Clinical Proteomics: Liquid Chromatography-Mass Spectrometry (LC-MS) Purification Systems

Multi-omics analysis of fecal samples in colorectal cancer Egyptians patients: a pilot study

BACKGROUND

Colorectal cancer (CRC) is a public health concern and the second most common disease worldwide. This is due to genetic coding and is influenced by environmental aspects, in which the gut microbiota plays a significant role. The purpose of this study was to compare the microbiota makeup of CRC patients with that of healthy control and to identify upregulated and downregulated proteins and metabolites in CRC patients. Using a next-generation sequencing approach, fecal samples of five females (4 CRC patients and one healthy control) were analyzed by BGI DNBSEQ-T7, Hong Kong, China. Furthermore, proteomics and metabolomics analysis were performed using LC-MS/MS technique.

RESULTS

Dysbiosis of gut microbiota has been observed in patients with CRC, with an increase in microbiota diversity at all taxonomic levels relative to healthy control. Where, at the functional level the bacterial species participate in many different pathways among them de novo nucleotide synthesis and amino acids pathways were aberrantly upregulated in CRC patients. Proteomics and metabolomics profiles of CRC patients showed different proteins and metabolites, a total of 360 and 158 proteins and metabolites, respectively were highly expressed compared to healthy control with fold change ≥ 1.2. Among the highly expressed proteins were transketolase, sushi domain-containing protein, sulfide quinone oxidoreductase protein, AAA family ATPase protein, carbonic anhydrase, IgG Fc-binding protein, nucleoside diphosphate kinase protein, arylsulfatase, alkaline phosphatase protein, phosphoglycerate kinase, protein kinase domain-containing protein, non-specific serine/threonine protein kinase, Acyl-CoA synthetase and EF-hand domain-containing protein. Some of the differential metabolites, Taurine, Taurocholic acid, 7-ketodeoxycholic acid, Glycochenodeoxycholic acid, Glycocholic acid, and Taurochenodeoxycholic acid that belong to bile acids metabolites.

CONCLUSIONS

Some bacterial species, proteins, and metabolites could be used as diagnostic biomarkers for CRC. Our study paves an insight into using multi-omics technology to address the relationship between gut microbiota and CRC.

Human corneal endothelial cells from older donors can be cultured and passaged on cell-derived extracellular matrix

PURPOSE

To investigate the effect of culturing human corneal endothelial cells (HCEnCs) from older donors on extracellular matrix (ECM) derived from human corneal endothelial cell line (HCEC-12).

METHODS

HCEC-12 cells were cultured on lab-tek chamber slides for 9 days. Upon confluence, the cells were ruptured using ammonium hydroxide leaving the released ECM on the slide surface which was visualized using scanning electron microscope (SEM). HCEnCs from old aged donor tissues (n = 40) were isolated and cultured on either fibronectin-collagen (FNC) or HCEC-12 ECM at passage (P) 0. At subsequent passages (P1 and P2), cells were sub-cultured on FNC and ECM separately. Live/dead analysis and tight junction using ZO-1 staining were used to record percentage viability and morphological changes. The protein composition of HCEC-12 ECM was then analysed using liquid chromatography-mass spectrometry.

RESULTS

SEM images showed long fibrillar-like structures and a fully laid ECM upon confluence. HCEnCs cultured from older donor tissues on this ECM showed significantly better proliferation and morphometric characteristics at subsequent passages. Out of 1307 proteins found from the HCEC-12 derived ECM, 93 proteins were evaluated to be matrix oriented out of which 20 proteins were exclusively found to be corneal endothelial specific.

CONCLUSIONS

ECM derived from HCEC-12 retains protein and growth factors that stimulate the growth of HCEnCs. As the current clinical trials are from younger donors that are not available routinely for cell culture, HCEnCs from older donors can be cultured on whole ECM and passaged successfully.

A proteomic profiling dataset of recombinant Chinese hamster ovary cells showing enhanced cellular growth following miR-378 depletion

The proteomic data presented in this article provide supporting information to the related research article "Depletion of endogenous miRNA-378-3p increases peak cell density of CHO DP12 cells and is correlated with elevated levels of Ubiquitin Carboxyl-Terminal Hydrolase 14" (Costello et al., in press) [1]. Control and microRNA-378 depleted CHO DP12 cells were profiled using label-free quantitative proteomic profiling. CHO DP12 cells were collected on day 4 and 8 of batch culture, subcellular proteomic enrichment was performed, and subsequent fractions were analyzed by liquid chromatography tandem mass spectrometry (LC-MS/MS). Here we provide the complete proteomic dataset of proteins significantly differentially expressed by greater than 1.25-fold change in abundance between control and miR-378 depleted CHO DP12 cells, and the lists of all identified proteins for each condition.