Tissue Biomarker Discovery
A non-destructive method for high-plex spatial profiling of proteins and genetic material as biomarkers
A non-destructive method for high-plex spatial profiling of proteins and genetic material as biomarkers.
Preserves the spatial context of cells within samples without disturbing their geometry and surrounding ECM. Spatial omics now combines molecular analysis with spatial information on the cell’s localization within the tissue.
Detection of biomolecules in tissues provides contextual information and the possibility to assess the interaction of different cell types and markers. Routine qualitative assessment of immune- and oligonucleotide-based methods in research and the clinic has been associated with assay variability because of lack of stringent validation and subjective interpretation of results.
Identification of biomolecules in tissues can have more value than circulating biomarkers as they are accompanied by spatial information, they are closer to the ‘site of action’, and they carry relative information.
Analysis of cells of the immune system and their response with respect to infection in a particular tissue/organ can be studied.
Synovial fluid analysis for cytokines like TNF-α associated with rheumatoid arthritis.
Normal/ Immune cell examination for tumors.
Rapid screening of tissues and organs before organ transplantation.
Screen respiratory washes from intubated patients.
Collection of tissues for biobanks
Case Study 1:
Tissues, not blood, are where immune cells act
About 3,04,58,251 cases of covid 19 have been registered in India as of June 2021. 2,95,48,302 patients have recovered and 4,00,312 deaths have been reported.
Something surprising was spotted early during the pandemic when people were severely ill with COVID-19 and on a ventilator, the daily rinses of the plastic tubes in their windpipes contained immune cells from the airway. More surprisingly, what was in these airway samples was very different from what was found in the same patient’s blood. The airway cells were producing high levels of cytokines — factors that recruit immune cells such as T cells to a tissue site and promote inflammation. By contrast, the corresponding blood samples were low in T cells, but high in other immune cells called monocytes, which were displaying unusual patterns of cell-surface receptors. Lung samples from patients who had died showed monocytes and a further type of immune cell (macrophages) clustered in the lung’s tiny air sacs; this is associated with the damage that typifies severe COVID-19.
The unusual receptors suggested to us that monocytes circulating in the blood had been both altered and summoned by the cytokines produced in the airway1. Had they not collected both airway and blood samples, they would not have put these pieces together.
The composition of immune cells is distinct which depends upon the type of tissue they act in. This is called a tissue-specific immune response. Screening for tissue biomarkers helps in understanding the spatial arrangement and organization of immune cells in these target tissues.
The pandemic has revealed major gaps in our understanding of the human immune system. One of the biggest is the reactions in tissues — at sites of infection and where disease manifests.
Case Study 2:
Tissues, not blood, are where immune cells act
The composition of immune cells is distinct in different tissues, with tissue-specific variation in gene expression, metabolic pathways and functional regulation. Defining these properties could target therapies to tissue immune responses — but that requires first looking at the tissues. Many tissue samples from living individuals can be collected during routine medical care. For instance, biopsies and elective surgeries allow collection of diseased and healthy tissue.
When a clinical team obtains the person’s organs for transplantation, the surgeon collects tissues for research — including the intestines, lungs, many lymph nodes, the thymus, spleen, bone marrow, skin, tonsils and salivary glands — and brings everything directly back to the laboratory for processing and sample storage. Linking tissue collection with organ donation is the best way to preserve the most tissue and the most-viable samples. So far, results from these tissues match those of tissue from living patients, although side-by-side comparisons are not always feasible.
So far, tissue samples from more than 500 donors have been obtained and screened. Samples have been shared with many collaborating investigators and are profiling them as part of the Human Cell Atlas, which aims to create comprehensive reference maps of all human cells.
Technological advances mean that RNA transcripts, protein content and gene modifications can be pinpointed even for single cells. Combined with computational analyses, these measurements allow the simultaneous identification of immune-cell composition, lineage and functional states. When applied to cells in blood, this detailed profiling has revealed immune signatures for certain infections and vaccines, from flu to SARS-CoV-2.
Ongoing studies aim in determining how tissue immune profiles correlate with factors such as sex and age.
tims TOF flex
timsTOF fleX is the ideal platform for performing spatially guided 4D-Proteomics™, SpatialOMx®, as it combines 4D-Omics and MALDI Imaging on a single platform.
nCounter® Analysis System
NanoString’s molecular barcoding technology uses color-coded molecular barcodes that can hybridize directly to many different types of target molecules. It is ideal for a range of applications requiring efficient, high-precision quantitation of hundreds of target molecules across a sample set. All nCounter assays generate high-quality results from challenging sample types, including FFPE and crude cell lysates.
RapifleX® MALDI Tissuetyper
Combining Mass Spectrometry with molecular imaging provides a deep understanding of the analysis of molecules and their spatial arrangement (histology) in the tissues.
Understanding tissue heterogeneity is critical to answering key biological questions in translational research. The current tissue analysis paradigm requires a tradeoff between morphological analysis or high-plex, sacrificing valuable information, or consuming precious samples.
(DSP) combines the best of spatial and molecular profiling technologies by generating a whole tissue image at single-cell resolution and digital profiling
GeoMx Digital Spatial Profiler (DSP)
Farber, D. (2021). Tissues, not blood, are where immune cells function. Nature, 593(7860), 506-509. DOI: 10.1038/d41586-021-01396-y
Brochure for tims TOF Flex- https://www.bruker.com/en/products-and-solutions/mass-spectrometry/timstof/timstof-flex/_jcr_content/root/sections/more_information/sectionpar/search_copy_copy_cop.download-asset.pdf/22bda39e-f2cc-4ffb-9c42-0a0470b632c5/1878001-4-reasons-for-4d-proteomics-ebook-rev-01.pdf
Brochure for nanostring nCounter- https://www.nanostring.com/wp-content/uploads/2020/12/BR_nCounterSystems_USNS_PM1093-01_R2.pdf