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A Transcriptomic Analysis and shRNA Screen for Intracellular Ion Channels and Transporters Regulating Pigmentation
Published in Bruno Gasnier, Michael X. Zhu, Ion and Molecule Transport in Lysosomes, 2020
Donald C. Koroma, Salwa Y. Hafez, Elena Oancea
An inherent characteristic of transcripts encoding melanosomal transporters, ion channels, and receptors is the presence of transmembrane domains. From the two sets of differentially expressed transcripts, we selected only those predicted to have >1 transmembrane domain based on UniProtKB database (www.uniprot.org). The Human Protein Atlas and GeneCards were then used to further select transcripts encoding proteins with predicted intracellular localization based on Compartments (compartments.jensenlab.org). We obtained 218 such transcripts common to both data sets, RR and H&O. We further selected these transcripts by calculating their fractional representation in HEMs compared to KERs, as shown in Figure 10.2A and setting the threshold to >10% enrichment in HEMs. The enrichment scores allowed for comparison of individual transcripts across both H&O and RR datasets and the scores for all the identified transcripts were positively correlated. In total, we obtained 182 transcripts that fulfilled all our selection criteria, not including known genes encoding melanosomal proteins. As expected, transcripts encoding known melanosomal proteins with a role in pigmentation, like OCA2, TPCN2, and SLC45A2 (the gene mutated in OCA4), fulfilled all the selection criteria, exhibiting a >80% enrichment in melanocytes (Figure 10.2B). A large majority of the 182 selected transcripts encode proteins with unknown function, in addition to other transcripts for which a function in melanocytes has not been characterized.
Recent advances in proteolytic stability for peptide, protein, and antibody drug discovery
Published in Expert Opinion on Drug Discovery, 2021
Xianyin Lai, Jason Tang, Mohamed E.H. ElSayed
The Human Protein Atlas is a database collecting human protein expression levels in blood, cells, tissues, and organs with specific locations based on various technologies, such as antibody-based imaging, mass spectrometry-based proteomics, transcriptomics, and systems biology. The program was initiated in 2003 with the Tissue Atlas and expanded to six sub-databases, each focusing on a specific aspect of the human proteins. The Tissue Atlas provides the expression and localization of human proteins across major tissues and organs [29,30], the Brain Atlas expands brain regions from a limited number of human brain regions in the Tissue Atlas to 10 major well-defined mammalian brain regions [31], the Cell Atlas shows high-resolution images of protein subcellular localization within cells [32], the Blood Atlas has proteins from blood cells and proteins secreted from other tissues into blood [33,34], the Metabolic Atlas shows protein function and gene expression in the context of the human metabolic network, and the Pathology Atlas includes the impact of protein levels for survival of patients with cancer [35].
Proteomics in the pharmaceutical and biotechnology industry: a look to the next decade
Published in Expert Review of Proteomics, 2021
Jennie R. Lill, William R. Mathews, Christopher M. Rose, Markus Schirle
Spatial proteomics is emerging on a number of fronts and in depth resources are now available to the community, mapping proteins and their interacting partners across tissues. Advances in microscopy, mass spectrometry, flow cytometry and machine learning has catapulted technology development to allow for more granular spatial cellular regulation. Various studies have been performed to probe the complex architecture that is the cell, including single-cell variations, dynamic protein translocations, changing interaction networks and proteins that can localize to various sub-cellular compartments, allowing researchers to further unravel human disease biology [195,196]. The Human Protein Atlas has been generated for probing a tissue based map of the human proteome, a wonderful resource for researchers who want to investigate the location of proteins at the tissue level [197].
Innate-like NKp30+CD8+ T cells armed with TCR/CAR target tumor heterogeneity
Published in OncoImmunology, 2021
Margareta P. Correia, Ana Stojanovic, Winfried S. Wels, Adelheid Cerwenka
Transcript expression data of ERBB2 and NCR3LG1 from several tumors from TCGA data sets (PanCancer Atlas) were extracted from the cBioPortal for Cancer Genomics (https://cbioportal.org). Graphs and correlations were generated in the cBioPortal software. Immunohistochemistry of tumor tissue slides of paired HER2 and B7H6 protein expression in breast cancer and colon carcinoma from patient samples was originally obtained from the Human Protein Atlas database (http://www.proteinatlas.org/).44 Tissue microarrays were stained with antibodies and labeled with DAB (3,3ʹ-diaminobenzidine) and counterstained with hematoxylin. Each sample is represented by 1 mm tissue cores. In the Human Protein Atlas database, all images of tissues stained by immunohistochemistry are manually annotated by two specialists sequentially. Annotation parameters include an evaluation of i) staining intensity (negative, weak, moderate or strong) and ii) fraction of stained cells within a sample (<25%, 25–75% or >75%). The staining intensity is classified as negative, weak, moderate or strong based on the laser power and detector gain settings used for image acquisition in combination with the visual appearance of the image.