Highly multiplexed spatial profiling with CODEX: bioinformatic analysis and application in human disease DOI Creative Commons
Wilson Kuswanto, Garry P. Nolan, Guolan Lu

et al.

Seminars in Immunopathology, Journal Year: 2022, Volume and Issue: 45(1), P. 145 - 157

Published: Nov. 21, 2022

Abstract Multiplexed imaging, which enables spatial localization of proteins and RNA to cells within tissues, complements existing multi-omic technologies has deepened our understanding health disease. CODEX, a multiplexed single-cell imaging technology, utilizes microfluidics system that incorporates DNA barcoded antibodies visualize 50 + cellular markers at the level. Here, we discuss latest applications CODEX studies cancer, autoimmunity, infection as well current bioinformatics approaches for analysis data from preprocessing cell segmentation marker quantification techniques. We conclude with commentary on challenges future developments profiling.

Language: Английский

Spatial Transcriptomics: A Powerful Tool in Disease Understanding and Drug Discovery DOI Creative Commons
Junxian Cao, Caifeng Li,

Zhao Cui

et al.

Theranostics, Journal Year: 2024, Volume and Issue: 14(7), P. 2946 - 2968

Published: Jan. 1, 2024

Recent advancements in modern science have provided robust tools for drug discovery. The rapid development of transcriptome sequencing technologies has given rise to single-cell transcriptomics and single-nucleus transcriptomics, increasing the accuracy accelerating discovery process. With evolution spatial (ST) technology emerged as a derivative approach. Spatial hot topic field omics research recent years; it not only provides information on gene expression levels but also offers expression. This shown tremendous potential disease understanding In this article, we introduce analytical strategies review its applications novel target mechanism unravelling. Moreover, discuss current challenges issues that need be addressed. conclusion, new perspective

Language: Английский

Citations

16
Mapping cancer biology in space: applications and perspectives on spatial omics for oncology DOI Creative Commons
Sumin Lee,

Gyeongjun Kim,

JinYoung Lee

et al.

Molecular Cancer, Journal Year: 2024, Volume and Issue: 23(1)

Published: Jan. 30, 2024

Technologies to decipher cellular biology, such as bulk sequencing technologies and single-cell technologies, have greatly assisted novel findings in tumor biology. Recent biology suggest that tumors construct architectures influence the underlying cancerous mechanisms. Increasing research has reported techniques map tissue a spatial context or targeted sampling-based characterization introduced solve oncology regarding heterogeneity, microenvironment, spatially located biomarkers. In this study, we address can delineate omics profile context, discovered via oncology, perspectives therapeutic approaches further technological developments.

Language: Английский

Citations

15
Single-cell spatial multiomics reveals tumor microenvironment vulnerabilities in cancer resistance to immunotherapy DOI Creative Commons
Camelia Quek, Aditya Pratapa, Xinyu Bai

et al.

Cell Reports, Journal Year: 2024, Volume and Issue: 43(7), P. 114392 - 114392

Published: June 29, 2024

Heterogeneous resistance to immunotherapy remains a major challenge in cancer treatment, often leading disease progression and death. Using CITE-seq matched 40-plex PhenoCycler tissue imaging, we performed longitudinal multimodal single-cell analysis of tumors from metastatic melanoma patients with innate resistance, acquired or response immunotherapy. We established the integration toolkit align transcriptomic features, cellular epitopes, spatial information provide deeper insights into tumors. With analysis, identified an "immune-striving" tumor microenvironment marked by peri-tumor lymphoid aggregates low infiltration T cells emergence MITF

Language: Английский

Citations

10
Tumor immune dysfunction and exclusion subtypes in bladder cancer and pan-cancer: a novel molecular subtyping strategy and immunotherapeutic prediction model DOI Creative Commons
Kun Zheng, Youlong Hai, Hongqi Chen

et al.

Journal of Translational Medicine, Journal Year: 2024, Volume and Issue: 22(1)

Published: April 17, 2024

Molecular subtyping is expected to enable precise treatment. However, reliable strategies for clinical application remains defective and controversial. Given the significance of tumor immune dysfunction exclusion (TIDE), we aimed develop a novel TIDE-based strategy guide personalized immunotherapy in bladder cancer (BC).

Language: Английский

Citations

9
Spatial transcriptomics: a new frontier in cancer research DOI Creative Commons
Siyuan Huang, Linkun Ouyang, Junjie Tang

et al.

Clinical Cancer Bulletin, Journal Year: 2024, Volume and Issue: 3(1)

Published: June 4, 2024

Abstract Tumor research is a fundamental focus of medical science, yet the intrinsic heterogeneity and complexity tumors present challenges in understanding their biological mechanisms initiation, progression, metastasis. Recent advancements single-cell transcriptomic sequencing have revolutionized way researchers explore tumor biology by providing unprecedented resolution. However, key limitation loss spatial information during preparation. Spatial transcriptomics (ST) emerges as cutting-edge technology that preserves RNA transcripts, thereby facilitating deeper heterogeneity, intricate interplay between cells microenvironment. This review systematically introduces ST technologies summarizes latest applications research. Furthermore, we provide thorough overview bioinformatics analysis workflow for data offer an online tutorial ( https://github.com/SiyuanHuang1/ST_Analysis_Handbook ). Lastly, discuss potential future directions ST. We believe will become powerful tool unraveling new insights effective treatment precision medicine oncology.

Language: Английский

Citations

9
Neuro-immune-cancer interactions: Mechanisms and therapeutic implications for tumor modulation DOI Creative Commons

Jianzhuang Wu,

Xinyi Lü, Chao Yan

et al.

Brain Behavior and Immunity Integrative, Journal Year: 2025, Volume and Issue: 10, P. 100119 - 100119

Published: April 1, 2025

Language: Английский

Citations

1
SPASCER: spatial transcriptomics annotation at single-cell resolution DOI Creative Commons
Zhiwei Fan, Yangyang Luo,

Huifen Lu

et al.

Nucleic Acids Research, Journal Year: 2022, Volume and Issue: 51(D1), P. D1138 - D1149

Published: Oct. 16, 2022

In recent years, the explosive growth of spatial technologies has enabled characterization heterogeneity tissue architectures. Compared to traditional sequencing, transcriptomics reserves information each captured location and provides novel insights into diverse spatially related biological contexts. Even though two databases exist, they provide limited analytical information. Information such as genes cells, cell-cell communication activities in space, cell type compositions microenvironment are critical clues unveil mechanism tumorigenesis embryo differentiation. Therefore, we constructed a new database, named SPASCER (https://ccsm.uth.edu/SPASCER), designed help understand organizations, region-specific microenvironment, intercellular interactions across architectures at multiple levels. contains datasets from 43 studies, including 1082 sub-datasets 16 organ types four species. scRNA-seq was integrated deconvolve/map transcriptomics, processed with interaction, gene pattern pathway enrichment analysis. Cell-cell regulation network matched were performed well. The application will architecture solid foundation for mechanistic understanding many processes healthy diseased tissues.

Language: Английский

Citations

35
The potential crosstalk between tumor and plasma cells and its association with clinical outcome and immunotherapy response in bladder cancer DOI Creative Commons
Fei Long, Wei Wang, Shuo Li

et al.

Journal of Translational Medicine, Journal Year: 2023, Volume and Issue: 21(1)

Published: May 3, 2023

Although immunotherapy is effective in improving the clinical outcomes of patients with bladder cancer (BC), it only a small percentage patients. Intercellular crosstalk tumor microenvironment strongly influences patient response to immunotherapy, while patterns plasma cells (PCs) as endogenous antibody-producing remain unknown. Here, we aimed explore heterogeneity PCs and their potential BC cells.

Language: Английский

Citations

22
Spatially Resolved Transcriptomics Technology Facilitates Cancer Research DOI Creative Commons
Qian Wang, Yuan Zhi,

Moxin Zi

et al.

Advanced Science, Journal Year: 2023, Volume and Issue: 10(30)

Published: Aug. 26, 2023

Single cell RNA sequencing (scRNA-seq) provides a great convenience for studying tumor occurrence and development its ability to study gene expression at the individual level. However, patient-derived tissues are composed of multiple types cells including adjacent non-malignant such as stromal immune cells. The spatial locations various in situ plays pivotal role tumors, which cannot be elucidated by scRNA-seq alone. Spatially resolved transcriptomics (SRT) technology emerges timely explore unrecognized relationship between background particular functions, is increasingly used cancer research. This review systematic overview SRT technologies that developed, more widely cutting-edge based on next-generation (NGS). In addition, main achievements precisely unveiling underappreciated function with unprecedented high-resolution research emphasized, aim developing effective clinical therapeutics oriented deeper understanding interaction surrounding

Language: Английский

Citations

21
Identifying novel biomarkers associated with bladder cancer treatment outcomes DOI Creative Commons
Peris Castaneda, Dan Theodorescu, Charles J. Rosser

et al.

Frontiers in Oncology, Journal Year: 2023, Volume and Issue: 13

Published: March 29, 2023

Bladder cancer is a complex disease with variable prognosis. Recent investigations into the molecular landscape of bladder have revealed frequent genetic alterations and subtypes therapeutic implications. Consequently, shift toward personalized treatment underway. To this end, several biomarkers been developed tested in their ability to predict response patients potentially help direct therapy. We performed search recently published PubMed articles using terms “biomarker,” “bladder cancer,” respective discussed (i.e., “neoadjuvant” or “BCG”). In review, we summarize latest studies on novel focus those intended improve risk stratification selection.

Language: Английский

Citations

20