2017 NIH SCAP-T: Challenges in collecting and pre-analytical processing of tissue

(Stephen Fisher) #1

Wed, June 28th, Pre-Meeting Breakout Session

Moderator: Robert Star (NIDDK)

There are many tissue collection and processing factors that influence data quality, from length of ischemia time to storage conditions and collection method. These factors influence the distribution and degradation of biomolecules at different rates. Therefore, it is critical to match the choice of tissue source, collection method and preservation technique with the types of biomolecules being studied by different downstream assays.

The purpose of this session is to identify some of the challenges in collecting, preserving, and annotating high quality human tissue that will be used for downstream analytical techniques in the HuBMAP program. These techniques include single cell RNAseq, FISH, immuno-fluorescence as well as emerging techniques such as MERFISH, FISSEQ, seqFISH, MIBI-TOF, and 3-dimensional high end imaging. Through the discussion, we hope to have a better understanding of the challenges HuBMAP might face in collecting and pre-analytical processing of tissue specimens and how this processing will impact the quality of data collected by different single cell, tissue, and imaging assays.

A number of components add to these challenges. One component is to record the spatial orientation of samples relative to anatomical landmarks (and build this into the sample management pipeline). A second component is the analysis, then integration and iteration of data from multiple imaging and omics assays to develop comprehensive molecular (and omic) profiles of the cells within the tissue, including location information. A third key component is to understand when sources of variability are biologically relevant (within tissue samples from same patient, across multiple tissues, and across multiple donors) or artifacts of the collection and processing of the samples.

Questions for the breakout session to consider include:

  • Quality: What are practical quality measures for assessing the impact of tissue collection methods and the degree of degradation? How does the magnitude of ischemia signatures compare with collection, dissociation or storage signatures? Is there a common set of quality biomarkers that can be used across all tissues and that are compatible with downstream assays?
  • Metadata: Beyond SPREC 2.0, are there common data elements describing collection and processing that are relevant to mapping DNA, RNA and proteins biomolecular distributions in tissues?
  • Assay Workflow: What are best practices for assessing the impact of single cell (liberase) and tissue (LCM, super-resolution, imaging MS/MS) based tissue “dissociation” methods on assay measurements? Can tissue sections be used for multiple assays (RNA in situ, then protein, then routine stains)?
  • Collection: For what assays and tissue types do tissues need to be collected from live donors? Rapid autopsy protocols?
  • Staining: Do common stains (e.g. H&E, trichrome, toluidine) influence the sensitivity and specificity of downstream assays?
  • Orientation: How do we preserve orientation of a tissue specimen through the processing chain?

(Stephen Fisher) #2

You can download the slides from this breakout discussion here:

(Xinghua Pan) #3

Failed to download, do not know why

(Stephen Fisher) #4

Sorry there is a problem with the slide deck download and it should be resolved shortly.

(Stephen Fisher) #5

Everything should be working now. If anyone has problems downloading the slide deck, please message me directly.

(Xinghua Pan) #6

Now I can download it well. Thanks a lot!

(Terence Shine) #7

I will figure it out. Just give me a sec. - t