Dataset Information

A Deg-protease family protein in marine Synechococcus is involved in outer membrane protein organization

ABSTRACT: In this study we inactivated SYNW2176 and characterized the stress response and outer membrane protein composition of the mutant in order to better understand the overlap between envelope stress and copper stress in marine Synechococcus.

INSTRUMENT(S): LTQ Orbitrap Velos, TripleTOF 5600

ORGANISM(S): Synechococcus Sp. (strain Wh8102)

TISSUE(S): Prokaryotic Cell

DISEASE(S): Multiple Chemical Sensitivity

SUBMITTER: Majid Ghassemian

LAB HEAD: Brian Palenik

PROVIDER: PXD000989 | Pride | 2019-12-17

REPOSITORIES: Pride

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Project description:Cancer cells metastasize through the bloodstream either as single migratory circulating tumor cells (CTCs) or as multicellular groupings (CTC-clusters). Existing technologies for CTC enrichment are designed primarily to isolate single CTCs, and while CTC-clusters are detectable in some cases, their true prevalence and significance remain to be determined. Here, we developed a microchip technology (Cluster-Chip) specifically designed to capture CTC-clusters independent of tumor-specific markers from unprocessed blood. CTC-clusters are isolated through specialized bifurcating traps under low shear-stress conditions that preserve their integrity and even two-cell clusters are captured efficiently. Highly parallel architecture of the chip allows deterministic screening of clinically relevant volumes of blood samples at slow, and hence, non-damaging flow rates. Using the Cluster-Chip, we identify CTC-clusters in 30-40% of patients with metastatic cancers of the breast, prostate and melanoma. RNA sequencing of CTC-clusters confirms their tumor origin and identifies leukocytes within the clusters as being tissue-derived macrophages. Together, the development of a device for efficient capture of CTC-clusters will enable detailed characterization of their biological properties and role in cancer metastasis. We used the Cluster-Chip to capture CTC-clusters from the blood of a breast cancer patient with high CTC counts, released CTC-clusters in solution, stained them with TexasRed-conjugated antibodies against the leukocyte cell surface markers CD45, CD14 and CD16, and then isolated intact CTC-clusters individually using a micromanipulator. From a single time point, we retrieved 15 CTC-clusters, and each of those clusters was individually subjected to RNA-sequencing analysis using a next generation platform (SOLiD 5500). In addition, two leukocytes were isolated from the blood of a healthy donor were individually subjected to RNA-sequencing analysis using the same platform.

Dataset Information

A Deg-protease family protein in marine Synechococcus is involved in outer membrane protein organization

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