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Connecting multiple microenvironment proteomes uncovers the biology in head and neck cancer

ABSTRACT: The poor prognosis of head and neck cancer (HNC) is associated with metastasis within the lymph nodes (LNs). Herein, the proteome of 140 multisite samples from a 59-HNC patient cohort, including primary and matched LN-negative or -positive tissues, saliva, and blood cells, reveals insights into the biology and potential metastasis biomarkers that may assist in clinical decision-making. Protein profiles are strictly associated with immune modulation across datasets, and this provides the basis for investigating immune markers associated with metastasis. The proteome of LN metastatic cells recapitulates the proteome of the primary tumor sites. Conversely, the LN microenvironment proteome highlights the candidate prognostic markers. By integrating prioritized peptide, protein, and transcript levels with machine learning models, we identified nodal metastasis signatures in blood and saliva. We present a proteomic characterization wiring multiple sites in HNC, thus providing a promising basis for understanding tumoral biology and identifying metastasis-associated signatures.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Adriana Franco Paes Leme

PROVIDER: MSV000099410 | MassIVE | Tue Oct 07 10:06:00 BST 2025

SECONDARY ACCESSION(S): PXD027780

REPOSITORIES: MassIVE

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Connecting multiple microenvironment proteomes uncovers the biology in head and neck cancer

Project description:The poor prognosis of head and neck cancer (HNC) is associated with metastasis within the lymph nodes (LNs). Herein, the proteome of 140 multisite samples from a 59-HNC patient cohort, including primary and matched LN-negative or -positive tissues, saliva, and blood cells, reveals insights into the biology and potential metastasis biomarkers that may assist in clinical decision-making. Protein profiles are strictly associated with immune modulation across datasets, and this provides the basis for investigating immune markers associated with metastasis. The proteome of LN metastatic cells recapitulates the proteome of the primary tumor sites. Conversely, the LN microenvironment proteome highlights the candidate prognostic markers. By integrating prioritized peptide, protein, and transcript levels with machine learning models, we identified nodal metastasis signatures in blood and saliva. We present a proteomic characterization wiring multiple sites in HNC, thus providing a promising basis for understanding tumoral biology and identifying metastasis-associated signatures.

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Expression data from 58 Synovial Sarcomas

Project description:Background: Synovial sarcoma (SS) occur in children as well as in adults, although metastatic events are much more common in the latter. Whereas the importance of the t(X;18) translocation in SS oncogenesis is well established, the genetic basis of SS metastasis is still poorly understood. We recently reported expression (CINSARC) and genomic (GI) prognostic signatures related to chromosome integrity in sarcomas and gastrointestinal stromal tumors (GISTs). Here we investigate whether these signatures can also predict outcomes in SS. Methods: One hundred primary untreated SS were selected for expression and genomic profiling in a training/validation approach. Results: CINSARC and GI have strong, independent and validated prognostic values (p<0.0001). Comparing expression profiles of tumors with or without metastasis, 14 genes common with the CINSARC signature were identified and the two top-ranked genes, KIF14 and CDCA2, were validated as prognostic markers in an independent cohort. Comparing genomic profiles of adult vs. pediatric SS, we show that metastasis is associated with genome complexity in both situations and that the adult genome is more frequently rearranged. Accordingly, pediatric patients with an even genomic profile do not develop metastasis. Conclusions: Metastasis development in SS is strongly associated with chromosome complexity, and CINSARC and GI are validated independent prognostic factors. The differences in metastasis frequency between adults and children are associated with genome instability, which is much more frequent in adults. GI is potentially the best overall biomarker, and clearly the most clinically relevant, considering that genome profiling from formalin fixed samples is already used in pathology. 58 Synovial Sarcomas hybridized to Agilent-014850 Whole Human Genome Microarray 4x44K G4112F

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