Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Whole exome sequencing of Lung Squamous Carcinoma Patients of Indian Origin

ABSTRACT: The study involves whole exome sequencing of 20 primary tumors obtained from lung squamous carcinoma patients of Indian origin. With this, we aim to describe the mutational profile of this specific subset of lung cancer patients. This knowledge will further allow us to gain an insight into potentially actionable genomic alterations prevalent in Indian lung squamous carcinoma.

INSTRUMENT(S): HiSeq X Ten

ORGANISM(S): Homo sapiens

SUBMITTER: Amit Dutt

PROVIDER: E-MTAB-8801 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Alterations in glycosylation are seen in many types of cancer, including colorectal cancer (CRC). CRC is known to display glycosylation alterations. Glycans, the sugar moieties of glycoconjugates, are involved in many important functions relevant to cancer, such as cell signaling and adhesion, and may can be of value as biomarkers. In this study, we have used mass spectrometry to analyze the N-glycan profiles of 35 CRC tissue samples from patients with tumors in the right or left colon and 10 healthy tissue samples from non-CRC patients who underwent operations for other reasons. The tumor samples were divided into groups depending on tumor location (right or left colon) and stage (II or III), while the healthy samples were divided into right or left side of the colon. The levels of neutral and acidic N-glycan compositions and glycan classes were analyzed in a total of ten different groups. Surprisingly, there were no significant differences in glycan levels when all right- and left-sided CRC samples were compared, and few differences (such as in the abundance of the neutral N-glycan H3N5) were seen when the samples were divided according to both location and stage. Multiple significant differences were found in the levels of glycans and glycan classes when stage II and III samples were compared, and these glycans could be of value as candidates for new markers of cancer progression. In order to validate our findings, we analyzed healthy tissue samples from the right and left colon and found no significant differences in the levels of any of the glycans analyzed, confirming that our findings when comparing CRC samples from the right and left colon are not due to normal variations in the levels of glycans between the healthy right and left colon. Additionally, the levels of the acidic glycans H4N3F1P1, H5N4F1P1, and S1H5N4F1 were found to change in a cancer-specific but colon location-nonspecific manner, indicating that CRC affects glycan levels in similar ways, regardless of tumor location.

Dataset Information

Whole exome sequencing of Lung Squamous Carcinoma Patients of Indian Origin

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