RNAseq analysis of samples from oral cancer and oral leukoplakias patients
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina NovaSeq 6000
ORGANISM(S): Homo sapiens
SUBMITTER: David Hervas
PROVIDER: E-MTAB-12205 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Oral squamous cell carcinoma (OSCC) is one of the most common cancers worldwide including the Asian subcontinent. Oral carcinoma exhibits inherent heterogeneity in terms of the sites involved, etiology and pathology. They occur at multiple sites such as tongue, buccal mucosa, maxilla. Effective approaches towards improving survival rates in OSCC patients are primarily focused on early detection of the disease. The early clinical indication of the disease follows the development of potentially malignant lesions (leukoplakia/erythro-leukoplakia) with varied rates of transformation. Currently histopathological evaluation of oral biopsy is generally practiced to evaluate potential malignancy. However, human saliva has been considered to be a valuable medium for discovering biomarker molecules for malignancy. Exfoliated cancer cells may release protein or RNA molecules into the saliva or free molecules may be secreted or leaked from cancer cells representing gene expression changes associated with tumor development. Salivary proteins thus provide a strong option for development of non-invasive, point-of-care assays for screening/early detection of oral cancers. Dysplastic leukoplakia (LP) of the oral cavity is a potentially malignant condition for oral squamous cell carcinoma (OSCC), early detection of which is an unmet clinical need. In an effort to develop non-invasive biomarker based method for early detection of the disease, we have used quantitative mass spectrometry to identify differently abundant salivary proteins in OSCC (buccal mucosa) patients and individuals with potential to develop cancer (oral dysplastic leukoplakia) in comparison to healthy controls (with risk habits such as tobacco chewing or smoking).
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Project description:This study aims to identify genes differentially expressed in oral CAFs with respect to their normal counterparts, i.e. oral NFs. We collected oral normal mucosal tissues and oral squamous cell carcinoma (OSCC) tissues from 12 healthy people and 12 OSCC patients, respectively, at West China Hospital of Stomatology, Sichuang University, P. R. China. The tissues were isolated, cultured and purified using standard protocols to obtain oral NFs and CAFs. Agilent 4×44K Whole Genome Oligo Microarrays were used to measure the gene expression profiles of the samples. Sample preparation and hybrid reactions were performed according to the manufacture’s instructions. RNA samples from NFs and CAFs were pooled respectively before hybridization. The chips were scanned and visualized using the Agilent DNA microarray scanner. Probe set intensities were measured using Agilent Feature Extraction software (version 10.5.1.1). Raw data were normalized in the Agilent GeneSpring GX software (version 11.0) using the Agilent FE one-color scenario (mainly median normalization). Oral NFs and CAFs were obtained from tissues derived from 12 healthy people undergoing plastic surgery and 12 OSCC patiens undergoing surgical resection. RNA samples from NFs and CAFs were pooled respectively before hybridization.
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Project description:Oral squamous cell carcinomas are neoplasms that are mostly preceded by precancerous lesions such as leukoplakia and erythroplakia. It is important for the clinician to know about the predilection and possibility of these precancerous conditions transforming to cancer. This will inturn help to efficiently treat and manage patients. It is therefore important to understand the molecular events that explain the biology of predilection and transformation of precancerous lesions such as erythroplakia and leukoplakia to cancer. Our study aims to identify potential biomarker proteins in precancerous lesions of leukoplakia and erythroplakia that can flag its transformation to oral cancer. Four biological replicate clinical phenotypes of healthy control, leukoplakia, erythroplakia, and oral carcinoma were recruited based on clinical screening and histopathological evaluation of buccal mucosa tissue. Differentially expressed proteins were delineated using Label-free quantitative proteomics experiment done on Orbitrap fusion Tribrid mass spectrometer in three technical replicate sets of samples. Raw files were processed using Maxquant version 2.0.1.0. and down stream analysis was done by Perseus version 1.6.15.0. Validation included functional annotation based on biological process and KEGG pathways using ClueGO plug-in of cytoscape. Hierarchical clustering, and principal component analysis were performed using ClustVis tool. Across control, leukoplakia, and cancer, l- lactate dehydrogenase A chain, plectin, and WD repeat-containing protein 1 were upregulated, whereas thioredoxin 1 and spectrin alpha chain non-erythrocytic 1 were downregulated. Across control, erythroplakia, and cancer, l- lactate dehydrogenase A chain was upregulated whereas aldehyde dehydrogenase 2, peroxiredoxin 1, Heat shock 70 kDa protein 1B, and spectrin alpha chain non-erythrocytic 1 were downregulated. We found proteins involved in leukoplakia were associated with alteration in cytoskeletal reorganization and glycolysis, while in erythroplakia they were associated with alteration in response to oxidative stress and glycolysis across phenotypes. Hierarchical clustering sub-grouped half of precancerous samples under the main branch of control and the remaining half under carcinoma. Similarly, principal component analysis identified segregated clusters of control, precancerous lesions, and cancer but erythroplakia phenotypes particularly overlapped more with cancer cluster. Label-free proteomics offers a good platform for identification of protein biomarkers that can flag premalignant conditions that could become malignant. Qualitative and quantitative protein signatures across control, precancer and cancer phenotypes explain the possible functional outcomes that dictate malignant transformation to oral carcinoma. The observations place the previously observed clinical findings of erythroplakia having more predilection for cancer, in the right perspective.
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Project description:Oral carcinogenesis is a multi-step process involving normal mucosa progressing to oral precancerous lesions and finally to oral squamous cell carcinoma (OSCC). This complex process encompasses various molecules, including non-coding RNAs (ncRNAs). In this study, we performed whole-transcriptome analyses on adjacent normal tissues, oral leukoplakia tissues, and OSCC tissues, with the goal of identifying key differentially expressed circRNAs, lncRNAs, miRNAs, and mRNAs associated with different stages of oral carcinogenesis. In our study, numerous differentially expressed circRNAs, lncRNAs, miRNAs, and mRNAs were identified in adjacent normal, oral leukoplakia, and OSCC tissues. Subsequently, we constructed two regulatory competitive endogenous RNA (ceRNA) networks and identified some potential critical molecules involved in oral carcinogenesis. In conclusion, based on the whole-transcriptome analyses, we mapped the molecular feathers at RNA level during the process of oral carcinogenesis and revealed certain ncRNAs with great research potential.
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Project description:Background. Oral carcinogenesis is a complex process involving multiple genes. However, the genetic changes involved in this process are not demonstrated in the identical oral squamous carcinomas (OSCCs). Methods. According to the pathological characteristics, parts of normal tissues, oral dysplastic lesions (ODLs), and invasive cancers were procured from the identical OSCCs using laser microdissection (LMD), and large scale gene expression profiling was carried out on 33 samples derived from 11 OSCCs. Results. We analyzed genes differentially expressed in normal tissues vs. ODLs and ODLs vs. invasive tumors and identified the 15 candidate genes that continuously increasing or decreasing in its expression during oral carcinogenesis. One of these, ISG15 was chosen for further characterization. Real-time quantitative reverse transcriptase-polymerase chain reaction and immunohistochmistry analysis confirmed that ISG15 expression was consistently increasing during oral tumorigenesis. ISG15 high expression was significantly associated with poor prognosis (P=0.027). In addition, patients whose tumor had high ISG15 expression had worse 5-year survival rate than patients whose tumors had a low expression level (P=0.019). Conclusions. We identified the 15 genes that are continuously increasing or decreasing in its expression during oral carcinogenesis. One of these, ISG15 is likely to be associated with both dysgenesis and tumorigenesis, and may be a potential prognostic marker in these malignancies. Microarray samples of invasive tumor, adjacent dysplastic lesions and noncancerous normal tissues were collected from 11 patients with primary OSCCs. We analyzed genes differentially expressed in (i) normal vs. dysplastic tissues and (ii) dysplastic vs. tumor tissues.
2012-09-11 | E-GEOD-35261 | biostudies-arrayexpress