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Plasma Multi-omics Nucleic Acid Landscape of Gastrointestinal Cancer [miRNA-seq]

ABSTRACT: We sequenced cell-free nucleaic acid (cfNA) for 2 major cancer types (44 samples of colorectal cancer and 36 samples of stomach cancer) and 81 samples of healthy individuals collected in China. Cancer related signaling pathway were identified. Cancer detection and specific classification were achieved through combining both cfRNA and cfDNA reads.

ORGANISM(S): Homo sapiens

PROVIDER: GSE186595 | GEO | 2023/09/28

REPOSITORIES: GEO

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Plasma Multi-omics Nucleic Acid Landscape of Gastrointestinal Cancer [long RNA]

Project description:We sequenced cell-free nucleaic acid (cfNA) for 2 major cancer types (44 samples of colorectal cancer and 36 samples of stomach cancer) and 81 samples of healthy individuals collected in China. Cancer related signaling pathway were identified. Cancer detection and specific classification were achieved through combining both cfRNA and cfDNA reads.

2023-09-28 | GSE186587 | GEO

Plasma Multi-omics Nucleic Acid Landscape of Gastrointestinal Cancer [MeDIP-seq]

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Cell-Free RNA Signature for Noninvasive Diagnosis of Hepatocellular Carcinoma Using MOF to Enrich Circulating Nucleic Acids

Project description:We developed a new method to extract cfNA (containing cfDNA, cfRNA and viral RNA) from serum/plasma based on the adsorption of nucleic acids by MOF materials (Co-IRMOF-74-IV), and compared the extraction capability with commercial kit method. We conducted a comprehensive characterization of the cell-free RNA in a small number of clinical samples, including patients with HCC (n=14), CHB (n=17) and normal individuals (n=8). And then we build a model with 6 cfRNA signature to diagnose liver cancer, and indicated high diagnostic efficiency (AUC=0.905) in the independent validation cohort (HCC n=7, CHB n=4 and normal individuals n=8)

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Project description:We sequenced cell-free RNA (cfRNA) for five cancer types (colorectal cancer, stomach cancer, liver cancer, lung cancer and esophageal cancer) and healthy individuals in 230 plasma samples collected from 6 clinical centers in China. Cancer related signaling pathway and microbial genus were identified. Cancer detection and specific classification were achieved through combining both host and microbial cfRNA reads.

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Liquid Biopsy Evaluation and Repository Development at Princess Margaret

Project description:The objective of this protocol is to develop an institution-wide liquid biopsy protocol that will establish a common process for collecting blood and corresponding archived tumor specimens for future research studies at the University Health Network’s Princess Margaret Cancer Centre. Circulating cell-free nucleic acids (cfNA), including cell-free DNA (cfDNA) and cell-free RNA (cfRNA), are non-invasive, real-time biomarkers that can provide diagnostic and prognostic information before cancer diagnosis, during cancer treatment, and at disease progression. Cancer research scientists and clinicians at the Princess Margaret are interested in incorporating the collection of peripheral blood samples ("liquid biopsies") into research protocols as a means of non-invasively assessing tumor progression and response to treatment at multiple time points during a patient’s course of disease.

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Plasma Multi-omics Nucleic Acid Landscape of Gastrointestinal Cancer [long RNA PBMC]

Project description:We sequenced 8 colorectal cancer patients' PBMC samples, and 6 healthy donors' PBMC samples. These individuals' plasma RNA have been profiled.

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Plasma Multi-omics Nucleic Acid Landscape of Gastrointestinal Cancer [Tissue RNA-seq]

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Transcriptomic analyses of gastrointestinal function in the “dwarf” and “medium” forms of Sthenoteuthis oualaniensis during sexual maturation

Project description:Sthenoteuthis oualaniensis (SA) is an important squid species in the South China Sea. Based on SA samples collected in 2016, SA was divided into the “dwarf” form (DF) and “medium” form (MF). To understand the changes in gastrointestinal function in SA during sexual maturation, we undertook transcriptomic analyses of the stomach and intestine tissues of the DF and MF of SA using the deep-sequencing platform Illumina HiSeq™. We exploited a high-throughput method to delineate differentially expressed genes (DEGs) in the DF and MF of SA. A total of 135,464 unigenes (68627 unigenes of the DG and 66837 unigenes of the MF) were generated. We identified 7965 and 4051 relative DEGs in the intestine and stomach tissue of the mature DF of SA compared with those of the immature DF of SA; and 22138 and 18460 DEGs in the intestine and stomach of the mature MF of SA compared with those of the immature MF of SA. Functional categorization and pathway analyses of these DEGs with regard to the metabolism of differentially expressed genes were noted. This work is the first to identify a set of genes associated with gastrointestinal function during the sexual maturation of SA.

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2017-09-22 | GSE104107 | GEO

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