Omics · dataset · 2026
Impact of immune status and clinical outcomes in oropharyngeal cancer
Listed in ZivaHub and Deakin Research Online and DMU Figshare — shown once because both records carry DOI 10.17034/32641686.v1
Description
Background
Oropharyngeal squamous cell carcinoma (OPSCC) is a biologically and clinically heterogeneous disease, known for having distinct molecular and prognostic features primarily driven by smoking, alcohol and human papillomavirus (HPV) infection. The immune system has emerged as a critical factor influencing cancer prognosis and survival. However, reliable, scalable, and interpretable approaches for defining the immune status of OPSCC patients and their impact in routine diagnostic settings remain limited. <br><br>Objectives: This thesis aims to comprehensively evaluate the prognostic and biological significance of OPSCC immune status through an integrative, multimodal approach: (1) to develop, evaluate and validate a tumour-infiltrating lymphocyte (TIL) classification in OPSCC, with attention to HPV-related differences and the prognostic significance of stromal TILs (STC%) in survival; (2) to identify enriched gene signatures from bulk RNA exome capture sequencing (ecRNA-seq) and validate these at the protein level via digital IHC analysis, considering associations with HPV, STC% and outcomes; (3) to explore systemic immunity using pre-treatment blood-based biomarkers, assessing links with outcomes, HPV status, and tumour TILs. <br><br>
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Methods
In Chapter 2, a hand-crafted algorithm was developed to classify STC% in digital H&E slides (WSIs and TMAs) and applied to a Northern Irish OPSCC cohort, with external validation. STC% was analysed in relation to survival, independent of HPV. Chapter 3 used ecRNA-seq to profile tumours stratified by STC% and HPV.
Enriched gene signatures linked to prognosis were validated by IHC (CD3, CD8, CD20) on matched TMAs. Chapter 4 analysed systemic immune biomarkers from blood counts in a later NI OPSCC cohort, evaluating prognostic impact and correlation with STC%. <br><br>Key Findings: The digital TIL algorithm showed prognostic value, with STC-high tumours independently associated with improved survival in both HPV+ and HPV− OPSCC. Transcriptomic profiling of STC-high cases revealed enrichment of B and T cell-related signatures linked to prognosis, validated by IHC.
Systemic immune biomarkers also predicted outcomes and showed a modest correlation with STC%. <br><br>Conclusion: This thesis presents a novel digital pathology algorithm for semi-automated quantification of stromal TILs, integrating transcriptomics, IHC and systemic biomarkers to reveal immune subclasses of OPSCC with prognostic significance, independent of HPV status. <br><br>Thesis is embargoed until 31 July 2028.<br>
Links
Where it is published
- DOI doi.org/10.17034/32641686.v1 ↗
DOI / persistent id · from zivahub uct ac za
Catalogue records · 1
- OAI-PMH record api.figshare.com/v2/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=oai%3Af… ↗
metadata API · from zivahub uct ac za
Topics
- From keywords
- Earth & Environmental Science · Earth & Environmental Science · Earth & Environmental Science · Life Sciences · Life Sciences · Life Sciences · Medicine & Health · Medicine & Health · Medicine & Health · RNA sequencing · RNA sequencing · RNA sequencing
- Inferred from text
- Cancer 75% · Disease 75% · Oncology and carcinogenesis 71% · Sequencing 75%
Provenance · 3 source records, 21 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| ZivaHub | oai:figshare.com:article/32641686 | 5 d ago | JSON v1 |
| Deakin Research Online | oai:figshare.com:article/32641686 | 5 d ago | JSON v1 |
| DMU Figshare | oai:figshare.com:article/32641686 | 5 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · zivahub uct ac za | connector:zivahub_uct_ac_za@1.0.0 | |
| concepts[disease].local:disease:cancer | enrichment · zivahub uct ac za | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[disease].local:disease:disease | enrichment · zivahub uct ac za | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[field].anzsrc:group:3211 | enrichment · zivahub uct ac za | taxonomy-embedding@1.1.0 | title+keywords+description (71%) |
| concepts[field].local:field:earth-environmental | mapping · figshare dmu ac uk | connector:figshare_dmu_ac_uk@1.0.0 | |
| concepts[field].local:field:earth-environmental | mapping · dro deakin edu au | connector:dro_deakin_edu_au@1.0.0 | |
| concepts[field].local:field:earth-environmental | mapping · zivahub uct ac za | connector:zivahub_uct_ac_za@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · dro deakin edu au | connector:dro_deakin_edu_au@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · zivahub uct ac za | connector:zivahub_uct_ac_za@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · figshare dmu ac uk | connector:figshare_dmu_ac_uk@1.0.0 | |
| concepts[field].local:field:medicine-health | mapping · zivahub uct ac za | connector:zivahub_uct_ac_za@1.0.0 | |
| concepts[field].local:field:medicine-health | mapping · figshare dmu ac uk | connector:figshare_dmu_ac_uk@1.0.0 | |
| concepts[field].local:field:medicine-health | mapping · dro deakin edu au | connector:dro_deakin_edu_au@1.0.0 | |
| concepts[modality].local:modality:rna-seq | mapping · zivahub uct ac za | vocabulary-mapper@1.0.0 | keywords['RNA-sequencing'] |
| concepts[modality].local:modality:rna-seq | mapping · dro deakin edu au | vocabulary-mapper@1.0.0 | keywords['RNA-sequencing'] |
| concepts[modality].local:modality:rna-seq | mapping · figshare dmu ac uk | vocabulary-mapper@1.0.0 | keywords['RNA-sequencing'] |
| concepts[modality].local:modality:sequencing | enrichment · zivahub uct ac za | keyword-concept-rules@1.0.0 | title+description (75%) |
| description | source · zivahub uct ac za | connector:zivahub_uct_ac_za@1.0.0 | /metadata/dc/description |
| license_text | source · zivahub uct ac za | connector:zivahub_uct_ac_za@1.0.0 | |
| publication_date | source · zivahub uct ac za | connector:zivahub_uct_ac_za@1.0.0 | |
| title | source · zivahub uct ac za | connector:zivahub_uct_ac_za@1.0.0 | /metadata/dc/title |