NBDC Research ID: hum0427.v2
SUMMARY
Aims:
- Head and neck malignancies originate in a wide variety of locations, including the pharynx, larynx, oral cavity, nose and paranasal sinuses, salivary glands, thyroid gland, and temporal bone. Their molecular biological characteristics differ depending on the location of origin. Therefore, it is necessary to establish a tailored treatment that is tailored to the molecular biological characteristics of each tumor. In the field of oncology, many researchers generally use cell lines obtained from cell banks. However, cell lines for head and neck malignancies available from cell banks are limited especially for rare-type cancers, resulting in difficulties in elucidation of biological characterization of such malignancies and establishment of therapeutic strategies. This study aimed to 1) conduct comprehensive genetic analysis of head and neck malignant tumor tissues and patient-derived blood, 2) establish cell lines of head and neck malignancies and to examine their tumorigenic abilities in immune-deficient animals, 3) deposit to cell banks. Using multi-omics approaches, we seek to elucidate the molecular mechanisms of oncogenes and to develop biomarkers for recurrence and metastasis prediction, as well as strategies for novel targeted therapies.
Methods:
- Genomic DNAs extracted from peripheral blood mononuclear cells (PBMC), the primary tumor tissues, and the cell line were used for whole exome sequencing analysis.
- Chromatin immunoprecipitation (ChIP) sequencing using H3K27Ac and YAP antibodies
Participants/Materials:
- PBMC and the primary tumor tissues were collected from a patient with external auditory canal squamous cell carcinoma, and a cell line was established from the primary tumor tissues. The cell line was deposited as SCEACono2 in RIKEN BioResource Research Center (https://cellbank.brc.riken.jp/cell_bank/CellInfo/?cellNo=RCB5515&lang=En).
- Five patients with temporal bone squamous cell carcinoma
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000645 | NGS (Exome) | Controlled-access (Type I) | 2023/11/02 |
| JGAS000645 (Data addition) | NGS (ChIP-seq) | Controlled-access (Type I) | 2026/06/16 |
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MOLECULAR DATA
| Participants/Materials |
external auditory canal squamous cell carcinoma (ICD10: C44.2): 1 case (3 samples) non-tumor tissue (PBMC), primary tumor tissue, cell line established from the primary tumor tissue: 1 sample each |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | MGI [DNBSEQ-G400] |
| Library Source | DNAs extracted from PBMC, the primary tumor tissues, and the cell line |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect Human All Exon V6 Kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000775 |
| Total Data Volume | 29.6 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Temporal bone squamous cell carcinoma (ICD10: C44.2): 5 cases [H3K27Ac] primary tumor tissues: 5 samples non-tumor tissues (normal skin): 2 samples [YAP] primary tumor tissues: 2 samples non-tumor tissues (normal skin): 2 samples Pooled input DNA obtained by mixing DNA from all patients: 1 sample |
| Targets | ChIP-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NextSeq 500] |
| Library Source | DNAs extracted from tumor and non-tumor tissues of patients with temporal bone squamous cell carcinoma, and immunoprecipitated with an anti-H3K27Ac and YAP antibody |
| Cell Lines | - |
| Library Construction (kit name) | DNA Library Prep Kit for Illumina |
| Fragmentation Methods | Ultrasonic fragmentation |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 75 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000775 |
| Total Data Volume | 25.0 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Takashi Nakagawa
Affiliation: Department of Otorhinolaryngology, Graduate School of Medical Sciences, Kyushu University
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (B) | Development of novel synthesizing treatment strategy by exhaustive research on temporal bone squamous cell carcinoma | 18H02951 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Elucidation of epigenetic tumor control mechanisms that determine the malignancy of squamous cell carcinoma of the temporal bone | 22H03236 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Elucidation of the Metastasis Regulatory Mechanism via NLRP3 Inflammasome Pathway in Temporal Bone Squamous Cell Carcinoma | 22K09745 |
| KAKENHI Grant-in-Aid for Early-Career Scientists | Investigation of transcriptional reprogramming mechanisms involved in invasion and metastasis of head and neck squamous cell caricnoma | 20K18300 |
| Research Grant, Soda Toyoji Memorial Foundation | Elucidation of Transcriptional Regulatory Mechanisms Contributing to the Progression of Squamous Cell Carcinoma of the External Auditory Canal via Multi-omics Analysis | - |
| Medical Research Grant, Takeda Science Foundation | Elucidation of the YAP1-mediated transcriptional reprogramming mechanism contributing to invasion and metastasis in head and neck squamous cell carcinoma | - |
| Cancer Research Grant, Shinnihon Foundation of Advanced Medical Treatment Research | Exploring Transcriptional Reprogramming Mechanisms Underlying Head and Neck Cancer Progression via Multi-omics Analysis | - |
| Cancer Research Grant, SGH Foundation | Elucidation of Transcriptional Reprogramming Mechanisms involved in Invasion and Metastasis in Head and Neck Squamous Cell Carcinoma | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Establishment and characterization of a primary cell culture derived from external auditory canal squamous cell carcinoma | doi: 10.1002/2211-5463.13225 | JGAD000775 |
| 2 | Aberrant Hippo-YAP/TEAD Signaling Drives Malignant Transcriptional Reprogramming in External Auditory Canal Squamous Cell Carcinoma | doi: 10.1158/2767-9764.CRC-25-0626 | JGAD000775 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
