06/19/2024] [Indexed: 07/04/2024]
Abstract
Early-stage disease detection, particularly in Point-Of-Care (POC) wearable formats, assumes pivotal role in advancing healthcare services and precision-medicine. Public benefits of early detection extend beyond cost-effectively promoting healthcare outcomes, to also include reducing the risk of comorbid diseases. Technological advancements enabling POC biomarker recognition empower discovery of new markers for various health conditions. Integration of POC wearables for biomarker detection with intelligent frameworks represents ground-breaking innovations enabling automation of operations, conducting advanced large-scale data analysis, generating predictive models, and facilitating remote and guided clinical decision-making. These advancements substantially alleviate socioeconomic burdens, creating a paradigm shift in diagnostics, and revolutionizing medical assessments and technology development. This review explores critical topics and recent progress in development of 1) POC systems and wearable solutions for early disease detection and physiological monitoring, as well as 2) discussing current trends in adoption of smart technologies within clinical settings and in developing biological assays, and ultimately 3) exploring utilities of POC systems and smart platforms for biomarker discovery. Additionally, the review explores technology translation from research labs to broader applications. It also addresses associated risks, biases, and challenges of widespread Artificial Intelligence (AI) integration in diagnostics systems, while systematically outlining potential prospects, current challenges, and opportunities.
Collapse
Affiliation(s)
- Fatemeh Haghayegh
- Laboratory of Advanced Biotechnologies for Health Assessments (Lab‐HA)Biomedical Engineering ProgramLassonde School of EngineeringYork UniversityTorontoM3J 1P3Canada
- Department of Electrical Engineering and Computer Science (EECS)Lassonde School of EngineeringYork UniversityTorontoONM3J 1P3Canada
| | - Alireza Norouziazad
- Laboratory of Advanced Biotechnologies for Health Assessments (Lab‐HA)Biomedical Engineering ProgramLassonde School of EngineeringYork UniversityTorontoM3J 1P3Canada
- Department of Electrical Engineering and Computer Science (EECS)Lassonde School of EngineeringYork UniversityTorontoONM3J 1P3Canada
| | - Elnaz Haghani
- Laboratory of Advanced Biotechnologies for Health Assessments (Lab‐HA)Biomedical Engineering ProgramLassonde School of EngineeringYork UniversityTorontoM3J 1P3Canada
- Department of Electrical Engineering and Computer Science (EECS)Lassonde School of EngineeringYork UniversityTorontoONM3J 1P3Canada
| | - Ariel Avraham Feygin
- Laboratory of Advanced Biotechnologies for Health Assessments (Lab‐HA)Biomedical Engineering ProgramLassonde School of EngineeringYork UniversityTorontoM3J 1P3Canada
- Department of Electrical Engineering and Computer Science (EECS)Lassonde School of EngineeringYork UniversityTorontoONM3J 1P3Canada
| | - Reza Hamed Rahimi
- Laboratory of Advanced Biotechnologies for Health Assessments (Lab‐HA)Biomedical Engineering ProgramLassonde School of EngineeringYork UniversityTorontoM3J 1P3Canada
- Department of Electrical Engineering and Computer Science (EECS)Lassonde School of EngineeringYork UniversityTorontoONM3J 1P3Canada
| | - Hamidreza Akbari Ghavamabadi
- Laboratory of Advanced Biotechnologies for Health Assessments (Lab‐HA)Biomedical Engineering ProgramLassonde School of EngineeringYork UniversityTorontoM3J 1P3Canada
- Department of Electrical Engineering and Computer Science (EECS)Lassonde School of EngineeringYork UniversityTorontoONM3J 1P3Canada
| | - Deniz Sadighbayan
- Department of BiologyFaculty of ScienceYork UniversityTorontoONM3J 1P3Canada
| | - Faress Madhoun
- Laboratory of Advanced Biotechnologies for Health Assessments (Lab‐HA)Biomedical Engineering ProgramLassonde School of EngineeringYork UniversityTorontoM3J 1P3Canada
- Department of Electrical Engineering and Computer Science (EECS)Lassonde School of EngineeringYork UniversityTorontoONM3J 1P3Canada
| | - Manos Papagelis
- Department of Electrical Engineering and Computer Science (EECS)Lassonde School of EngineeringYork UniversityTorontoONM3J 1P3Canada
| | - Tina Felfeli
- Department of Ophthalmology and Vision SciencesUniversity of TorontoOntarioM5T 3A9Canada
- Institute of Health PolicyManagement and EvaluationUniversity of TorontoOntarioM5T 3M6Canada
| | - Razieh Salahandish
- Laboratory of Advanced Biotechnologies for Health Assessments (Lab‐HA)Biomedical Engineering ProgramLassonde School of EngineeringYork UniversityTorontoM3J 1P3Canada
- Department of Electrical Engineering and Computer Science (EECS)Lassonde School of EngineeringYork UniversityTorontoONM3J 1P3Canada
| |
Collapse
|
15
|
Guo X, Su L, Shi M, Sun L, Chen W, Geng J, Li J, Zong Y, He Z, Du R. Network Pharmacology and Transcriptomics to Explore the Pharmacological Mechanisms of 20(S)-Protopanaxatriol in the Treatment of Depression. Int J Mol Sci 2024; 25:7574. [PMID: 39062817 PMCID: PMC11276827 DOI: 10.3390/ijms25147574] [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: 04/25/2024] [Revised: 06/15/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024] Open
Abstract
Depression is one of the most common psychological disorders nowadays. Studies have shown that 20(S)-protopanaxatriol (PPT) can effectively improve depressive symptoms in mice. However, its mechanism needs to be further explored. In this study, we used an integrated approach combining network pharmacology and transcriptomics to explore the potential mechanisms of PPT for depression. First, the potential targets and pathways of PPT treatment of depression were screened through network pharmacology. Secondly, the BMKCloud platform was used to obtain brain tissue transcription data of chronic unpredictable mild stress (CUMS) model mice and screen PPT-altered differential expression genes (DEGs). Gene ontology (GO) analysis and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed using network pharmacology and transcriptomics. Finally, the above results were verified by molecular docking, Western blotting, and quantitative real-time polymerase chain reaction (qRT-PCR). In this study, we demonstrated that PPT improved depression-like behavior and brain histopathological changes in CUMS mice, downregulated nitric oxide (NO) and interleukin-6 (IL-6) levels, and elevated serum levels of 5-hydroxytryptamine (5-HT) and brain-derived neurotrophic factor (BDNF) after PPT treatment compared to the CUMS group. Eighty-seven potential targets and 350 DEGs were identified by network pharmacology and transcriptomics. Comprehensive analysis showed that transthyretin (TTR), klotho (KL), FOS, and the phosphatidylinositol 3-kinase-protein kinase B (PI3K-AKT) signaling pathway were closely associated with the therapeutic effects of PPT. Molecular docking results showed that PPT had a high affinity for PI3K, AKT, TTR, KL, and FOS targets. Gene and protein level results showed that PPT could increase the expression of PI3K, phosphorylation of PI3K (p-PI3K), AKT, phosphorylation of AKT (p-AKT), TTR, and KL and inhibit the expression level of FOS in the brain tissue of depressed mice. Our data suggest that PPT may achieve the treatment of depression by inhibiting the expression of FOS, enhancing the expression of TTR and KL, and modulating the PI3K-AKT signaling pathway.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Zhongmei He
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun 130118, China; (X.G.); (L.S.); (M.S.); (L.S.); (W.C.); (J.G.); (J.L.); (Y.Z.)
| | - Rui Du
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun 130118, China; (X.G.); (L.S.); (M.S.); (L.S.); (W.C.); (J.G.); (J.L.); (Y.Z.)
| |
Collapse
|
16
|
Wang Y, Yu Z, Cheng M, Hu E, Yan Q, Zheng F, Guo X, Zhang W, Li H, Li Z, Zhu W, Wu Y, Tang T, Li T. Buyang huanwu decoction promotes remyelination via miR-760-3p/GPR17 axis after intracerebral hemorrhage. JOURNAL OF ETHNOPHARMACOLOGY 2024; 328:118126. [PMID: 38556140 DOI: 10.1016/j.jep.2024.118126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/02/2024] [Accepted: 03/27/2024] [Indexed: 04/02/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The repairment of myelin sheaths is crucial for mitigating neurological impairments of intracerebral hemorrhage (ICH). However, the current research on remyelination processes in ICH remains limited. A representative traditional Chinese medicine, Buyang Huanwu decoction (BYHWD), shows a promising therapeutic strategy for ICH treatment. AIM OF THE STUDY To investigate the pro-remyelination effects of BYHWD on ICH and explore the underlying mechanisms. MATERIALS AND METHODS The collagenase-induced mice ICH model was created for investigation. BYHWD's protective effects were assessed by behavioral tests and histological staining. Transmission electron microscopy was used for displaying the structure of myelin sheaths. The remyelination and oligodendrocyte differentiation were evaluated by the expressions of myelin proteolipid protein (PLP), myelin basic protein (MBP), MBP/TAU, Olig2/CC1, and PDGFRα/proliferating cell nuclear antigen (PCNA) through RT-qPCR and immunofluorescence. Transcriptomics integrated with disease database analysis and experiments in vivo and in vitro revealed the microRNA-related underlying mechanisms. RESULTS Here, we reported that BYHWD promoted the neurological function of ICH mice and improved remyelination by increasing PLP, MBP, and TAU, as well as restoring myelin structure. Besides, we showed that BYHWD promoted remyelination by boosting the differentiation of PDGFRα+ oligodendrocyte precursor cells into olig2+/CC1+ oligodendrocytes. Additionally, we demonstrated that the remyelination effects of BYHWD worked by inhibiting G protein-coupled receptor 17 (GPR17). miRNA sequencing integrated with miRNA database prediction screened potential miRNAs targeting GPR17. By applying immunofluorescence, RNA in situ hybridization and dual luciferase reporter gene assay, we confirmed that BYHWD suppressed GPR17 and improved remyelination by increasing miR-760-3p. CONCLUSIONS BYHWD improves remyelination and neurological function in ICH mice by targeting miR-760-3p to inhibit GPR17. This study may shed light on the orchestration of remyelination mechanisms after ICH, thus providing novel insights for developing innovative prescriptions with brain-protective properties.
Collapse
Affiliation(s)
- Yang Wang
- Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, PR China; NATCM Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, PR China; Xiangya Hospital, Central South University, Jiangxi, Nanchang, PR China
| | - Zhe Yu
- Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, PR China; NATCM Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
| | - Menghan Cheng
- Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, PR China; NATCM Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
| | - En Hu
- Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, PR China; NATCM Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, PR China; Xiangya Hospital, Central South University, Jiangxi, Nanchang, PR China
| | - Qiuju Yan
- Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, PR China; NATCM Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
| | - Fei Zheng
- The College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, PR China
| | - Xiaohang Guo
- School of Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, PR China
| | - Wei Zhang
- The College of Integrated Traditional Chinese and Western Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, PR China
| | - Haigang Li
- Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha, Hunan, PR China
| | - Zhilin Li
- Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, PR China; NATCM Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
| | - Wenxin Zhu
- Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, PR China; NATCM Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
| | - Yao Wu
- Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, PR China; NATCM Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
| | - Tao Tang
- Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, PR China; NATCM Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, PR China; Xiangya Hospital, Central South University, Jiangxi, Nanchang, PR China
| | - Teng Li
- Institute of Integrative Medicine, Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, PR China; NATCM Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, PR China; Xiangya Hospital, Central South University, Jiangxi, Nanchang, PR China.
| |
Collapse
|
17
|
Chee CW, Mohd Hashim N, Abdullah I, Nor Rashid N. RNA Sequencing and Bioinformatics Analysis Reveals the Downregulation of DNA Replication Genes by Morindone in Colorectal Cancer Cells. Appl Biochem Biotechnol 2024; 196:3216-3233. [PMID: 37642925 DOI: 10.1007/s12010-023-04690-9] [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] [Accepted: 08/16/2023] [Indexed: 08/31/2023]
Abstract
Morindone, a natural anthraquinone compound, has been reported to have significant pharmacological properties in different cancers. However, its anticancer effects in colorectal cancer (CRC) and the underlying molecular mechanisms remain obscure. In this study, RNA sequencing was used to assess the differentially expressed genes (DEGs) following morindone treatment in two CRC cell lines, HCT116 and HT29 cells. Functional enrichment analysis of overlapping DEGs revealed that negative regulation of cell development from biological processes and the MAPK signalling pathway were the most significant Gene Ontology terms and Kyoto Encyclopaedia of Genes and Genome pathway, respectively. Seven hub genes were identified among the overlapping genes, including MCM5, MCM6, MCM10, GINS2, POLE2, PRIM1, and WDHD1. All hub genes were found downregulated and involved in DNA replication fork. Among these, GINS2 was identified as the most cancer-dependent gene in both cells with better survival outcomes. Validation was performed on seven hub genes with rt-qPCR, and the results were consistent with the RNA sequencing findings. Collectively, this study provides corroboration of the potential therapeutic benefits and suitable pharmacological targets of morindone in the treatment of CRC.
Collapse
Affiliation(s)
- Cheok Wui Chee
- Department of Molecular Medicine, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Najihah Mohd Hashim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
- Centre for Natural Products Research and Drug Discovery, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
- Drug Design and Development Research Group, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Iskandar Abdullah
- Drug Design and Development Research Group, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
- Department of Chemistry, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Nurshamimi Nor Rashid
- Department of Molecular Medicine, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
- Centre for Natural Products Research and Drug Discovery, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
- Drug Design and Development Research Group, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
| |
Collapse
|
18
|
Qiao Z, Teng X, Liu A, Yang W. Novel Isolating Approaches to Circulating Tumor Cell Enrichment Based on Microfluidics: A Review. MICROMACHINES 2024; 15:706. [PMID: 38930676 PMCID: PMC11206030 DOI: 10.3390/mi15060706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/14/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024]
Abstract
Circulating tumor cells (CTCs), derived from the primary tumor and carrying genetic information, contribute significantly to the process of tumor metastasis. The analysis and detection of CTCs can be used to assess the prognosis and treatment response in patients with tumors, as well as to help study the metastatic mechanisms of tumors and the development of new drugs. Since CTCs are very rare in the blood, it is a challenging problem to enrich CTCs efficiently. In this paper, we provide a comprehensive overview of microfluidics-based enrichment devices for CTCs in recent years. We explore in detail the methods of enrichment based on the physical or biological properties of CTCs; among them, physical properties cover factors such as size, density, and dielectric properties, while biological properties are mainly related to tumor-specific markers on the surface of CTCs. In addition, we provide an in-depth description of the methods for enrichment of single CTCs and illustrate the importance of single CTCs for performing tumor analyses. Future research will focus on aspects such as improving the separation efficiency, reducing costs, and increasing the detection sensitivity and accuracy.
Collapse
Affiliation(s)
- Zezheng Qiao
- School of Electromechanical and Automotive Engineering, Yantai University, Yantai 264005, China; (Z.Q.); (X.T.)
| | - Xiangyu Teng
- School of Electromechanical and Automotive Engineering, Yantai University, Yantai 264005, China; (Z.Q.); (X.T.)
| | - Anqin Liu
- School of Mechanical and Electrical Engineering, Yantai Institute of Technology, Yantai 264005, China
| | - Wenguang Yang
- School of Electromechanical and Automotive Engineering, Yantai University, Yantai 264005, China; (Z.Q.); (X.T.)
| |
Collapse
|
19
|
Matsukiyo Y, Yamanaka C, Yamanishi Y. De Novo Generation of Chemical Structures of Inhibitor and Activator Candidates for Therapeutic Target Proteins by a Transformer-Based Variational Autoencoder and Bayesian Optimization. J Chem Inf Model 2024; 64:2345-2355. [PMID: 37768595 DOI: 10.1021/acs.jcim.3c00824] [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: 09/29/2023]
Abstract
Deep generative models for molecular generation have been gaining much attention as structure generators to accelerate drug discovery. However, most previously developed methods are chemistry-centric approaches, and comprehensive biological responses in the cell have not been taken into account. In this study, we propose a novel computational method, TRIOMPHE-BOA (transcriptome-based inference and generation of molecules with desired phenotypes using the Bayesian optimization algorithm), to generate new chemical structures of inhibitor or activator candidates for therapeutic target proteins by integrating chemically and genetically perturbed transcriptome profiles. In the algorithm, the substructures of multiple molecules that were selected based on the transcriptome analysis are fused in the design of new chemical structures by exploring the latent space of a Transformer-based variational autoencoder using Bayesian optimization. Our results demonstrate the usefulness of the proposed method in terms of having high reproducibility of existing ligands for 10 therapeutic target proteins when compared with previous methods. Moreover, this method can be applied to proteins without detailed 3D structures or known ligands and is expected to become a powerful tool for more efficient hit identification.
Collapse
Affiliation(s)
- Yuki Matsukiyo
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
| | - Chikashige Yamanaka
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
| | - Yoshihiro Yamanishi
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
- Graduate School of Informatics, Nagoya University, Chikusa, Nagoya, Aichi 464-8601, Japan
| |
Collapse
|
20
|
Mohammadi E, Dashti S, Shafizade N, Jin H, Zhang C, Lam S, Tahmoorespur M, Mardinoglu A, Sekhavati MH. Drug repositioning for immunotherapy in breast cancer using single-cell analysis. NPJ Syst Biol Appl 2024; 10:37. [PMID: 38589404 PMCID: PMC11001976 DOI: 10.1038/s41540-024-00359-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/13/2024] [Indexed: 04/10/2024] Open
Abstract
Immunomodulatory peptides, while exhibiting potential antimicrobial, antifungal, and/or antiviral properties, can play a role in stimulating or suppressing the immune system, especially in pathological conditions like breast cancer (BC). Thus, deregulation of these peptides may serve as an immunotherapeutic strategy to enhance the immune response. In this meta-analysis, we utilized single-cell RNA sequencing data and known therapeutic peptides to investigate the deregulation of these peptides in malignant versus normal human breast epithelial cells. We corroborated our findings at the chromatin level using ATAC-seq. Additionally, we assessed the protein levels in various BC cell lines. Moreover, our in-house drug repositioning approach was employed to identify potential drugs that could positively impact the relapse-free survival of BC patients. Considering significantly deregulated therapeutic peptides and their role in BC pathology, our approach aims to downregulate B2M and SLPI, while upregulating PIGR, DEFB1, LTF, CLU, S100A7, and SCGB2A1 in BC epithelial cells through our drug repositioning pipeline. Leveraging the LINCS L1000 database, we propose BRD-A06641369 for B2M downregulation and ST-4070043 and BRD-K97926541 for SLPI downregulation without negatively affecting the MHC complex as a significantly correlated pathway with these two genes. Furthermore, we have compiled a comprehensive list of drugs for the upregulation of other selected immunomodulatory peptides. Employing an immunotherapeutic approach by integrating our drug repositioning pipeline with single-cell analysis, we proposed potential drugs and drug targets to fortify the immune system against BC.
Collapse
Affiliation(s)
- Elyas Mohammadi
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden.
- Department of Animal Science, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Samira Dashti
- Department of Internal Medicine, Mashhad University of Medical Science, Mashhad, Iran
| | - Neda Shafizade
- Department of Internal Medicine, Mashhad University of Medical Science, Mashhad, Iran
| | - Han Jin
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Cheng Zhang
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Simon Lam
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | - Adil Mardinoglu
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK
| | | |
Collapse
|
21
|
Li P, Jiang Z, Liu T, Liu X, Qiao H, Yao X. Improving drug response prediction via integrating gene relationships with deep learning. Brief Bioinform 2024; 25:bbae153. [PMID: 38600666 PMCID: PMC11006795 DOI: 10.1093/bib/bbae153] [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: 12/26/2023] [Revised: 03/05/2024] [Accepted: 03/18/2024] [Indexed: 04/12/2024] Open
Abstract
Predicting the drug response of cancer cell lines is crucial for advancing personalized cancer treatment, yet remains challenging due to tumor heterogeneity and individual diversity. In this study, we present a deep learning-based framework named Deep neural network Integrating Prior Knowledge (DIPK) (DIPK), which adopts self-supervised techniques to integrate multiple valuable information, including gene interaction relationships, gene expression profiles and molecular topologies, to enhance prediction accuracy and robustness. We demonstrated the superior performance of DIPK compared to existing methods on both known and novel cells and drugs, underscoring the importance of gene interaction relationships in drug response prediction. In addition, DIPK extends its applicability to single-cell RNA sequencing data, showcasing its capability for single-cell-level response prediction and cell identification. Further, we assess the applicability of DIPK on clinical data. DIPK accurately predicted a higher response to paclitaxel in the pathological complete response (pCR) group compared to the residual disease group, affirming the better response of the pCR group to the chemotherapy compound. We believe that the integration of DIPK into clinical decision-making processes has the potential to enhance individualized treatment strategies for cancer patients.
Collapse
Affiliation(s)
- Pengyong Li
- School of Computer Science and Technology,Xidian University, 710126 Xi’an, Shaanxi, China
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, 519020 Macau, China
| | - Zhengxiang Jiang
- School of Electronic Engineering, Xidian University, 710126 Xi’an, Shaanxi, China
| | - Tianxiao Liu
- School of Computer Science and Technology,Xidian University, 710126 Xi’an, Shaanxi, China
| | - Xinyu Liu
- Beijing Laboratory of Biomedical Materials, Department of Geriatric Dentistry, Peking University School and Hospital of Stomatology, 100081 Beijing, China
| | - Hui Qiao
- Department of Oncology, Tai’an Municipal Hospital, 271021 Tai’an, Shandong, China
| | - Xiaojun Yao
- Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, 999078 Macao, China
| |
Collapse
|
22
|
Liu T, Xu C, Guo J, He Z, Zhang Y, Feng Y. Whole Blood Transcriptome Analysis in Patients with Trigeminal Neuralgia: a Prospective Clinical Study. J Mol Neurosci 2024; 74:16. [PMID: 38300339 DOI: 10.1007/s12031-024-02195-6] [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: 11/11/2023] [Accepted: 01/28/2024] [Indexed: 02/02/2024]
Abstract
Trigeminal neuralgia (TN) brings a huge burden to patients, without long-term effective treatment. This study aimed to explore the differentially expressed genes (DEGs) and related enrichment pathways in patients with TN. This was a study of transcriptome sequencing and bioinformatics analysis of human samples. Whole blood samples were collected from the TN patients and pain-free controls. RNA was extracted to conduct the RNA-sequencing and the subsequent bioinformatics analysis. DEGs between the two groups were derived. Kyoto encyclopedia of genes and genomes (KEGG) and Gene ontology (GO) was used to find the enrichment pathways of DEGs. Protein protein interaction (PPI) network was used to depict the interaction between DEGs and find the most important gene, hub gene. Compared with the control group, there were 117 up-regulated DEGs and 103 down-regulated DEGs in the whole blood of patients in the TN group. Pathway enrichment analysis showed that DEGs were mainly enriched in the neuroimmune and metabolic pathways. The PPI network demonstrated that colony stimulating factor 2 (CSF2) was the most important hub gene in the whole blood of TN patients. This study shows the expression of the transcriptome in the whole blood samples of TN patients. The neuroimmune responses and key hub gene CSF2 in the whole blood cells play a vital role in the occurrence of TN. Our research provides a theoretical basis for the diagnosis and treatments of TN. This study was registered at clinicaltrials.gov in June 2021 (No. NCT04923399).
Collapse
Affiliation(s)
- Tianyu Liu
- Department of Anesthesiology, Peking University People's Hospital, Xizhimen South Street 11, Beijing, 100044, China
| | - Chao Xu
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jiaqi Guo
- Shanghai Minhang Center for Disease Control and Prevention, Shanghai, China
| | - Zile He
- Department of Anesthesiology, Peking University People's Hospital, Xizhimen South Street 11, Beijing, 100044, China
| | - Yunpeng Zhang
- Department of Anesthesiology, Peking University People's Hospital, Xizhimen South Street 11, Beijing, 100044, China
| | - Yi Feng
- Department of Anesthesiology, Peking University People's Hospital, Xizhimen South Street 11, Beijing, 100044, China.
- Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Xueyuan road 38, Beijing, 100191, China.
| |
Collapse
|
23
|
Cheng M, Li T, Hu E, Yan Q, Li H, Wang Y, Luo J, Tang T. A novel strategy of integrating network pharmacology and transcriptome reveals antiapoptotic mechanisms of Buyang Huanwu Decoction in treating intracerebral hemorrhage. JOURNAL OF ETHNOPHARMACOLOGY 2024; 319:117123. [PMID: 37673200 DOI: 10.1016/j.jep.2023.117123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 09/08/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Buyang Huanwu Decoction (BYHWD), as a traditional Chinese medical prescription, has been used to treat intracerebral hemorrhage (ICH) for hundreds of years, but the antiapoptotic properties have not yet been studied. AIM OF THE STUDY This study aims to elucidate the antiapoptotic mechanism of BYHWD in ICH. MATERIALS AND METHODS The therapeutic effect of BYHWD on ICH was assessed by modified neurological severity scores (mNSS), foot fault, and histopathological staining. Then, we used a modified comprehensive strategy by integrating transcriptome and network pharmacology to reveal the underlying mechanism. TUNEL assay, qRT-PCR, and western blot were further applied to evaluate the antiapoptotic effect of BYHWD on ICH. Dual-luciferase reporter assay and plasmid transfections were implemented to validate the potential competing endogenous RNAs (ceRNA) mechanism of Sh2b3. RESULTS Network pharmacology analysis indicated that the regulation of the apoptotic process was the highest enriched GO term, and that MAP kinase activity, ERK1, and ERK2 cascade were strongly correlated. Transcriptome analysis screened 180 differentially expressed mRNAs, which were highly enriched in the immune system process and negative regulation of programmed cell death. By checking the literature, we found that Sh2b3 was of great importance to apoptosis by modulating MAPK cascades. TUNEL assay validated the anti-apoptotic effect of BYHWD. Moreover, BYHWD was proven to regulate the Sh2b3-mediated ERK1/2 signaling pathway in ICH mice by qRT-PCR and western blot. We further explored the lncRNA-miRNA-mRNA network underlying the therapeutic effect, among which 4933404O12Rik/miR-185-5p is the upstream regulatory mechanism of Sh2b3. CONCLUSIONS We explored the antiapoptotic mechanism of BYHWD in treating ICH by a novel integrated strategy, which involved the 4933404O12Rik/miR-185-5p/Sh2b3 ceRNAs axis.
Collapse
Affiliation(s)
- Menghan Cheng
- Institute of Integrative Chinese Medicine, Department of Integrated Chinese Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China; NATCM Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China; Hunan Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China
| | - Teng Li
- Institute of Integrative Chinese Medicine, Department of Integrated Chinese Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China; Department of Neurology of Integrated Chinese Medicine, Xiangya Jiangxi Hospital, Central South University, Nanchang, 330006, PR China; NATCM Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China; Hunan Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China
| | - En Hu
- Institute of Integrative Chinese Medicine, Department of Integrated Chinese Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China; Department of Neurology of Integrated Chinese Medicine, Xiangya Jiangxi Hospital, Central South University, Nanchang, 330006, PR China; NATCM Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China; Hunan Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China
| | - Qiuju Yan
- Institute of Integrative Chinese Medicine, Department of Integrated Chinese Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China; NATCM Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China; Hunan Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China
| | - Haigang Li
- Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha, Hunan, 410219, PR China
| | - Yang Wang
- Institute of Integrative Chinese Medicine, Department of Integrated Chinese Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China; Department of Neurology of Integrated Chinese Medicine, Xiangya Jiangxi Hospital, Central South University, Nanchang, 330006, PR China; NATCM Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China; Hunan Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China
| | - Jiekun Luo
- Institute of Integrative Chinese Medicine, Department of Integrated Chinese Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China; Department of Neurology of Integrated Chinese Medicine, Xiangya Jiangxi Hospital, Central South University, Nanchang, 330006, PR China; NATCM Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China; Hunan Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China
| | - Tao Tang
- Institute of Integrative Chinese Medicine, Department of Integrated Chinese Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China; Department of Neurology of Integrated Chinese Medicine, Xiangya Jiangxi Hospital, Central South University, Nanchang, 330006, PR China; NATCM Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China; Hunan Key Laboratory of TCM Gan, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China.
| |
Collapse
|
24
|
Hou D, Lin H, Feng Y, Zhou K, Li X, Yang Y, Wang S, Yang X, Wang J, Zhao H, Zhang X, Fan J, Lu S, Wang D, Zhu L, Ju D, Chen YZ, Zeng X. CMAUP database update 2024: extended functional and association information of useful plants for biomedical research. Nucleic Acids Res 2024; 52:D1508-D1518. [PMID: 37897343 PMCID: PMC10767869 DOI: 10.1093/nar/gkad921] [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: 09/05/2023] [Revised: 09/23/2023] [Accepted: 10/10/2023] [Indexed: 10/30/2023] Open
Abstract
Knowledge of the collective activities of individual plants together with the derived clinical effects and targeted disease associations is useful for plant-based biomedical research. To provide the information in complement to the established databases, we introduced a major update of CMAUP database, previously featured in NAR. This update includes (i) human transcriptomic changes overlapping with 1152 targets of 5765 individual plants, covering 74 diseases from 20 027 patient samples; (ii) clinical information for 185 individual plants in 691 clinical trials; (iii) drug development information for 4694 drug-producing plants with metabolites developed into approved or clinical trial drugs; (iv) plant and human disease associations (428 737 associations by target, 220 935 reversion of transcriptomic changes, 764 and 154121 associations by clinical trials of individual plants and plant ingredients); (v) the location of individual plants in the phylogenetic tree for navigating taxonomic neighbors, (vi) DNA barcodes of 3949 plants, (vii) predicted human oral bioavailability of plant ingredients by the established SwissADME and HobPre algorithm, (viii) 21-107% increase of CMAUP data over the previous version to cover 60 222 chemical ingredients, 7865 plants, 758 targets, 1399 diseases, 238 KEGG human pathways, 3013 gene ontologies and 1203 disease ontologies. CMAUP update version is freely accessible at https://bidd.group/CMAUP/index.html.
Collapse
Affiliation(s)
- Dongyue Hou
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Hanbo Lin
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Yuhan Feng
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Kaicheng Zhou
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Xingxiu Li
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Yuan Yang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Shuaiqi Wang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Xue Yang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Jiayu Wang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Hui Zhao
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Xuyao Zhang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Jiajun Fan
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - SongLin Lu
- The State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Dan Wang
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China
| | - Lyuhan Zhu
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China
| | - Dianwen Ju
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| | - Yu Zong Chen
- The State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China
- Shenzhen Bay Laboratory, Shenzhen 518000, China
| | - Xian Zeng
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai 201203, China
| |
Collapse
|
25
|
Nazli A, Qiu J, Tang Z, He Y. Recent Advances and Techniques for Identifying Novel Antibacterial Targets. Curr Med Chem 2024; 31:464-501. [PMID: 36734893 DOI: 10.2174/0929867330666230123143458] [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: 05/24/2022] [Revised: 10/30/2022] [Accepted: 11/11/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND With the emergence of drug-resistant bacteria, the development of new antibiotics is urgently required. Target-based drug discovery is the most frequently employed approach for the drug development process. However, traditional drug target identification techniques are costly and time-consuming. As research continues, innovative approaches for antibacterial target identification have been developed which enabled us to discover drug targets more easily and quickly. METHODS In this review, methods for finding drug targets from omics databases have been discussed in detail including principles, procedures, advantages, and potential limitations. The role of phage-driven and bacterial cytological profiling approaches is also discussed. Moreover, current article demonstrates the advancements being made in the establishment of computational tools, machine learning algorithms, and databases for antibacterial target identification. RESULTS Bacterial drug targets successfully identified by employing these aforementioned techniques are described as well. CONCLUSION The goal of this review is to attract the interest of synthetic chemists, biologists, and computational researchers to discuss and improve these methods for easier and quicker development of new drugs.
Collapse
Affiliation(s)
- Adila Nazli
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Jingyi Qiu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 266 Fangzheng Avenue, Chongqing, 400714, P. R. China
| | - Ziyi Tang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 266 Fangzheng Avenue, Chongqing, 400714, P. R. China
| | - Yun He
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| |
Collapse
|
26
|
Zhu A, Liu Y, Liu Y. Identification of key genes and regulatory mechanisms in adult degenerative scoliosis. J Clin Neurosci 2024; 119:170-179. [PMID: 38103507 DOI: 10.1016/j.jocn.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 12/19/2023]
Abstract
BACKGROUND Adult degenerative scoliosis (ADS) is a spinal disorder, but its pathogenesis remain unclear. Therefore, in this study, we utilized data from the GEO database and explored the key genes and regulatory mechanisms involved in ADS. METHODS We performed bioinformatics analysis on the GSE209825 dataset of GEO database. Weighted gene co-expression network analysis (WGCNA) was used to identify ADS-related gene modules, and we performed gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. We constructed a protein-protein interaction (PPI) network using the STRING database. We validated the specificity of hub genes in ADS using the GSE34095 dataset and plotted ROC curves for the identification of different degenerative spinal diseases based on the hub genes expression RESULTS: We identified 113 differentially expressed lncRNAs. WGCNA identified the MEblack module had the strongest correlation to ADS. GO and KEGG analyses of target genes in lncRNAs revealed their involvement in immune responses, inflammation, cellular processes, and metabolic pathways. Through PPI and ROC analysis, 10 hub genes linked to ADS diseases with certain specificity were found: ELANE, LTF, DEFA1B, SLC2A4, DEFA1, FAXDC2, LCN2, CTSB, FDFT1, and AURKA. CONCLUSIONS We identified 10 potential hub genes associated with ADS and constructed a transcription factors (TFs)-lncRNAs-hub genes regulatory network. These findings provide a new direction and research basis for the targeted treatment and mechanism research of ADS.
Collapse
Affiliation(s)
- Aoran Zhu
- Department of Spinal Surgery, The First Hospital of Jilin University, Changchun 130021, China
| | - Ying Liu
- Department of Spinal Surgery, The First Hospital of Jilin University, Changchun 130021, China
| | - Yan Liu
- Department of Spinal Surgery, The First Hospital of Jilin University, Changchun 130021, China.
| |
Collapse
|
27
|
Vasilopoulos SN, Güner H, Uça Apaydın M, Pavlopoulou A, Georgakilas AG. Dual Targeting of DNA Damage Response Proteins Implicated in Cancer Radioresistance. Genes (Basel) 2023; 14:2227. [PMID: 38137049 PMCID: PMC10742610 DOI: 10.3390/genes14122227] [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: 11/26/2023] [Revised: 12/13/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Ionizing radiation can induce different types of DNA lesions, leading to genomic instability and ultimately cell death. Radiation therapy or radiotherapy, a major modality in cancer treatment, harnesses the genotoxic potential of radiation to target and destroy cancer cells. Nevertheless, cancer cells have the capacity to develop resistance to radiation treatment (radioresistance), which poses a major obstacle in the effective management of cancer. It has been shown that administration of platinum-based drugs to cancer patients can increase tumor radiosensitivity, but despite this, it is associated with severe adverse effects. Several lines of evidence support that activation of the DNA damage response and repair machinery in the irradiated cancer cells enhances radioresistance and cellular survival through the efficient repair of DNA lesions. Therefore, targeting of key DNA damage repair factors would render cancer cells vulnerable to the irradiation effects, increase cancer cell killing, and reduce the risk of side effects on healthy tissue. Herein, we have employed a computer-aided drug design approach for generating ab initio a chemical compound with drug-like properties potentially targeting two proteins implicated in multiple DNA repair pathways. The findings of this study could be taken into consideration in clinical decision-making in terms of co-administering radiation with DNA damage repair factor-based drugs.
Collapse
Affiliation(s)
- Spyridon N. Vasilopoulos
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Zografou Campus, 15780 Athens, Greece;
- Department of Science and Mathematics, Deree-The American College of Greece, 6 Gravias Street, 15342 Athens, Greece
| | - Hüseyin Güner
- Izmir Biomedicine and Genome Center (IBG), 35340 Izmir, Turkey; (H.G.); (M.U.A.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, 35340 Izmir, Turkey
- Department of Molecular Biology and Genetics, Faculty of Life and Natural Science, Abdullah Gül University, 38080 Kayseri, Turkey
| | - Merve Uça Apaydın
- Izmir Biomedicine and Genome Center (IBG), 35340 Izmir, Turkey; (H.G.); (M.U.A.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, 35340 Izmir, Turkey
| | - Athanasia Pavlopoulou
- Izmir Biomedicine and Genome Center (IBG), 35340 Izmir, Turkey; (H.G.); (M.U.A.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, 35340 Izmir, Turkey
| | - Alexandros G. Georgakilas
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Zografou Campus, 15780 Athens, Greece;
| |
Collapse
|
28
|
Lin K, Deng T, Qu H, Ou H, Huang Q, Gao B, Li X, Wei N. Gastric protective effect of Alpinia officinarum flavonoids: mediating TLR4/NF-κB and TRPV1 signalling pathways and gastric mucosal healing. PHARMACEUTICAL BIOLOGY 2023; 61:50-60. [PMID: 36541204 PMCID: PMC9788718 DOI: 10.1080/13880209.2022.2152058] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/03/2022] [Accepted: 11/19/2022] [Indexed: 06/17/2023]
Abstract
CONTEXT Our previous studies have found that total flavonoid of Alpinia officinarum Hance (Zingiberaceae) (F.AOH) had protective effects on gastric ulcer (GU). OBJECTIVE To investigate the protective mechanism of F.AOH on acetic acid-induced chronic GUs in rats and ethanol-induced GES-1 cells damage. MATERIALS AND METHODS In vivo: Gastric damage was induced in SD rats by administering acetic acid after oral treatment with F-AOH at 54, 27 and 13.5 mg/kg (2 weeks of continuous gavage). After a comprehensive evaluation of rats' serum and gastric tissue-related indicators, gene transcriptome sequencing, qPCR and Western blotting were used to investigate the mechanism further. In vivo: GES-1 cells were incubated with F-AOH (8, 4 and 2 μg/mL) for 16 h and treated with 7% ethanol for 4 h. Transwell and flow cytometry were employed to detect migration and apoptosis of cells. RESULTS F.AOH effectively reduced the area of GUs in rats (from 11.2 ± 1.89 to 2.19 ± 0.95), reversing ethanol-induced cells apoptosis (from 23 ± 1.3 to 8.11 ± 0.93%). It also inhibited the expression of endothelin-1 (ET-1) and iNOS proteins, decreasing the levels of TNF-α IL-6 in serum, improving oxidative stress levels and increasing the expression of Bcl-2/Bax dimer genes. In addition, 4005 differentially expressed genes between the acetic acid model and the drug groups. Through experimental verification, F.AOH can inhibit the activation of TLR4/NF-κB signalling pathway and TRPV1 receptor. CONCLUSIONS F.AOH, as an effective gastric protective plant component, had potential therapeutic value in anti-inflammatory pain and antioxidative stress gastrointestinal diseases.
Collapse
Affiliation(s)
- Kaiwen Lin
- School of Pharmacy, Hainan Medical University, Haikou, China
- Hainan Women and Children’s Medical Center, Haikou, China
| | - Tang Deng
- School of Pharmacy, Hainan Medical University, Haikou, China
- First Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Huijuan Qu
- School of Pharmacy, Hainan Medical University, Haikou, China
| | - Hongya Ou
- School of Pharmacy, Hainan Medical University, Haikou, China
| | - Qifeng Huang
- School of Pharmacy, Hainan Medical University, Haikou, China
- First Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Bingmiao Gao
- School of Pharmacy, Hainan Medical University, Haikou, China
| | - Xiaoliang Li
- School of Pharmacy, Hainan Medical University, Haikou, China
| | - Na Wei
- School of Pharmacy, Hainan Medical University, Haikou, China
| |
Collapse
|
29
|
Atay S. A 15-Gene-Based Risk Signature for Predicting Overall Survival in SCLC Patients Who Have Undergone Surgical Resection. Cancers (Basel) 2023; 15:5219. [PMID: 37958393 PMCID: PMC10649828 DOI: 10.3390/cancers15215219] [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: 09/28/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
Small cell lung cancer (SCLC) is a malignancy with a poor prognosis whose treatment has not progressed for decades. The survival benefit of surgery and the selection of surgical candidates are still controversial in SCLC. This study is the first report to identify transcriptomic alterations associated with prognosis and propose a gene expression-based risk signature that can be used to predict overall survival (OS) in SCLC patients who have undergone potentially curative surgery. An integrative transcriptome analysis of three gene expression datasets (GSE30219, GSE43346, and GSE149507) revealed 1734 up-regulated and 2907 down-regulated genes. Cox-Mantel test, Cox regression, and Lasso regression analyses were used to identify genes to be included in the risk signature. EGAD00001001244 and GSE60052-cohorts were used for internal and external validation, respectively. Overall survival was significantly poorer in patients with high-risk scores compared to the low-risk group. The discriminatory performance of the risk signature was superior to other parameters. Multivariate analysis showed that the risk signature has the potential to be an independent predictor of prognosis. The prognostic genes were enriched in pathways including regulation of transcription, cell cycle, cell metabolism, and angiogenesis. Determining the roles of the identified prognostic genes in the pathogenesis of SCLC may contribute to the development of new treatment strategies. The risk signature needs to be validated in a larger cohort of patients to test its usefulness in clinical decision-making.
Collapse
Affiliation(s)
- Sevcan Atay
- Department of Medical Biochemistry, Faculty of Medicine, Ege University, 35100 Izmir, Turkey
| |
Collapse
|
30
|
Liu J, Wu R, Yuan S, Kelleher R, Chen S, Chen R, Zhang T, Obaidi I, Sheridan H. Pharmacogenomic Analysis of Combined Therapies against Glioblastoma Based on Cell Markers from Single-Cell Sequencing. Pharmaceuticals (Basel) 2023; 16:1533. [PMID: 38004399 PMCID: PMC10675611 DOI: 10.3390/ph16111533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 10/01/2023] [Accepted: 10/19/2023] [Indexed: 11/26/2023] Open
Abstract
Glioblastoma is the most common and aggressive form of primary brain cancer and the lack of viable treatment options has created an urgency to develop novel treatments. Personalized or predictive medicine is still in its infancy stage at present. This research aimed to discover biomarkers to inform disease progression and to develop personalized prophylactic and therapeutic strategies by combining state-of-the-art technologies such as single-cell RNA sequencing, systems pharmacology, and a polypharmacological approach. As predicted in the pyroptosis-related gene (PRG) transcription factor (TF) microRNA (miRNA) regulatory network, TP53 was the hub gene in the pyroptosis process in glioblastoma (GBM). A LASSO Cox regression model of pyroptosis-related genes was built to accurately and conveniently predict the one-, two-, and three-year overall survival rates of GBM patients. The top-scoring five natural compounds were parthenolide, rutin, baeomycesic acid, luteolin, and kaempferol, which have NFKB inhibition, antioxidant, lipoxygenase inhibition, glucosidase inhibition, and estrogen receptor agonism properties, respectively. In contrast, the analysis of the cell-type-specific differential expression-related targets of natural compounds showed that the top five subtype cells targeted by natural compounds were endothelial cells, microglia/macrophages, oligodendrocytes, dendritic cells, and neutrophil cells. The current approach-using the pharmacogenomic analysis of combined therapies-serves as a model for novel personalized therapeutic strategies for GBM treatment.
Collapse
Affiliation(s)
- Junying Liu
- NatPro Center, School of Pharmacy and Pharmaceutical Sciences, Trinity College Dublin, D02 PN40 Dublin, Ireland; (T.Z.); (I.O.); (H.S.)
| | - Ruixin Wu
- Preclinical Department, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, No. 274, Zhijiang Road, Jing’an District, Shanghai 200071, China;
| | - Shouli Yuan
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China;
| | - Robbie Kelleher
- School of Medicine, Trinity College Dublin, D02 PN40 Dublin, Ireland;
| | - Siying Chen
- The Second Affiliated Hospital, Nanchang University, Nanchang 330031, China;
| | - Rongfeng Chen
- National Center for Occupational Safety and Health, NHC, Beijing 102308, China;
| | - Tao Zhang
- NatPro Center, School of Pharmacy and Pharmaceutical Sciences, Trinity College Dublin, D02 PN40 Dublin, Ireland; (T.Z.); (I.O.); (H.S.)
- School of Food Science & Environmental Health, Technological University Dublin, D07 EWV4 Dublin, Ireland
| | - Ismael Obaidi
- NatPro Center, School of Pharmacy and Pharmaceutical Sciences, Trinity College Dublin, D02 PN40 Dublin, Ireland; (T.Z.); (I.O.); (H.S.)
| | - Helen Sheridan
- NatPro Center, School of Pharmacy and Pharmaceutical Sciences, Trinity College Dublin, D02 PN40 Dublin, Ireland; (T.Z.); (I.O.); (H.S.)
| |
Collapse
|
31
|
Wang Y, Diao S, Li H, Ye L, Suo Y, Zheng Y, Sun P, Han W, Fu J. Comparative Metabolomic and Transcriptomic Analyses Reveal Distinct Ascorbic Acid (AsA) Accumulation Patterns between PCA and PCNA Persimmon Developing Fruit. Int J Mol Sci 2023; 24:15362. [PMID: 37895041 PMCID: PMC10607040 DOI: 10.3390/ijms242015362] [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: 07/21/2023] [Revised: 10/07/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
Persimmon fruit has a high nutritional value and significantly varies between pollination-constant astringent (PCA) and pollination-constant non-astringent (PCNA) persimmons. The astringency type affects sugar, flavonoids, and tannin accumulation and is well known in persimmon fruit. However, the impact of the fruit astringency type on ascorbic acid (AsA) accumulation is limited. In this study, typical PCA varieties ('Huojing' and 'Zhongshi5') and PCNA varieties ('Yohou' and 'Jiro') of persimmon fruit were sampled at four developing stages (S1-S4) to provide valuable information on AsA content variation in PCA and PCNA persimmon. Persimmon fruit is rich in ascorbic acid; the AsA content of the four varieties 'Zhongshi5', 'Huojing', 'Jiro', and 'Youhou' mature fruit reached 104.49, 48.69, 69.69, and 47.48 mg/100 g. Fruit of the same astringency type persimmon showed a similar AsA accumulation pattern. AsA content was significantly higher in PCA than PCNA fruit at S1-S3. The initial KEGG analysis of metabolites showed that galactose metabolism is the major biosynthetic pathway of AsA in persimmon fruit. There were significant differences in galactose pathway-related metabolite content in developing PCA and PCNA fruit, such as Lactose, D-Tagatose, and D-Sorbitol content in PCA being higher than that of PCNA. Combined gene expression and WGCNA analyses showed that the expression of the GME (evm.TU.contig4144.37) gene was higher in PCA-type than in PCNA-type fruit in S1-S3 and exhibited the highest correlation with AsA content (r = 690 **, p < 0.01). Four hub genes, including the DNA methylation gene, methyltransferase gene, F-box, and Actin-like Protein, were identified as potential regulators of the GME gene. These results provide basic information on how astringency types affect AsA accumulation and will provide valuable information for further investigation on AsA content variation in persimmon fruit.
Collapse
Affiliation(s)
- Yiru Wang
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.W.); (S.D.); (H.L.); (L.Y.); (Y.S.); (Y.Z.); (P.S.)
| | - Songfeng Diao
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.W.); (S.D.); (H.L.); (L.Y.); (Y.S.); (Y.Z.); (P.S.)
| | - Huawei Li
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.W.); (S.D.); (H.L.); (L.Y.); (Y.S.); (Y.Z.); (P.S.)
| | - Lingshuai Ye
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.W.); (S.D.); (H.L.); (L.Y.); (Y.S.); (Y.Z.); (P.S.)
- Research Institute of Fast-Growing Trees, Chinese Academy of Forestry, Zhanjiang 524022, China
| | - Yujing Suo
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.W.); (S.D.); (H.L.); (L.Y.); (Y.S.); (Y.Z.); (P.S.)
| | - Yanhao Zheng
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.W.); (S.D.); (H.L.); (L.Y.); (Y.S.); (Y.Z.); (P.S.)
| | - Peng Sun
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.W.); (S.D.); (H.L.); (L.Y.); (Y.S.); (Y.Z.); (P.S.)
| | - Weijuan Han
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.W.); (S.D.); (H.L.); (L.Y.); (Y.S.); (Y.Z.); (P.S.)
| | - Jianmin Fu
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.W.); (S.D.); (H.L.); (L.Y.); (Y.S.); (Y.Z.); (P.S.)
| |
Collapse
|
32
|
Corbett J, Young JS, Tipton MJ, Costello JT, Williams TB, Walker EF, Lee BJ, Stevens CE. Molecular biomarkers for assessing the heat-adapted phenotype: a narrative scoping review. J Physiol Sci 2023; 73:26. [PMID: 37848829 DOI: 10.1186/s12576-023-00882-4] [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: 06/13/2023] [Accepted: 10/03/2023] [Indexed: 10/19/2023]
Abstract
Heat acclimation/acclimatisation (HA) mitigates heat-related decrements in physical capacity and heat-illness risk and is a widely advocated countermeasure for individuals operating in hot environments. The efficacy of HA is typically quantified by assessing the thermo-physiological responses to a standard heat acclimation state test (i.e. physiological biomarkers), but this can be logistically challenging, time consuming, and expensive. A valid molecular biomarker of HA would enable evaluation of the heat-adapted state through the sampling and assessment of a biological medium. This narrative review examines candidate molecular biomarkers of HA, highlighting the poor sensitivity and specificity of these candidates and identifying the current lack of a single 'standout' biomarker. It concludes by considering the potential of multivariable approaches that provide information about a range of physiological systems, identifying a number of challenges that must be overcome to develop a valid molecular biomarker of the heat-adapted state, and highlighting future research opportunities.
Collapse
Affiliation(s)
- J Corbett
- Extreme Environments Laboratory, School of Sport Health and Exercise Sciences, University of Portsmouth, Portsmouth, UK.
| | - J S Young
- National Horizons Centre, Teesside University, Darlington, UK
| | - M J Tipton
- Extreme Environments Laboratory, School of Sport Health and Exercise Sciences, University of Portsmouth, Portsmouth, UK
| | - J T Costello
- Extreme Environments Laboratory, School of Sport Health and Exercise Sciences, University of Portsmouth, Portsmouth, UK
| | - T B Williams
- Extreme Environments Laboratory, School of Sport Health and Exercise Sciences, University of Portsmouth, Portsmouth, UK
| | - E F Walker
- Defence Science and Technology Laboratory, Porton Down, Salisbury, UK
| | - B J Lee
- Occupational and Environmental Physiology Group, Centre for Sport, Exercise and Life Sciences, Faculty of Health and Life Sciences, Coventry University, Coventry, UK
| | - C E Stevens
- Extreme Environments Laboratory, School of Sport Health and Exercise Sciences, University of Portsmouth, Portsmouth, UK
| |
Collapse
|
33
|
Kumar N, Skubleny D, Parkes M, Verma R, Davis S, Kumar L, Aissiou A, Greiner R. Learning Individual Survival Models from PanCancer Whole Transcriptome Data. Clin Cancer Res 2023; 29:3924-3936. [PMID: 37463063 PMCID: PMC10543961 DOI: 10.1158/1078-0432.ccr-22-3493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/11/2023] [Accepted: 07/11/2023] [Indexed: 07/20/2023]
Abstract
PURPOSE Personalized medicine attempts to predict survival time for each patient, based on their individual tumor molecular profile. We investigate whether our survival learner in combination with a dimension reduction method can produce useful survival estimates for a variety of patients with cancer. EXPERIMENTAL DESIGN This article provides a method that learns a model for predicting the survival time for individual patients with cancer from the PanCancer Atlas: given the (16,335 dimensional) gene expression profiles from 10,173 patients, each having one of 33 cancers, this method uses unsupervised nonnegative matrix factorization (NMF) to reexpress the gene expression data for each patient in terms of 100 learned NMF factors. It then feeds these 100 factors into the Multi-Task Logistic Regression (MTLR) learner to produce cancer-specific models for each of 20 cancers (with >50 uncensored instances); this produces "individual survival distributions" (ISD), which provide survival probabilities at each future time for each individual patient, which provides a patient's risk score and estimated survival time. RESULTS Our NMF-MTLR concordance indices outperformed the VAECox benchmark by 14.9% overall. We achieved optimal survival prediction using pan-cancer NMF in combination with cancer-specific MTLR models. We provide biological interpretation of the NMF model and clinical implications of ISDs for prognosis and therapeutic response prediction. CONCLUSIONS NMF-MTLR provides many benefits over other models: superior model discrimination, superior calibration, meaningful survival time estimates, and accurate probabilistic estimates of survival over time for each individual patient. We advocate for the adoption of these cancer survival models in clinical and research settings.
Collapse
Affiliation(s)
- Neeraj Kumar
- Alberta Machine Intelligence Institute, Edmonton, Alberta, Canada
| | - Daniel Skubleny
- Department of Surgery, University of Alberta, Edmonton, Alberta, Canada
| | - Michael Parkes
- Computing Science Department, University of Alberta, Edmonton, Alberta, Canada
| | - Ruchika Verma
- Alberta Machine Intelligence Institute, Edmonton, Alberta, Canada
| | - Sacha Davis
- Alberta Machine Intelligence Institute, Edmonton, Alberta, Canada
| | - Luke Kumar
- Microsoft, Vancouver, British Columbia, Canada
| | | | - Russell Greiner
- Alberta Machine Intelligence Institute, Edmonton, Alberta, Canada
- Computing Science Department, University of Alberta, Edmonton, Alberta, Canada
| |
Collapse
|
34
|
Hasib RA, Ali MC, Rahman MH, Ahmed S, Sultana S, Summa SZ, Shimu MSS, Afrin Z, Jamal MAHM. Integrated gene expression profiling and functional enrichment analyses to discover biomarkers and pathways associated with Guillain-Barré syndrome and autism spectrum disorder to identify new therapeutic targets. J Biomol Struct Dyn 2023; 42:11299-11321. [PMID: 37776011 DOI: 10.1080/07391102.2023.2262586] [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: 03/15/2023] [Accepted: 09/17/2023] [Indexed: 10/01/2023]
Abstract
Guillain-Barré syndrome (GBS) is one of the most prominent and acute immune-mediated peripheral neuropathy, while autism spectrum disorders (ASD) are a group of heterogeneous neurodevelopmental disorders. The complete mechanism regarding the neuropathophysiology of these disorders is still ambiguous. Even after recent breakthroughs in molecular biology, the link between GBS and ASD remains a mystery. Therefore, we have implemented well-established bioinformatic techniques to identify potential biomarkers and drug candidates for GBS and ASD. 17 common differentially expressed genes (DEGs) were identified for these two disorders, which later guided the rest of the research. Common genes identified the protein-protein interaction (PPI) network and pathways associated with both disorders. Based on the PPI network, the constructed hub gene and module analysis network determined two common DEGs, namely CXCL9 and CXCL10, which are vital in predicting the top drug candidates. Furthermore, coregulatory networks of TF-gene and TF-miRNA were built to detect the regulatory biomolecules. Among drug candidates, imatinib had the highest docking and MM-GBSA score with the well-known chemokine receptor CXCR3 and remained stable during the 100 ns molecular dynamics simulation validated by the principal component analysis and the dynamic cross-correlation map. This study predicted the gene-based disease network for GBS and ASD and suggested prospective drug candidates. However, more in-depth research is required for clinical validation.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Rizone Al Hasib
- Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia, Bangladesh
- Laboratory of Medical and Environmental Biotechnology Islamic University, Kushtia, Bangladesh
| | - Md Chayan Ali
- Department of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Md Habibur Rahman
- Department of Computer Science and Engineering, Islamic University, Kushtia, Bangladesh
- Center for Advanced Bioinformatics and Artificial Intelligent Research, Islamic University, Kushtia, Bangladesh
| | - Sabbir Ahmed
- Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia, Bangladesh
| | - Shaharin Sultana
- Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia, Bangladesh
- Laboratory of Medical and Environmental Biotechnology Islamic University, Kushtia, Bangladesh
| | - Sadia Zannat Summa
- Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia, Bangladesh
- Laboratory of Medical and Environmental Biotechnology Islamic University, Kushtia, Bangladesh
| | | | - Zinia Afrin
- Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia, Bangladesh
| | - Mohammad Abu Hena Mostofa Jamal
- Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia, Bangladesh
- Laboratory of Medical and Environmental Biotechnology Islamic University, Kushtia, Bangladesh
| |
Collapse
|
35
|
Andersson H, Sobti A, Jimenez DG, de Coaña YP, Ambarkhane SV, Hägerbrand K, Smith KE, Lindstedt M, Ellmark P. Early Pharmacodynamic Changes Measured Using RNA Sequencing of Peripheral Blood from Patients in a Phase I Study with Mitazalimab, a Potent CD40 Agonistic Monoclonal Antibody. Cells 2023; 12:2365. [PMID: 37830579 PMCID: PMC10572020 DOI: 10.3390/cells12192365] [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: 08/23/2023] [Revised: 09/18/2023] [Accepted: 09/22/2023] [Indexed: 10/14/2023] Open
Abstract
CD40-targeting therapies can enhance the dendritic cell priming of tumor-specific T cells and repolarize intratumoral macrophages to alleviate the tumoral immunosuppressive environment and remodel the extracellular matrix. Mitazalimab is a potent agonistic CD40 monoclonal IgG1 antibody currently under clinical development. This study used RNA sequencing of blood samples from a subset of patients from a Phase I trial with mitazalimab (NCT02829099) to assess peripheral pharmacodynamic activity. We found that mitazalimab induced transient peripheral transcriptomic alterations (at 600 µg/kg and 900 µg/kg dose administered intravenously), which mainly were attributed to immune activation. In particular, the transcriptomic alterations showed a reduction in effector cells (e.g., CD8+ T cells and natural killer cells) and B cells peripherally with the remaining cells (e.g., dendritic cells, monocytes, B cells, and natural killer cells) showing transcription profiles consistent with activation. Lastly, distinct patient subgroups based on the pattern of transcriptomic alterations could be identified. In summary, the data presented herein reinforce the anticipated mode of action of mitazalimab and support its ongoing clinical development.
Collapse
Affiliation(s)
- Hampus Andersson
- Alligator Bioscience AB, 223 81 Lund, Sweden; (H.A.); (A.S.); (D.G.J.); (Y.P.d.C.); (M.L.)
- Department of Immunotechnology, Lund University, 223 81 Lund, Sweden
| | - Aastha Sobti
- Alligator Bioscience AB, 223 81 Lund, Sweden; (H.A.); (A.S.); (D.G.J.); (Y.P.d.C.); (M.L.)
| | - David Gomez Jimenez
- Alligator Bioscience AB, 223 81 Lund, Sweden; (H.A.); (A.S.); (D.G.J.); (Y.P.d.C.); (M.L.)
| | - Yago Pico de Coaña
- Alligator Bioscience AB, 223 81 Lund, Sweden; (H.A.); (A.S.); (D.G.J.); (Y.P.d.C.); (M.L.)
| | | | - Karin Hägerbrand
- Alligator Bioscience AB, 223 81 Lund, Sweden; (H.A.); (A.S.); (D.G.J.); (Y.P.d.C.); (M.L.)
| | - Karin Enell Smith
- Alligator Bioscience AB, 223 81 Lund, Sweden; (H.A.); (A.S.); (D.G.J.); (Y.P.d.C.); (M.L.)
| | - Malin Lindstedt
- Alligator Bioscience AB, 223 81 Lund, Sweden; (H.A.); (A.S.); (D.G.J.); (Y.P.d.C.); (M.L.)
- Department of Immunotechnology, Lund University, 223 81 Lund, Sweden
| | - Peter Ellmark
- Alligator Bioscience AB, 223 81 Lund, Sweden; (H.A.); (A.S.); (D.G.J.); (Y.P.d.C.); (M.L.)
- Department of Immunotechnology, Lund University, 223 81 Lund, Sweden
| |
Collapse
|
36
|
Karousi P, Kontos CK, Papakotsi P, Kostakis IK, Skaltsounis AL, Scorilas A. Next-generation sequencing reveals altered gene expression and enriched pathways in triple-negative breast cancer cells treated with oleuropein and oleocanthal. Funct Integr Genomics 2023; 23:299. [PMID: 37707691 PMCID: PMC10501944 DOI: 10.1007/s10142-023-01230-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/06/2023] [Accepted: 09/06/2023] [Indexed: 09/15/2023]
Abstract
Triple-negative breast cancer (TNBC) is a subtype of breast cancer characterized by poor prognosis and limited treatment options. Oleuropein and oleocanthal are bioactive chemicals found in extra-virgin olive oil; they have been shown to have anti-cancer potential. In this study, we examined the inhibitory effects of these two natural compounds, on MDA-MB-231 and MDA-MB-468 TNBC cell lines. The human TNBC MDA-MB-231 and MDA-MB-468 cell lines were treated with oleuropein or oleocanthal at ranging concentrations for 48 h. After determining the optimum concentration to reach IC50, using the sulforhodamine B assay, total RNA was extracted after 12, 24, and 48 h from treated and untreated cells. Poly(A)-RNA selection was conducted, followed by library construction and RNA sequencing. Differential gene expression (DEG) analysis was performed to identify DEGs between treated and untreated cells. Pathway analysis was carried out using the KEGG and GO databases. Oleuropein and oleocanthal considerably reduced the proliferation of TNBC cells, with oleocanthal having a slightly stronger effect than oleuropein. Furthermore, multi-time series RNA sequencing showed that the expression profile of TNBC cells was significantly altered after treatment with these compounds, with temporal dynamics and groups of genes consistently affected at all time points. Pathway analysis revealed several significant pathways associated with TNBC, including cell death, apoptotic process, programmed cell death, response to stress, mitotic cell cycle process, cell division, and cancer progression. Our findings suggest that oleuropein and oleocanthal have potential therapeutic benefits for TNBC and can be further investigated as alternative treatment options.
Collapse
Affiliation(s)
- Paraskevi Karousi
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Christos K Kontos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece.
| | | | - Ioannis K Kostakis
- Division of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Alexios-Leandros Skaltsounis
- Division of Pharmacognosy & Natural Products Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece.
| |
Collapse
|
37
|
Parreau S, Molina E, Dumonteil S, Goulabchand R, Naves T, Bois MC, Akil H, Terro F, Fauchais AL, Liozon E, Jauberteau MO, Weyand CM, Ly KH. Use of high-plex data provides novel insights into the temporal artery processes of giant cell arteritis. Front Immunol 2023; 14:1237986. [PMID: 37744332 PMCID: PMC10512077 DOI: 10.3389/fimmu.2023.1237986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 08/21/2023] [Indexed: 09/26/2023] Open
Abstract
Objective To identify the key coding genes underlying the biomarkers and pathways associated with giant cell arteritis (GCA), we performed an in situ spatial profiling of molecules involved in the temporal arteries of GCA patients and controls. Furthermore, we performed pharmacogenomic network analysis to identify potential treatment targets. Methods Using human formalin-fixed paraffin-embedded temporal artery biopsy samples (GCA, n = 9; controls, n = 7), we performed a whole transcriptome analysis using the NanoString GeoMx Digital Spatial Profiler. In total, 59 regions of interest were selected in the intima, media, adventitia, and perivascular adipose tissue (PVAT). Differentially expressed genes (DEGs) (fold-change > 2 or < -2, p-adjusted < 0.01) were compared across each layer to build a spatial and pharmacogenomic network and to explore the pathophysiological mechanisms of GCA. Results Most of the transcriptome (12,076 genes) was upregulated in GCA arteries, compared to control arteries. Among the screened genes, 282, 227, 40, and 5 DEGs were identified in the intima, media, adventitia, and PVAT, respectively. Genes involved in the immune process and vascular remodeling were upregulated within GCA temporal arteries but differed across the arterial layers. The immune-related functions and vascular remodeling were limited to the intima and media. Conclusion This study is the first to perform an in situ spatial profiling characterization of the molecules involved in GCA. The pharmacogenomic network analysis identified potential target genes for approved and novel immunotherapies.
Collapse
Affiliation(s)
- Simon Parreau
- Division of Rheumatology, Mayo Clinic, Rochester, MN, United States
- Division of Internal Medicine, Dupuytren University Hospital, Limoges, France
- INSERM U1308, Faculty of Medicine, University of Limoges, Limoges, France
| | - Elsa Molina
- Stem Cell Genomics Core, Stem Cell Program, University of California, San Diego, La Jolla, CA, United States
- Next Generation Sequencing Core, Salk Institute for Biological Studies, La Jolla, CA, United States
| | - Stéphanie Dumonteil
- Division of Internal Medicine, Dupuytren University Hospital, Limoges, France
| | - Radjiv Goulabchand
- Division of Internal Medicine, Nîmes University Hospital, University of Montpellier, Nîmes, France
- Division of Gastroenterology, Department of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Thomas Naves
- INSERM U1308, Faculty of Medicine, University of Limoges, Limoges, France
| | - Melanie C. Bois
- Division of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
| | - Hussein Akil
- INSERM U1308, Faculty of Medicine, University of Limoges, Limoges, France
| | - Faraj Terro
- Cell Biology, Dupuytren University Hospital, Limoges, France
| | - Anne-Laure Fauchais
- Division of Internal Medicine, Dupuytren University Hospital, Limoges, France
- INSERM U1308, Faculty of Medicine, University of Limoges, Limoges, France
| | - Eric Liozon
- Division of Internal Medicine, Dupuytren University Hospital, Limoges, France
| | | | | | - Kim-Heang Ly
- Division of Internal Medicine, Dupuytren University Hospital, Limoges, France
- INSERM U1308, Faculty of Medicine, University of Limoges, Limoges, France
| |
Collapse
|
38
|
Mariani NAP, Silva JV, Fardilha M, Silva EJR. Advances in non-hormonal male contraception targeting sperm motility. Hum Reprod Update 2023; 29:545-569. [PMID: 37141450 DOI: 10.1093/humupd/dmad008] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 03/23/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND The high rates of unintended pregnancy and the ever-growing world population impose health, economic, social, and environmental threats to countries. Expanding contraceptive options, including male methods, are urgently needed to tackle these global challenges. Male contraception is limited to condoms and vasectomy, which are unsuitable for many couples. Thus, novel male contraceptive methods may reduce unintended pregnancies, meet the contraceptive needs of couples, and foster gender equality in carrying the contraceptive burden. In this regard, the spermatozoon emerges as a source of druggable targets for on-demand, non-hormonal male contraception based on disrupting sperm motility or fertilization. OBJECTIVE AND RATIONALE A better understanding of the molecules governing sperm motility can lead to innovative approaches toward safe and effective male contraceptives. This review discusses cutting-edge knowledge on sperm-specific targets for male contraception, focusing on those with crucial roles in sperm motility. We also highlight challenges and opportunities in male contraceptive drug development targeting spermatozoa. SEARCH METHODS We conducted a literature search in the PubMed database using the following keywords: 'spermatozoa', 'sperm motility', 'male contraception', and 'drug targets' in combination with other related terms to the field. Publications until January 2023 written in English were considered. OUTCOMES Efforts for developing non-hormonal strategies for male contraception resulted in the identification of candidates specifically expressed or enriched in spermatozoa, including enzymes (PP1γ2, GAPDHS, and sAC), ion channels (CatSper and KSper), transmembrane transporters (sNHE, SLC26A8, and ATP1A4), and surface proteins (EPPIN). These targets are usually located in the sperm flagellum. Their indispensable roles in sperm motility and male fertility were confirmed by genetic or immunological approaches using animal models and gene mutations associated with male infertility due to sperm defects in humans. Their druggability was demonstrated by the identification of drug-like small organic ligands displaying spermiostatic activity in preclinical trials. WIDER IMPLICATIONS A wide range of sperm-associated proteins has arisen as key regulators of sperm motility, providing compelling druggable candidates for male contraception. Nevertheless, no pharmacological agent has reached clinical developmental stages. One reason is the slow progress in translating the preclinical and drug discovery findings into a drug-like candidate adequate for clinical development. Thus, intense collaboration among academia, private sectors, governments, and regulatory agencies will be crucial to combine expertise for the development of male contraceptives targeting sperm function by (i) improving target structural characterization and the design of highly selective ligands, (ii) conducting long-term preclinical safety, efficacy, and reversibility evaluation, and (iii) establishing rigorous guidelines and endpoints for clinical trials and regulatory evaluation, thus allowing their testing in humans.
Collapse
Affiliation(s)
- Noemia A P Mariani
- Department of Biophysics and Pharmacology, Institute of Biosciences of Botucatu, São Paulo State University, Botucatu, Brazil
| | - Joana V Silva
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
- QOPNA & LAQV, Department of Chemistry, University of Aveiro, Aveiro, Portugal
- Multidisciplinary Research in Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Margarida Fardilha
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
| | - Erick J R Silva
- Department of Biophysics and Pharmacology, Institute of Biosciences of Botucatu, São Paulo State University, Botucatu, Brazil
| |
Collapse
|
39
|
Hasankhani A, Bakherad M, Bahrami A, Shahrbabak HM, Pecho RDC, Shahrbabak MM. Integrated analysis of inflammatory mRNAs, miRNAs, and lncRNAs elucidates the molecular interactome behind bovine mastitis. Sci Rep 2023; 13:13826. [PMID: 37620551 PMCID: PMC10449796 DOI: 10.1038/s41598-023-41116-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 08/22/2023] [Indexed: 08/26/2023] Open
Abstract
Mastitis is known as intramammary inflammation, which has a multifactorial complex phenotype. However, the underlying molecular pathogenesis of mastitis remains poorly understood. In this study, we utilized a combination of RNA-seq and miRNA-seq techniques, along with computational systems biology approaches, to gain a deeper understanding of the molecular interactome involved in mastitis. We retrieved and processed one hundred transcriptomic libraries, consisting of 50 RNA-seq and 50 matched miRNA-seq data, obtained from milk-isolated monocytes of Holstein-Friesian cows, both infected with Streptococcus uberis and non-infected controls. Using the weighted gene co-expression network analysis (WGCNA) approach, we constructed co-expressed RNA-seq-based and miRNA-seq-based modules separately. Module-trait relationship analysis was then performed on the RNA-seq-based modules to identify highly-correlated modules associated with clinical traits of mastitis. Functional enrichment analysis was conducted to understand the functional behavior of these modules. Additionally, we assigned the RNA-seq-based modules to the miRNA-seq-based modules and constructed an integrated regulatory network based on the modules of interest. To enhance the reliability of our findings, we conducted further analyses, including hub RNA detection, protein-protein interaction (PPI) network construction, screening of hub-hub RNAs, and target prediction analysis on the detected modules. We identified a total of 17 RNA-seq-based modules and 3 miRNA-seq-based modules. Among the significant highly-correlated RNA-seq-based modules, six modules showed strong associations with clinical characteristics of mastitis. Functional enrichment analysis revealed that the turquoise module was directly related to inflammation persistence and mastitis development. Furthermore, module assignment analysis demonstrated that the blue miRNA-seq-based module post-transcriptionally regulates the turquoise RNA-seq-based module. We also identified a set of different RNAs, including hub-hub genes, hub-hub TFs (transcription factors), hub-hub lncRNAs (long non-coding RNAs), and hub miRNAs within the modules of interest, indicating their central role in the molecular interactome underlying the pathogenic mechanisms of S. uberis infection. This study provides a comprehensive insight into the molecular crosstalk between immunoregulatory mRNAs, miRNAs, and lncRNAs during S. uberis infection. These findings offer valuable directions for the development of molecular diagnosis and biological therapies for mastitis.
Collapse
Affiliation(s)
- Aliakbar Hasankhani
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran.
| | - Maryam Bakherad
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Abolfazl Bahrami
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran.
| | - Hossein Moradi Shahrbabak
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran.
| | | | - Mohammad Moradi Shahrbabak
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| |
Collapse
|
40
|
Yamanaka C, Uki S, Kaitoh K, Iwata M, Yamanishi Y. De novo drug design based on patient gene expression profiles via deep learning. Mol Inform 2023; 42:e2300064. [PMID: 37475603 DOI: 10.1002/minf.202300064] [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: 03/16/2023] [Revised: 05/25/2023] [Accepted: 07/20/2023] [Indexed: 07/22/2023]
Abstract
Computational de novo drug design is a challenging issue in medicine, and it is desirable to consider all of the relevant information of the biological systems in a disease state. Here, we propose a novel computational method to generate drug candidate molecular structures from patient gene expression profiles via deep learning, which we call DRAGONET. Our model can generate new molecules that are likely to counteract disease-specific gene expression patterns in patients, which is made possible by exploring the latent space constructed by a transformer-based variational autoencoder and integrating the substructures of disease-correlated molecules. We applied DRAGONET to generate drug candidate molecules for gastric cancer, atopic dermatitis, and Alzheimer's disease, and demonstrated that the newly generated molecules were chemically similar to registered drugs for each disease. This approach is applicable to diseases with unknown therapeutic target proteins and will make a significant contribution to the field of precision medicine.
Collapse
Affiliation(s)
- Chikashige Yamanaka
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
| | - Shunya Uki
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
| | - Kazuma Kaitoh
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
- Graduate School of Informatics, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Michio Iwata
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
| | - Yoshihiro Yamanishi
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
- Graduate School of Informatics, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| |
Collapse
|
41
|
Viñas R, Joshi CK, Georgiev D, Lin P, Dumitrascu B, Gamazon ER, Liò P. Hypergraph factorization for multi-tissue gene expression imputation. NAT MACH INTELL 2023; 5:739-753. [PMID: 37771758 PMCID: PMC10538467 DOI: 10.1038/s42256-023-00684-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 06/02/2023] [Indexed: 09/30/2023]
Abstract
Integrating gene expression across tissues and cell types is crucial for understanding the coordinated biological mechanisms that drive disease and characterise homeostasis. However, traditional multitissue integration methods cannot handle uncollected tissues or rely on genotype information, which is often unavailable and subject to privacy concerns. Here we present HYFA (Hypergraph Factorisation), a parameter-efficient graph representation learning approach for joint imputation of multi-tissue and cell-type gene expression. HYFA is genotype-agnostic, supports a variable number of collected tissues per individual, and imposes strong inductive biases to leverage the shared regulatory architecture of tissues and genes. In performance comparison on Genotype-Tissue Expression project data, HYFA achieves superior performance over existing methods, especially when multiple reference tissues are available. The HYFA-imputed dataset can be used to identify replicable regulatory genetic variations (eQTLs), with substantial gains over the original incomplete dataset. HYFA can accelerate the effective and scalable integration of tissue and cell-type transcriptome biorepositories.
Collapse
Affiliation(s)
- Ramon Viñas
- Department of Computer Science and Technology, University of Cambridge
| | | | - Dobrik Georgiev
- Department of Computer Science and Technology, University of Cambridge
| | - Phillip Lin
- Division of Genetic Medicine, Vanderbilt University Medical Center
| | - Bianca Dumitrascu
- Department of Statistics and Irving Institute for Cancer Dynamics, Columbia University
| | - Eric R. Gamazon
- Vanderbilt Genetics Institute and Data Science Institute, MRC Epidemiology Unit, University of Cambridge
| | - Pietro Liò
- Department of Computer Science and Technology, University of Cambridge
| |
Collapse
|
42
|
Bakhsh MR, Rouhi L, Ghaedi K, Hashemi M, Peymani M, Samarghandian S. Therapeutic effects of guanidine hydrochloride on breast cancer through targeting KCNG1 gene. Biomed Pharmacother 2023; 164:114982. [PMID: 37311278 DOI: 10.1016/j.biopha.2023.114982] [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: 03/24/2023] [Revised: 05/28/2023] [Accepted: 06/01/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) is one of the subtypes of breast cancer (BC) that is associated with poor survival rates and failure to respond to hormonal and targeted therapies. OBJECTIVE The aim of this study was to identify a specific gene at the expression level for TNBC and targeting of this type of breast cancer based on it. Using TCGA database, genes that are particularly high expression in TNBC subtypes compared to other BC subtypes (in terms of receptor status) and normal samples were identified and their sensitivity and specificity were evaluated. Using PharmacoGX and Drug Bank data, drug sensitivity and drug-appropriate genes were identified, respectively. The effects of the identified drug on triple-negative cell lines (MDA-MB-468) were evaluated in comparison with the cell line of other subtypes (MCF7) by apoptosis and MTS tests. RESULTS Data analyzes showed that the expression level of KCNG1 gene in the TNBC subgroup was significantly higher compared to other BC subtypes from the KCN gene family and ROC results showed that this gene had highest sensitivity and specificity in TNBC subtype. The results of drug resistance and sensitivity showed that an increase in the expression level of KCNG1 was associated with sensitivity to Cisplatin and Oxaliplatin. Moreover, Drug Bank results showed that Guanidine hydrochloride (GuHCl) was a suitable inhibitor for KCNG1. In vitro results showed that the expression level of KCNG1 was higher in MDA-MB-468 compared to MCF7. In addition, the rate of apoptosis in response to GuHCl treatment in MDA-MB-468 cell line as TNBC cell model was higher than MCF7 in the same concentration. CONCLUSION This study revealed that GuHCl could be a suitable treatment for TNBC subtype by targeting of KCNG1.
Collapse
Affiliation(s)
- Mehdi Roshanian Bakhsh
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, the Islamic Republic of Iran
| | - Leila Rouhi
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, the Islamic Republic of Iran
| | - Kamran Ghaedi
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, the Islamic Republic of Iran; Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, the Islamic Republic of Iran
| | - Mehrdad Hashemi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, the Islamic Republic of Iran; Farhikhtegan Medical Convergence sciences Research Center, Farhikhtegan Hospital Tehran Medical sciences, Islamic Azad University, Tehran, the Islamic Republic of Iran.
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, the Islamic Republic of Iran.
| | - Saeed Samarghandian
- Healthy Ageing Research Centre, Neyshabur University of Medical Sciences, Neyshabur, the Islamic Republic of Iran.
| |
Collapse
|
43
|
Gigliotta A, Trontti K, Väänänen J, Hovatta I. Gene expression profiling reveals a role of immune system and inflammation in innate and stress-induced anxiety-like behavior. Front Genet 2023; 14:1173376. [PMID: 37260777 PMCID: PMC10229056 DOI: 10.3389/fgene.2023.1173376] [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: 02/24/2023] [Accepted: 05/04/2023] [Indexed: 06/02/2023] Open
Abstract
Anxiety is an evolutionarily conserved response that is essential for survival. Pathological anxiety, however, is a maladaptive response to nonthreatening situations and greatly affects quality of life. The recent COVID-19 pandemic has increased the prevalence of anxiety symptoms and highlighted the urge to identify the molecular events that initiate pathological anxiety. To this aim, we investigated the extent of similarity of brain region-specific gene expression patterns associated with innate and stress-induced anxiety-like behavior. We compared the cortico-frontal (FCx) and hippocampal (Hpc) gene expression patterns of five inbred mouse strains with high or low levels of innate anxiety-like behavior with gene expression patterns of mice subjected to chronic social defeat stress. We found significantly large overlap of the Hpc but small overlap of the FCx gene expression patterns in innate and stress-induced anxiety, that however, converged onto common inflammation and immune system canonical pathways. Comparing the gene expression data with drug-gene interaction datasets revealed drug candidates, including medrysone, simvastatin, captopril, and sulpiride, that produced gene expression changes opposite to those observed in innate or stress-induced anxiety-like behavior. Together, our data provide a comprehensive overview of FCx and Hpc gene expression differences between innate and stress-induced anxiety and support the role of inflammation and immune system in anxiety-like behavior.
Collapse
|
44
|
Liu J, Lyu X, Zhou Z, Yang L, Zeng J, Yang Y, Zhao Z, Chen R, Tong X, Li J, Liu H, Zou Y. Multifunctional Droplets Formed by Interfacially Self-Assembled Fluorinated Magnetic Nanoparticles for Biocompatible Single Cell Culture and Magnet-Driven Manipulation. ACS APPLIED MATERIALS & INTERFACES 2023; 15:17324-17334. [PMID: 36962257 DOI: 10.1021/acsami.2c23003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The ability to encapsulate and manipulate droplets with a picoliter volume of samples and reagents shows great potential for practical applications in chemistry, biology, and materials science. Magnetic control is a promising approach for droplet manipulation due to its ability for wireless control and its ease of implementation. However, it is challenged by the poor biocompatibility of magnetic materials in aqueous droplets. Moreover, current droplet technology is problematic because of the molecule leakage between droplets. In the paper, we propose multifunctional droplets with the surface coated by a layer of fluorinated magnetic nanoparticles for magnetically actuated droplet manipulation. Multifunctional droplets show excellent biocompatibility for cell culture, nonleakage of molecules, and high response to a magnetic field. We developed a strategy of coating the F-MNP@SiO2 on the outer surface of droplets instead of adding magnetic material into droplets to enable droplets with a highly magnetic response. The encapsulated bacteria and cells in droplets did not need to directly contact with the magnetic materials at the outer surface, showing high biocompatibility with living cells. These droplets can be precisely manipulated based on magnet distance, the time duration of the magnetic field, the droplet size, and the MNP composition, which well match with theoretical analysis. The precise magnetically actuated droplet manipulation shows great potential for accurate and sensitive droplet-based bioassays like single cell analysis.
Collapse
Affiliation(s)
- Jiahe Liu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Xiaoyan Lyu
- Department of Dermatology, Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ziwei Zhou
- Central Laboratory of Yongchuan Hospital, Chongqing Medical University, Chongqing 402160, China
| | - Lin Yang
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Jie Zeng
- College of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Yao Yang
- Department of Dermatology, Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zhenghuan Zhao
- College of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Rui Chen
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Xin Tong
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Jiaqi Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Hailan Liu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Yuan Zou
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| |
Collapse
|
45
|
Wang Y, Liu X, Jia H, Zhang R, Guan J, Zhang L. Integrative analysis of transcriptome and metabolome reveals probiotic effects on cecal metabolism in broilers. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:2876-2888. [PMID: 36519671 DOI: 10.1002/jsfa.12387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/07/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Probiotics play an important role in the host and have attracted widespread attention as an alternative to antibiotics. Arbor Acres broilers were used in the present experiment and fed different doses of compound probiotics at 1, 5, and 10 g kg-1 . The effects of compound probiotics on broiler growth performance and cecal transcriptome and metabolome were investigated. RESULTS We discovered 425 differentially expressed genes (DEGs; upregulated: 256; downregulated: 169) in the cecal transcriptome study. These DEGs were assigned to fat metabolic pathways, such as the peroxisome proliferator-activated receptor (PPAR) signaling pathway, according to KEGG analysis. Probiotics downregulated LPL and upregulated PPARα expression in the cecum. In metabolome analysis of the cecum of cecum, we screened 86 differential metabolites and performed KEGG enrichment analysis of these metabolites. The KEGG analysis showed that these differentially expressed metabolites were annotated to nucleotide metabolism-related pathways, such as purine metabolism. In the cecum, probiotics upregulated the content of guanine, AMP, 3'-AMP, adenylosuccinate, deoxyguanosine, and ADP-ribose, whereas they downregulated the content of 5-hydroxyisourate. Comprehensive transcriptome and metabolome analysis revealed that glycolysis, gluconeogenesis, and glycerophospholipid metabolism pathways were jointly enriched in cecum of broilers fed a probiotic-containing diet. CONCLUSION This study provides valuable information for studying the regulation and gene metabolism network of probiotics on cecal metabolism in broilers. © 2022 Society of Chemical Industry.
Collapse
Affiliation(s)
- Yanfei Wang
- Shanxi Key Laboratory for Modernization of TCVM, College of Life and Science, Shanxi Agricultural University, Taigu, China
| | - Xuan Liu
- Shanxi Key Laboratory for Modernization of TCVM, College of Life and Science, Shanxi Agricultural University, Taigu, China
| | - Hao Jia
- Shanxi Key Laboratory for Modernization of TCVM, College of Life and Science, Shanxi Agricultural University, Taigu, China
| | - Ruonan Zhang
- Shanxi Key Laboratory for Modernization of TCVM, College of Life and Science, Shanxi Agricultural University, Taigu, China
| | - Jiawei Guan
- Shanxi Key Laboratory for Modernization of TCVM, College of Life and Science, Shanxi Agricultural University, Taigu, China
| | - Lihuan Zhang
- Shanxi Key Laboratory for Modernization of TCVM, College of Life and Science, Shanxi Agricultural University, Taigu, China
| |
Collapse
|
46
|
Li J, Huang HY, Lin YCD, Zuo H, Tang Y, Huang HD. Cinnamomi ramulus inhibits cancer cells growth by inducing G2/M arrest. Front Pharmacol 2023; 14:1121799. [PMID: 37007025 PMCID: PMC10063822 DOI: 10.3389/fphar.2023.1121799] [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: 12/12/2022] [Accepted: 02/13/2023] [Indexed: 03/19/2023] Open
Abstract
Introduction: Cinnamomi ramulus (CR) is one of the most widely used traditional Chinese medicine (TCM) with anti-cancer effects. Analyzing transcriptomic responses of different human cell lines to TCM treatment is a promising approach to understand the unbiased mechanism of TCM. Methods: This study treated ten cancer cell lines with different CR concentrations, followed by mRNA sequencing. Differential expression (DE) analysis and gene set enrichment analysis (GSEA) were utilized to analyze transcriptomic data. Finally, the in silico screening results were verified by in vitro experiments. Results: Both DE and GSEA analysis suggested the Cell cycle pathway was the most perturbated pathway by CR across these cell lines. By analyzing the clinical significance and prognosis of G2/M related genes (PLK1, CDK1, CCNB1, and CCNB2) in various cancer tissues, we found that they were up-regulated in most cancer types, and their down-regulation showed better overall survival rates in cancer patients. Finally, in vitro experiments validation on A549, Hep G2, and HeLa cells suggested that CR can inhibit cell growth by suppressing the PLK1/CDK1/ Cyclin B axis. Discussion: This is the first study to apply transcriptomic analysis to investigate the cancer cell growth inhibition of CR on various human cancer cell lines. The core effect of CR on ten cancer cell lines is to induce G2/M arrest by inhibiting the PLK1/CDK1/Cyclin B axis.
Collapse
Affiliation(s)
- Jing Li
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Hsi-Yuan Huang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Yang-Chi-Dung Lin
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Huali Zuo
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Yun Tang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Hsien-Da Huang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| |
Collapse
|
47
|
Oumeddour A. Screening of potential hub genes and key pathways associated with breast cancer by bioinformatics tools. Medicine (Baltimore) 2023; 102:e33291. [PMID: 36930083 PMCID: PMC10019133 DOI: 10.1097/md.0000000000033291] [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: 11/19/2022] [Accepted: 02/24/2023] [Indexed: 03/18/2023] Open
Abstract
Breast cancer (BC) remains the leading cause of cancer-related death in women worldwide. The development of new targeted therapies that may improve patient survival remains an area of growing interest. This study aimed to identify new biomarkers involved in BC progression that could be used as potential targeted therapies. DEGs were selected from three gene expression profiles, GSE55715, GSE124646, and GSE87049, using the GEO2R tool and Venn diagram software. Gene Ontology and KEGG pathways were then performed using DAVID software. Next, the PPI network was constructed using STRING and visualized using Cytoscape software, and hub genes were extracted using the cytoHubba plug-in. Survival analysis was performed using the Kaplan-Meier Plotter, while the expression of hub genes in BC was verified using the GEPIA2 tool. Finally, transcription the factors of hub genes were determined using the NetworkAnalyst database, and the TIMER tool was employed to explore the infiltration levels of tumor immune cells with related genes. A total of 146 DEGs were identified in the three datasets, including 60 upregulated genes that were enriched in the cell cycle, and 86 downregulated genes that were mainly enriched in the TNF signaling pathway and pathways in cancer. Ten genes were identified: BUB1, CDK1, HMMR, MAD2L1, CEP55, AURKA, CCNB2, TPX2, MELK, and KIF20A. The overexpression of hub genes, except CDK1, was associated with poor survival in BC and was regulated by several transcription factors involved in DNA binding activity and transcription regulation. The infiltration levels of immune cells were positively correlated with hub genes, particularly macrophages and CD4+ T cells. This study identified new reliable molecular biomarkers that can serve as potential therapeutic targets for BC treatment.
Collapse
Affiliation(s)
- Abdelkader Oumeddour
- Department of Natural Sciences and Life, 8 May 1945 University of Guelma, Guelma, Algeria
| |
Collapse
|
48
|
Chiang CC, Yeh H, Lim SN, Lin WR. Transcriptome analysis creates a new era of precision medicine for managing recurrent hepatocellular carcinoma. World J Gastroenterol 2023; 29:780-799. [PMID: 36816628 PMCID: PMC9932421 DOI: 10.3748/wjg.v29.i5.780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/23/2022] [Accepted: 01/10/2023] [Indexed: 02/06/2023] Open
Abstract
The high incidence of hepatocellular carcinoma (HCC) recurrence negatively impacts outcomes of patients treated with curative intent despite advances in surgical techniques and other locoregional liver-targeting therapies. Over the past few decades, the emergence of transcriptome analysis tools, including real-time quantitative reverse transcription PCR, microarrays, and RNA sequencing, has not only largely contributed to our knowledge about the pathogenesis of recurrent HCC but also led to the development of outcome prediction models based on differentially expressed gene signatures. In recent years, the single-cell RNA sequencing technique has revolutionized our ability to study the complicated crosstalk between cancer cells and the immune environment, which may benefit further investigations on the role of different immune cells in HCC recurrence and the identification of potential therapeutic targets. In the present article, we summarized the major findings yielded with these transcriptome methods within the framework of a causal model consisting of three domains: primary cancer cells; carcinogenic stimuli; and tumor microenvironment. We provided a comprehensive review of the insights that transcriptome analyses have provided into diagnostics, surveillance, and treatment of HCC recurrence.
Collapse
Affiliation(s)
- Chun-Cheng Chiang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, United States
| | - Hsuan Yeh
- School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Siew-Na Lim
- Department of Neurology, Linkou Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - Wey-Ran Lin
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Department of Gastroenterology and Hepatology, Linkou Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
| |
Collapse
|
49
|
The Sesquiterpene Lactone-Rich Fraction of Inula helenium L. Enhances the Antitumor Effect of Anti-PD-1 Antibody in Colorectal Cancer: Integrative Phytochemical, Transcriptomic, and Experimental Analyses. Cancers (Basel) 2023; 15:cancers15030653. [PMID: 36765611 PMCID: PMC9913754 DOI: 10.3390/cancers15030653] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023] Open
Abstract
Treatment strategies combining immune checkpoint inhibitors with sesquiterpene lactones have attracted much attention as a promising approach for cancer treatment. We systemically analyzed gene expression profiles of cells in response to two major sesquiterpene lactones, alantolactone and isoalantolactone, and determined whether the sesquiterpene lactone-rich fraction of Inula helenium L. (SFIH) enhances the antitumor effect of anti-PD-1 antibody in MC38 colorectal cancer-bearing mice. Gene expression and pathway analysis using RNA sequencing data were used to identify the SFIH-driven combined activity with anti-PD-1 antibody. The results showed that SFIH significantly enhanced the antitumor effect of anti-PD-1 antibody by reducing tumor growth and increasing the survival time of mice. Specifically, SFIH exhibited antitumor activity when combined with anti-PD-1 antibody, and the effects were further enhanced compared with monotherapy. An analysis of immune cells indicated that combination treatment with SFIH and anti-PD-1 antibody significantly increased the proportion of CD8+ T cells. Moreover, combination treatment enhanced antitumor immunity by decreasing the population of myeloid-derived suppressor cells and increasing the number of M1-like macrophages. Pathway enrichment analysis revealed that combination therapy activated immune-related pathways to a greater extent than monotherapy. In conclusion, our integrative analysis demonstrates that SFIH enhances the response of murine tumors to anti-PD-1 antibody. These findings provide insight into developing integrative therapeutics and molecular data for the use of natural products as an adjunct treatment for colorectal cancer.
Collapse
|
50
|
Arumugam P, Ramesh V, Sampathkumar B, Perumalsamy H, Balusamy SR, Suganya K, Balraj S, Nachimuthu SK, Sundaravadivelu S. Integrative transcriptome analysis of triple negative breast cancer profiles for identification of druggable targets. J Biomol Struct Dyn 2023; 41:12106-12119. [PMID: 36617953 DOI: 10.1080/07391102.2022.2164795] [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: 11/30/2021] [Accepted: 12/29/2022] [Indexed: 01/10/2023]
Abstract
As triple negative breast cancer (TNBC) lacks a specific target, exploration of abnormally expressed genes during the progression of TNBC is important for a better understanding of tumorigenesis and to find a specific target. We intended to figure out genes associated with TNBC, which can provide unique insights into gene dysregulation in TNBC while also pointing to new possible therapeutic targets for TNBC. A meta-analysis of multiple TNBC mRNA profiles was performed to identify consistently differentially expressed genes (CDGs). The pathways involved in modulating these genes were analyzed by MsigDB, and the interaction map was constructed. These CDGs were evaluated for their expression in cell lines, and drugs that could modulate the expression of CDGs were obtained using the connectivity map. CDGs were docked with doxorubicin and anethole, which is a phytocompound. The expression of selected CDGs was analyzed in MDA-MB-231 cells after treatment with doxorubicin and anethole. We found 45 CDGs, out of which 36 were upregulated and 9 were downregulated. MDA-MB-231 cell line was found to have high expression of CDGs, and drug that could modulate the expression of CDGs was doxorubicin. Docking results revealed that anethole and doxorubicin had good interaction with the CDGs especially with the genes AURKA, CDC6, DEPDC1, KIF23, KPNA2, MELK, CTNNB1, FLI1 and E2F1. Gene expression studies of the selected CDGs showed that the synergistic effect of anethole and doxorubicin effectively downregulated the expression. The CDGs identified from multiple cohorts have clinical significance and may be effectively exploited in the targeted therapy for TNBC.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Poornima Arumugam
- Department of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education For Women, Coimbatore, Tamil Nadu, India
| | - Vignesh Ramesh
- International Center for Clinical Research, Friedrich Alexander University, Erlangen-Nurnberb, Germany
| | - Banupriya Sampathkumar
- Department of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education For Women, Coimbatore, Tamil Nadu, India
| | - Haribalan Perumalsamy
- Graduate School of Biotechnology, College of Life Science, Kyung Hee University, Yongin, Republic of Korea
| | | | - Kanagaraj Suganya
- Department of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education For Women, Coimbatore, Tamil Nadu, India
| | - Sudha Balraj
- Department of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education For Women, Coimbatore, Tamil Nadu, India
| | | | - Sumathi Sundaravadivelu
- Department of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education For Women, Coimbatore, Tamil Nadu, India
| |
Collapse
|