Spatial Omics: A Disruptive Innovation Poised to Unlock a $15B+ Market and Transform Clinical Diagnostics

In an era where innovation is cloaked in rhetoric, where can true innovation be found?

Throughout the history of scientific and technological development, the most groundbreaking innovations have almost invariably originated from research laboratories. New products based on these innovative technologies often create new markets and transform people’s lives. For instance, the Internet, which is ubiquitous in our daily lives, originated from the European Organization for Nuclear Research (CERN).

From the perspective of investors who prioritize “early-stage, small-scale, and innovative” ventures, the current market is rife with “pseudo-innovations.” To identify genuine innovative projects and uncover valuable technological breakthroughs, a growing number of investors are turning their attention upstream—to scientific research laboratories.

Focusing on the cutting edge of technology, investors have uncovered a series of disruptive projects and revolutionary innovative technologies, such as spatial omics. In 2022, the prestigious international academic journal Nature named spatial omics one of the seven most disruptive technologies of the year. In 2023, the World Economic Forum released its Top 10 Emerging Technologies of 2023 report, in which spatial omics was listed alongside other well-known innovations such as flexible batteries, generative artificial intelligence, and sustainable aviation fuels.

Not only investors, but also the industrial sector are bullish on spatial omics. According to market reports from DeciBio and JPMorgan Chase, the global market size for spatial omics could reach $15 billion in 2022. In terms of industry landscape, global giants such as Roche Diagnostics and Danaher, as well as leading single-cell sequencing company 10x Genomics, are all making strategic moves in spatial omics. Moreover, the total amount of acquisitions and financing in the spatial omics industry has exceeded $1 billion over the past two years.

What Is Spatial Omics? Why Is It Considered a Disruptive Technology? How Large Will the Blue-Ocean Market Be? Read On.

Spatial omics is an emerging technology in the life sciences that correlates molecular mechanisms with their tissue context in situ. It enables the visualization of cellular composition and native gene expression across distinct tissue regions, revealing the spatial heterogeneity of omics data. This approach facilitates the elucidation of cell–cell interactions, thereby advancing researchers’ understanding of the tissue microenvironment and tissue growth.

In layman's terms, spatial multi-omics technology primarily labels nucleic acids or proteins of different cell types within the tissue microenvironment to capture complex cellular phenotypes, functional states, and the spatial structural relationships between cells and their tissue microenvironment, thereby enabling the visualization of biomarkers and the establishment of corresponding data analysis models.Spatial omics data provides significant benefits for tumor research, immunology, developmental biology, neuroscience, and pathology.。

Taking tumor research as an example, high-dimensional single-cell data from tumor lesions can reveal transcriptional patterns that determine biological differences among samples, as well as the underlying genes driving these differences. This information provides researchers with clues to understand the state transitions between normal and cancerous cells within the samples. By using these patterns as a lens, other transcriptional datasets—including those collected at different stages of tumor progression—can be evaluated, thereby offering pathways for predicting carcinogenesis and guiding therapeutic interventions.

Historically, researchers in the life sciences have used bulk sequencing to rapidly obtain information about specific cells or tissues under particular conditions. However, bulk sequencing involves homogenizing samples prior to sequencing, yielding data that represent the average across all cells. Given the significant heterogeneity among different cell types, this averaged expression profile masks intercellular differences and obscures the heterogeneity inherent in cells and tissues.

Subsequently, the emergence of single-cell omics technologies has enabled researchers to measure comprehensive information at the level of individual cells, including genomics, transcriptomics, epigenomics, and proteomics, thereby revealing cellular and tissue heterogeneity. However,Single-cell omics technologies fail to capture spatial information of cells, failing to reveal the local networks of intercellular communication, thereby isolating samples from their native microenvironment and resulting in the loss of critical information.

In the field of biology,Spatial Information Is CrucialSpatial context influences cellular phenotype, state, and function. For instance, a cell’s position relative to its neighboring cells within the human body determines the signals it receives. These signals may arise from cell-cell interactions, soluble messenger molecules, or therapeutic agents. Disruption of intercellular interactions in the human body can lead to severe diseases. Therefore, when investigating the biological mechanisms underlying human development and disease, researchers must carefully assess how a cell’s microenvironment affects its normal function or dysfunction.

Given the importance of spatial information, numerous scientists have previously employed various techniques and instruments to perform spatial profiling of biomolecules. Unfortunately, conventional methods are limited to capturing a restricted number of targets at low resolution, thereby offering limited value.

Effort pays off. Thanks to continuous improvements by scientists, spatial omics—a field capable of providing information on the spatial relationships between tissues and cells—finally surged in 2016, witnessing an explosive growth in related technologies and various supporting instruments.Spatial omics, by enabling researchers to gain deeper insights into complex biological issues such as cellular interactions, signaling pathways, and regulatory mechanisms within organisms, has been regarded in the past two years as the next major trend in the life sciences field.。

Today, spatial omics is applied in numerous scientific research scenarios within the life sciences, including basic research, translational research, pathological studies, and new drug development. Meanwhile, by detecting target molecular features on tissue samples, spatial omics holds the promise of revolutionizing pathological techniques and expanding into broader applications such as clinical diagnosis and precision medicine.

An investor stated, “Spatial omics is one of the most watched tracks among innovative omics tools, with a large potential market, high technical barriers, and rapid growth globally,”Poised to Reach a Critical Inflection Point for Translation from the Research Market to the Clinical Market in the Coming Years。”

According to market reports from DeciBio and JPMorgan, the global market size for spatial omics reached $15 billion in 2022. The market is expected to experience explosive growth in the coming years as spatial omics technologies are increasingly adopted in clinical settings.

Perhaps due to the market-disruptive potential and future growth prospects of spatial omics, numerous investment firms—including Yuanhe Origin, Xingze Capital, Xianfeng Qiyun, ZhenFund, and Longpan Investment—collectively bet on this sector in 2023. Innovative companies specializing in spatial omics, such as Salus, Dynamic Biosystems, Yuanxing Zhizao, and Gewu Zhihe, all secured new rounds of financing during the first half of the year, a period often referred to as a “capital winter.”

As the potential of spatial omics gradually comes to light, major global leaders and innovative enterprises have begun to position themselves in the field of spatial omics.

Among them, 10x Genomics, the leader in the single-cell sequencing industry, has demonstrated the greatest urgency. It acquired Spatial Transcriptomics, a leading company in the field of spatial genomics, in 2018; purchased ReadCoor, a spatial multi-omics platform, for $350 million in cash and stock in 2020; and acquired Cartana, a developer of in situ RNA analysis technology, for $41.2 million, thereby making a strong entry into the spatial omics sector.

Perhaps recognizing the rarity of this opportunity, Bio-Techne, a global leader in life science reagents, also chose to rapidly expand its presence through acquisitions. In April 2023, Bio-Techne first entered into a strategic partnership with Lunaphore, a developer of automated spatial biology solutions, to jointly develop an automated spatial multi-omics workflow by leveraging Lunaphore’s instrumentation and antibody panels alongside Bio-Techne’s RNAscope HiPlex technology. Bio-Techne anticipated that this workflow would enable highly multiplexed, simultaneous detection of protein and RNA biomarkers at single-cell resolution on the same slide. Two months after establishing the strategic partnership (in June 2023), Bio-Techne acquired Lunaphore outright to accelerate its expansion in the spatial omics sector.

In addition to 10x Genomics and Bio-Techne, other prominent companies such as Roche Diagnostics, Danaher, MGI Tech, Nanostring, and AKOYA Bioscience, as well as innovative enterprises including Vizgen, GeWuZhiHe, Salus, Dynamic Biosystems, Beijing Fenuoweikang Biotechnology Co., Ltd., and Yuanxing Zhizao, are also expanding into the field of spatial omics.

To date, a variety of differentiated spatial omics technologies have emerged in the market. Among them, the technology platforms of companies such as 10x Genomics, NanoString, MGI Tech, and Vizgen have garnered significant industry attention.

As one of the earliest companies to heavily invest in spatial omics, 10x Genomics launched its new spatial omics technology platform—the Xenium In Situ Analysis Platform for Tissue—at the end of 2022. This platform comprises the Xenium Analyzer, reagents and consumables, and analysis software. It integrates single-molecule RNA and protein detection capabilities with optical components, data acquisition, and decoding technologies, enabling targeted in situ analysis of gene and protein expression at subcellular resolution.

According to reports, the Xenium in situ tissue analysis platform is a newly optimized system built upon the previously acquired ReadCoor and Cartana technologies. It is compatible with various sample types, including fresh frozen (FF) tissues and formalin-fixed paraffin-embedded (FFPE) tissues, offering the advantage of flexible input sample requirements.

Meanwhile, the Xenium platform also offers advantages such as ultra-high throughput, scalable applications, and comprehensive data analysis.

Specifically, in terms of throughput, the imaging area of the Xenium platform slide is 12 mm × 24 mm, and two slides can be loaded into the analyzer simultaneously for each run, which takes approximately two days to complete.

In terms of applications, the targeted panels of the Xenium platform can be expanded to accommodate different tissue types and use cases. Currently, 10x Genomics enables the detection of 400 RNA transcripts, with expectations to achieve simultaneous detection of 1,000 analytes in the future. Additionally, 10x Genomics offers custom panel design, allowing customers to add 100 genes to its commercial panels.

In terms of data analysis, the analytical software provided by 10x Genomics offers robust and comprehensive capabilities for primary and secondary data analysis, as well as for data visualization.

Furthermore, Xenium technology can be integrated with single-cell and spatial discovery technologies to deliver higher in situ resolution. Leveraging the high-resolution in situ spatial capabilities of Xenium technology, it will help researchers gain deeper insights into the tumor microenvironment, cell specificity, biological development, and other areas.

An industry insider commented, “This more targeted analysis is particularly well-suited for in-depth investigation of genes of interest identified following single-cell sequencing or unbiased spatial transcriptomics studies.”

From a financial perspective, 10x Genomics reported revenue of $146.8 million in the second quarter of 2023, representing a 28% year-over-year increase. A key driver was strong shipment growth for the Xenium platform, with momentum further accelerated by the launch of multiple new curated and customizable gene panels, as well as significant updates to its onboard software.

Vizgen, an innovative company in spatial omics, was founded in 2019 and completed three rounds of financing between 2020 and 2022, raising a total of approximately $136 million. According to reports, Vizgen is dedicated to developing next-generation spatially resolved single-cell transcriptomics solutions and has launched the MERSCOPE platform based on Harvard University’s MERFISH technology.

David Walt, Professor at Harvard University and Co-founder of Vizgen, stated, “MERFISH technology has broad applications in the fields of basic biology and medicine, and Vizgen’s proprietary technology is crucial for enhancing single-molecule detection capabilities.”

It is reported that Vizgen’s MERSCOPE platform comprises custom targeted gene panels, reagent kits and consumables, the MERSCOPE instrument, analysis computers, and visualization and analysis software, providing technical support from sample preparation to data analysis. Leveraging the MERSCOPE platform, Vizgen can map each cell’s response signals back to spatial coordinates within tissue samples, thereby generating detailed tissue maps and precisely defining the cellular microenvironment experienced by each cell in the sample.

In terms of applications, the MERSCOPE platform is capable of analyzing a variety of sample types, including fresh or fixed-frozen tissues, PBMCs, and adherent or suspension cells. It enables spatial transcriptomic analysis and supports imaging analysis ranging from whole tissue sections to single-cell and subcellular resolutions.

This spatial omics technology platform provides innovative tools for basic research and translational medicine in fields such as neuroscience, infectious diseases, cancer research, drug development, the Human Brain Project, and cell and gene therapy, holding significant value for drug discovery and development.

Compared to other spatial omics technologies, the MERSCOPE platform offers advantages such as high throughput, subcellular resolution, and higher detection sensitivity, enabling the characterization of low-abundance genes.

As a rising star, Vizgen had installed 100 MERSCOPE instruments by the end of July 2023. Previously, data analytics provider OMAPiX partnered with Vizgen to leverage its MERSCOPE platform technology, offering a comprehensive suite of customized spatial transcriptomics and proteomics data services for large-scale pharmaceutical and academic research projects, thereby accelerating drug development and life sciences research.

In recent years, spatial omics has gained significant traction, with academic publications in this field experiencing exponential growth. As the application and research of spatial omics become increasingly mature, its adoption in the clinical market is expected to accelerate.

Compared to the rapid adoption of spatial omics overseas, China's spatial omics industry is still in its nascent stage.

However, while overseas competitors are extremely powerful, domestic spatial omics companies are also entering the market by leveraging their differentiated advantages.

For example, Yuanxing Zhizao has achieved multidimensional breakthroughs in engineering design and reagent development. Its independently developed high-end instrument for single-cell spatial multi-omics can perform tissue section pretreatment, antigen retrieval, staining, imaging, and image preprocessing, offering advantages such as subcellular resolution, simultaneous high-sensitivity detection of 100+ plex proteins and RNA, and high throughput. Combined with its proprietary CFPTM reagent technology, the spatial omics platform is fully compatible with existing detection antibodies and nucleic acid probes on the market, enabling users to achieve rapid and cost-effective technological upgrades.

Yuanxing Zhizao stated, “These engineering designs and key technologies give the company a unique advantage as it enters the translational research and clinical diagnostics markets.”

Salus has launched multiple super-resolution spatial omics chips, featuring super-resolution analysis and high-capacity tissue loading capabilities. Its omics chips have achieved submicron-level resolution, enabling the acquisition of transcriptomic information at the subcellular organelle level within tissues. Currently, Salus has partnered with several renowned research institutions to promote the application of super-resolution spatial omics tools in scientific research and clinical diagnostics.

Unlike companies that start with scientific research and then expand into clinical settings, Fenuoweikang directly targets clinical applications, choosing spatially resolved pathological visualization as its entry point for clinical implementation. The company is dedicated to developing solutions capable of simultaneously capturing multi-omics spatial information—including DNA, RNA, and proteins—on a single platform.

Dynamic Biosystems has pioneered a novel in situ RNA sequencing technology in the field of spatial omics. As a key spatial omics technique, in situ sequencing enables direct visualization of gene expression at subcellular resolution within the native tissue context, holding significant promise for advancing precise pathological diagnosis of tissue-derived specimens, diagnostics related to tumor immunotherapy, and analysis of the tumor microenvironment.

Currently, Dynamic Biosystems has established strategic partnerships with leading IVD companies to leverage its Digital-seq single-cell omics technology for clinical applications, and is collaborating with top-tier Grade A tertiary hospitals to accelerate the clinical translation of spatial omics technologies.

Currently, the global spatial omics market is in its early stages of development, presenting domestic companies with an opportunity to carve out a niche in the research sector and lay the groundwork for future clinical applications.