Differentially expressed proteins in positive versus negative HNSCC lymph nodes

A Systemic and Integrated Analysis of p63-Driven Regulatory Networks in Mouse Oral Squamous Cell Carcinoma

Oral squamous cell carcinoma (OSCC) is the most common malignancy of the oral cavity and is linked to tobacco exposure, alcohol consumption, and human papillomavirus infection. Despite therapeutic advances, a lack of molecular understanding of disease etiology, and delayed diagnoses continue to negatively affect survival. The identification of oncogenic drivers and prognostic biomarkers by leveraging bulk and single-cell RNA-sequencing datasets of OSCC can lead to more targeted therapies and improved patient outcomes. However, the generation, analysis, and continued utilization of additional genetic and genomic tools are warranted. Tobacco-induced OSCC can be modeled in mice via 4-nitroquinoline 1-oxide (4NQO), which generates a spectrum of neoplastic lesions mimicking human OSCC and upregulates the oncogenic master transcription factor p63. Here, we molecularly characterized established mouse 4NQO treatment-derived OSCC cell lines and utilized RNA and chromatin immunoprecipitation-sequencing to uncover the global p63 gene regulatory and signaling network. We integrated our p63 datasets with published bulk and single-cell RNA-sequencing of mouse 4NQO-treated tongue and esophageal tumors, respectively, to generate a p63-driven gene signature that sheds new light on the role of p63 in murine OSCC. Our analyses reveal known and novel players, such as COTL1, that are regulated by p63 and influence various oncogenic processes, including metastasis. The identification of new sets of potential biomarkers and pathways, some of which are functionally conserved in human OSCC and can prognosticate patient survival, offers new avenues for future mechanistic studies.

Identifying KRT20 as a Potential Key Gene in Lymphatic Metastasis of Head and Neck Squamous Cell Carcinoma

Background: Head and neck squamous cell carcinoma (HNSCC) was the seventh most common cancer worldwide in 2018. Lymphatic metastasis (LM) is closely related to HNSCC prognosis and recurrence. However, the underlying mechanism of LM remains unclear. Therefore, this study aimed to identify the key genes in the LM of HNSCC. Methods: We used The Cancer Genome Atlas (TCGA) to identify differentially expressed genes (DEGs) between LM and non-LM cases. A random forest model, the Search Tool for the Retrieval of Interacting Genes, Cytoscape, and cytoHubba were used to identify hub genes among DEGs, including KRT20 (Cytokeratins 20). We analyzed the survival of KRT20 in TCGA, and we overexpressed KRT20 in HNSCC cell lines to investigate its effects on migration and invasion. We also correlated the expression of KRT20 in HNSCC tissue microarrays with survival and clinicopathological features. Results: We identified 243 DEGs—143 upregulated genes and 100 downregulated genes. Further analysis revealed that KRT20 is a potential key gene associated with LM and overall survival rates among patients with HNSCC. Overexpression of KRT20 increased the migration and invasion ability of HNSCC cell lines Tu686 and FD-LSC-1. Tissue microarray studies demonstrated an overexpression of KRT20 among N1+ patients (including N1-N3 patients). Survival analysis results and the clinicopathological features of HNSCC tissue microarrays were consistent with our analysis of TCGA. Thus, a high KRT20 expression level might suggest an adverse HNSCC prognosis. Our gene set enrichment analysis showed that KRT20 participates in many metabolic pathways, including those related to tumorigenesis and cancer development. Conclusions: We propose that KRT20 may be a key gene in HNSCC with LM.

Investigating proteome changes between primary and metastatic cutaneous squamous cell carcinoma using SWATH mass spectrometry

BACKGROUND

Cutaneous squamous cell carcinoma (cSCC) is a common malignancy worldwide and the first as the cause of death from keratinocytic carcinomas. Around 5% of primary cSCCs metastasize, leading to a 5-year survival rate of only 11 %.

OBJECTIVE

This paper aims to investigate the proteome profile of primary and metastatic cSCC lesions for the identification of potential diagnostic biomarkers and molecular alterations.

METHODS

Liquid chromatography coupled with SWATH-MS workflow was used to analyse the proteome profile of formalin-fixed and paraffin-embedded samples of primary (n = 20) and metastatic cSCC (n = 25) lesions. Statistical and bioinformatics analysis was performed to identify differentially abundant proteins and molecular alterations between the lesions.

RESULTS

A total of 5037 proteins were identified across the samples of which 19 proteins including ISG15, APOA1 and MARCKS with roles in metastasis were increased and 11 proteins including DMKN, APCS and CST6 decreased in metastatic cSCC lesions relative to the primary phenotypes (adj. p-value <0.05). The proteomic data separated the lesions based on their histopathological diagnosis. Bioinformatics analysis revealed that cell migration, cell survival and immune response are likely activated, and apoptosis is inhibited in metastatic cSCC lesions, indicating increased lesion complexity as the disease progresses from primary to the metastatic phenotype. Two samples were reclassified after PCA analysis.

CONCLUSION

SWATH-MS analysis identified important molecular changes between primary and metastatic cSCC samples. Exploring these findings further will allow their translation into the clinic for improved tumour diagnosis, staging and therapeutic intervention.

Prognostic implication of proteomic profiles in head and neck squamous cell carcinoma

BACKGROUND AND OBJECTIVE

Head and neck squamous cell carcinoma (HNSCC) is one of the malignant cancers with poor prognosis. However, clinicopathologic and histological criteria were finite to predict the prognosis of HNSCC. We aimed to characterize the proteomic profile of prognosis from HNSCC patients.

MATERIAL AND METHODS

Reverse phase protein array (RPPA) data in HNSCC were downloaded from The Cancer Proteome Atlas (TCPA). Independent prognostic-related proteins (IPP) were screened by Cox regression model and Kaplan-Meier methods. IPP signature (IPPS) including selected proteins was conducted for prognostic prediction for HNSCC. Protein-protein network analysis and gene ontology (GO) enrichment were used to identify related functional proteins and pathways.

RESULTS

Based on the IPP, IPPS for HNSCC was constructed: risk score = (1.541* IRF1) + (1.460 * SMAD4) + (1.396 * LKB1) + (0.746* Cyclin E2) + (0.618* Paxillin) + (0.499* p-PEA-15 (Ser116)). The IPPS in HNSCC showed good predictive performance (area under curve = 0.779) with moderate sensitivity and specificity. Protein-protein network analysis and functional enrichment indicated an implication of response to decreased oxygen levels in HNSCC.

CONCLUSION

The identified proteomic signature might function as a prognostic tool for the management of HNSCC and provide novel target for the treatment of HNSCC.

Enhancing the Bystander and Abscopal Effects to Improve Radiotherapy Outcomes

In this paper, we summarize published articles and experiences related to the attempt to improve radiotherapy outcomes and, thus, to personalize the radiation treatment according to the individual characteristics of each patient. The evolution of ideas and the study of successively published data have led us to envisage new biophysical models for the interpretation of tumor and healthy normal tissue response to radiation. In the development of the model, we have shown that when mesenchymal stem cells (MSCs) and radiotherapy are administered simultaneously in experimental radiotherapy on xenotumors implanted in a murine model, the results of the treatment show the existence of a synergic mechanism that is able to enhance the local and systemic actions of the radiation both on the treated tumor and on its possible metastasis. We are convinced that, due to the physical hallmarks that characterize the neoplastic tissues, the physical-chemical tropism of MSCs, and the widespread functions of macromolecules, proteins, and exosomes released from activated MSCs, the combination of radiotherapy plus MSCs used intratumorally has the effect of counteracting the pro-tumorigenic and pro-metastatic signals that contribute to the growth, spread, and resistance of the tumor cells. Therefore, we have concluded that MSCs are appropriate for therapeutic use in a clinical trial for rectal cancer combined with radiotherapy, which we are going to start in the near future.

A Chemical Probe for Tudor Domain Protein Spindlin1 to Investigate Chromatin Function

Modifications of histone tails, including lysine/arginine methylation, provide the basis of a "chromatin or histone code". Proteins that contain "reader" domains can bind to these modifications and form specific effector complexes, which ultimately mediate chromatin function. The spindlin1 (SPIN1) protein contains three Tudor methyllysine/arginine reader domains and was identified as a putative oncogene and transcriptional coactivator. Here we report a SPIN1 chemical probe inhibitor with low nanomolar in vitro activity, exquisite selectivity on a panel of methyl reader and writer proteins, and with submicromolar cellular activity. X-ray crystallography showed that this Tudor domain chemical probe simultaneously engages Tudor domains 1 and 2 via a bidentate binding mode. Small molecule inhibition and siRNA knockdown of SPIN1, as well as chemoproteomic studies, identified genes which are transcriptionally regulated by SPIN1 in squamous cell carcinoma and suggest that SPIN1 may have a role in cancer related inflammation and/or cancer metastasis.