biostudies-literatureRoostee SVetenskapsrådetFru Berta Kamprads StiftelseStig and Ragna Gorthon FoundationALFThelma Zoégas Foundation for Medicinal ResearchCancerfonden21417https://www.ebi.ac.uk/biostudies/studies/S-EPMC11399404biostudies-literatureUnknown14(1)The tumour immune microenvironment (TIME) in breast cancer is acknowledged with an increasing role in treatment response and prognosis. With a growing number of immune markers analysed, digital image analysis may facilitate broader TIME understanding, even in single-plex IHC data. To facilitate analyses of the latter an open-source image analysis pipeline, Tissue microarray MArker Quantification (TMArQ), was developed and applied to single-plex stainings for p53, CD3, CD4, CD8, CD20, CD68, FOXP3, and PD-L1 (SP142 antibody) in a 218-patient triple negative breast cancer (TNBC) cohort with complementary pathology scorings, clinicopathological, whole genome sequencing, and RNA-sequencing data. TMArQ's cell counts for analysed immune markers were on par with results from alternative methods anScientific reportsTumour immune characterisation of primary triple-negative breast cancer using automated image quantification of immunohistochemistry-stained immune cells.PMC113994042022-2796FBKS-2020-5 + FBKS-21-27(328)CAN 2021/14072021-018002022/12052022/0021Jonsson GStaaf JPhung BRoostee SJonsson MEhinger DAine MSjodahl GfalseTumour immune characterisation of primary triple-negative breast cancer using automated image quantification of immunohistochemistry-stained immune cells.The tumour immune microenvironment (TIME) in breast cancer is acknowledged with an increasing role in treatment response and prognosis. With a growing number of immune markers analysed, digital image analysis may facilitate broader TIME understanding, even in single-plex IHC data. To facilitate analyses of the latter an open-source image analysis pipeline, Tissue microarray MArker Quantification (TMArQ), was developed and applied to single-plex stainings for p53, CD3, CD4, CD8, CD20, CD68, FOXP3, and PD-L1 (SP142 antibody) in a 218-patient triple negative breast cancer (TNBC) cohort with complementary pathology scorings, clinicopathological, whole genome sequencing, and RNA-sequencing data. TMArQ's cell counts for analysed immune markers were on par with results from alternative methods an2024-01-01T00:00:00Z2024 Sep2026-06-02T23:38:34.442Z2025-04-04T08:17:58.917ZS-EPMC113994043927191010.1038/s41598-024-72306-1