Feasibility of mass cytometry proteomic characterisation of circulating tumour cells in head and neck squamous cell carcinoma for deep phenotyping

Karl Payne; Jill Brooks; Nikolaos Batis; Naeem Khan; Mohammed El-Asrag; Paul Nankivell; Hisham Mehanna; Graham Taylor

doi:10.1038/s41416-023-02428-2

Feasibility of mass cytometry proteomic characterisation of circulating tumour cells in head and neck squamous cell carcinoma for deep phenotyping

Karl Payne, Jill Brooks, Nikolaos Batis, Naeem Khan, Mohammed El-Asrag, Paul Nankivell, Hisham Mehanna, Graham Taylor^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

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Abstract

Background: Circulating tumour cells (CTCs) are a potential cancer biomarker, but current methods of CTC analysis at single-cell resolution are limited. Here, we describe high-dimensional single-cell mass cytometry proteomic analysis of CTCs in HNSCC.

Methods: Parsortix microfluidic-enriched CTCs from 14 treatment-naïve HNSCC patients were analysed by mass cytometry analysis using 41 antibodies. Immune cell lineage, epithelial-mesenchymal transition (EMT), stemness, proliferation and immune checkpoint expression was assessed alongside phosphorylation status of multiple signalling proteins. Patient-matched tumour gene expression and CTC EMT profiles were compared. Standard bulk CTC RNAseq was performed as a baseline comparator to assess mass cytometry data.

Results: CTCs were detected in 13/14 patients with CTC counts of 2–24 CTCs/ml blood. Unsupervised clustering separated CTCs into epithelial, early EMT and advanced EMT groups that differed in signalling pathway activation state. Patient-specific CTC cluster patterns separated into immune checkpoint low and high groups. Patient tumour and CTC EMT profiles differed. Mass cytometry outperformed bulk RNAseq to detect CTCs and characterise cell phenotype.

Discussion: We demonstrate mass cytometry allows high-plex proteomic characterisation of CTCs at single-cell resolution and identify common CTC sub-groups with potential for novel biomarker development and immune checkpoint inhibitor treatment stratification.

Original language	English
Pages (from-to)	1590-1598
Number of pages	9
Journal	British Journal of Cancer
Volume	129
Issue number	10
Early online date	21 Sept 2023
DOIs	https://doi.org/10.1038/s41416-023-02428-2
Publication status	Published - 9 Nov 2023

Bibliographical note

Funding Information:
This project was primarily funded by a Cancer Research UK grant to KP (C11497/A28789). The Parsortix device was purchased with a grant to KP from the Queen Elizabeth Hospital Birmingham charity. HM is a National Institute for Health Research (NIHR) Senior Investigator. The views expressed in this article are those of the author(s) and not necessarily those of the NIHR, CRUK or the Department of Health and Social Care.

Publisher Copyright:
© 2023, The Author(s).

ASJC Scopus subject areas

Oncology
Cancer Research

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1038/s41416-023-02428-2Licence: Creative Commons: Attribution (CC BY)

PayneK2023FeasibilityFinal published version, 1.63 MBLicence: Creative Commons: Attribution (CC BY)

Validating a novel method for the isolation and single-cell characterisation of circulating tumour cells in head and neck cancer: a step towards personalised medicine
Mehanna, H., Yau, C., Payne, K. & Nankivell, P.
Cancer Research Uk
1/10/19 → 31/12/24
Project: Research
Identification of genetic factors that predispose to either immune checkpoint inhibitor or conventional chemotherapy toxicity
Palles, C., Middleton, G. & Steven, N.
Cancer Research Uk
1/09/19 → 31/12/24
Project: Research
The Birmingham CRUK Centre Clinical Academic Training Programme
Middleton, G., Brain, K., Thomas, K., Sundar, S., Harper, L. & Tennant, D.
Cancer Research Uk
1/04/19 → 31/03/27
Project: Research

Cite this

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title = "Feasibility of mass cytometry proteomic characterisation of circulating tumour cells in head and neck squamous cell carcinoma for deep phenotyping",

abstract = "Background: Circulating tumour cells (CTCs) are a potential cancer biomarker, but current methods of CTC analysis at single-cell resolution are limited. Here, we describe high-dimensional single-cell mass cytometry proteomic analysis of CTCs in HNSCC. Methods: Parsortix microfluidic-enriched CTCs from 14 treatment-na{\"i}ve HNSCC patients were analysed by mass cytometry analysis using 41 antibodies. Immune cell lineage, epithelial-mesenchymal transition (EMT), stemness, proliferation and immune checkpoint expression was assessed alongside phosphorylation status of multiple signalling proteins. Patient-matched tumour gene expression and CTC EMT profiles were compared. Standard bulk CTC RNAseq was performed as a baseline comparator to assess mass cytometry data. Results: CTCs were detected in 13/14 patients with CTC counts of 2–24 CTCs/ml blood. Unsupervised clustering separated CTCs into epithelial, early EMT and advanced EMT groups that differed in signalling pathway activation state. Patient-specific CTC cluster patterns separated into immune checkpoint low and high groups. Patient tumour and CTC EMT profiles differed. Mass cytometry outperformed bulk RNAseq to detect CTCs and characterise cell phenotype. Discussion: We demonstrate mass cytometry allows high-plex proteomic characterisation of CTCs at single-cell resolution and identify common CTC sub-groups with potential for novel biomarker development and immune checkpoint inhibitor treatment stratification.",

author = "Karl Payne and Jill Brooks and Nikolaos Batis and Naeem Khan and Mohammed El-Asrag and Paul Nankivell and Hisham Mehanna and Graham Taylor",

note = "Funding Information: This project was primarily funded by a Cancer Research UK grant to KP (C11497/A28789). The Parsortix device was purchased with a grant to KP from the Queen Elizabeth Hospital Birmingham charity. HM is a National Institute for Health Research (NIHR) Senior Investigator. The views expressed in this article are those of the author(s) and not necessarily those of the NIHR, CRUK or the Department of Health and Social Care. Publisher Copyright: {\textcopyright} 2023, The Author(s).",

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AU - Payne, Karl

AU - Brooks, Jill

AU - Batis, Nikolaos

AU - Khan, Naeem

AU - El-Asrag, Mohammed

AU - Nankivell, Paul

AU - Mehanna, Hisham

AU - Taylor, Graham

N1 - Funding Information: This project was primarily funded by a Cancer Research UK grant to KP (C11497/A28789). The Parsortix device was purchased with a grant to KP from the Queen Elizabeth Hospital Birmingham charity. HM is a National Institute for Health Research (NIHR) Senior Investigator. The views expressed in this article are those of the author(s) and not necessarily those of the NIHR, CRUK or the Department of Health and Social Care. Publisher Copyright: © 2023, The Author(s).

PY - 2023/11/9

Y1 - 2023/11/9

N2 - Background: Circulating tumour cells (CTCs) are a potential cancer biomarker, but current methods of CTC analysis at single-cell resolution are limited. Here, we describe high-dimensional single-cell mass cytometry proteomic analysis of CTCs in HNSCC. Methods: Parsortix microfluidic-enriched CTCs from 14 treatment-naïve HNSCC patients were analysed by mass cytometry analysis using 41 antibodies. Immune cell lineage, epithelial-mesenchymal transition (EMT), stemness, proliferation and immune checkpoint expression was assessed alongside phosphorylation status of multiple signalling proteins. Patient-matched tumour gene expression and CTC EMT profiles were compared. Standard bulk CTC RNAseq was performed as a baseline comparator to assess mass cytometry data. Results: CTCs were detected in 13/14 patients with CTC counts of 2–24 CTCs/ml blood. Unsupervised clustering separated CTCs into epithelial, early EMT and advanced EMT groups that differed in signalling pathway activation state. Patient-specific CTC cluster patterns separated into immune checkpoint low and high groups. Patient tumour and CTC EMT profiles differed. Mass cytometry outperformed bulk RNAseq to detect CTCs and characterise cell phenotype. Discussion: We demonstrate mass cytometry allows high-plex proteomic characterisation of CTCs at single-cell resolution and identify common CTC sub-groups with potential for novel biomarker development and immune checkpoint inhibitor treatment stratification.

AB - Background: Circulating tumour cells (CTCs) are a potential cancer biomarker, but current methods of CTC analysis at single-cell resolution are limited. Here, we describe high-dimensional single-cell mass cytometry proteomic analysis of CTCs in HNSCC. Methods: Parsortix microfluidic-enriched CTCs from 14 treatment-naïve HNSCC patients were analysed by mass cytometry analysis using 41 antibodies. Immune cell lineage, epithelial-mesenchymal transition (EMT), stemness, proliferation and immune checkpoint expression was assessed alongside phosphorylation status of multiple signalling proteins. Patient-matched tumour gene expression and CTC EMT profiles were compared. Standard bulk CTC RNAseq was performed as a baseline comparator to assess mass cytometry data. Results: CTCs were detected in 13/14 patients with CTC counts of 2–24 CTCs/ml blood. Unsupervised clustering separated CTCs into epithelial, early EMT and advanced EMT groups that differed in signalling pathway activation state. Patient-specific CTC cluster patterns separated into immune checkpoint low and high groups. Patient tumour and CTC EMT profiles differed. Mass cytometry outperformed bulk RNAseq to detect CTCs and characterise cell phenotype. Discussion: We demonstrate mass cytometry allows high-plex proteomic characterisation of CTCs at single-cell resolution and identify common CTC sub-groups with potential for novel biomarker development and immune checkpoint inhibitor treatment stratification.

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Feasibility of mass cytometry proteomic characterisation of circulating tumour cells in head and neck squamous cell carcinoma for deep phenotyping

Abstract

Bibliographical note

ASJC Scopus subject areas

UN SDGs

Access to Document

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Projects

Validating a novel method for the isolation and single-cell characterisation of circulating tumour cells in head and neck cancer: a step towards personalised medicine

Identification of genetic factors that predispose to either immune checkpoint inhibitor or conventional chemotherapy toxicity

The Birmingham CRUK Centre Clinical Academic Training Programme

Cite this