Spatiotemporal transcriptomic analyses reveal molecular gradient patterning during development and the tonotopic organization along cochlear axis DOI Open Access
Mengzhen Yan, Penghui Zhang, Yafan Wang

et al.

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

Published: Oct. 31, 2024

Abstract Disruption of cochlear architecture and development can lead to malfunction, resulting in hearing defects. However, the spatial molecular profiles critical for function remain poorly understood due structural complexity cochlea. In this study, we performed comprehensive spatiotemporal transcriptomic analyses on developing adult cochlea, identifying numerous genes with gradient expression patterns hair cells (HCs) spiral ganglion neurons (SGNs) across apical-to-basal axis. The gene Myo7a , a well-known HC marker, established decreasing outer (OHCs) from apical basal regions adulthood. contrast, other class exhibited an opposing pattern along axis adulthood, such as Calb2 HCs Nefh SGNs, which potentially corresponds tuning properties sensing frequency sounds. Importantly, our provided compelling evidences existence distinct subtypes OHCs. revealed regional heterogeneity cell communication intensity between weakest at apex, aligning region detection low-frequency sound. This study systematically characterized fine organizations HCs, their regionalized cell-communications within offering insights into morphological foundations underlying tonotopic organization discrimination.

Language: Английский

ShinyCellPlus: an improved ShinyCell application for the interactive visualization of single cell dat DOI Creative Commons
Drew Moore, Bryan Granger, Stefano Berto

et al.

F1000Research, Journal Year: 2025, Volume and Issue: 14, P. 338 - 338

Published: March 27, 2025

Motivation With the growing complexity of single-cell data, there is a need for more sophisticated sharing tools. To address this, we developed ShinyCellPlus, an enhanced version ShinyCell, that offers advanced, interactive visualizations and functionalities RNA-seq data Results The library facilitates visualization, shares tab-separated tables from marker detection or differential expression analyses, implements functional enrichment analysis, provides easy access to gene set enrichments. Availability implementation Code documentation ShinyCellPlus are currently available at https://github.com/BioinformaticsMUSC/ShinyCellPlus

Language: Английский

Citations

0
From Invaginating Site to Deep Lesion: Spatial Transcriptomics Unravels Ectopic Endometrial Penetration Features in Adenomyosis DOI Creative Commons
Boyu Li, Jia Qi,

Yumeng Cao

et al.

Advanced Science, Journal Year: 2025, Volume and Issue: unknown

Published: April 7, 2025

Abstract Adenomyosis, characterized by clinical intractability, significantly impacts female fertility and life quality due to the absence of definitive diagnostic markers effective treatment options. The invagination theory is a primary hypothesis for adenomyosis, but underlying molecular mechanisms remain unclear. In this study, spatial transcriptional landscape adenomyosis with an evident structure mapped from endometrial invaginating site ectopic lesions utilizing transcriptomics single‐cell RNA sequencing. addition, authors employ bulk sequencing deconvolution assess significance core ecotypes, use histological techniques target specific cell types, conduct in vitro experiments validation. At site, SFRP5 + epithelial cells promote proliferation angiogenesis through secretion IHH. During invading process, ESR1 smooth muscle (SMCs) facilitate invasion creating migratory tracts via collagen degradation. Within deep lesions, CNN1 stromal fibroblasts induce fibrosis undergoing fibroblast‐to‐myofibroblast transition (FMT) response pathologic profibrogenic signals microenvironment lesions. This work offers in‐depth understanding pathological processes invagination. Furthermore, introduces first web source which expected be valuable resource subsequent research.

Language: Английский

Citations

0
New horizons at the interface of artificial intelligence and translational cancer research DOI
Josephine Yates, Eliezer M. Van Allen

Cancer Cell, Journal Year: 2025, Volume and Issue: 43(4), P. 708 - 727

Published: April 1, 2025

Language: Английский

Citations

0
Single-Cell RNA-Sequencing: Opening New Horizons for Breast Cancer Research DOI Open Access
Lingyan Xiang,

Jie Rao,

Jingping Yuan

et al.

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(17), P. 9482 - 9482

Published: Aug. 31, 2024

Breast cancer is the most prevalent malignant tumor among women with high heterogeneity. Traditional techniques frequently struggle to comprehensively capture intricacy and variety of cellular states interactions within breast cancer. As global precision medicine rapidly advances, single-cell RNA sequencing (scRNA-seq) has become a highly effective technique, revolutionizing research by offering unprecedented insights into heterogeneity complexity This cutting-edge technology facilitates analysis gene expression profiles at level, uncovering diverse cell types microenvironment. By dissecting composition transcriptional signatures cells, scRNA-seq provides new perspectives for understanding mechanisms behind therapy, drug resistance metastasis in In this review, we summarized working principle workflow emphasized major applications discoveries research, highlighting its impact on our comprehension biology potential guiding personalized treatment strategies.

Language: Английский

Citations

1
Spatiotemporal transcriptomic analyses reveal molecular gradient patterning during development and the tonotopic organization along cochlear axis DOI Open Access
Mengzhen Yan, Penghui Zhang, Yafan Wang

et al.

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

Published: Oct. 31, 2024

Abstract Disruption of cochlear architecture and development can lead to malfunction, resulting in hearing defects. However, the spatial molecular profiles critical for function remain poorly understood due structural complexity cochlea. In this study, we performed comprehensive spatiotemporal transcriptomic analyses on developing adult cochlea, identifying numerous genes with gradient expression patterns hair cells (HCs) spiral ganglion neurons (SGNs) across apical-to-basal axis. The gene Myo7a , a well-known HC marker, established decreasing outer (OHCs) from apical basal regions adulthood. contrast, other class exhibited an opposing pattern along axis adulthood, such as Calb2 HCs Nefh SGNs, which potentially corresponds tuning properties sensing frequency sounds. Importantly, our provided compelling evidences existence distinct subtypes OHCs. revealed regional heterogeneity cell communication intensity between weakest at apex, aligning region detection low-frequency sound. This study systematically characterized fine organizations HCs, their regionalized cell-communications within offering insights into morphological foundations underlying tonotopic organization discrimination.

Language: Английский

Citations

0