There as been a lot of advancements in the omics world and one very exciting emerging technology is spatial omics. I created a series on LinkedIn that broke down the spatial omics industry, what the technology is and the specialist companies in the market including product manufacturers, service providers and software companies. You can read my full blog below.
What is spatial omics?
The omics revolution has expanded our ability to characterize cells through interrogation of the full genome, transcriptome, or proteome. Until recently, these techniques couldn’t be applied in situ, resulting in the loss of spatial relationships.
Spatial omics offer high-throughput solutions to assess the spatial organization and cell types within niches and understand their intercellular communication. Spatial omics combines next generation sequencing / high level multiplexing with imaging modalities, which gives depth and clarity to our insights into the spatial distribution of gene expression, cell-state transitions and cell-cell interactions.
The technology
Spatial technologies fall into two categories: NGS or imaging-based approaches. These include:
In situ sequencing (ISS) enables direct read-out transcript sequences within a tissue via ligation, gene barcodes, or sort fragment cDNAs. RNA is reverse transcribed and amplified by rolling circle amplification, followed by sequencing.
Applications: FISSEQ, starMAP, etc.
In-situ hybridization (ISH) builds on ISS technology, facilitating target sequence detection using fluorescent labelled probes. Sequential rounds of hybridization and imagine combined with barcoding enable substantial multiplexing.
Applications: MERFISH, seqFISH, smFISH, etc.
NGS-based methods build on the innovation of single cell RNA sequencing (scRNA-seq) to incorporate spatially barcoded RNAs on microarray slides. These barcodes are used to map spatial position, while traditional sequencing reads map to the genome. These approaches offer the advantage of unbiased interrogation of large regions of tissue.
Applications: DBIT-Seq, HDST, Pixel-seq, Slide-seq, etc.
Multi-omics approaches continue to develop, expanding the focus from the transcriptome to the proteome, epigenome and metabolome. Targeted co-detection of proteins or DNA genomic loci via high-throughput spatial mapping paired with spatial transcriptome data are starting to reveal snapshots of tissue complexity.
Applications: Multiplexed RNA-protein ISH, MIBI, etc.
The market
The spatial omics solution market size was valued at 250million in 2022, and is predicted to reach 671million by 2031 at 11.9% CAGR during the forecasted period.
Market segmentation:
Product types are instruments, kits, consumables and services
Application areas include: diagnostics, translation research, drug discovery and development, single-cell analysis and cell biology etc.
Samples that are analysed include: DNA, RNA and proteins
End-users include: biopharma and biotech companies, academic and research institutions and contract research organisations (CROs)
Benefits
The ability to chart cellular activity in normal v diseased tissues
Preservation of spatial information
Identify and characterize cellular heterogeneity
Discovery of biomarkers
Validation of results from traditional omics studies
Aids drug discovery and development by revealing how drugs interact with different cells in tissues
Gives a single cell resolution
Generates complex data that can be visualised in spatially accurate maps
Greater insights into cellular diversity and tissue architecture
Greater insights into cellular communication and interactions within a tissue microenvironment
Discovery of novel genes and regulatory elements
Potential to contribute to personalised treatment strategies and disease monitoring
Drawbacks
Technically complex
Large amounts of complex data that can be hard to process, analyse and interpret
High cost
Limit on how many genes or molecules that can be simultaneously analysed
Sample preparation may impact the preservation of cellular morphology and molecular content
Complex data can be hard to analyse and interpret
Difficult to find techniques to validate spatial omics findings
May be a lack of standardized protocols and benchmarks for data quality, due to being new
Requires substantial computational resources, including processing power and memory
Ethical considerations: consent, privacy and data sharing
Market breakdown
Companies who specialise in spatial tools and products:
Stellaromics Inc.,
Pixelgen
Cell Signaling Technology
AtlasXomics
Centrillion Tech.
Rarecyte
Neogenomics’s
Navinci Diagnostics
Standard Biotools
STOmics
Complete Genomics
Steam Instruments
Resolve Biosciences
10x Genomics
Nanostring Technologies
Vizgen
Akoya Biosciences
Ultivue
Canopy Biosciences
Flagship Biosciences
Ionpath
Miltenyi Biotec
Lunaphore (acquired by Bio-Techne)
Rebus Biosystems
Spatial Genomics, Inc.
Veranome Biosystems
Curio Bioscience
Advanced Cell Diagnostics
Acuity Spatial Genomics (a Bruker company)
For an more detail on each company’s technology, you can read Katie’s article.
Companies who specialise in spatial software/data:
Alpenglow Biosciences
ai
Aspect Analytics
Bioturing
Enable Medicine
Excelra
Indica Labs
Leica Microsystems
Medgenome
mosaic (Owkin initiative)
Nexco Analytics
Nucleai
Partek
PathAI
PredxBio (previously SpIntellx)
ProCogia
Qiagen
ROSALIND
powered by ONRAMP
Visiopharm
For more detail on each company’s technology, you can read Katie’s article over on LinkedIn.
Service providers
I identified 58 companies who offer spatial omics services. All of the companies identified offer spatial transcriptomics services and a high percentage also offer spatial proteomic services. There was only a handful of companies offering additional spatial services, these include:
Aliri = Spatial Transcriptomic, Metabolomic and Proteomic services
CapitalBio Technology = Spatial Transcriptomic and Metabolomic services
CD Genomics = Spatial Genomics, Transcriptomics, Proteomics, Metabolomics, and Epigenomics services
Oebiotech =Spatial Transcriptomics and Metabolomics services
The technology
The technology being used by these service providers includes:
Visium and Xenium from 10x Genomics
CosMx and GeoMx from NanoString Technologies, Inc.
Hyperion from Standard BioTools
PhenoCycler and PhenoImager from Akoya Biosciences, Inc.
CellScape from Canopy Biosciences
Curio Seeker from Curio Bioscience
MiBi from Ionpath
Cell DIVE from Leica Microsystems
COMET from Lunaphore
InSituPlex® from Ultivue
Merscope from Vizgen.
Companies who offer spatial omics services:
Abiosciences
AcelaBio
Aliri
AMKbiotech
Arkana Laboratories
Azenta Life Sciences
BioChain Institute, Inc.
BostonGene
Canopy Biosciences
CapitalBio Technology
CD Genomics mics
Cerba Research
CellCarta
Cellecta, Inc.
Citogen
Concept Life Sciences
Covance
Crown Bioscience
CyberomiX Inc.
Discovery Life Sciences
Dxome CLIA Laboratory
Ebiogen
Enable Medicine
Ensigna Biosystems, Inc.
Explicyte
Flagship Biosciences, Inc.
Fortis Life Sciences
Fulgent Genetics
Fynn Bio
Geninus Inc.
A*STAR – Agency for Science, Technology and Research
Hawayen Bio
iCura Diagnostics, Inc
Integrated Sciences
Invicro
Ionpath
K2bio
KOTAI Biotechnologies, Inc.
Labcorp
Lanterne Dx
MacroGenics, Inc.
Navigate BioPharma Services, Inc.
NeoGenomics Laboratories
Novelbio
Novogene Global
OEbiotech
ORGANOIDSCIENCES 오가노이드사이언스
Presage Biosciences, Inc.
Propath UK
Psomagen
Q² Solutions
Single Cell Discoveries
Sirona Dx
Source BioScience
Strand Life Sciences
theraCUES
YuceBio
You can read the full article over on my LinkedIn here.
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