IFDlong: an isoform and fusion detector for accurate annotation and quantification of long-read RNA-seq data DOI Creative Commons
Wenjia Wang, Yuzhen Li, Sungjin Ko

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 14, 2024

Advancements in long-read transcriptome sequencing (long-RNA-seq) technology have revolutionized the study of isoform diversity. These full-length transcripts enhance detection various structural variations, including novel isoforms, alternative splicing events, and fusion transcripts. By shifting open reading frame or altering gene expressions, studies proved that these transcript alterations can serve as crucial biomarkers for disease diagnosis therapeutic targets. In this project, we proposed IFDlong, a bioinformatics biostatistics tool to detect using bulk single-cell long-RNA-seq data. Specifically, software performed annotation each long-read, defined quantified expression by expectation-maximization algorithm, profiled For evaluation, IFDlong pipeline achieved overall best performance when compared with several existing tools large-scale simulation studies. both quantification, is able reach more than 0.8 Spearman's correlation truth, 0.9 cosine similarity distinguishing multiple events. simulation, successfully balance sensitivity (higher 90%) specificity 90%). Furthermore, has its accuracy robustness diverse in-house public datasets on healthy tissues, cell lines types diseases. Besides long-RNA-seq, compatibility This new may hold promise significant impact analysis. The available at https://github.com/wenjiaking/IFDlong.

Language: Английский

A Narrative Review of Cytokine Networks: Pathophysiological and Therapeutic Implications for Inflammatory Bowel Disease Pathogenesis DOI Creative Commons

Marek Vébr,

Renata Pomahačová, Josef Sýkora

et al.

Biomedicines, Journal Year: 2023, Volume and Issue: 11(12), P. 3229 - 3229

Published: Dec. 6, 2023

Inflammatory bowel disease (IBD) is a lifelong inflammatory immune mediated disorder, encompassing Crohn's (CD) and ulcerative colitis (UC); however, the cause specific pathogenesis of IBD yet incompletely understood. Multiple cytokines produced by different cell types results in complex functional networks that constitute highly regulated messaging network signaling pathways. Applying biological mechanisms underlying at single omic level, technologies genetic engineering enable quantification pattern released new insights into cytokine landscape IBD. We focus on existing literature dealing with biology pro- or anti-inflammatory interactions facilitate cell-based modulation system for inflammation. summarize main roles substantial related to homeostatic tissue functions remodeling IBD, which may be specifically valuable successful cytokine-targeted therapies via marketed products. Cytokines their receptors are validated targets multiple therapeutic areas, we review current strategies intervention developing therapies. New biologics have shown efficacy last few decades management IBD; unfortunately, many patients nonresponsive develop therapy resistance over time, creating need novel therapeutics. Thus, treatment options beyond immune-modifying anti-TNF agents combination expanding rapidly. Further studies needed fully understand response, cytokines, direct pathogenetic relevance regarding individually tailored, safe efficient targeted-biotherapeutics.

Language: Английский

Citations

26
Cytokines and soluble mediators as architects of tumor microenvironment reprogramming in cancer therapy DOI
Suling Xu,

Qing-Qing Wang,

Wenxue Ma

et al.

Cytokine & Growth Factor Reviews, Journal Year: 2024, Volume and Issue: 76, P. 12 - 21

Published: Feb. 28, 2024

Language: Английский

Citations

13
Endothelial and Macrophage Interactions in the Angiogenic Niche. DOI
Fahad Hassan Shah, Heon‐Woo Lee

Cytokine & Growth Factor Reviews, Journal Year: 2024, Volume and Issue: 78, P. 64 - 76

Published: July 14, 2024

Language: Английский

Citations

9
The pharmacoepigenetic paradigm in cancer treatment DOI Creative Commons

Belén Ocaña-Paredes,

Sebastián Rivera-Orellana, David Ramírez

et al.

Frontiers in Pharmacology, Journal Year: 2024, Volume and Issue: 15

Published: April 24, 2024

Epigenetic modifications, characterized by changes in gene expression without altering the DNA sequence, play a crucial role development and progression of cancer significantly influencing activity cellular function. This insight has led to novel class therapeutic agents, known as epigenetic drugs. These drugs, including histone deacetylase inhibitors, acetyltransferase methyltransferase aim modulate curb growth uniquely landscape cells. Ongoing research clinical trials are rigorously evaluating efficacy these particularly their ability improve outcomes when used combination with other treatments. Such therapies may more effectively target potentially overcome challenge drug resistance, significant hurdle therapy. Additionally, importance nutrition, inflammation control, circadian rhythm regulation modulating responses been increasingly recognized, highlighting critical modifiers thereby effectiveness pharmacological interventions patient outcomes. drugs represent paradigm shift treatment, offering targeted that promise precise approach treating wide spectrum tumors, fewer side effects compared traditional chemotherapy. progress marks step towards personalized interventions, leveraging unique profiles individual tumors optimize treatment strategies.

Language: Английский

Citations

8
Sprouting sympathetic fibres release CXCL16 and norepinephrine to synergistically mediate sensory neuronal hyperexcitability in a rodent model of neuropathic pain DOI Creative Commons
Chen Wang,

Anjie Di,

Yan Yan Wu

et al.

British Journal of Anaesthesia, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Chronic neuropathic pain generally has a poor response to treatment with conventional drugs. Sympathectomy can alleviate in some patients, suggesting that abnormal sympathetic-somatosensory signaling interactions might underlie forms of pain. The molecular mechanisms underlying remain obscure. Lumbar sympathectomy was performed spared nerve injury (SNI) mice or rats, and the up-down method used measure mechanical paw withdrawal threshold. Dorsal root ganglia (DRG) injection perfusion were deliver virus Methylated RNA immunoprecipitation sequencing, RNA-sequencing, immunoelectron microscopy identify neurotransmitters. We found sprouting tyrosine hydroxylase-positive sympathetic fibres DRG mediated maintenance allodynia after SNI (day 28, P<0.001). further significantly increased N6-methyladenosine level CXCL16 messenger P<0.001), which attributable reduced demethylase fat mass obesity-associated protein (P=0.002) interaction YTHDF1 (P=0.013) ganglion. Enhanced expression lead increases release into act synergistically norepinephrine from terminals enhance neuronal excitability. Norepinephrine co-released contribute rodent model.

Language: Английский

Citations

1
Single Cell Transcriptome Signatures of Sarcoidosis in Lung Immune Cell Populations DOI Open Access
Camille M. Moore, Shu‐Yi Liao, Cheyret Wood

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 22, 2025

To identify cell specific molecular changes associated with sarcoidosis risk and progression, we aimed to characterize the cellular composition, gene expression patterns, cell-cell interactions in BAL cells from patients (both progressive non-progressive) healthy controls. Single RNA-seq data were collected on 12 4 control participants. We combined scRNA-seq these participants our previously 10 for a final sample size of 16 cases (8 8 14 Following initial preprocessing CellRanger, quality controlled, combined, clustered Seurat. tested differences proportions by disease group using F-tests pseudobulk analysis. Cell communication pathway analysis performed CellChat. identified five macrophage populations: resident, high metallothionein (MT) recruited, profibrotic proliferating macrophages. Each subpopulation displayed unique profiles, notable differential genes pathways linked resident macrophages, recruited also observed progression In non-macrophages cells, significant reduction number B compared Among T populations, transcriptional alterations at level. Additionally, distinct cell-to-cell macrophages between These findings underscore complexity immune involvement highlight potential targets further investigation.

Language: Английский

Citations

1
Targeting CXCR2 signaling in inflammatory lung diseases: neutrophil-driven inflammation and emerging therapies DOI
Md Sadique Hussain, Ahsas Goyal,

Kavita Goyal

et al.

Naunyn-Schmiedeberg s Archives of Pharmacology, Journal Year: 2025, Volume and Issue: unknown

Published: March 6, 2025

Language: Английский

Citations

1
Conserved spatial subtypes and cellular neighborhoods of cancer-associated fibroblasts revealed by single-cell spatial multi-omics DOI
Yunhe Liu, Ansam Sinjab, Jimin Min

et al.

Cancer Cell, Journal Year: 2025, Volume and Issue: unknown

Published: March 1, 2025

Language: Английский

Citations

1
Unveiling the genetic and epigenetic landscape of colorectal cancer: new insights into pathogenic pathways DOI
Humzah Postwala, Yesha Shah, Priyajeet S. Parekh

et al.

Medical Oncology, Journal Year: 2023, Volume and Issue: 40(11)

Published: Oct. 19, 2023

Language: Английский

Citations

12
Identification of human genes interacting with HIV attachment receptors and potentially involved in disease pathogenesis based on multi-network bioinformatics analysis DOI Open Access
V. S. Davydenko, Yu. V. Ostankova, A. N. Shchemelev

et al.

HIV Infection and Immunosuppressive Disorders, Journal Year: 2025, Volume and Issue: 16(4), P. 28 - 44

Published: Feb. 13, 2025

The aim of the study was to search for candidate genes interacting with HIV attachment receptors (CCR5, CXCR4, CCR2, CD4) and potentially involved in disease pathogenesis, based on complex silico network algorithms. Materials methods. A number web applications were used analyse genetic protein-protein networks, algorithms databases which are complementary. CD4 receptor chemokine co-receptor CCR5, CXCR4 CCR2 as background/baseline all cases, their protein products play a key role process virus cell. data analysed, including two-stage ranking identified according interaction background presence results analysis different resources. Results discussion. According results, using three resources: HumanNet — 451 genes, GeneMania 86, STRING 61. Based crossing resources, total associated 511. rank above 4 points 68. Of these, 31 (45.6%) encoding C-C/C-X-C family ligands, 12 (17.6%) C-C/C-XC receptors, 8 (11.8%) other types, 17 (25%) proteins types. following that not members C-C/C/C-X-C families indicated groups have been identified: ARRB2, TLR2, ADRA1A, ARRB1, FPR1, FPR3, GNAI1, PF4, PIK3CG, PPIA, S1PR3, GNA11, GNAI2, GNG2, PTPRC, ADRA1B, ADRB1, AFP, CD164, DBN1, GNB1, ITCH, RNF113A, SLC1A1, USP14. Conclusion. Most pathogenesis those progression infection is known or under active investigation. At same time, whose never considered possible participants identified, but suggest they may regulation entry and/or modulation immune response organism. Further bioinformatic experimental studies functions polymorphic variants these will help improve understanding basis identify new directions therapeutic approaches.

Language: Английский

Citations

0