scTrends: A living review of commercial single-cell and spatial 'omic technologies DOI Creative Commons
Joachim De Jonghe, James W. Opzoomer, Amaia Vilas‐Zornoza

et al.

Cell Genomics, Journal Year: 2024, Volume and Issue: 4(12), P. 100723 - 100723

Published: Dec. 1, 2024

Understanding the rapidly evolving landscape of single-cell and spatial omic technologies is crucial for advancing biomedical research drug development. We provide a living review both mature emerging commercial platforms, highlighting key methodologies trends shaping field. This spans from foundational such as microfluidics plate-based methods to newer approaches like combinatorial indexing; on side, we consider next-generation sequencing imaging-based transcriptomics. Finally, highlight that may fundamentally expand scope data generation within pharmaceutical research, creating opportunities discover validate novel mechanisms. Overall, this serves critical resource navigating commercialization application in academic research.

Language: Английский

Attractor Landscape Analysis Reveals a Reversion Switch in the Transition of Colorectal Tumorigenesis DOI Creative Commons
Dongkwan Shin, Jeong‐Ryeol Gong,

Sang Kwon Jeong

et al.

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

Published: Jan. 22, 2025

Abstract A cell fate change such as tumorigenesis incurs critical transition. It remains a longstanding challenge whether the underlying mechanism can be unraveled and molecular switch that reverse transition is found. Here systems framework, REVERT, presented with which reconstruct core regulatory network model reversion based on single‐cell transcriptome data over process identified. The usefulness of REVERT demonstrated by applying it to patient‐derived matched organoids colon cancer normal colon. generic framework applied investigate various phenomena.

Language: Английский

Citations

1
Connecting genotype and phenotype in minor spliceosome diseases DOI Open Access
Antto J. Norppa, Mariia Shcherbii, Mikko J. Frilander

et al.

RNA, Journal Year: 2025, Volume and Issue: 31(3), P. 284 - 299

Published: Jan. 6, 2025

Minor spliceosome is responsible for recognizing and excising a specific subset of divergent introns during the pre-mRNA splicing process. Mutations in unique snRNA protein components minor are increasingly being associated with variety germline somatic human disorders, collectively termed as spliceosomopathies. Understanding mechanistic basis these diseases has been challenging due to limited functional information on many components. However, recently published cryo-electron microscopy (cryo-EM) structures various assembly intermediates have marked significant advancement elucidating roles splicing. These structural breakthroughs not only enhanced our comprehension spliceosome's functionality but also shed light how disease-associated mutations disrupt its functions. Consequently, research focus now shifting toward investigating defects translate into broader pathological processes within gene expression pathways. Here we outline current knowledge spliceosome, explore consequences mutations, discuss emerging challenges connecting molecular dysfunctions clinical phenotypes.

Language: Английский

Citations

0
Single-Cell RNA Sequencing in Unraveling Acquired Resistance to EGFR-TKIs in Non-Small Cell Lung Cancer: New Perspectives DOI Open Access
Peng Lin,

Siyou Deng,

Jinjie Li

et al.

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(4), P. 1483 - 1483

Published: Feb. 11, 2025

Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) have demonstrated remarkable efficacy in treating non-small cell lung cancer (NSCLC), but acquired resistance greatly reduces and poses a significant challenge to patients. While numerous studies investigated the mechanisms underlying EGFR-TKI resistance, its complexity diversity make existing understanding still incomplete. Traditional approaches frequently struggle adequately reveal process of drug development through mean value analysis at overall cellular level. In recent years, rapid single-cell RNA sequencing technology has introduced transformative method for analyzing gene expression changes within tumor cells resolution. It not only deepens our microenvironment heterogeneity associated with also identifies potential biomarkers resistance. this review, we highlight critical role research, particular focus on application exploring EGFR-TKI-acquired NSCLC. We emphasize elucidating mechanism promise informing more precise personalized treatment strategies. Ultimately, approach aims advance NSCLC toward new era precision medicine.

Language: Английский

Citations

0
Towards understanding cancer dormancy over strategic hitching up mechanisms to technologies DOI Creative Commons
Sumin Yang, Jieun Seo, Jeong‐Hyeon Choi

et al.

Molecular Cancer, Journal Year: 2025, Volume and Issue: 24(1)

Published: Feb. 14, 2025

Delving into cancer dormancy has been an inherent task that may drive the lethal recurrence of after primary tumor relief. Cells in quiescence can survive for a short or long term silence, undergo genetic epigenetic changes, and initiate relapse through certain contextual cues. The state be induced by multiple conditions including drug treatment, turn, undergoes life cycle generally occurs dissemination, invasion, intravasation, circulation, immune evasion, extravasation, colonization. Throughout this cascade, cellular machinery governs fate individual cells, largely affected gene regulation. Despite its significance, precise view is yet hampered. Revolutionizing advanced single cell read sequencing analysis methodologies artificial intelligence, most recent stage research tool progress, expected to provide holistic diverse aspects dormancy.

Language: Английский

Citations

0
RNA splicing: novel star in pulmonary diseases with a treatment perspective DOI Creative Commons

Zhihui Niu,

Bingqian Xu, Xing Li

et al.

Acta Pharmaceutica Sinica B, Journal Year: 2025, Volume and Issue: unknown

Published: March 1, 2025

Language: Английский

Citations

0
Plate-based long-read single cell gene- and isoform transcriptome profiling using scLIS-seq DOI Creative Commons
Koen Deserranno,

Elise Callens,

Danique Berrevoet

et al.

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

Published: March 21, 2025

Abstract While contemporary short-read single cell RNA-sequencing allows to decipher tissue composition, discrimination between transcript isoforms remains challenging. Here, we propose long-read isoform sequencing (scLIS-seq), and highlight its performance on Jurkat HEK293T cells in direct comparison Smart-seq3xpress (SS3X). scLIS-seq demonstrates sensitive gene detection with high correlation compared SS3X detects at least 10 of over 2600 genes, while 17.1–21.6% the reads supported novel isoforms. Direct SS3X-reconstructed demonstrated scLIS-seq’s superiority. Overall, provides a powerful scRNA-seq strategy, enabling transcriptome analysis detection.

Language: Английский

Citations

0
Alternative transcriptomes and plant resilience: technological innovations and biological insights DOI
Ashish Pathak, Raja Jeet,

Mathilde Moens

et al.

Journal of Plant Biochemistry and Biotechnology, Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 29, 2024

Language: Английский

Citations

0
Potenzial und Anwendungsmöglichkeiten der Analyse einzelner Zellen: Hochauflösende Analytik DOI
Stefan Kirsch, Bernhard Polzer

Trillium Diagnostik, Journal Year: 2024, Volume and Issue: 22(3), P. 166 - 168

Published: Sept. 13, 2024

Die Analyse von Einzelzellen birgt großes Potenzial für die Diagnostik und Therapie verschiedenster Erkrankungen. In der Onkologie werden bereits im Rahmen Liquid Biopsy einzelne zirkulierende Tumorzellen Blut charakterisiert, um Krankheitsverläufe zu überwachen oder optimal anzupassen. Weiterentwicklung Einzelzellanalyse beispielsweise durch Spatial-Omics-Technologien sowie bioinformatische Auswertung verschiedener Informationsebenen lässt hoffen, dass in Zukunft bei komplexen physiologischen Prozessen pathogene Abweichungen nur wenigen Zellen frühzeitig identifiziert können.

Citations

0
Unlocking the Potential of Metagenomics with the PacBio High-Fidelity Sequencing Technology DOI Creative Commons

Yanhua Han,

J. He, Minghui Li

et al.

Microorganisms, Journal Year: 2024, Volume and Issue: 12(12), P. 2482 - 2482

Published: Dec. 2, 2024

Traditional methods for studying microbial communities have been limited due to difficulties in culturing and sequencing all species. Recent advances third-generation technologies, particularly PacBio’s high-fidelity (HiFi) sequencing, significantly advanced metagenomics by providing accurate long-read sequences. This review explores the role of HiFi overcoming limitations previous methods, including high error rates fragmented assemblies. We discuss benefits applications across various environments, such as human gut soil, which provides broader context further exploration. Key studies are discussed highlight sequencing’s ability recover complete coherent genomes from complex microbiomes, showcasing its superior accuracy continuity compared other technologies. Additionally, we explore potential quantitative analysis, well detection single nucleotide variations (SNVs) structural (SVs). PacBio is establishing a new benchmark metagenomics, with enhance our understanding ecology drive forward advancements both environmental clinical applications.

Language: Английский

Citations

0
scTrends: A living review of commercial single-cell and spatial 'omic technologies DOI Creative Commons
Joachim De Jonghe, James W. Opzoomer, Amaia Vilas‐Zornoza

et al.

Cell Genomics, Journal Year: 2024, Volume and Issue: 4(12), P. 100723 - 100723

Published: Dec. 1, 2024

Understanding the rapidly evolving landscape of single-cell and spatial omic technologies is crucial for advancing biomedical research drug development. We provide a living review both mature emerging commercial platforms, highlighting key methodologies trends shaping field. This spans from foundational such as microfluidics plate-based methods to newer approaches like combinatorial indexing; on side, we consider next-generation sequencing imaging-based transcriptomics. Finally, highlight that may fundamentally expand scope data generation within pharmaceutical research, creating opportunities discover validate novel mechanisms. Overall, this serves critical resource navigating commercialization application in academic research.

Language: Английский

Citations

0