Genome-wide copy number analysis for occult lymph node metastasis in oral squamous cell carcinoma
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ABSTRACT: Using Affymetrix Mapping 250K array, we studied copy number aberrations in oral squamous cell carcinoma (OSCC) to identified biomarkers associated with occult lymph node metastasis. We used frozen specimens from 60 OSCC patients. Copy number analysis was performed using homogenized samples of 60 oral squamous cell carcinoma patients by GeneChip Human Mapping 250k Sty arrays. As a reference, SNP array data set of 50 normal Asians (Japanese & Chinese) from HapMap database was used.
Project description:Using Affymetrix Mapping 250K array, we studied copy number aberrations in oral squamous cell carcinoma (OSCC) to identified biomarkers associated with occult lymph node metastasis. We used frozen specimens from 60 OSCC patients.
Project description:The development of oral squamous cell carcinoma (OSCC) is a multistep process requiring the accumulation of genetic alterations. Oral carcinogenesis is a multifactorial process involving numerous genetic changes that affect the activity of oncogenes, tumor suppressor genes and other classes of disease-related genes.Therefore, to identify the responsive genes for progression of oral dysplasia or OSCC, we here performed CGH analysis to DNA from oral dysplasia and OSCC by microdissection Copy number analysis of Affymetrix 250K SNP arrays was performed for 8 oral dysplasia samples, 8 oral squamous cell carcinoma samples, using microdissection
Project description:The development of oral squamous cell carcinoma (OSCC) is a multistep process requiring the accumulation of genetic alterations. To identify genes responsible for OSCC development, we performed high-density single-nucleotide polymorphism array analysis and genome-wide gene expression profiling on OSCC tumors. These analyses identified "absent in melanoma (AIM2)" and "interferon-inducible gene 16 (IFI16)," mapped to the hematopoietic IFN-inducible nuclear proteins with 200-amino acid repeat (HIN-200) gene cluster in the amplified region of chromosome 1q23, with overexpression in OSCCs. AIM2 and IFI16 are cytoplasmic double-stranded DNA sensors for innate immunity and act as tumor suppressors in several human cancers. Knockdown of AIM2 or IFI16 in OSCC cells resulted in the suppression of cell growth and the induction of apoptosis, accompanied by the downregulation of NF-κB activation. Because all of the OSCC cell lines had impairment of p53 activity, wild-type p53 was introduced in p53-deficient OSCC cells, and as a result, the expression of wild-type p53 suppressed cell growth and induced apoptosis via suppression of NF-κB activity. Finally, the coexpression of AIM2 and IFI16 significantly enhanced cell growth in p53-deficient cells; in contrast, the expression of AIM2 and/or IFI16 in cells bearing wild-type p53 suppressed cell growth. Moreover, AIM2 and IFI16 synergistically enhanced NF-κB signaling in p53-deficient cells. Thus, expression of AIM2 and IFI16 may have oncogenic functions in OSCC cells inactivating p53 system. Copy number analysis of Affymetrix 250K SNP arrays was performed for 5 oral leukoplakia samples, 20 oral squamous cell carcinoma samples, and 8 oral squamous cell carcinoma cell lines.
Project description:Oral squamous cell carcinoma (OSCC) is associated with high case-fatality. To gain insight into the complexity of OSCC and to identify potential chromosomal changes that may be associated with OSCC mortality, we examined paired DNA from peripheral blood and tumor cells to assess genome-wide LOH and DNA copy number alteration (CNA) and their associations with risk factors, tumor characteristics, and disease-specific mortality among 75 patients with HPV-negative OSCC. We found a highly heterogeneous and complex genomic landscape of HPV-negative tumors, and identified regions in 4q, 8p, 9p, and 11q that seem to play an important role in oral cancer biology and survival from this disease. We used Affymetrix 6.0 SNP arrays to test paired DNA from peripheral blood and tumor cells isolated by laser capture microdissection from 75 patients with HPV-negative OSCC. Peripheral blood DNA is used as reference for CNA to LOH.
Project description:In order to identify biomarkers that contribute to genetic causes of OSCC, we attempt to identify copy number variation regions (CNV) in patients with OSCC. We identified and confirmed the clinical significance of amplification regions scattered from 8q22.2 to 8q24.3. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from normal oral tissues and OSCC specimens. Copy number analysis of Affymetrix SNP 6.0 arrays was performed for 112 OSCC specimens and 10 non-cancerous samples.
Project description:We report an epitranscriptome-wide mapping of m6A-modified circRNAs (m6A-circRNA) in oral squamous cell carcinoma (OSCC). Utilizing the data of m6A-circRNAs epitranscriptomic microarray analysis, we found that m6A-circRNAs exhibited their particular modification style in OSCC. anti-m6A antibody Synaptic Systems, cat. No. 202003)
Project description:Oral squamous cell carcinoma (OSCC) is associated with high case-fatality. To gain insight into the complexity of OSCC and to identify potential chromosomal changes that may be associated with OSCC mortality, we examined paired DNA from peripheral blood and tumor cells to assess genome-wide LOH and DNA copy number alteration (CNA) and their associations with risk factors, tumor characteristics, and disease-specific mortality among 75 patients with HPV-negative OSCC. We found a highly heterogeneous and complex genomic landscape of HPV-negative tumors, and identified regions in 4q, 8p, 9p, and 11q that seem to play an important role in oral cancer biology and survival from this disease.
Project description:RNA-Seq was applied to oral squamous cell carcinomas and matched normal oral tissue to measure gene expression patterns and identify examples of allelic imbalance. Oral squamous cell carcinomas (OSCC) and matched normal tissue from 3 patients.
Project description:Oral potentially malignant disorders (OPMDs) may precede oral squamous cell carcinoma (OSCC). Early detection of OPMDs has a crucial role in OSCC prevention. DNA aneuploidy and chromosomal aberrations are markers of genomic DNA damage and chromosomal instability (CIN), which is involved in cancer development. We explored the relationship among genomic DNA copy number aberrations (CNAs), histological diagnosis and DNA aneuploidy in OPMDs/OSCCs. Samples from OPMDs and OSCCs were processed for high resolution DNA flow cytometry (hr DNA-FCM) to determine the relative DNA content expressed with the DNA index (DI). Additionally, on a subset of these samples, array-Comparative Genomic Hybridization (aCGH) analysis was performed on DNA obtained from diploid nuclei suspension or from aneuploid-enriched nuclei suspensions. DNA copy number aberrations were determined using high resolution arrays on 151 samples (2x105K, n=82 samples, and 4x180K, n=69 samples) (Agilent Technologies, Palo Alto, CA, USA). Labeling, hybridization, scanning and feature extraction were performed as previously described using the cross hybridization method previously described [Castagnola P, Malacarne D, Scaruffi P, Maffei M, Donadini A, et al. (2011) Chromosomal aberrations and aneuploidy in oral potentially malignant lesions: distinctive features for tongue. BMC Cancer 11: 445.].
Project description:Hypoxic microenvironment plays important roles in the progression of solid tumors including oral squamous cell carcinoma (OSCC). Long noncoding RNAs (lncRNAs) have gained much attention in the past few years. However, it is not clear whether lncRNAs could regulate hypoxia-adaptation of OSCC, and which lncRNAs participate in this process. Using an lncRNA microarray, we analyzed the aberrant lncRNA expression profiles in OSCC tissues compared with paired normal oral mucosa as well as in hypoxic OSCC cells compared with normoxic OSCC cells. Our data revealed 2053 differentially expressed (Fold Change >= 2.0, P-value <= 0.05) lncRNAs, among which 934 lncRNAs were significantly up-regulated and 1119 lncRNAs were down-regulated in OSCC compared with paired normal mucosa. Six OSCC tissues and paired normal oral mucosa were obtained from 6 patients with OSCC. LncRNA expression profiles were evaluated by an Agilent Human LncRNA Array v3.0 (8 x 60K, Arraystar).