Chromosome 19 Annotations with Disease Speciation: A First Report from the Global Research Consortium

Abstract

A first research development progress report of the Chromosome 19 Consortium with members from Sweden, Norway, Spain, USA, China and India, a part of the Chromosome-Centric Human Proteome Project (C-HPP) global initiative is presented (http://www.c-hpp.org). From the chromosome 19 peptide-targeted library constituting 6159 peptides, a pilot study was conducted using a sub-set with 125 isotope-labeled peptides. We applied an annotation strategy with triple quadrupole, ESI-Qtrap, and MALDI mass spectrometry platforms, comparing the quality of data within, and in-between these instrumental set-ups. LC-MS conditions were outlined by multiplex assay developments, followed by MRM assay developments. SRM was applied to biobank samples, quantifying kallikrein 3 (prostate specific antigen) in plasma from prostate cancer patients. The antibody production has been initiated for more than 1200 genes from the entire chromosome 19, and the progress developments are presented. We developed a dedicated transcript microarray, to serve as the mRNA identifier by screening cancer cell lines. NAPPA protein arrays were built to align with the transcript data with the Chromosome 19 NAPPA chip, dedicated to 90 proteins, as the first development delivery. We have introduced an IT-infrastructure utilizing a LIMS system that serves as the key interface for the research teams in order to share and explore data generated within the project. The cross-site data repository will form the basis for sample processing, including biological samples, as well as patient samples from national Biobanks.

Association of chromosome 19 to lung cancer genotypes and phenotypes

“…The Chromosome 19 Consortium has investigated gene expression using complementary analysis platforms, to provide a genomewide human protein resource database, and detailed maps of protein molecular pathways, interactions, and networks. The Chromosome 19 project has already contributed to the annotations of severe diseases, especially glioblastoma [11][12][13].…”

Quantitative proteomics and transcriptomics reveals metabolic differences in attracting and non-attracting human-in-mouse glioma stem cell xenografts and stromal cells

“…We utilized label-free quantitative proteomics as a reliable technique previously employed by our lab [23,50] that is cost effective, yields high proteome coverage, and does not suffer from dynamic range limitations [37,51]. We also utilized a targeted transcriptomic platform [45][46][47], which contains genesets related to GBM biology, in parallel to label-free proteomics (Fig. 1).…”

“…A custom targeted microarray containing functional human gene sets related to glioma biology was used to measure the relative expression of epigenetics-, radiation sensitivity-, ion-, metabolomics-, ER stress-, and unfolded protein response-, ubiquitination, chromosome 19-, and all cloned glycogene-related transcripts compiled from the NCBI human sequence and CAZy (www.cazy.org) databases totaling 2577 transcripts [45][46][47]. Each transcript-specific oligonucleotide was spotted in triplicate on the microarray.…”

“…Significance analysis of microarrays algorithm (SAM, v4.0, Stanford University, Palo Alto, CA) [49] was used with minimum 5000 permutations to determine statistically significant differentially expressed genes. The significance cutoff in these experiments was set to a FDR of <10% [45][46][47]. Positive fold change values are indicative of an increase in transcript expression in attractors relative to non-attractors and negative fold change values are indicative of a decrease in transcript expression in attractors relative to non-attractors (Supplementary Table S5).…”

Integrated Transcriptomic and Glycomic Profiling of Glioma Stem Cell Xenografts

“…A universal human reference (Stratagene, La Jolla, CA) was labeled with Cy3 32 . Data from chips scanned with a confocal laser (ScanArray 4000XL; Packard Biochip Technologies, Billerica, MA) were processed with BlueFuse (Illumina Fulbourn, Cambridge, UK) 21, 29-31 and analyzed by significance of analysis of microarrays algorithm (SAM, v4.0, Stanford University, Palo Alto, CA) 33 . The significance cutoff was set to an FDR of < 10% 21, 29-31 .…”