Quantifying Protein Expression in PDAC Tumors

A TMA of treatment-naive PDAC tumours was constructed from 1 mm punch biopsies of well-demarcated tumours from paraffin-embedded tissue blocks by a pathologist. An Aperio Scan-Scope XT Slide Scanner (Aperio Technologies) was used to acquire 20× images. A previously validated tumour-specific nuclear algorithm (IHC-MARK) was used to quantify protein expression.14 22 (link) Positive staining was normalised to total tissue surface area and the mean intensity or cellular density per cm² was used to classify samples into high, mid and low cohorts and overall survival following PDAC resection compared (online supplementary figure S1).

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Nywening T.M., Belt B.A., Cullinan D.R., Panni R.Z., Han B.J., Sanford D.E., Jacobs R.C., Ye J., Patel A.A., Gillanders W.E., Fields R.C., DeNardo D.G., Hawkins W.G., Goedegebuure P, & Linehan D.C. (2017). Targeting both tumour-associated CXCR2+ neutrophils and CCR2+ macrophages disrupts myeloid recruitment and improves chemotherapeutic responses in pancreatic ductal adenocarcinoma. Gut, 67(6), 1112-1123.

Publication 2017

Scan-Scope XT Slide Scanner

Biopsies Paraffin Pathologist Pdac Protein Scan Tissue Tumour

Corresponding Organization : University of Rochester Medical Center

Other organizations : Washington University in St. Louis

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Variable analysis

independent variables

Treatment status of PDAC tumours (treatment-naive)

dependent variables

Protein expression
Overall survival following PDAC resection

control variables

Paraffin-embedded tissue blocks
20× images acquired using Aperio Scan-Scope XT Slide Scanner
Tumour-specific nuclear algorithm (IHC-MARK) used to quantify protein expression

controls

Positive control: Not explicitly mentioned
Negative control: Not explicitly mentioned

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