Subcellular spatial molecular imager for in-situ hi-plex multi-omic analysis of biological tissue specimens

CONTEXT OF RESEARCH
In the 1600s pioneers of the microscope, coined the term 'cell' to describe structures observed under magnification; 400 years later, the word and concept remains. Indeed, our understanding of 'cell theory' underpins every aspect of health and disease, from immune cells making antibodies against viruses, or neurons storing memories.

To truly understand a complex organ such as the brain it is imperative to have a census not only of cell types that compose it, but also their functions. Previously, to measure which genes were 'switched-on or off', tissue samples had to be digested before analysis and so 'geography' of position of diseased tissue or immune cells on the disease battlefield' was lost.

We are realising that the same cell may have a completely different role depending on its position in an organ or diseased tissue like cancer. This idea underpins the concept of spatial biology. In essence how does the environment that cell resides in impact what it does, how does it influence surrounding cells, and can this information help us understand how a disease might progress or respond to treatment? Furthermore, it is becoming apparent of the importance of knowing where in the cell the gene resides (nucleus, membrane, cytoplasm) as this may impact what role it has.

OVERALL AIM
We plan to use a novel molecular microscope (CosMx Spatial Molecular Imager) to measure exact 3-dimensional location of thousands of genes and protein molecules simultaneously within a cell using real-world sections of human tissue while maintaining the tissue architecture.

OBJECTIVES
-We will generate incredibly detailed 'Spatial Maps' providing information on type and location of every normal cell, immune cell and diseased cell in a tissue specimen.
-We will discover how cells in this immune system 'atlas' interact in healthy and diseased tissues.
-We will focus the microscope to even higher resolutions to study the position of genes and proteins within cell compartments providing truly novel discovery in human disease.
-We will study the 'cancer immune battlefield', in terms of: Location, Activity, Inter-relationships between the immune cells and cancer cells to identify how targeting the immune system could help more patients with cancer?

Our objective is for the technology to be housed in a central facility to enable access for researchers from all specialties to study a wide spectrum of diseases and allowing answers to questions such as:
-Why do therapies for rheumatoid arthritis not work for all patients?
-What impact do infections like COVID19 have on the immune system in different organs?
-How the immune system lead to degenerative changes in the brain?
-How malarial parasites interact with blood vessels?

POTENTIAL APPLICATIONS AND BENEFITS
The potential applications of this molecular microscope technology are vast. As a result of studying real-world tissue on normal glass microscope slides, it allows us to unlock tissue archives of diseases and investigate with incredible detail to make discovery that could help future patients.

It has implications for a broad range of diseases from cancer, autoimmune, infection as well as study of the normal development of organs.

This technology could impact upon how pathologists practice as rather than traditional 'visual' analysis of tissue, a comprehensive, molecular tissue exploration is now possible enabling every cell present to be not only identified but also to have its activity measured.

Importantly these broad and detailed analysis can be performed in small biopsies from patients resulting in huge amounts of information that could in the future guide what therapy a patient receives from the time of diagnosis.

Overall, this technology has potential to lay the foundation of the development of a precision medicine strategy providing the right treatment for the right patient at the right time for many diseases in particular cancer.

BACKGROUND
Increasingly single-cell and spatial-omics approaches are required to fulfil understanding of genomic, temporal and phenotypic dimensions of normal development and disease. We aim to apply, highly multiplexed, high-resolution imaging and high-throughput spatially resolved transcriptomics using a novel Spatial Molecular Imager (SMI) approach to enable robust comprehensive spatial assessment of cell types across multiple pathologies.

OBJECTIVES
Single-cell Spatial-omics Methodology
The Nanostring CosMx SMI platform is an integrated system with mature cyclic in situ hybridization chemistry, aligned with ultra-high-resolution imaging enabling customisable multiplexing of RNAs (1000s) and proteins (100s) simultaneously at single cell and subcellular (<100nm) levels while maintaining tissue topography.

EXPERIMENTAL DESIGN
CosMx SMI provides an end-to-end pipeline from fixed tissue/ organoids on standard microscopy slides to automated hybridization and target molecule detection with image-based spatial coordinates exported for visualisation. Using molecularly characterised biobanked specimens, clinical trial samples and preclinical models, an extensive catalogue of pathologies will undergoing spatial-omic characterisation including:
-Primary/metastatic cancers
-Host-parasite states
-Neuroinflammation
-Autoimmune disorders
-Cardiovascular disease
-COVID-19 infected tissue

Integrated and open-source options enable cell typing, dimension reduction, neighbourhood and cell-cell ligand/receptor interaction analyses.

SCIENTIFIC AND MEDICAL OPPORTUNITIES
The proposed technology implementation is significant, facilitating in human tissues:
1)Discovery of cell-type-specific changes in development, disease and preclinical models (cell atlasing)
2)Development of novel spatial-omic biomarkers correlated with treatment response and survival outcomes
3)Identification, mapping and therapeutic targeting of crucial inter-cellular interactions