Quantifying and interpreting biologically meaningful spatial signatures within tumor microenvironments DOI Creative Commons
Siyu Jing,

He-qi Wang,

Ping Lin

et al.

npj Precision Oncology, Journal Year: 2025, Volume and Issue: 9(1)

Published: March 11, 2025

The tumor microenvironment (TME) plays a crucial role in orchestrating cell behavior and cancer progression. Recent advances spatial profiling technologies have uncovered novel signatures, including univariate distribution patterns, bivariate relationships, higher-order structures. These signatures the potential to revolutionize mechanism treatment. In this review, we summarize current state of signature research, highlighting computational methods uncover spatially relevant biological significance. We discuss impact these on fundamental biology translational address challenges future research directions.

Language: Английский

Enablers and challenges of spatial omics, a melting pot of technologies DOI Creative Commons
Theodore Alexandrov, Julio Sáez-Rodríguez, Sinem K. Saka

et al.

Molecular Systems Biology, Journal Year: 2023, Volume and Issue: 19(11)

Published: Oct. 16, 2023

Abstract Spatial omics has emerged as a rapidly growing and fruitful field with hundreds of publications presenting novel methods for obtaining spatially resolved information any data type on spatial scales ranging from subcellular to organismal. From technology development perspective, is highly interdisciplinary that integrates imaging omics, molecular analyses, sequencing mass spectrometry, image analysis bioinformatics. The emergence this not only opened window into biology, but also created multiple opportunities, questions, challenges method developers. Here, we provide the perspective developers what makes unique. After providing brief overview state art, discuss technological enablers present our vision about future applications impact melting pot.

Language: Английский

Citations

17
Cancer metastasis through the lymphatic versus blood vessels DOI Creative Commons
Stanley P. L. Leong, Marlys H. Witte

Clinical & Experimental Metastasis, Journal Year: 2024, Volume and Issue: 41(4), P. 387 - 402

Published: June 28, 2024

Abstract Whether cancer cells metastasize from the primary site to distant sites via lymphatic vessels or blood directly into circulation is still under intense study. In this review article, we follow journey of metastasizing sentinel lymph nodes and beyond sites. We emphasize heterogeneity microenvironment as major determinants metastasis. Multiple molecules have been found be associated with complicated process Based on large node data, it reasonable conclude that may through in some cases but most cases, they use gateway enter

Language: Английский

Citations

6
The current landscape of spatial biomarkers for prediction of response to immune checkpoint inhibition DOI Creative Commons
Hannah L. Williams, A. Frei,

Thibaud Koessler

et al.

npj Precision Oncology, Journal Year: 2024, Volume and Issue: 8(1)

Published: Aug. 13, 2024

Enabling the examination of cell-cell relationships in tissue, spatially resolved omics technologies have revolutionised our perspectives on cancer biology. Clinically, development immune checkpoint inhibitors (ICI) has advanced therapeutics. However, a major challenge effective implementation is identification predictive biomarkers response. In this review we examine potential added value spatial response to ICI beyond current clinical benchmarks.

Language: Английский

Citations

6
Using Transcriptomics and Cell Morphology Data in Drug Discovery: The Long Road to Practice DOI Creative Commons
Lavinia-Lorena Pruteanu, Andreas Bender

ACS Medicinal Chemistry Letters, Journal Year: 2023, Volume and Issue: 14(4), P. 386 - 395

Published: March 22, 2023

Gene expression and cell morphology data are high-dimensional biological readouts of much recent interest for drug discovery. They able to describe systems in different states (e.g., healthy diseased), as well before after compound treatment, they hence useful matching both spaces repurposing) characterizing compounds with respect efficacy safety endpoints. This Microperspective describes advances this direction a focus on applied discovery repurposing, outlining what else is needed advance further, particular better understanding the applicability domain their relevance decision making, which currently often still unclear.

Language: Английский

Citations

14
Single-cell and spatially resolved transcriptomics for liver biology DOI
Ping Lin, Xi Yan, Siyu Jing

et al.

Hepatology, Journal Year: 2023, Volume and Issue: 80(3), P. 698 - 720

Published: April 1, 2023

Single-cell transcriptomics enables the identification of rare cell types and inference state transitions, whereas spatially resolved allows quantification cells genes in context tissues. The recent progress these new technologies is improving our understanding landscape its roles diseases. Here, we review key biological insights into liver homeostasis, development, regeneration, chronic disease, cancer obtained from single-cell transcriptomics. We highlight atlas that characterizes comprehensive cellular composition; diversity function; spatial architecture such as zonation, communication, proximity; identity conversion cell-specific alterations are associated with pathology; therapeutic targets. further discuss outstanding challenges, advanced experimental technologies, computational methods help to address challenges.

Language: Английский

Citations

12
Steps to Improve Precision Medicine in Epilepsy DOI Creative Commons
Simona Balestrini, Davide Mei, Sanjay M. Sisodiya

et al.

Molecular Diagnosis & Therapy, Journal Year: 2023, Volume and Issue: 27(6), P. 661 - 672

Published: Sept. 27, 2023

Precision medicine is an old concept, but it not widely applied across human health conditions as yet. Numerous attempts have been made to apply precision in epilepsy, this has based on a better understanding of aetiological mechanisms and deconstructing disease into multiple biological subsets. The scope provide effective strategies for treating individual patients with specific agent(s) that are likely work best the causal make-up. We overview main applications including current limitations pitfalls, propose potential implementation achieve higher rate success patient care. Such include establishing definition its outcomes; learning from past experiences, failures other fields (e.g. oncology); using appropriate drug repurposing versus traditional discovery process); adequate methods assess efficacy randomised controlled trials alternative trial designs). Although progress diagnostic techniques now allows comprehensive characterisation each epilepsy condition molecular, biological, structural clinical perspective, there remain challenges integration data practice domain.

Language: Английский

Citations

12
Metabolomics at the tumor microenvironment interface: Decoding cellular conversations DOI Creative Commons

Naomi Berrell,

Habib Sadeghirad,

Tony Blick

et al.

Medicinal Research Reviews, Journal Year: 2023, Volume and Issue: 44(3), P. 1121 - 1146

Published: Dec. 26, 2023

Cancer heterogeneity remains a significant challenge for effective cancer treatments. Altered energetics is one of the hallmarks and influences tumor growth drug resistance. Studies have shown that exists within metabolic profile tumors, personalized-combination therapy with relevant interventions could improve patient response. Metabolomic studies are identifying novel biomarkers therapeutic targets improved treatment The spatial location elements in microenvironment becoming increasingly important understanding disease progression. evolution metabolomics analysis now allows scientists to deeply understand how metabolite distribution contributes biology. Recently, these techniques spatially resolved subcellular level. It has been proposed mapping outcomes by improving precision medicine, enabling earlier diagnosis intraoperatively margins. This review will discuss altered pathways contribute progression resistance explore current capabilities technologies be integrated into clinical practice outcomes.

Language: Английский

Citations

11
Redefining clinical practice through spatial profiling: a revolution in tissue analysis DOI Creative Commons

EJ Mulholland,

SJ Leedham

Annals of The Royal College of Surgeons of England, Journal Year: 2024, Volume and Issue: 106(4), P. 305 - 312

Published: March 31, 2024

Spatial biology, which combines molecular biology and advanced imaging, enhances our understanding of tissue cellular organisation. Despite its potential, spatial omics encounters challenges related to data complexity, computational requirements standardisation analysis. In clinical applications, has the potential revolutionise biomarker discovery, disease stratification personalised treatments. It can identify disease-specific cell patterns, could help risk stratify patients for trials disease-appropriate therapies. Although there are in adopting it practice, significantly enhance patient outcomes. this paper, we discuss recent evolution improving level treatment disease, advance precision effectiveness healthcare interventions.

Language: Английский

Citations

4
Applications of single-cell technologies in drug discovery for tumor treatment DOI Creative Commons
Bingyu Liu, Shunfeng Hu, Xin Wang

et al.

iScience, Journal Year: 2024, Volume and Issue: 27(8), P. 110486 - 110486

Published: July 11, 2024

Language: Английский

Citations

4
SANTO: a coarse-to-fine alignment and stitching method for spatial omics DOI Creative Commons
Haoyang Li, Yingxin Lin, Wenjia He

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: July 18, 2024

Abstract With the flourishing of spatial omics technologies, alignment and stitching slices becomes indispensable to decipher a holistic view 3D molecular profile. However, existing methods are unpractical process large-scale image-based dataset due extreme time consumption unsatisfactory accuracy. Here we propose SANTO, coarse-to-fine method targeting tasks for omics. SANTO firstly rapidly supplies reasonable positions two identifies overlap region. Then, refines by considering patterns. Comprehensive experiments demonstrate superior performance over methods. Specifically, stitches cross-platform breast cancer samples, enabling integration complementary features synergistically explore tumor microenvironment. is then applied 3D-to-3D spatiotemporal study development mouse embryo. Furthermore, enables cross-modality transcriptomic epigenomic data understand interactions.

Language: Английский

Citations

4