12. February 2024

Exploring the Tissue Microenvironment with High-throughput Cytometers

Understanding the interactions of cellular, multi-cellular, and non-cellular components that make up our tissues is an important foundation of medical research. Information on the components, spatial relationships, and molecular exchanges in tissue microenvironments is central to disease research and treatment. Current advancements in this field have resulted in the need for high-throughput imaging methods for rapid screening.

What is the Tissue Microenvironment?

Tissues have a specific microenvironment of a multifaceted mixture of 3D components, all vital in maintaining normal biological and physiological functions in organs, as well as playing an essential role in combatting malignant cell growth.1 The dynamic group of cellular and non-cellular entities that form the tissue microenvironment vary from tissue to tissue and work together to form a complex and comprehensive regulatory network that maintain organ homeostasis.2 Tissue microenvironments are generally composed of stromal cells, parenchymal cells, structural extracellular matrix proteins, and signaling molecules.1

The influence of the tissue microenvironment in the development and progression of disease is increasingly evident and understanding the mechanisms within tissue microenvironments is key in the prevention, treatment, and cure of diseases.3 Knowledge on different components’ roles and how they interact and coordinate for healthy tissue functioning enables better detection and identification of disease.1

Disease Biomarkers

Because tissue microenvironment analysis provides a picture of the spatial and molecular relationships between cellular and non-cellular components, that we previously had difficulty examining, it is highly important in the discovery of biomarkers. Biomarker research is at the forefront of disease prognosis, diagnosis, and treatment, propelling drug development and playing a foundational role in the field of precision medicine.5

Biomarkers provide critical insights into all stages of disease development/treatment. They can be used to assess a patient’s disease risk and provide early screening methods. The important information biomarkers provide on the efficacy and safety of treatments, and when monitoring a patient’s response to treatment, is driving innovative medical practices.5

Biomarkers encompass a large variety of different biochemical molecules involved in multifaceted interactions. High-throughput screening techniques are required to examine the extremely vast number of biomarker candidates in the tissue microenvironment. As biomarker research skyrockets, with more than 200,000 PubMed citations between 2010 and 2015, there is continuous need for high-throughput techniques that can rapidly examine a vast array of biomarkers.5

High-throughput Imaging

Advancements of high-throughput techniques in more recent years, digital pathology and image analysis, also known as tissue cytometry, have evolved significantly.6 One of the most rapidly evolving digital imaging techniques is whole slide scanning which creates high resolution images of entire tissue samples. High-throughput scanning devices examine hundreds of slides per assay, accommodating large, busy clinical laboratories and tissue research facilities that must scan masses of samples on a daily basis.

High-throughput methods have proven to be essential in evaluating the clinical utility of novel biomarkers. Large, multiplexed tissue microarray analysis (TMA) provides complex analysis of numerous biomarkers, facilitating high-throughput experiments in drug discovery.7 Combined with high-throughput image analysis, TMAs deliver quantitative data and have become a prioritized method for validating biomarkers for disease screening and treatment of large groups of patients.6

High-throughput tissue cytometry techniques are required to accommodate the vast diversity and multifaceted nature of examining tissue microenvironments for biomarker discovery. Their application in oncology has significantly aided the defining of biomarkers that have prognostic and theragnostic significance for treatments of well-established and novel druggable targets, as well as enhancing our knowledge on cancer progression and resistance mechanisms.7


High-throughput tissue cytometry is central to exploring the tissue microenvironment for the discovery of biomarkers for disease diagnosis and treatment. TissueGnostics, a leader in tissue analysis, offers high-throughput cytometers, such as TissueFAXS SL, to meet largescale scanning of tissue samples and thus investigate tissue microenvironment. With the ability to conduct live imaging, whole-slide confocal fluorescent imaging can scan a large array of slides. With a slide loader for 120 standard slides, TissueGnostics’ TissueFAXS imaging system can meet all your high-throughput scanning requirements.

Using the StrataQuest software by TissueGnostics for in-depth image analysis, you can document the interactions and spatial relationships to facilitate the identification of novel biomarkers. TissueGnostics provides you with advanced high-throughput techniques for more efficient research into disease for faster development of more effective treatments. Reach out to us today for more information on our revolutionary image analysis systems.



1. Alphonso, A. and Alahari, S.K.,2009. Stromal cells and integrins: conforming to the needs of the tumor microenvironment. Neoplasia. 11(12), pp.1264-1271.
2. Rani, B., Cao, Y., Malfettone, A., Tomuleasa, C., Fabregat, I. and Giannelli, G. 2014. Role of the tissue microenvironment as a therapeutic target in hepatocellular carcinoma. World Journal of Gastroenterology: WJG. 20(15), p.4128.
3. Sachs, P.C., Mollica, P.A. and Bruno, R.D. 2017. Tissue specific microenvironments: a key tool for tissue engineering and regenerative medicine. Journal of biological engineering. 11, pp.1-11.
4. https://tissuegnostics.com/what-tissue-microenvironment-analysis
5. Kumar, M. and Sarin, S.K., 2009. Biomarkers of diseases in medicine. Curr Trends Sci. 70, pp.403-17.
6. Hamilton, P.W., Bankhead, P., Wang, Y., Hutchinson, R., Kieran, D., McArt, D.G., James, J. and Salto-Tellez, M. 2014. Digital pathology and image analysis in tissue biomarker research. Methods. 70(1), pp.59-73.
7. Wang, Y., Savage, K., Grills, C., McCavigan, A., James, J.A., Fennell, D.A. and Hamilton, P.W. 2011. A TMA de-arraying method for high throughput biomarker discovery in tissue research. PLoS One. 6(10), p.e26007.
8. Le Rochais, M., Hemon, P., Pers, J.O. and Uguen, A. 2022. Application of high-throughput imaging mass cytometry Hyperion in cancer research. Frontiers in Immunology. 13, p.859414.


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