Gaeklrr: A Novel Clustering Method of the Low-Rank Represent Based on Graph Auto-Encoder and Relaxed K-Means for Single Cell Type Identification DOI

Linping Wang,

Jin‐Xing Liu, Junliang Shang

et al.

Published: Jan. 1, 2023

With the rapid advancement of single-cell RNA sequencing (scRNA-seq) technology, disease mechanism research has advanced to a new level. Clustering is critical for scRNA-seq because it reveals similarity expression patterns. However, data contains numerous noises and outliers. Traditional clustering algorithms may fail capture accurate information. In this study, we propose GAEKLRR method type identification, which low-rank representation (LRR) based on graph auto-encoder (GAE) relaxed k-means. consists gedLRR Among them, LRR algorithm GAE. made up an encoder decoder. Firstly, reduce impact noise outliers mapping benchmark, generates robust embedding dictionary using gedLRR. by GAE structural information node features. Due reconstruction inner product distance, interpretability. Secondly, information, utilizes seek matrix while k-means update centroid. It worth noting that indication captured labels, can be used directly tasks. Finally, experiments real datasets demonstrate significant advantages clustering.

Language: Английский

A single-cell atlas of the aging mouse ovary DOI Creative Commons

José V. V. Isola,

Sarah R. Ocañas,

Chase R. Hubbart

et al.

Nature Aging, Journal Year: 2024, Volume and Issue: 4(1), P. 145 - 162

Published: Jan. 10, 2024

Abstract Ovarian aging leads to diminished fertility, dysregulated endocrine signaling and increased chronic disease burden. These effects begin emerge long before follicular exhaustion. Female humans experience a sharp decline in fertility around 35 years of age, which corresponds declines oocyte quality. Despite growing body work, the field lacks comprehensive cellular map transcriptomic changes mouse ovary identify early drivers ovarian decline. To fill this gap we performed single-cell RNA sequencing on tissue from young (3-month-old) reproductively aged (9-month-old) mice. Our analysis revealed doubling immune cells ovary, with lymphocyte proportions increasing most, was confirmed by flow cytometry. We also found an age-related downregulation collagenase pathways stromal fibroblasts, rises fibrosis. Follicular displayed stress-response, immunogenic fibrotic pathway inductions aging. This report provides critical insights into mechanisms responsible for phenotypes. The data can be explored interactively via Shiny-based web application.

Language: Английский

Citations

63
Advances in single-cell transcriptomics in animal research DOI Creative Commons

Yunan Yan,

Senlin Zhu, Minghui Jia

et al.

Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology, Journal Year: 2024, Volume and Issue: 15(1)

Published: Aug. 2, 2024

Abstract Understanding biological mechanisms is fundamental for improving animal production and health to meet the growing demand high-quality protein. As an emerging biotechnology, single-cell transcriptomics has been gradually applied in diverse aspects of research, offering effective method study gene expression high-throughput single cells different tissues/organs animals. In unprecedented manner, researchers have identified cell types/subtypes their marker genes, inferred cellular fate trajectories, revealed cell‒cell interactions animals using transcriptomics. this paper, we introduce development technology review processes, advancements, applications research. We summarize recent efforts obtain a more profound understanding nutrition health, reproductive performance, genetics, disease models livestock species. Moreover, practical experience accumulated based on large number cases highlighted provide reference determining key factors (e.g., sample size, clustering, type annotation) analysis. also discuss limitations outlook current stage. This paper describes comprehensive progress novel insights sustainable advancements agricultural productivity health.

Language: Английский

Citations

7
Single-cell transcriptomics reveals the mechanisms of lung injury induced by Galt gene editing in mouse DOI Creative Commons
Zhihao Li, Ning Wang, Haobo Wang

et al.

Biochemical and Biophysical Research Communications, Journal Year: 2025, Volume and Issue: 763, P. 151780 - 151780

Published: April 11, 2025

Galactosemia, caused by mutations in the GALT gene, leads to multi-organ damage. This study investigates impact of Galt c.847 + 1G > T mutation on lung tissue using single-cell transcriptomics. We employed CRISPR/Cas9 generate a gene-edited mouse model with c. 847 and assessed expression through PCR Western blotting. Histopathological analysis revealed significant structural changes, including alveolar congestion inflammation. Single-cell RNA sequencing demonstrated marked reduction immune cells (NK, T, macrophages, B cells) an increase type II cells, vascular endothelial myofibroblasts GAL mouse. The increased abundance indicated impaired differentiation repair. Metabolic abnormalities linked mutation, disruptions TGF-β1, FGF, Mif pathways contributing cellular dysfunction exacerbated injury. provides insights into molecular mechanisms injury galactosemia, highlighting alterations cell populations key signaling pathways.

Language: Английский

Citations

0
Single-cell RNA sequencing characterization of Holstein cattle blood and milk immune cells during a chronic Staphylococcus aureus mastitis infection DOI Creative Commons
Jayne E Wiarda, Kaitlyn M. Sarlo Davila, Julian Trachsel

et al.

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: April 12, 2025

Language: Английский

Citations

0
Single-cell transcriptomic analysis reveals regulative mechanisms of follicular selection and atresia in chicken granulosa cells DOI

Wenhui Zhang,

Xuejiao Chen, Ruixue Nie

et al.

Food Research International, Journal Year: 2024, Volume and Issue: 198, P. 115368 - 115368

Published: Nov. 17, 2024

Language: Английский

Citations

3
Follicular development and ovary aging: single-cell studies DOI
Hong Zhao, Yifu Wang, Yihua Yang

et al.

Biology of Reproduction, Journal Year: 2023, Volume and Issue: 109(4), P. 390 - 407

Published: July 28, 2023

Abstract Follicular development is a critical process in reproductive biology that determines the number of oocytes and interacts with various cells within follicle (such as oocytes, granulosa cells, cumulus theca cells), plays vital role fertility health because dogma limited oogonia. Dysregulation follicular can lead to infertility problems other disorders. To explore physiological pathological mechanisms development, immunology-based methods, microarrays, next-generation sequencing have traditionally been used for characterization at tissue level. However, proliferation single-cell techniques, research has uncovered unique molecular individual masked by previous holistic analyses. In this review, we briefly summarize achievements limitations traditional methods study development. Simultaneously, focus on how understand level reveal relevant intervention targets. Moreover, also delineate application prospects research.

Language: Английский

Citations

5
A single-cell atlas of the aging murine ovary DOI Creative Commons

José V. V. Isola,

Sarah R. Ocañas,

Chase R. Hubbart

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: April 29, 2023

ABSTRACT Ovarian aging leads to diminished fertility, dysregulated endocrine signaling, and increased chronic disease burden. These effects begin emerge long before follicular exhaustion. Around 35 years old, women experience a sharp decline in corresponding declines oocyte quality. Despite growing body of work, the field lacks comprehensive cellular map transcriptomic changes ovary identify early drivers ovarian decline. To fill this gap, we performed single-cell RNA sequencing on tissue from young (3-month-old) reproductively aged (9-month-old) mice. Our analysis revealed doubling immune cells ovary, with lymphocyte proportions increasing most, which was confirmed by flow cytometry. We also found an age-related downregulation collagenase pathways stromal fibroblasts, corresponds rises fibrosis. Follicular displayed stress response, immunogenic, fibrotic signaling pathway inductions aging. This report raises provides critical insights into mechanisms responsible for phenotypes.

Language: Английский

Citations

4
Single-Cell RNA Sequencing Reveals the Cellular Landscape of Longissimus Dorsi in a Newborn Suhuai Pig DOI Open Access
Xiao Wei,

Nengjing Jiang,

Zhengyu Ji

et al.

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(2), P. 1204 - 1204

Published: Jan. 18, 2024

The introduction of single-cell RNA sequencing (scRNA-seq) technology has spurred additional advancements in analyzing the cellular composition tissues. longissimus dorsi (LD) pigs serves as primary skeletal muscle for studying meat quality pig industry. However, profile porcine LD is still its infancy stage. In this study, we profiled transcriptomes 16,018 cells a newborn Suhuai at resolution. Subsequently, constructed atlas LD, identifying 11 distinct cell populations, including endothelial (24.39%), myotubes (18.82%), fibro-adipogenic progenitors (FAPs, 18.11%), satellite (16.74%), myoblasts (3.99%), myocytes (5.74%), Schwann (3.81%), smooth (3.22%), dendritic (2.99%), pericytes (1.86%), and neutrophils (0.33%). CellChat was employed to deduce cell–cell interactions by evaluating gene expression receptor–ligand pairs across different types. results show that FAPs are signal contributors LD. addition, delineated developmental trajectory myogenic examined alterations various marker genes molecular events throughout stages differentiation. Moreover, found can be divided into three subclusters (NR2F2-FAPs, LPL-FAPs, TNMD-FAPs) according their biological functions, suggesting could associated with differentiation tendon cell. Taken together, communication network pig, analyzed heterogeneity subpopulation cells. This enhances our comprehension features involved development control pigs.

Language: Английский

Citations

1
Exploring the induction of endometrial epithelial cell apoptosis in clinical-type endometritis in yaks through the cyt-c/caspase-3 signaling axis DOI
Zhipeng Cao, Shuo Wang, Ming Qi

et al.

Microbial Pathogenesis, Journal Year: 2023, Volume and Issue: 186, P. 106470 - 106470

Published: Dec. 2, 2023

Language: Английский

Citations

3
Gaeklrr: A Novel Clustering Method of the Low-Rank Represent Based on Graph Auto-Encoder and Relaxed K-Means for Single Cell Type Identification DOI

Linping Wang,

Jin‐Xing Liu, Junliang Shang

et al.

Published: Jan. 1, 2023

With the rapid advancement of single-cell RNA sequencing (scRNA-seq) technology, disease mechanism research has advanced to a new level. Clustering is critical for scRNA-seq because it reveals similarity expression patterns. However, data contains numerous noises and outliers. Traditional clustering algorithms may fail capture accurate information. In this study, we propose GAEKLRR method type identification, which low-rank representation (LRR) based on graph auto-encoder (GAE) relaxed k-means. consists gedLRR Among them, LRR algorithm GAE. made up an encoder decoder. Firstly, reduce impact noise outliers mapping benchmark, generates robust embedding dictionary using gedLRR. by GAE structural information node features. Due reconstruction inner product distance, interpretability. Secondly, information, utilizes seek matrix while k-means update centroid. It worth noting that indication captured labels, can be used directly tasks. Finally, experiments real datasets demonstrate significant advantages clustering.

Language: Английский

Citations

0