Expression & Epigenetic Silencing of MicroRNA for Predicting Therapeutic Response and Prognosis of HPV-negative HNSCC

NCT03953443 | Completed

• 1 other identifier: INST 1008
• Study Type: observational
• Target: 25
• Locations: 1 country
• Sites: 1

Brief Summary

A two-part molecular epidemiological study will be conducted to comprehensively assess the association between miR expression and miR promoter methylation and the response to therapy and prognosis in primary, HPV-negative HNSCC patients. Part 1 will be a prospective collection of 25 pairs of fresh tumor-distant normal mucosal tissue in patients with HNSCC. Ultimately, 15 HPV-negative tumor-mucosal pairs will be utilized for discovery work in identifying miRs whose expression is up- or down-regulated in tumors. Part 2 will test the association between miR expression and miR promoter methylation, and therapeutic response and survival in all archived surgical cases of HPV-negative HNSCC at University of New Mexico Hospital (UNMH) collected after 1990.

Conditions

Head and Neck Squamous Cell Carcinoma

Outcome Measures

Primary Outcomes (3)

• Identify tumor specific microRNAs (miRs) whose expression increases or decreases by over 2 fold in fresh tumor vs. distant normal mucosa from patients with head and neck squamous cell carcinoma (HNSCC) negative for human papillomavirus (HPV)

  SOLiD sequencing of fresh tumor-distant normal pairs will discover miRs whose expression is altered in HNSCC tumors. SOLiD sequencing will provide fully quantitative data for the expression of known and novel miRs. Because HPV-related tumors comprise approximately 20% of all HNSCC and are biologically distinct from HPV negative tumors classically associated with tobacco and alcohol, only HNSCC without p16 overexpression will be used in this discovery experiment. This restriction will increase homogeneity of the samples and the power to detect miRs associated with the etiology of HPV-negative HNSCC. The miRs identified will be validated using qPCR assay in the tumor-normal pairs and in p16-negative HNSCC cell lines (n\>15). In addition, miRs previously reported to be dysregulated in HNSCC will be subjected to similar validation, even if not identified during the SOLiD sequencing discovery phase.

  As long as needed to collect 15 HPV-negative tumor-mucosal sample pairs and complete sequencing, up to 10 years

• Identify miRs whose reduced expression in HPV-negative HNSCC is due to promoter methylation

  miRs with reduced expression in tumor tissue identified under Outcome 1 will be scrutinized for CpG rich promoters by checking the UCSC database. The methylation status of CpG rich promoters of miRs will be examined by COBRA assay in tumor vs. normal pairs (n=15) and in p16-negative HNSCC cell lines (n\>15). The heterogeneity of methylation status across the CpG rich promoter will be characterized by bisulfate sequencing using the COBRA PCR product. The silencing of miRs by promoter methylation will be examined by comparing mean miR expression levels between the methylation categories for the tumor-normal pairs and for the HNSCC cell lines. This is primarily a descriptive study.

  As long as needed to complete sequencing and analyze results, up to 5 years

• Define the statistical association between the expression of tumor specific miRs, miR methylation, and the therapeutic response and prognosis of HPV-negative HNSCC using patient medical records

  The therapeutic response and prognosis of HPV-negative HNSCC will be collected from two sources: the patient's case file from the New Mexico Tumor Registry (NMTR) and from the patient's UNMH medical record. qRT PCR will be designed to quantify the miR expression in RNA extracted from the formalin-fixed, paraffin embedded (FFPE) tissues. A methylation-specific PCR (MSP) will be designed to facilitate the large-scale methyl-typing in all retrospective clinical samples. The primary analysis will be performed in HPV-negative HNSCC. A secondary analysis will be conducted to include all HNSCC, with and without p16 overexpression. p16 overexpression status will be adjusted in the secondary analysis. The association between miR expression status (high or low) and miR methylation status (yes or no), and patient's PFS and OS will be examined using Kaplan-Meier survival plots and the log-rank test.

  As long as needed to collect and analyze information from medical records, up to 5 years

Interventions

Not interventional OTHER

Eligibility Criteria

• Age: 18 Years+
• Sex: all
• Healthy Volunteers: No
• Age Groups: Adult (18-64), Older Adult (65+)
• Sampling Method: Non-Probability Sample

Study Population

Patients with known or suspected HNSCC

You may qualify if:

• Patients with a known or suspected diagnosis of HNSCC
• Any primary site may be included, except nonkeratinizing nasopharyngeal SCC or lip SCC.
• Patients are planned for diagnostic biopsies for suspected HNSCC, or for therapeutic surgery for HNSCC.
• Patients are naïve to radiation to the head and neck, prior to research biopsies.
• Patients have not received chemotherapy for the diagnosis of HNSCC, prior to research biopsies.
• Age \> 18 years.
• Eastern Cooperative Oncology Group (ECOG) performance status of 0-2.
• Patients sign an informed consent, agreeing to fresh tumor biopsy as well as distant normal mucosal biopsy for purposes of described research. Research biopsies will be in addition to planned surgery. In cases where tumor resection is planned, a representative part of the tumor will be submitted for research purposes.

You may not qualify if:

• Nonkeratinizing nasopharyngeal carcinoma
• Lip squamous cell carcinoma

Sponsors & Collaborators

• New Mexico Cancer Research Alliance: lead

Study Sites (1)

University of New Mexico - Cancer Center

Albuquerque, New Mexico, 87106, United States

Location

Biospecimen

Retention: SAMPLES WITH DNA

Fresh HNSCC tumor-distant normal mucosal tissue

MeSH Terms

Conditions

Squamous Cell Carcinoma of Head and Neck

Condition Hierarchy (Ancestors)

Carcinoma, Squamous Cell; Carcinoma; Neoplasms, Glandular and Epithelial; Neoplasms by Histologic Type; Neoplasms; Head and Neck Neoplasms; Neoplasms by Site

Study Officials

• Garth Olson, MD

  University of New Mexico Comprehensive Cancer Center

  PRINCIPAL INVESTIGATOR

Study Design

• Study Type: observational
• Observational Model: CASE ONLY
• Time Perspective: PROSPECTIVE
• Sponsor Type: OTHER
• Responsible Party: SPONSOR

Study Record Dates

• First Submitted: May 8, 2019
• First Posted: May 16, 2019
• Study Start: December 17, 2010
• Primary Completion: February 13, 2020
• Study Completion: March 14, 2023
• Last Updated: May 22, 2025

Record last verified: 2025-05

Data Sharing

• IPD Sharing: Will not share

Locations

US (1)