"Chromosome 17 team has been mostly focused on supporting neXtProt and the whole HPP effort with the I-TASSER/COFACTOR functional annotation pipeline. During 2020-2021 the pipeline has been enhanced as D-I-TASSER/COFACTOR. Hundreds of requests for functional annotation have been addressed"
PI: Gilbert S. OMENN
The Chromosome 17 team has dedicated our effort to working with Eric Deutsch at PeptideAtlas and Lydie Lane at neXtProt to enhance data quality and create and apply the HPP Guidelines for Interpretation of Mass Spectrometry Data (versions 1.0, 2.1, 3.0). This work supports the HPP goal to document expression of the proteins on the human proteome parts list at neXtProt. This work supports the C-HPP goals to identify neXtProt PE2,3,4 Missing Proteins (MP50 Challenge) and to functionally annotate unannotated uPE1 proteins (CP50 Challenge). We document the increase in PE1 proteins and the reduction of PE2,3,4 missing proteins. This work is reported in the annual HPP Metrics publication in the HPP special issue of Journal of Proteome Research (JPR). See Omenn et al, JPR 2020, for the most recent publication. Metrics 2021 will be finalized and submitted to JPR during June 2021.
As shown in Table 2 of the Metrics papers, since the announcement of the MP50 Challenge in October 2016, the number of PE2,3,4 proteins for Chromosome 17 has been reduced from 148 to 58 (-90), while the total across all chromosomes is a reduction from 2949 in 2016 to 1421 in neXtProt release 2021-02 (-1528).
The Chromosome 17 team also adapted and applied the I-TASSER/COFACTOR algorithm to predict functions based on Gene Ontology terms for the uPE1 proteins. See Zhang C, et al, JPR 2018 and JPR 2019. At the Adelaide World Congress of Proteomics Lydie Lane of neXtProt announced that each protein’s page in neXtProt henceforth contains a link in the lower left to this algorithmic prediction of function. Many HPP investigators and others have utilized this service.
We have not performed specific laboratory experiments.
PI: Robert MORITZ
"For in vitro translation and transcription (IVTT)-assisted SRM, we have been generating IVTT-compatible plasmids for the missing and the uPE1 proteins and assembled and distributed a comprehensive collection representing 90% of all human protein-coding genes through our repository DNASU"
PI: Joshua LABAER
To unveil the function of the uPE1 or the “Dark proteins”, we are utilizing CRISPR-based genome-wide functional genomics screens, targeting to identify genes and mutations that promote progression of breast cancer, especially the highly aggressive basal-like subtype with TP53 mutations. As a model system, we employ MCF10A cell lines expressing 10 prevalent mutant forms of p53 proteins that have been comprehensively analyzed for cancer-related phenotypes and molecular profiles by RNA-Seq and ChIP-Seq. From in vitro and xenograft-based screens on these cell lines, a few hundred hits, including several uPE1 proteins, have been identified to promote more aggressive behaviors of cells expressing different p53 mutants. We are currently performing individual validation of the hits in parallel with integrated bioinformatics analysis to infer their cellular functions.