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Single-sample signature score

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Mao Y, Gide TN, Adegoke NA, Quek C, Maher N, Potter A, Patrick E, Saw RPM, Thompson JF, Spillane AJ, Shannon KF, Carlino MS, Lo SN, Menzies AM, da Silva IP, Long GV, Scolyer RA, Wilmott JS. Cross-platform comparison of immune signatures in immunotherapy-treated patients with advanced melanoma using a rank-based scoring approach. J Transl Med 2023;21:257. [PMID: 37055772 PMCID: PMC10103529 DOI: 10.1186/s12967-023-04092-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 03/27/2023] [Indexed: 04/15/2023] Open

Abstract

BACKGROUND

Gene expression profiling is increasingly being utilised as a diagnostic, prognostic and predictive tool for managing cancer patients. Single-sample scoring approach has been developed to alleviate instability of signature scores due to variations from sample composition. However, it is a challenge to achieve comparable signature scores across different expressional platforms.

METHODS

The pre-treatment biopsies from a total of 158 patients, who have received single-agent anti-PD-1 (n = 84) or anti-PD-1 + anti-CTLA-4 therapy (n = 74), were performed using NanoString PanCancer IO360 Panel. Multiple immune-related signature scores were measured from a single-sample rank-based scoring approach, singscore. We assessed the reproducibility and the performance in reporting immune profile of singscore based on NanoString assay in advance melanoma. To conduct cross-platform analyses, singscores between the immune profiles of NanoString assay and the previous orthogonal whole transcriptome sequencing (WTS) data were compared through linear regression and cross-platform prediction.

RESULTS

singscore-derived signature scores reported significantly high scores in responders in multiple PD-1, MHC-1-, CD8 T-cell-, antigen presentation-, cytokine- and chemokine-related signatures. We found that singscore provided stable and reproducible signature scores among the repeats in different batches and cross-sample normalisations. The cross-platform comparisons confirmed that singscores derived via NanoString and WTS were comparable. When singscore of WTS generated by the overlapping genes to the NanoString gene set, the signatures generated highly correlated cross-platform scores (Spearman correlation interquartile range (IQR) [0.88, 0.92] and r² IQR [0.77, 0.81]) and better prediction on cross-platform response (AUC = 86.3%). The model suggested that Tumour Inflammation Signature (TIS) and Personalised Immunotherapy Platform (PIP) PD-1 are informative signatures for predicting immunotherapy-response outcomes in advanced melanoma patients treated with anti-PD-1-based therapies.

CONCLUSIONS

Overall, the outcome of this study confirms that singscore based on NanoString data is a feasible approach to produce reliable signature scores for determining patients' immune profiles and the potential clinical utility in biomarker implementation, as well as to conduct cross-platform comparisons, such as WTS.

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Affiliation(s)

Yizhe Mao Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
Tuba N Gide Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
Nurudeen A Adegoke Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
Camelia Quek Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
Nigel Maher Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, NSW, Australia
Alison Potter Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, NSW, Australia
Ellis Patrick School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, Australia The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW, Australia
Robyn P M Saw Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia Royal Prince Alfred Hospital, Camperdown, NSW, Australia Mater Hospital, North Sydney, Sydney, NSW, Australia
John F Thompson Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia Royal Prince Alfred Hospital, Camperdown, NSW, Australia Mater Hospital, North Sydney, Sydney, NSW, Australia
Andrew J Spillane Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia Mater Hospital, North Sydney, Sydney, NSW, Australia Royal North Shore Hospital, Sydney, Australia
Kerwin F Shannon Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia Royal Prince Alfred Hospital, Camperdown, NSW, Australia Mater Hospital, North Sydney, Sydney, NSW, Australia Chris O'Brien Lifehouse, Camperdown, NSW, Australia
Matteo S Carlino Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia Westmead and Blacktown Hospitals, Sydney, NSW, Australia
Serigne N Lo Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
Alexander M Menzies Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia Mater Hospital, North Sydney, Sydney, NSW, Australia Royal North Shore Hospital, Sydney, Australia
Inês Pires da Silva Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia Chris O'Brien Lifehouse, Camperdown, NSW, Australia
Georgina V Long Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia Mater Hospital, North Sydney, Sydney, NSW, Australia Royal North Shore Hospital, Sydney, Australia
Richard A Scolyer Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, NSW, Australia
James S Wilmott Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia. Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia. Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia.

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