THE HUMAN PROTEOME ARRAY: HuProt™
HuProt™ in the News
HuProt™ — The Human Proteome Microarray
>21,000 GST-purified recombinant proteins. Expressed in yeast from sequence-confirmed plasmids. Piezoelectrically printed with duplicate spots. Confirmed folding by kinase autophosphorylation assay. Batches of up to 1000 slides.
There have been other protein microarrays, but none were made from a protein library as comprehensive or thoroughly validated as HuProt. HuProt arrays allow for pan-isotype autoantibody biomarker profiling versus properly folded, three-dimensional human proteins.
HuProt™ — Content Library
The new HuProt v4.0 consists of >21,000 unique human proteins, isoform variants, and protein fragments – covering 16,794 unique genes. This includes 15,889 of the 19,613 canonical human proteins described in the Human Protein Atlas, with broad coverage across protein subclasses:
HuProt™ — Production and QA/QC
Each HuProt array begins as CDI’s ORF collection, which we mobilize into a yeast galactose-inducible GST fusion vector (pEGH-A) using Gateway-mediated site-specific recombination. Each of our >21,000 clones is individually verified to have correct inserts by both BsrGI digestion and plasmid DNA sequencing. Clones with confirmed size, sequence, and high copy number are preserved in our library, which is routinely transformed into yeast for large-scale protein expression and N-terminal GST tag purification.
CDI uses its Arrayjet Ultra Marathon II non-contact piezoelectric (inkjet) printer to manufacture microarrays with significant performance advantages over contact print methods used in older-generation protein microarrays:
• precise spot morphology (see figure, above)
• Up to 1000 array print batch sizes for large cohort analysis
• rapid production of custom control configured arrays
• reduced inter- and intra-array variability
• greater data reproducibility (see below)
After purification, the GST-tagged proteins are piezoelectrically printed on glass slides in duplicate, along with control proteins (GST, BSA, Histones, IgG, etc.). Slides are barcoded for tracking and archiving. Each microarray batch is routinely evaluated by anti-GST staining to demonstrate quality of expression and printing. Slides can be PATH™ nitrocellulose or SuperEpoxy2™.
Learn more about our ANTYGEN™ HuProt™ analysis services — standalone or as part of a Grand Seromics™ assay:
HuProt Literature Citations
Autoantibody Profiling
- Fan W et al. (2019) Sa1679–Multiple rather than specific Antibodies were identified in Irritable Bowel Syndrome using Huprot™ Microarray Approach Gastroenterology 156 (6), Supplement 1, Page S-364
- Lastwika KJ et al. (2019) Tumor-derived autoantibodies identify malignant pulmonary nodules. Am J Respir Crit Care Med, 199 (10)
- Ye S et al. (2019) Plasma proteomic and autoantibody profiles reveal the proteomic characteristics involved in longevity families in Bama, China Clin Proteomics,16:22
- Gowen MF et al. (2018) Baseline antibody profiles predict toxicity in melanoma patients treated with immune checkpoint inhibitors. J. Transl. Med., 16(1):82
- Bigley V et al. (2018) Biallelic interferon regulatory factor 8 mutation: A complex immunodeficiency syndrome with dendritic cell deficiency, monocytopenia, and immune dysregulation. J. Allergy Clin Immunol, 141(6):2234-2248
- Bremer HD et al. (2018) ILF2 and ILF3 are autoantigens in canine systemic autoimmune disease Sci.Rep. 8(1):4852
- Chung JM et al. (2018) Identification of the thioredoxin-Like 2 Autoantibody as a Specific Biomarker for Triple-Negative Breast Cancer. J Breast Cancer 21:87-90
- Pan J et al. (2017) Identification of Serological Biomarkers for Early Diagnosis of Lung Cancer Using a Protein Array-Based Approach. Mol Cell Proteomics 16 (12):2069-2078
- Wang J et al. (2017) PTMA, a new identified autoantigen for oral submucous fibrosis, regulates oral submucous fibroblast proliferation and extracellular matrix. Oncotarget. 8(43): 74806–74819.
- Gupta S et al. (2017) Serum Profiling for Identification of Autoantibody Signatures in Diseases Using Protein Microarrays. Methods Mol Biol 1619:303-315.
- Gupta S et al. (2017) Evaluation of autoantibody signatures in meningioma patients using human proteome arrays. Oncotarget 8 (35): 58443-58456
- Chung et al. (2017) Phenotyping and auto-antibody production by liver-infiltrating B cells in primary sclerosing cholangitis and primary biliary cholangitis J. Autoimmun 77:45-54
- Ogishi et al. (2016) Delineation of autoantibody repertoire through differential proteogenomics in hepatitis C virus-induced cryoglobulinemia. Sci Rep 6:29532.
- Yang L et al. (2016) Identification of serum biomarkers for gastric cancer diagnosis using a human proteome microarray. Mol Cell Proteomics 15(2):614-23.
- Fiorentino DF et al. (2016) PUF60: a prominent new target of the autoimmune response in dermatomyositis and Sjögren’s syndrome. Ann Rheum Dis 75(6): 1145–1151.
- Hu CJ et al. (2016) Identification of Novel Biomarkers for Behcet Disease Diagnosis Using HuProt Array Approach. Mol Cell Proteomics 16(2):147-156
- Shi L et al. (2016) Application of high-throughput protein array in clinical screening for tumor markers. Int J Clin Exp Med 9:8529-8535.
- Syed P et al. (2015) Autoantibody profiling of glioma serum samples to identify biomarkers using human proteome arrays Sci Rep 15(5):13895
- Hu C et al. (2015) Autoantibody profiling on human proteome microarray for biomarker discovery in cerebrospinal fluid and sera of neuropsychiatric lupus. PLoS One 10(5):e0126643
- Hu CJ et al. (2012). Identification of new autoantigens for primary biliary cirrhosis using human proteome microarrays. Mol Cell Proteomics 11(9):669-80.
Antibody Specificity and Crossreactivity
- Venkataraman A et al. (2018) A toolbox of immunoprecipitation-grade monoclonal antibodies to human transcription factors. Nat Methods , in press
- Ramos-López et al. (2018) Antibody Specificity Profiling using Protein Microarrays. In: Rockberg J., Nilvebrant J. (eds) Epitope Mapping Protocols, Methods in Molecular Biology, vol 1785. e0181251.
- Washburn N et al. (2017) High-resolution physicochemical characterization of different intravenous immunoglobulin products. PLoS One 2017 Jul 31
- Sterner E et al. (2017) Therapeutic Antibodies to Ganglioside GD2 Evolved from Highly Selective Germline Antibodies. Cell Rep 20(7):1681-1691
- Kim YP et al (2014) Effective Therapeutic Approach for Head and Neck Cancer by an Engineered Minibody Targeting the EGFR Receptor. PLoS One. 1;9(12):e113442.
- Liu S et al. (2014) Characterization of monoclonal antibody’s binding kinetics using oblique-incidence reflectivity difference approach. MAbs 7:110-119
- Jeong JS et al. (2012) Rapid identification of monospecific monoclonal antibodies using a human proteome microarray. Mol Cell Proteomics 11(6):O111.016253
Protein Interactomics
- Zhao T et al. (2019) DNA methylation-regulated QPCT promotes sunitinib resistance by increasing HRAS stability in renal cell carcinoma Theranostics; 9(21): 6175–6190
- Song G et al. (2019) Proteome-wide Tyrosine Phosphorylation Analysis Reveals Dysregulated Signaling Pathways in Ovarian Tumors. Mol Cell Proteomics. 18(3):448-460.
- Cao T et al. (2019) A Two-Way Proteome Microarray Strategy to Identify Novel Mycobacterium tuberculosis-Human Interactors. Front. Cell. Infect. Microbiol, 28;9:65
- Cho HM et al. (2019) Drp1-Zip1 Interaction Regulates Mitochondrial Quality Surveillance System Mol Cell. 73(2):364-376.e8
- Wu FL et al. (2018) Global profiling of PknG interactions using a human proteome microarray reveals novel connections with CypA. Proteomics, Dec;18(23):e1800265
- Feng Y et al. (2018) High-Throughput Chip Assay for Investigating Escherichia coli Interaction with the Blood-Brain Barrier Using Microbial and Human Proteome Microarrays (Dual-Microarray Technology) Anal Chem 90(18):10958-10966
- Guo G et al. (2018) The cytomegalovirus protein US31 induces inflammation through mono-macrophages in systemic lupus erythematosus by promoting NF-κB2 activation. Cell Death Dis 24(9):2
- Choi S et al (2018) PELI1 Selectively Targets Kinase-Active RIP3 for Ubiquitylation-Dependent Proteasomal Degradation. Mol Cell. 70(5):920-935.e7.
- Bao Y et al (2018) Angiopoietin-like protein 3 blocks nuclear import of FAK and contributes to sorafenib response. Br J Cancer. 119(4):450-461.
- Yang Z et al. (2017) A Human Proteome Array Approach to Identifying Key Host Proteins Targeted by Toxoplasma Kinase ROP18. Mol Cell Proteomics 16:469-484
- Cox E et al. (2017) Global Analysis of SUMO-Binding Proteins Identifies SUMOylation as a Key Regulator of the INO80 Chromatin Remodeling Complex. Mol Cell Proteomics 16:812-23
- Liu M et al. (2017) Disruption of Ssp411 causes impaired sperm head formation and male sterility in mice. Biochim Biophys Acta Gen Subj. 1862(3):660-668.
- Li H et al. (2016) Penetrance of Congenital Heart Disease in a Mouse Model of Down Syndrome Depends on a Trisomic Potentiator of a Disomic Modifier. Genetics 203(2):763-70
- Wang Y et al. (2016) A nuclease that mediates cell death induced by DNA damage and poly(ADP-ribose) polymerase-1. Science 354 (6308)
- Ainscough J et al. (2015) Interleukin-1β Processing Is Dependent on a Calcium-mediated Interaction with Calmodulin. J. Biol. Chem. 290(52):31151-61
- Hu J et al. (2015) Systematic prediction of scaffold proteins reveals new design principles in scaffold-mediated signal transduction. PLoS Comput Biol 11(9):e1004508
- Jung JG et al. (2014) Notch3 interactome analysis identified WWP2 as a negative regulator of Notch3 signaling in ovarian cancer. PLos Genet10:e1004751.
- Ma TM et al. (2014) Serine racemase regulated by binding to stargazin and PSD-95: Potential NMDA-AMPA glutamate neurotransmission cross-talk. J Biol Chem. 289(43):29631-41
- Deng, RP et al. (2014) Global Identification of O-GlcNAc Transferase (OGT) Interactors by a Human Proteome Microarray and the Construction of an OGT Interactome. Proteomics 14:1020-30.
- Fan, Q et al. (2014) Identification of proteins that interact with alpha A-crystallin using a human proteome microarray. Mol Vis 20:117-124.
- Chen Y et al. (2013) Bcl2-associated Athanogene 3 Interactome Analysis Reveals a New Role in Modulating Proteasome Activity. Mol Cell Proteomics 12(10):2804-19.
- Huang Y. et al (2012) Global tumor protein p53/p63 interactome: making a case for cisplatin chemoresistance. Cell Cycle 11(12):2367-79.
Kinase assays
- Hu J et al. (2015) Systematic prediction of scaffold proteins reveals new design principles in scaffold-mediated signal transduction. PLoS Comput Biol 11(9):e1004508
- Tarrant MK et al. (2012) Regulation of CK2 by phosphorylation and O-GlcNAcylation revealed by semisynthesis. Nat Chem Biol 8(3):262-9.
Other enzyme assays
- Uzoma I et al. (2018) Global Identification of Small Ubiquitin-related Modifier (SUMO) Substrates Reveals Crosstalk between SUMOylation and Phosphorylation Promotes Cell Migration. Mol. Cell. Proteomics 17(5):871-888
- Xu Z et al. (2017) Systematic identification of the protein substrates of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase-T1/T2/T3 using a human proteome microarray. Proteomics 17:11
- Cox E et al. (2015) Identification of SUMO E3 ligase-specific substrates using the HuProt human proteome microarray. Methods Mol Biol. 1295:455-63
- Lee YI et al. (2013) Protein microarray characterization of the S-nitrosoproteome. Mol Cell Proteomics 13:63-72.
Nucleic Acid Binding
- Kang CL et al. (2019) LncRNA AY promotes hepatocellular carcinoma metastasis by stimulating ITGAV transcription Theranostics 9(15):4421-4436
- Liu L et al. (2019) Insight into novel RNA-binding activities via large-scale analysis of lncRNA-bound proteome and IDH1-bound transcriptome. Nucleic Acid Res. 47(5):2244-2262
- McClymont et al. (2018) Parkinson-Associated SNCA Enhancer Variants Revealed by Open Chromatin in Mouse Dopamine Neurons. Am J Hum Genet 103(6):874-892
- Qin M et al. (2018) Circ-UBR5: An exonic circular RNA and novel small nuclear RNA involved in RNA splicing. Biochem Biophys Res Comm 503 (2):1027-1034.
- Wang Y et al. (2018) HIC1 deletion promotes breast cancer progression by activating tumor cell/fibroblast crosstalk. J Clin Invest. 128(12):5235-5250.
- Barry G et al. (2017) The long non-coding RNA NEAT1 is responsive to neuronal activity and is associated with hyperexcitability states. Sci Rep 7:40127
- Barry G et al. (2014) The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicing. Molec Psychiatry. 19(4):486-94.
- Donnelly CJ et al. (2013) RNA toxicity from the ALS/FTD C9ORF72 expansion is mitigated by antisense intervention. Neuron 80(2):415-28.
- Fan B et al. (2013) A human proteome microarray identifies that the heterogeneous nuclear ribonucleoprotein K (hnRNP K) recognizes the 5′ terminal sequence of the hepatitis C virus RNA. Mol Cell Proteomics. 13(1):84-92.
- Hu S. et al (2009) Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling. Cell. 139(3):610-22.
Small molecule profiling
- Jia D et al (2019) Cardioprotective mechanism study of salvianic acid A sodium based on a proteome microarray approach and metabolomic profiling of rat serum Mol. Omics 2019 15(4):271-279.
- Zhang HN et al (2015) Systematic identification of arsenic-binding proteins reveals that hexokinase-2 is inhibited by arsenic. Proc Natl Acad Sci U.S.A. 112 (49):15084-9
Other
- Syu GD (2019) Development and application of a high-content virion display human GPCR array. Nature Communications 10: 1997
- Coll JM (2018) Herpesvirus infection induces both specific and heterologous antiviral antibodies in carp. Front Immunol. 9 (39) Jan 2018
- Azevedo C (2018) Screening a Protein Array with synthetic biotinylated Inorganic Polyphosphate to define the human PolyP-ome. ACS Chem Biol. 13 (8):1958-1963