Spatial organization and molecular correlation of tumor-infiltrating lymphocytes using deep learning on pathology images
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Published version
Author(s)
Type
Journal Article
Abstract
Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumor-infiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment.
Date Issued
2018-04-03
Date Acceptance
2018-03-20
Citation
Cell Reports, 2018, 23 (1), pp.181-193.e7
ISSN
2211-1247
Publisher
Elsevier
Start Page
181
End Page
193.e7
Journal / Book Title
Cell Reports
Volume
23
Issue
1
Copyright Statement
© 2018 The Authors. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
Sponsor
SAIC-F-Frederick, Inc
Leidos Biomedical Research, Inc.
Identifier
http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000429092900017&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=1ba7043ffcc86c417c072aa74d649202
Grant Number
TCGA Pilot Program
15Y011ST
Subjects
Science & Technology
Life Sciences & Biomedicine
Cell Biology
SQUAMOUS-CELL CARCINOMA
STANDARDIZED METHOD
IMMUNE CONTEXTURE
GENOMIC ANALYSES
SOLID TUMORS
CANCER
MELANOMA
SUBTYPES
PROPOSAL
BREAST
Publication Status
Published
Date Publish Online
2018-04-05