Advancements in the Application of scRNA-Seq in Breast Research: A Review DOI Open Access
Zhenyu Zhang,

Xiao‐Ming Ma,

Yongfu La

et al.

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(24), P. 13706 - 13706

Published: Dec. 22, 2024

Single-cell sequencing technology provides apparent advantages in cell population heterogeneity, allowing individuals to better comprehend tissues and organs. Sequencing is currently moving beyond the standard transcriptome single-cell level, which likely bring new insights into function of breast cells. In this study, we examine primary types involved development, as well achievements study scRNA-seq microenvironment, stressing finding novel subsets using approaches analyzing problems solutions scRNA-seq. Furthermore, are excited about field’s promising future.

Language: Английский

Spatial multi-omics: deciphering technological landscape of integration of multi-omics and its applications DOI Creative Commons

Xiaojie Liu,

Ting Peng,

Miaochun Xu

et al.

Journal of Hematology & Oncology, Journal Year: 2024, Volume and Issue: 17(1)

Published: Aug. 24, 2024

The emergence of spatial multi-omics has helped address the limitations single-cell sequencing, which often leads to loss context among cell populations. Integrated analysis genome, transcriptome, proteome, metabolome, and epigenome enhanced our understanding biology molecular basis human diseases. Moreover, this approach offers profound insights into interactions between intracellular intercellular mechanisms involved in development, physiology, pathogenesis In comprehensive review, we examine current advancements technologies, focusing on their evolution refinement over past decade, including improvements throughput resolution, modality integration, accuracy. We also discuss pivotal contributions revealing heterogeneity, constructing detailed atlases, deciphering crosstalk tumor immunology, advancing translational research cancer therapy through precise mapping.

Language: Английский

Citations

15
Interleukin‐5 as a pleiotropic cytokine orchestrating airway type 2 inflammation: Effects on and beyond eosinophils DOI Creative Commons
Kathleen M. Buchheit, Dominick Shaw, Geoffrey Chupp

et al.

Allergy, Journal Year: 2024, Volume and Issue: 79(10), P. 2662 - 2679

Published: Oct. 1, 2024

Abstract Interleukin (IL)‐5 is the key cytokine in maturation, activation, proliferation, migration and survival of eosinophils, which are effector cells many upper lower airway diseases. Through its effects on IL‐5 indirectly contributes to various pathophysiological processes including tissue damage, repair remodelling. Understanding importance eosinophil‐associated diseases led development anti‐IL‐5 therapies, provide clinical benefits across a range conditions. However, recent evidence suggests that eosinophil‐depletion alone may not account for all therapeutic therapy also contribute disease independently eosinophils. Indeed, from ex vivo studies targeted demonstrates inhibition affects much broader beyond epithelial cells, plasma mast basophils, neutrophils, type 2 innate lymphoid T regulatory fibroblasts. This review will an update supporting breadth biology relevant pathogenesis inflammation, where there need additional insight, implications more central role inflammation.

Language: Английский

Citations

6
Single-cell sequencing in diabetic retinopathy: progress and prospects DOI Creative Commons
Tianshu Yang, Ningzhi Zhang, Ning Yang

et al.

Journal of Translational Medicine, Journal Year: 2025, Volume and Issue: 23(1)

Published: Jan. 13, 2025

Diabetic retinopathy is a major ocular complication of diabetes, characterized by progressive retinal microvascular damage and significant visual impairment in working-age adults. Traditional bulk RNA sequencing offers overall gene expression profiles but does not account for cellular heterogeneity. Single-cell overcomes this limitation providing transcriptomic data at the individual cell level distinguishing novel subtypes, developmental trajectories, intercellular communications. Researchers can use single-cell to draw atlases identify features cells, enhancing our understanding pathogenesis pathological changes diabetic retinopathy. Additionally, widely employed analyze organoids single extracellular vesicles. multi-omics integrates omics information, whereas stereo-sequencing analyzes spatiotemporal simultaneously. This review discusses protocols obtaining cells from retina accurate data. It highlights applications advancements study normal retinas associated with underscores potential these technologies deepen that may lead introduction new therapeutic strategies.

Language: Английский

Citations

0
Analysis and Validation of Autophagy-Related Gene Biomarkers and Immune Cell Infiltration Characteristic in Bronchopulmonary Dysplasia by Integrating Bioinformatics and Machine Learning DOI Creative Commons
Shuzhe Xiao,

Yue Ding,

Chen Du

et al.

Journal of Inflammation Research, Journal Year: 2025, Volume and Issue: Volume 18, P. 549 - 563

Published: Jan. 1, 2025

Autophagy and immunity play important regulatory roles in lung developmental disorders. However, there is currently a lack of bioinformatics analysis on autophagy-related genes (ARGs) immune infiltration bronchopulmonary dysplasia (BPD). We aim to screen validate the signature BPD by vivo experiment. GSE8586 was obtained from Gene Expression Omnibus (GEO) database. The differentially expressed (DEGs) were identified using R program. Using cell-type identification with CIBERSORT analyze inflammatory status BPD. Subsequently, hub Lasso Cytoscape three machine-learning algorithms (MCC, Degree MCODE). In addition, validated ROC, single-cell sequence IHC hyperoxia rats. Finally, we searched drug targets these genes, established nomogram model for predicting risk There 73 (DE-ARGs) overlapping DEGs ARGs. Five BRIX1, JUN, PES1, NR4A1 RRP9, lowly group had high diagnostic value model. All are mainly located B cell, epithelial fibroblast, endothelial smooth muscle cell pneumocyte sequencing. Moreover, showed cells higher closely associated genes. also predict result rats that expression BRX1, lower compared normoxia group. NR4A1, may be promising therapeutic Our findings provided researchers clinicians more evidence regarding immunotherapeutic strategies treatment.

Language: Английский

Citations

0
Integrated spatial transcriptome and metabolism study reveals metabolic heterogeneity in human bladder cancer DOI Creative Commons
Yu Lu, Fangdie Ye,

Xuedan Han

et al.

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 28, 2025

Abstract Bladder cancer (BC) is a malignancy that originates from the cells lining bladder and one of most common cancers urinary system, capable occurring in any part bladder. However, molecular mechanisms underlying malignant transformation BC have not been systematically studied. This study integrated cutting-edge techniques spatial transcriptomics (ST) metabolomics (SM) to capture transcriptomic metabolomic landscapes both adjacent normal tissues. ST results revealed significant upregulation genes associated with choline metabolism glucose metabolism, while related sphingolipid tryptophan were significantly downregulated. Additionally, metabolic reprogramming was observed tissues, including as well downregulation metabolism. These alterations may play crucial role promoting tumorigenesis immune evasion BC. The interpretation SM data this offers new insights into progression provides valuable clues for prevention treatment

Language: Английский

Citations

0
Single-cell RNA sequencing reveals the impaired epidermal differentiation and pathological microenvironment in diabetic foot ulcer DOI Creative Commons
Y. Liu, Peng Wang, Jingting Li

et al.

Burns & Trauma, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 17, 2025

Diabetic foot ulcer (DFU) is one of the most common and complex complications diabetes, but underlying pathophysiology remains unclear. Single-cell RNA sequencing (scRNA-seq) has been conducted to explore novel cell types or molecular profiles DFU from various perspectives. This study aimed comprehensively analyze potential mechanisms impaired re-epithelization in a single-cell perspective. We scRNA-seq on tissues human normal skin, acute wound, investigate epidermal differentiation pathological microenvironment. Pseudo-time lineage inference analyses revealed distinct states transition trajectories cells under different conditions. Transcription factor analysis regulatory mechanism key subtypes keratinocytes. Cell-cell interaction network between proinflammatory microenvironment cells. Laser-capture microscopy coupled with (LCM-seq) multiplex immunohistochemistry were used validate expression location Our research provided comprehensive map phenotypic dynamic changes that occur during differentiation, alongside corresponding networks DFU. Importantly, we identified two keratinocytes: basal (BC-2) diabetes-associated keratinocytes (DAK) might play crucial roles impairment homeostasis. BC-2 DAK showed marked increase DFU, an inactive state insufficient motivation for differentiation. was involved cellular response apoptosis processes, high TXNIP, IFITM1, IL1R2. Additionally, pro-differentiation transcription factors downregulated indicating process be inhibited associated glucose Furthermore, increased CCL2 + CXCL2+ fibroblasts, VWA1+ vascular endothelial cells, GZMA+CD8+ T detected These wound could regulate fate through TNFSF12-TNFRSF12A, IFNG-IFNGR1/2, IL-1B-IL1R2 pathways, which result persistent inflammation findings offer insights into present therapeutic targets improve care treatment outcomes patients.

Language: Английский

Citations

0
Spatial transcriptomics in autoimmune rheumatic disease: potential clinical applications and perspectives DOI Creative Commons
Akira Miyamoto, Hiroshi Shimagami, Atsushi Kumanogoh

et al.

Inflammation and Regeneration, Journal Year: 2025, Volume and Issue: 45(1)

Published: Feb. 20, 2025

Spatial transcriptomics is a cutting-edge technology that analyzes gene expression at the cellular level within tissues while integrating spatial location information. This concept, which combines high-plex RNA sequencing with data, emerged in early 2010s. has rapidly expanded development of technologies such as situ hybridization, sequencing, barcoding, and microdissection-based methods. Each technique offers advanced mapping resolution precise assessments single-cell level. Over past decade, use on clinical samples enabled researchers to identify expressions specific diseased foci, significantly enhancing our understanding interactions disease processes. In field rheumatology, complex elusive pathophysiology diseases rheumatoid arthritis, systemic lupus erythematosus, Sjögren's syndrome remains challenge for personalized treatment. provides insights into how different cell populations interact synovial tissue, kidneys, salivary glands. review summarizes current autoimmune rheumatic diseases, focusing immune distribution tissues. We also explore potential from perspective discuss possibilities translating this bedside.

Language: Английский

Citations

0
Mapping molecular landscapes in triple-negative breast cancer: insights from spatial transcriptomics DOI
Fares Saeed H. Al-Mansour, Hassan H. Almasoudi, Ali Albarrati

et al.

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

Published: March 22, 2025

Language: Английский

Citations

0
Neoantigen vaccines: advancing personalized cancer immunotherapy DOI Creative Commons
Alaa A. A. Aljabali,

Yassmen Hamzat,

Alaa Alqudah

et al.

Exploration of Immunology, Journal Year: 2025, Volume and Issue: 5

Published: April 8, 2025

Neoantigen vaccines are a promising strategy in cancer immunotherapy that leverage tumor-specific mutations to elicit targeted immune responses. Although they have considerable potential, development challenges related antigen prediction accuracy, manufacturing complexity, and scalability remain key obstacles their widespread clinical use. This literature review was conducted using PubMed, Scopus, Web of Science, Google Scholar databases identify relevant studies. Keywords included “neoantigen vaccines,” “personalized immunotherapy,” “tumor heterogeneity,” “bioinformatics pipelines,” “prediction algorithms”. Clinical trial data were sourced from ClinicalTrials.gov, Trialtrove, other publicly available registries. Eligible studies peer-reviewed research articles, systematic reviews, trials focusing on neoantigen vaccine development, bioinformatic strategies, immunotherapy. Tumor heterogeneity clonal evolution significantly impact efficacy, necessitating multi-epitope targeting adaptive design. Current algorithms suffer high false-positive false-negative rates, requiring further integration with multi-omics machine learning enhance accuracy. Manufacturing remains complex, time-intensive, costly, advancements standardization automation. Combination therapies, such as checkpoint inhibitors adoptive cell counteract the immunosuppressive tumor microenvironment, improving treatment outcomes. hold great potential for personalized therapy but require bioinformatics, scalability, immunomodulatory strategies efficacy. Continued interdisciplinary collaboration essential refining applications.

Language: Английский

Citations

0
Unveiling hypoxia-related prognostic and immunotherapeutic biomarkers in lung adenocarcinoma through single-cell and bulk RNA sequencing: Including insights into PGF DOI
Shengqiang Mao, Lü Chen, Qingyan Li

et al.

International Journal of Biological Macromolecules, Journal Year: 2025, Volume and Issue: 309, P. 143056 - 143056

Published: April 12, 2025

Language: Английский

Citations

0