spatial biology

Spatial transcriptomics measures mRNA transcript abundance and distribution in situ across a tissue.{{cite journal |last1=Jena |first1=Siddhartha G. |last2=Verma |first2=Archit |last3=Engelhardt |first3=Barbara E. |date=4 September 2024 |title=Answering open questions in biology using spatial genomics and structured methods |journal=BMC Bioinformatics |volume=25 |issue=1 |page=291 |doi=10.1186/s12859-024-05912-5 |pmc=11375982 |pmid=39232666 |doi-access=free}} Spatial method for RNA in situ detection is first described in a 1969 landmark paper{{Cite journal |last1=Gall |first1=Joseph G. |last2=Pardue |first2=Mary Lou |date=June 1969 |title=Formation and detection of rna-dna hybrid molecules in cytological preparations* |journal=Proceedings of the National Academy of Sciences |volume=63 |issue=2 |pages=378–383 |doi=10.1073/pnas.63.2.378 |doi-access=free |pmc=223575 |pmid=4895535|bibcode=1969PNAS...63..378G }} by Joseph G. Gall and Mary-Lou Pardue. Previous to spatial transcriptomics techniques, whole transcriptome profiling lacked spatial context because tissues were ground up in bulk RNA-seq or dissociated into single cells suspensions in single cell RNA-seq. Although some literature refers to "spatial genomics" for RNA,{{Cite journal |last1=Jena |first1=Siddhartha G. |last2=Verma |first2=Archit |last3=Engelhardt |first3=Barbara E. |date=2024-09-04 |title=Answering open questions in biology using spatial genomics and structured methods |journal=BMC Bioinformatics |language=en |volume=25 |issue=1 |doi=10.1186/s12859-024-05912-5 |doi-access=free |issn=1471-2105 |pmc=11375982 |pmid=39232666}} growing consensus has settled on usage of "spatial transcriptomics" or "spatially resolved transcriptomics."{{Cite journal |last=Marx |first=Vivien |date=January 2021 |title=Method of the Year: spatially resolved transcriptomics |url=https://www.nature.com/articles/s41592-020-01033-y |journal=Nature Methods |language=en |volume=18 |issue=1 |pages=9–14 |doi=10.1038/s41592-020-01033-y |issn=1548-7105}}

Spatial proteomics measures the localization and abundance of proteins at the subcellular level across a tissue.{{cite journal |last1=Lundberg |first1=Emma |last2=Borner |first2=Georg H. H. |date=May 2019 |title=Spatial proteomics: a powerful discovery tool for cell biology |journal=Nature Reviews Molecular Cell Biology |volume=20 |issue=5 |pages=285–302 |doi=10.1038/s41580-018-0094-y |pmid=30659282}} Immunohistochemistry-based spatial proteomic methods include oligo barcoded antibodies, cyclic immunofluorescence (cycIF), co-detection by indexing (CODEX), iterative bleaching extends multiplicity (IBEX), multiplexed ion beam imaging (MIBI) and imaging mass cytometry (IMC).{{Cite journal |date=December 2024 |title=Method of the Year 2024: spatial proteomics |url=https://www.nature.com/articles/s41592-024-02565-3 |journal=Nature Methods |language=en |volume=21 |issue=12 |pages=2195–2196 |doi=10.1038/s41592-024-02565-3 |issn=1548-7105|doi-access=free }} Other methods includes deep visual proteomics that profile protein expression in single cells by laser capture microdissection and mass spectroscopy. The term "spatial medicine" is recently coined by Eric Topol to refer to a study that used deep visual proteomics to find a therapeutic treatment for patients with a rare skin condition.{{Cite web |last=Topol |first=Eric |date=2024-10-26 |title=The Dawn of Spatial Medicine |url=https://erictopol.substack.com/p/the-dawn-of-spatial-medicine |access-date=2025-01-04 |website=Ground Truths}}

Spatial genomics localizes the native three dimensional genome architecture within the nucleus.{{Cite journal |last1=Kempfer |first1=Rieke |last2=Pombo |first2=Ana |date=April 2020 |title=Methods for mapping 3D chromosome architecture |url=https://www.nature.com/articles/s41576-019-0195-2 |journal=Nature Reviews Genetics |language=en |volume=21 |issue=4 |pages=207–226 |doi=10.1038/s41576-019-0195-2 |issn=1471-0064|url-access=subscription }} Nuclear organization of chromosomes and how chromosomes are positioned and folded has implications for gene regulation, transcription, DNA replication, DNA damage repair, and cell division.

Spatial omics refers to the collection of high-throughput molecular profiling techniques that measure and spatially map the distribution of transcriptome, proteome or other biomolecules in a tissue. Spatial biology is a more general term that encompasses the science and techniques, but often spatial biology and spatial omics are used interchangeably.

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Category:Biology