High-resolution spatially resolved proteomics of complex tissues based on microfluidics and transfer learning

Cell, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Despite recent advances in imaging- and antibody-based methods, achieving in-depth, high-resolution protein mapping across entire tissues remains a significant challenge spatial proteomics. Here, we present parallel-flow projection transfer learning omics data (PLATO), an integrated framework combining microfluidics with deep to enable of thousands proteins whole tissue sections. We validated the PLATO by profiling proteome mouse cerebellum, identifying 2,564 groups single run. then applied rat villus human breast cancer samples, resolution 25 μm uncovering proteomic dynamics associated disease states. This approach revealed spatially distinct tumor subtypes, identified key dysregulated proteins, provided novel insights into complexity microenvironment. believe that represents transformative platform for exploring regulation its interplay genetic environmental factors.

Language: Английский

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Strategies for Accurate Cell Type Identification in CODEX Multiplexed Imaging Data

Frontiers in Immunology, Journal Year: 2021, Volume and Issue: 12

Published: Aug. 13, 2021

Multiplexed imaging is a recently developed and powerful single-cell biology research tool. However, it presents new sources of technical noise that are distinct from other types data, necessitating practices for multiplexed processing analysis, particularly regarding cell-type identification. Here we created datasets by performing CODEX on four sections the human colon (ascending, transverse, descending, sigmoid) using panel 47 oligonucleotide-barcoded antibodies. After cell segmentation, implemented five different normalization techniques crossed with unsupervised clustering algorithms, resulting in 20 unique annotations same dataset. We generated two standard annotations: hand-gated produced over-clustering spatial verification. then compared these at levels granularity. First, increasing granularity led to decreased labeling accuracy; therefore, subtle phenotype should be avoided step. Second, accuracy identification varied more choice than algorithm. Third, better accounted segmentation during annotation hand-gating. Fourth, Z-score was generally effective mitigating effects imaging. Variation will lead significant differential results such as cellular neighborhood analysis; consequently, also make recommendations accurately assigning labels

Language: Английский

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A robust multiplex immunofluorescence and digital pathology workflow for the characterisation of the tumour immune microenvironment

Molecular Oncology, Journal Year: 2020, Volume and Issue: 14(10), P. 2384 - 2402

Published: July 16, 2020

Multiplex immunofluorescence is a powerful tool for the simultaneous detection of tissue-based biomarkers, revolutionising traditional immunohistochemistry. The Opal methodology allows up to eight biomarkers be measured concomitantly without cross-reactivity, permitting identification different cell populations within tumour microenvironment. In this study, we aimed validate multiplex workflow in two complementary panels and evaluate immune microenvironment colorectal cancer (CRC) formalin-fixed paraffin-embedded tissue. We stained CRC tonsil samples using on Leica BOND RX immunostainer. then acquired images an Akoya Vectra Polaris performed multispectral unmixing inform. Antibody were validated tissue microarray sections containing cores from six normal types, qupath image analysis. Comparisons between chromogenic immunohistochemistry consecutive same showed significant correlation (r

Language: Английский

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Prognostic Significance of CD4+ and CD8+ Tumor-Infiltrating Lymphocytes in Head and Neck Squamous Cell Carcinoma: A Meta-Analysis

Cancers, Journal Year: 2021, Volume and Issue: 13(4), P. 781 - 781

Published: Feb. 13, 2021

It has been suggested that the presence of tumor-infiltrating lymphocytes (TILs) in tumor microenvironment is associated with a better prognosis different types cancer. In this systematic review and meta-analysis, we investigated prognostic role CD4+ CD8+ TILs head neck squamous cell carcinoma (HNSCC).PubMed, Cochrane, Embase, Scopus, Web Science were searched up to September 2020. This study was conducted following preferred reporting items for reviews meta-analyses (PRISMA) checklist. Risk ratios from individual studies displayed forest plots pooled hazard (HR) death corresponding confidence intervals (CI) calculated according random-effects models. bias included assessed through Newcastle-Ottawa scale.28 met inclusion criteria. Studies on HNSCC subsites combined reported significant reduction risk both high (HR: 0.77; 95% CI: 0.65-0.93) 0.64; 0.47-0.88). High significantly overall survival among oropharyngeal 0.52; 0.31-0.89), as well TILS Human papillomavirus -ve +ve cancers 0.39; 0.16-0.93 HR: 0.40; CI 0.21-0.76 respectively). also improved hypopharyngeal (HR = 0.43 0.30-0.63). No association emerged patients cancer oral cavity or larynx.The findings meta-analysis demonstrate significance variation subsite warrants further focused investigation. We highlight how may serve predictive biomarkers stratify into treatment groups, applications immune-checkpoint inhibitors notable areas research.

Language: Английский

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Image-based cell phenotyping with deep learning

Current Opinion in Chemical Biology, Journal Year: 2021, Volume and Issue: 65, P. 9 - 17

Published: May 21, 2021

Language: Английский

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