HuProt: THE HUMAN PROTEOME MICROARRAY

The world’s largest collection of full-length human proteins.

There have been other protein microarrays, but none were made from a protein library as comprehensive or thoroughly validated as HuProt™. Created by faculty at the High Throughput Biology (HIT) Center at the Johns Hopkins University School of Medicine, HuProt was the brainchild of CDI co-founders Jef Boeke, Heng Zhu, Dan Eichinger, & Seth Blackshaw. Original development on HuProt was funded by the NIH Common Fund Support for the Development of Protein Capture Reagents and Technologies, a major project which resulted in HuProt-validated monospecific monoclonal antibodies for human transcription factors. These antibodies, along with many others, are now sold by CDI as Monomabs™.

The collection starts with sequence-confirmed plasmids, which are used to make >21,000 GST-purified recombinant proteins in yeast.  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™.  HuProt arrays have been used to evaluate DNA & RNA nucleotide binding, antibody specificity, small molecule binding, protein-protein interactions, and more to  properly folded, three-dimensional human proteins.

Technology overview.

Next-generation technology.  More content, cleaner data.

We start with sequence-confirmed plasmids, then individually express and GST-purify proteins from S. cerevisiae. Piezoelectric printing is used to spot these in duplicate alongside controls in batches of up to 1000 arrays; quality confirmed with anti-GST QA/QC. Successful folding demonstrated by kinase autophosphorylation assay. Service available.

Broad coverage of the human proteome.

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.

Content includes major functional classes such as intracellular proteins, membrane proteins, enzymes, secreted proteins, transcription factors, transporters, GPCRs, cytokines, immune receptors, immune checkpoints, CD markers, ion channels, cytosolic proteins, nuclear receptors. Additionally there is thorough coverage for proteins enriched in major tissues of interest such as testis, cerebral cortex, thyroid gland, skin, fallopian tube, liver, parathyroid, intestine, kidney, spleen, muscle, epididymis, lymph node, bone marrow, adrenal gland, esophagus, heart, appendix, tonsil, prostate, rectum, adipose tissue, stomach, colon, cervix, uterus, gallbladder, seminal vesicle, breast, ovary, endometrium, smooth muscle, salivary gland, pancreas, and bladder.

Reproducible protein distribution.

CDI’s non-contact piezoelectric ‘inkjet’ process uses next-generation ArrayJet printers and allows for rapid production of high quality microarray slides time after time. Versus older contact pin printing methods – HuProt™ arrays are made with improved accuracy and reproducibility with excellent spot morphology.

Reproducible serum profiling.

Reproducible Proteome-Wide IgG Autoantibody Immunoprofiling of a Healthy Human Male Within and Across HuProt Proteome Microarray Batches. Serum was collected from a healthy adult human male donor, incubated on pairs (Rep1, Rep2) of HuProt proteome microarrays across three print batches (Batch 1 Feb12_2020, Batch 2 Dec09_2019, Batch 3 Oct01_2019), and stained with anti-IgG (red) & anti-IgA (green) secondaries. Raw data were plotted on a log scale and linear regression analysis was performed. Intra-lot correlations of spot pair averages (red boxes) was >.95 R^2 within all three batches. Slide-to slide cross pairings across all possible pairs of the six slides was a >.90 R^2 correlation – demonstrating robust reproducibility of HuProt microarray data between any individual slide; these results demonstrate multi-isotype analysis requiring multiple slides should be reliable.

Learn more about our ANTYGEN™ HuProt™ analysis services.

huprot the human antigen matrix microarray button by CDI Labs
CDI Labs Order Product Button

Deep dive on HuProt™ proteome microarray technology and QA/QC.

HuProt™ Microarray Production. The HuProt™ Human Proteome Microarray is the most comprehensive human proteome array created to date (Jeong et al, 2012).  It contains over 21,000 human proteins and protein isoforms, including >81% of canonically expressed proteins as defined by the Human Protein Atlas, and allows hundreds of interactions to be profiled in high-throughput.  HuProt™ can be used for a wide range of applications-this includes mapping antigen-specific immunity as multi-isotype profiles in serum, determining monoclonal antibody specificity, and studying protein-protein interaction, substrate identification, protein-DNA binding, protein-RNA binding, and binding of some small molecules.  CDI Labs’ latest version of the array, HuProt™ v4.0, contains >81% of human proteins in each major functional Gene Ontology protein category (Venkataraman et al, 2018).

Creation of HuProt™ Library. HuProt™ library clones were derived from public ORF libraries or independently synthesized; entry clones are from the laboratories of Heng Zhu and Seth Blackshaw (The Johns Hopkins University). Using the Gateway recombinant cloning system (Invitrogen, CA), human ORFs were shuttled from the entry clones to a yeast high-copy expression vector (pEGH-A) that produces GST-His6 fusion proteins under the control of the galactose-inducible GAL1 promoter. Plasmids were rescued into E. coli and verified by restriction endonuclease digestion. Plasmids with inserts of correct size were transformed into yeast for protein purification (Hu S et al, 2009; Jeong J et al, 2012)

Validating and Curating Clones used in HuProt™. To check and confirm the identity of each human ORF in the HuProt™ libary, bidirectional Sanger sequencing was conducted on both the entry clones and the yeast expression vectors that were derived from them (Venkataraman A et al, 2018). Blast+ was used to align the ORF sequence to multiple public databases (UniProt, CCDS, RefSeq, and Ensembl) to generate an integrated alignment score for each clone.  If a clone covered the entire sequence of a known protein, the clone is considered full length (F), whereas partial matches were regarded as indicative of truncated (TRUNC) clones. Because the source clones included ORFs containing untranslated regions, unannotated splice variants, and single-nucleotide polymorphisms, the clones were categorized into groups ranging from perfect matches to the known protein-coding transcriptome, to as-yet potential protein-coding ORFs that are not yet reviewed.  A detailed breakdown of this classification, along with the threshold parameters, can be accessed at https://collection.cdi-lab.com/public.

Protein Purification from the HuProt™ Library. Proteins were purified from yeast transformed with expression vectors encoding the human ORFs. Human proteins were purified as GST-His6 fusion proteins from yeast using a previously described high-throughput purification protocol (Hu S et al, 2009; Zhu et al., 2001). Using a 96-well format, the samples are purified from yeast extracts using glutathione-agarose beads.  0.1% Triton is included in the lysis buffer and washers to ensure that the purified proteins are free of lipids.

Protein Microarray Production & Testing.  The purified human proteins were arrayed in a 384-well format and printed on PATH slides (GraceBio, USA), using an Arrayjet UltraMarathon printer (Arrayjet, UK) to create a block format.  Arrays that show >95% of the spots with a foreground/background signal (F/B) ratio of at least 1.5 in an anti-GST assay are classified usableA number of controls that are reactive with secondary detection reagents are included on HuProt™. Controls include titrated GST protein, histones, mouse and rabbit anti-biotin, mouse IgM, and biotin-tagged control for streptavidin detection.  Each block also contains a row of control spots, including Alex Fluor 555/647 as landmarks.

Tests show that HuProt™ arrays contain a majority of the annotated, full-length proteome in native conformation. Tests on HuProt™ show that the proteins are folded in native conformation and retain function (Hu S. poster; Venkataraman A., et al., 2018). When both native and denatured HuProt™ arrays were probed with monoclonal antibodies that selectively recognize either linear or folded epitopes of their cognate antigen, the antibodies were found to recognize the appropriate antigen form (Venkataraman A., et al., 2018). Further tests (RNA binding) showed that proteins on HuProt™ do retain function (Venkataraman A., et al., 2018).

HuProt References: Autoantibody Seromics

[1]
L. Zhuang, C. Huang, Z. Ning, L. Yang, W. Zou, P. Wang, C. Cheng, Z. Meng, Circulating tumor‐associated autoantibodies as novel diagnostic biomarkers in pancreatic adenocarcinoma, Intl Journal of Cancer. 152 (2023) 1013–1024. https://doi.org/10.1002/ijc.34334.
[2]
Q. Yang, H. Ye, G. Sun, K. Wang, L. Dai, C. Qiu, J. Shi, J. Zhu, X. Wang, P. Wang, Human Proteome Microarray identifies autoantibodies to tumor‐associated antigens as serological biomarkers for the diagnosis of hepatocellular carcinoma, Molecular Oncology. 17 (2023) 887–900. https://doi.org/10.1002/1878-0261.13371.
[3]
X. Xie, L. Tian, Y. Zhao, F. Liu, S. Dai, X. Gu, Y. Ye, L. Zhou, X. Liu, Y. Sun, X. Zhao, BACH1-induced ferroptosis drives lymphatic metastasis by repressing the biosynthesis of monounsaturated fatty acids, Cell Death Dis. 14 (2023) 48. https://doi.org/10.1038/s41419-023-05571-z.
[4]
Y. Wang, J. Li, X. Zhang, M. Liu, L. Ji, T. Yang, K. Wang, C. Song, P. Wang, H. Ye, J. Shi, L. Dai, Autoantibody signatures discovered by HuProt protein microarray to enhance the diagnosis of lung cancer, Clinical Immunology. 246 (2023) 109206. https://doi.org/10.1016/j.clim.2022.109206.
[5]
T.L. Voyer, A. Gervais, J. Rosain, A. Parent, A. Cederholm, D. Rinchai, L. Bizien, G. Hancioglu, Q. Philippot, M.S. Gueye, M.R. Luxman, M. Renkilaraj, M. Ogishi, C. Soudée, M. Migaud, F. Rozenberg, M. Momenilandi, Q. Riller, L. Imberti, O. Delmonte, G. Müller, B. Keller, J. Orrego, W.A. Gallego, T. Rubin, M. Emiroglu, N. Parvaneh, D. Eriksson, M. Aranda-Guillen, D.I. Berrios, L. Vong, C.H. Katelaris, P. Mustillo, J. Rädler, J. Bohlen, J.B. Celik, C. Astudillo, S. Winter, A. Guichard, V. Béziat, J. Bustamante, Q. Pan-Hammarström, Y. Zhang, L.B. Rosen, S.M. Holland, H. Kenney, K. Boztuğ, N. Mahlaoui, S. Latour, R. Abraham, V. Lougaris, F. Hauck, A. Sediva, F. Atschekzei, M.C. Poli, M.A. Slatter, B. Palterer, M.D. Keller, A. Pinzon-Charry, A. Sullivan, L. Droney, D. Suan, N. Aladjidi, M. Hie, E. Lazaro, J. Franco, S. Keles, M. Malphette, M. Pasquet, M.E. Maccari, A. Meinhardt, A. Ikinciogullari, M. Shahrooei, F. Celmeli, P. Frosk, C.C. Goodnow, P.E. Gray, A. Belot, H.S. Kuehn, S.D. Rosenzweig, F. Licciardi, A. Servettaz, V. Barlogis, G.L. Guenno, V.-M. Herrmann, T. Kuijpers, G. Ducoux, F. Sarrot-Reynauld, C. Schuetz, C. Cunningham-Rundles, F. Rieux-Laucat, S.G. Tangye, C. Sobacchi, R. Doffinger, K. Warnatz, B. Grimbacher, C. Fieschi, L. Berteloot, V. Bryant, S.T. Assant, L.D. Notarangelo, H. Su, B. Neven, L. Abel, Q. Zhang, B. Boisson, A. Cobat, E. Jouanguy, O. Kampe, P. Bastard, C. Roifman, N. Landegren, M.S. Anderson, J.-L. Casanova, A. Puel, Impaired thymic AIRE expression underlies autoantibodies against type I IFNs in humans with inborn errors of the alternative NF-kB pathway, Preprints, 2023. https://doi.org/10.22541/au.167330741.18394805/v1.
[6]
G.-D. Syu, F.X.R. Sutandy, K. Chen, Y. Cheng, C.-S. Chen, J.C. Shih, Autoantibody profiling of monoamine oxidase A knockout mice, an autism spectrum disorder model, Brain, Behavior, and Immunity. 107 (2023) 193–200. https://doi.org/10.1016/j.bbi.2022.10.001.
[7]
E. Shenderov, A.M. De Marzo, T.L. Lotan, H. Wang, S. Chan, S.J. Lim, H. Ji, M.E. Allaf, C. Chapman, P.A. Moore, F. Chen, K. Sorg, A.M. White, S.E. Church, B. Hudson, P.A. Fields, S. Hu, S.R. Denmeade, K.J. Pienta, C.P. Pavlovich, A.E. Ross, C.G. Drake, D.M. Pardoll, E.S. Antonarakis, Neoadjuvant enoblituzumab in localized prostate cancer: a single-arm, phase 2 trial, Nat Med. 29 (2023) 888–897. https://doi.org/10.1038/s41591-023-02284-w.
[8]
F. Moadab, X. Wang, R. Najjar, K.C. Ukadike, S. Hu, T. Hulett, A.A. Bengtsson, C. Lood, T. Mustelin, Argonaute, vault, and ribosomal proteins targeted by autoantibodies in systemic lupus erythematosus, J Rheumatol. (2023) jrheum.2022-1327. https://doi.org/10.3899/jrheum.2022-1327.
[9]
B.D. Michael, C. Dunai, E.J. Needham, K. Tharmaratnam, R. Williams, Y. Huang, S.A. Boardman, J. Clark, P. Sharma, K. Subramaniam, G.K. Wood, C. Collie, R. Digby, A. Ren, E. Norton, M. Leibowitz, S. Ebrahimi, A. Fower, H. Fox, E. Tato, M. Ellul, G. Sunderland, M. Held, C. Hetherington, F. Nkongho, A. Palmos, A. Grundmann, J.P. Stewart, M. Griffiths, T. Solomon, G. Breen, A. Coles, J. Cavanagh, S.R. Irani, A. Vincent, L. Taams, D.K. Menon, Para-infectious brain injury in COVID-19 persists at follow-up despite attenuated cytokine and autoantibody responses, Infectious Diseases (except HIV/AIDS), 2023. https://doi.org/10.1101/2023.04.03.23287902.
[10]
C. Mandel-Brehm, S.E. Vazquez, C. Liverman, M. Cheng, Z. Quandt, A.F. Kung, A. Parent, B. Miao, E. Disse, C. Cugnet-Anceau, S. Dalle, E. Orlova, E. Frolova, D. Alba, A. Michels, B.E. Oftedal, M.S. Lionakis, E.S. Husebye, A.K. Agarwal, X. Li, C. Zhu, Q. Li, E. Oral, R. Brown, M.S. Anderson, A. Garg, J.L. DeRisi, Autoantibodies to Perilipin-1 Define a Subset of Acquired Generalized Lipodystrophy, Diabetes. 72 (2023) 59–70. https://doi.org/10.2337/db21-1172.
[11]
L. Malle, R.S. Patel, M. Martin-Fernandez, O.J. Stewart, Q. Philippot, S. Buta, A. Richardson, V. Barcessat, J. Taft, P. Bastard, J. Samuels, C. Mircher, A.-S. Rebillat, L. Maillebouis, M. Vilaire-Meunier, K. Tuballes, B.R. Rosenberg, R. Trachtman, J.-L. Casanova, L.D. Notarangelo, S. Gnjatic, D. Bush, D. Bogunovic, Autoimmunity in Down’s syndrome via cytokines, CD4 T cells and CD11c+ B cells, Nature. 615 (2023) 305–314. https://doi.org/10.1038/s41586-023-05736-y.
[12]
N. Lou, C. Zheng, Y. Wang, C. Liang, Q. Tan, R. Luo, L. Zhang, T. Xie, Y. Shi, X. Han, Identification of novel serological autoantibodies in Chinese prostate cancer patients using high-throughput protein arrays, Cancer Immunol Immunother. 72 (2023) 235–247. https://doi.org/10.1007/s00262-022-03242-0.
[13]
P. Laudański, G. Rogalska, D. Warzecha, M. Lipa, G. Mańka, M. Kiecka, R. Spaczyński, P. Piekarski, B. Banaszewska, A. Jakimiuk, T. Issat, W. Rokita, J. Młodawski, M. Szubert, P. Sieroszewski, G. Raba, K. Szczupak, T. Kluz, M. Kluza, T. Neuman, P. Adler, H. Peterson, A. Salumets, M. Wielgos, Autoantibody screening of plasma and peritoneal fluid of patients with endometriosis, Human Reproduction. 38 (2023) 629–643. https://doi.org/10.1093/humrep/dead011.
[14]
X. Feng, W. Tong, J. Li, Y. Xu, S. Zhu, W. Xu, Diagnostic value of anti-Kaiso autoantibody in axial spondyloarthritis, Front. Immunol. 14 (2023) 1156350. https://doi.org/10.3389/fimmu.2023.1156350.
[15]
A. Barpanda, C. Tuckley, A. Ray, A. Banerjee, S.P. Duttagupta, C. Kantharia, S. Srivastava, A protein microarray‐based serum proteomic investigation reveals distinct autoantibody signature in colorectal cancer, Proteomics Clinical Apps. 17 (2023) 2200062. https://doi.org/10.1002/prca.202200062.
[16]
C. Auger, H. Moudgalya, M.R. Neely, J.T. Stephan, I. Tarhoni, D. Gerard, S. Basu, C.L. Fhied, A. Abdelkader, M. Vargas, S. Hu, T. Hulett, M.J. Liptay, P. Shah, C.W. Seder, J.A. Borgia, Development of a Novel Circulating Autoantibody Biomarker Panel for the Identification of Patients with ‘Actionable’ Pulmonary Nodules, Cancers. 15 (2023) 2259. https://doi.org/10.3390/cancers15082259.
[17]
C. Auger, H. Moudgalya, P. Shah, M. Liptay, C. Seder, J. Borgia, PP01.33 Serum Autoantibodies may help Identify Individuals with Actionable Pulmonary Nodules on LDCT Scan, Journal of Thoracic Oncology. 18 (2023) e24. https://doi.org/10.1016/j.jtho.2022.09.059.
[18]
A.R. Ahmadi, G. Song, T. Gao, J. Ma, X. Han, M. Hu, A.M. Cameron, R. Wesson, B. Philosophe, S. Ottmann, E.A. King, A. Gurakar, L. Qi, B. Peiffer, J. Burdick, R.A. Anders, Z. Zhou, D. Feng, H. Lu, C.-S. Chen, J. Qian, B. Gao, H. Zhu, Z. Sun, Discovery and characterization of cross-reactive intrahepatic antibodies in severe alcoholic hepatitis, Pathology, 2023. https://doi.org/10.1101/2023.02.23.529702.
[19]
J. Wu, P. Wang, Z. Han, T. Li, C. Yi, C. Qiu, Q. Yang, G. Sun, L. Dai, J. Shi, K. Wang, H. Ye, A novel immunodiagnosis panel for hepatocellular carcinoma based on bioinformatics and the autoantibody‐antigen system, Cancer Science. 113 (2022) 411–422. https://doi.org/10.1111/cas.15217.
[20]
S.-M. Shim, Y.H. Koh, J.-H. Kim, J.-P. Jeon, A combination of multiple autoantibodies is associated with the risk of Alzheimer’s disease and cognitive impairment, Sci Rep. 12 (2022) 1312. https://doi.org/10.1038/s41598-021-04556-2.
[21]
K. Sacco, R. Castagnoli, S. Vakkilainen, C. Liu, O.M. Delmonte, C. Oguz, I.M. Kaplan, S. Alehashemi, P.D. Burbelo, F. Bhuyan, A.A. De Jesus, K. Dobbs, L.B. Rosen, A. Cheng, E. Shaw, M.S. Vakkilainen, F. Pala, J. Lack, Y. Zhang, D.L. Fink, V. Oikonomou, A.L. Snow, C.L. Dalgard, J. Chen, B.A. Sellers, G.A. Montealegre Sanchez, K. Barron, E. Rey-Jurado, C. Vial, M.C. Poli, A. Licari, D. Montagna, G.L. Marseglia, F. Licciardi, U. Ramenghi, V. Discepolo, A. Lo Vecchio, A. Guarino, E.M. Eisenstein, L. Imberti, A. Sottini, A. Biondi, S. Mató, D. Gerstbacher, M. Truong, M.A. Stack, M. Magliocco, M. Bosticardo, T. Kawai, J.J. Danielson, T. Hulett, M. Askenazi, S. Hu, NIAID Immune Response to COVID Group, J. Barnett, X. Cheng, K. Kaladi, V. Kuram, J. Mackey, N.M. Bansal, A.J. Martins, B. Palterer, H. Matthews, U. Mudunuri, M. Nambiar, A.J. Oler, A. Rastegar, S. Samuel, C. Shyu, V. Waingankar, S. Weber, S. Xirasagar, Chile MIS-C Group, Y. Espinosa, C. Astudillo, C. Piñera, R. González, Pavia Pediatric COVID-19 Group, M. De Filippo, M. Votto, L. Montagna, J.I. Cohen, H.C. Su, D.B. Kuhns, M.S. Lionakis, T.M. Snyder, S.M. Holland, R. Goldbach-Mansky, J.S. Tsang, L.D. Notarangelo, Immunopathological signatures in multisystem inflammatory syndrome in children and pediatric COVID-19, Nat Med. 28 (2022) 1050–1062. https://doi.org/10.1038/s41591-022-01724-3.
[22]
E.J. Needham, A.L. Ren, R.J. Digby, E.J. Norton, S. Ebrahimi, J.G. Outtrim, D.A. Chatfield, A.E. Manktelow, M.M. Leibowitz, V.F.J. Newcombe, R. Doffinger, G. Barcenas-Morales, C. Fonseca, M.J. Taussig, R.M. Burnstein, R.J. Samanta, C. Dunai, N. Sithole, N.J. Ashton, H. Zetterberg, M. Gisslén, A. Edén, E. Marklund, P.J.M. Openshaw, J. Dunning, M.J. Griffiths, J. Cavanagh, G. Breen, S.R. Irani, A. Elmer, N. Kingston, C. Summers, J.R. Bradley, L.S. Taams, B.D. Michael, E.T. Bullmore, K.G.C. Smith, P.A. Lyons, A.J. Coles, D.K. Menon, Cambridge NeuroCOVID Group, F. Anwar, K. Allinson, J. Bhatti, E.T. Bullmore, D.A. Chatfield, D. Christmas, A.J. Coles, J.P. Coles, M. Correia, T. Das, P.C. Fletcher, A.W. Jubb, V.C. Lupson, A.E. Manktelow, D.K. Menon, A. Michell, E.J. Needham, V.F.J. Newcombe, J.G. Outtrim, L. Pointon, C.T. Rodgers, J.B. Rowe, C. Rua, N. Sithole, L.R.B. Spindler, E.A. Stamatakis, J. Taylor, F. Valerio, B. Widmer, G.B. Williams, P.F. Chinnery, CITIID-NIHR COVID-19 BioResource Collaboration, J. Allison, G. Alvio, A. Ansaripour, S. Baker, S. Baker, L. Bergamaschi, A. Bermperi, A. Betancourt, H. Biggs, S.-H. Bong, G. Bower, J.R. Bradley, K. Brookes, A. Bucke, B. Bullman, K. Bunclark, H. Butcher, S. Caddy, J. Calder, L. Caller, L. Canna, D. Caputo, M. Chandler, Y. Chaudhry, P. Chinnery, D. Clapham-Riley, D. Cooper, C. Cossetti, C. Crucusio, I. Cruz, M. Curran, J.D. Coudert, E.M.D.D.D. Bie, R.D. Jesus, A.D. Sa, A.-M. Dean, K. Dempsey, E. Dewhurst, G.D. Stefano, J. Domingo, G. Dougan, B.J. Dunmore, A. Elmer, M. Epping, C. Fahey, S. Fawke, T. Feltwell, C. Fernandez, S. Fuller, A. Furlong, I. Georgana, A. George, N. Gleadall, I.G. Goodfellow, S. Gräf, B. Graves, J. Gray, R. Grenfell, R.K. Gupta, G. Hall, W. Hamilton, J. Harris, S. Hein, C. Hess, S. Hewitt, A. Hinch, J. Hodgson, M. Hosmillo, E. Holmes, C. Houldcroft, C. Huang, O. Huhn, K. Hunter, T. Ivers, A. Jahun, S. Jackson, I. Jarvis, E. Jones, H. Jones, S. Jose, M. Josipović, M. Kasanicki, J. Kennet, F. Khokhar, Y. King, N. Kingston, J. Kourampa, E.L. Gresley, E. Laurenti, E. Legchenko, P.J. Lehner, D. Lewis, E. Li, R. Linger, P.A. Lyons, M. Mackay, J.C. Marioni, J. Marsden, J. Martin, C. Matara, N.J. Matheson, C. McMahon, A. Meadows, S. Meloy, V. Mendoza, L. Meredith, N. Mende, F. Mescia, A. Michael, A. Moulton, R. Michel, L. Mwaura, F. Muldoon, F. Nice, C. O’Brien, C. Ocaya, C. O’Donnell, G. Okecha, O. Omarjee, N. Ovington, W.H. Owehand, S. Papadia, R. Paraschiv, S. Parmar, C. Pascuale, C. Patterson, C. Penkett, M. Perales, M. Perera, I. Phelan, M. Pinckert, L. Pointon, P. Polgarova, G. Polwarth, N. Pond, J. Price, V. Ranganath, C. Publico, R. Rastall, C. Ribeiro, N. Richoz, V. Romashova, S. Rossi, J. Rowlands, V. Ruffolo, J. Sambrook, C. Saunders, N.S. Yarkoni, K. Schon, M. Selvan, R. Sharma, J. Shih, K.G.C. Smith, S. Spencer, L. Stefanucci, H. Stark, J. Stephens, K.E. Stirrups, M. Strezlecki, C. Summers, R. Sutcliffe, J.E.D. Thaventhiran, T. Tilly, Z. Tong, H. Tordesillas, C. Treacy, M. Toshner, P. Townsend, C. Treacy, L. Turner, P. Vargas, B. Vergese, J.V. Ziegenweidt, N. Walker, L. Watson, J. Webster, M.P. Weekes, N.K. Wilson, J. Wood, J. Worsley, M. Wylot, A. Yakovleva, C.Y.A.J.-A. Zerrudo, Cambridge NIHR Clinical Research Facility, C. Saunders, A. Elmer, Brain injury in COVID-19 is associated with dysregulated innate and adaptive immune responses, Brain. 145 (2022) 4097–4107. https://doi.org/10.1093/brain/awac321.
[23]
R. Luo, C. Zheng, W. Song, Q. Tan, Y. Shi, X. Han, High‐throughput and multi‐phases identification of autoantibodies in diagnosing early‐stage breast cancer and subtypes, Cancer Science. 113 (2022) 770–783. https://doi.org/10.1111/cas.15227.
[24]
D. Kumar, C. Prince, T. Hulett, P. Ramos, O. Candelario, L. Youngblood, M. Briones, C. Bennett, S. Chandrakasan, Pediatric Evans Syndrome Displays Broad Immune Dysregulation Characterized By Extra-Follicular B-Cell Responses and Unique Autoantibody Repertoire, Blood. 140 (2022) 1646–1647. https://doi.org/10.1182/blood-2022-169527.
[25]
P. Johannet, W. Liu, D. Fenyo, M. Wind-Rotolo, M. Krogsgaard, J.M. Mehnert, J.S. Weber, J. Zhong, I. Osman, Baseline Serum Autoantibody Signatures Predict Recurrence and Toxicity in Melanoma Patients Receiving Adjuvant Immune Checkpoint Blockade, Clinical Cancer Research. 28 (2022) 4121–4130. https://doi.org/10.1158/1078-0432.CCR-22-0404.
[26]
A. Gandhi, J. Taylor, M. Morici, A. Reid, T. Meniawy, M.A. Khattak, E. Gray, M. Millward, P. Zaenker, Autoantibodies as potential biomarkers of immune-related adverse events in patients with advanced cutaneous melanoma treated with immune checkpoint inhibitors., JCO. 40 (2022) 9536–9536. https://doi.org/10.1200/JCO.2022.40.16_suppl.9536.
[27]
W. Fan, X. Fang, C. Hu, G. Fei, Q. Xiao, Y. Li, X. Li, J.D. Wood, X. Zhang, Multiple rather than specific autoantibodies were identified in irritable bowel syndrome with HuProtTM proteome microarray, Front. Physiol. 13 (2022) 1010069. https://doi.org/10.3389/fphys.2022.1010069.
[28]
T.V. Clendenen, S. Hu, Y. Afanasyeva, M. Askenazi, K.L. Koenig, T. Hulett, M. Liu, S. Liu, F. Wu, A. Zeleniuch-Jacquotte, Y. Chen, Temporal reproducibility of IgG and IgM autoantibodies in serum from healthy women, Sci Rep. 12 (2022) 6192. https://doi.org/10.1038/s41598-022-10174-3.
[29]
L. Cinquanta, M. Infantino, N. Bizzaro, Detecting Autoantibodies by Multiparametric Assays: Impact on Prevention, Diagnosis, Monitoring, and Personalized Therapy in Autoimmune Diseases, The Journal of Applied Laboratory Medicine. 7 (2022) 137–150. https://doi.org/10.1093/jalm/jfab132.
[30]
M.O. Borghi, M. Bombaci, C. Bodio, P.A. Lonati, A. Gobbini, M. Lorenzo, E. Torresani, A. Dubini, I. Bulgarelli, F. Solari, F. Pregnolato, A. Bandera, A. Gori, G. Parati, S. Abrignani, R. Grifantini, P.L. Meroni, Anti-Phospholipid Antibodies and Coronavirus Disease 2019: Vaccination Does Not Trigger Early Autoantibody Production in Healthcare Workers, Front. Immunol. 13 (2022) 930074. https://doi.org/10.3389/fimmu.2022.930074.
[31]
A. Banerjee, A. Ray, A. Barpanda, A. Dash, I. Gupta, M.U. Nissa, H. Zhu, A. Shah, S.P. Duttagupta, A. Goel, S. Srivastava, Evaluation of autoantibody signatures in pituitary adenoma patients using human proteome arrays, Proteomics Clinical Apps. 16 (2022) 2100111. https://doi.org/10.1002/prca.202100111.
[32]
H.R. Ahn, G.O. Baek, M.G. Yoon, J.A. Son, J.H. Yoon, J.Y. Cheong, H.J. Cho, H.C. Kang, J.W. Eun, S.S. Kim, Hypomethylation-mediated upregulation of the WASF2 promoter region correlates with poor clinical outcomes in hepatocellular carcinoma, J Exp Clin Cancer Res. 41 (2022) 158. https://doi.org/10.1186/s13046-022-02365-7.
[33]
A.K.H. Wong, I. Woodhouse, F. Schneider, D.A. Kulpa, G. Silvestri, C.L. Maier, Broad auto-reactive IgM responses are common in critically ill patients, including those with COVID-19, Cell Reports Medicine. 2 (2021) 100321. https://doi.org/10.1016/j.xcrm.2021.100321.
[34]
X. Wen, G. Song, C. Hu, J. Pan, Z. Wu, L. Li, C. Liu, X. Tian, F. Zhang, J. Qian, H. Zhu, Y. Li, Identification of Novel Serological Autoantibodies in Takayasu Arteritis Patients Using HuProt Arrays, Molecular & Cellular Proteomics. 20 (2021) 100036. https://doi.org/10.1074/mcp.RA120.002119.
[35]
C. Qiu, B. Wang, P. Wang, X. Wang, Y. Ma, L. Dai, J. Shi, K. Wang, G. Sun, H. Ye, J. Zhang, Identification of novel autoantibody signatures and evaluation of a panel of autoantibodies in breast cancer, Cancer Sci. 112 (2021) 3388–3400. https://doi.org/10.1111/cas.15021.
[36]
C.P. Moritz, Y. Tholance, O. Stoevesandt, K. Ferraud, J.-P. Camdessanché, J.-C. Antoine, CIDP Antibodies Target Junction Proteins and Identify Patient Subgroups: An Autoantigenomic Approach, Neurol Neuroimmunol Neuroinflamm. 8 (2021) e944. https://doi.org/10.1212/NXI.0000000000000944.
[37]
C.P. Moritz, O. Stoevesandt, Y. Tholance, J.-P. Camdessanché, J.-C. Antoine, Proper definition of the set of autoantibody-targeted antigens relies on appropriate reference group selection, New Biotechnology. 60 (2021) 168–172. https://doi.org/10.1016/j.nbt.2020.08.007.
[38]
R. McGregor, M.L. Tay, L.H. Carlton, P. Hanson-Manful, J.M. Raynes, W.O. Forsyth, D.T. Brewster, M.J. Middleditch, J. Bennett, W.J. Martin, N. Wilson, P. Atatoa Carr, M.G. Baker, N.J. Moreland, Mapping Autoantibodies in Children With Acute Rheumatic Fever, Front. Immunol. 12 (2021) 702877. https://doi.org/10.3389/fimmu.2021.702877.
[39]
M.A. Hutchinson, H.-S. Park, K.J. Zanotti, J. Alvarez-Gonzalez, J. Zhang, L. Zhang, R. Telljohann, M. Wang, E.G. Lakatta, P.J. Gearhart, R.W. Maul, Auto-Antibody Production During Experimental Atherosclerosis in ApoE-/- Mice, Front. Immunol. 12 (2021) 695220. https://doi.org/10.3389/fimmu.2021.695220.
[40]
C. Cui, Y. Duan, C. Qiu, P. Wang, G. Sun, H. Ye, L. Dai, Z. Han, C. Song, K. Wang, J. Shi, J. Zhang, Identification of Novel Autoantibodies Based on the Human Proteomic Chips and Evaluation of Their Performance in the Detection of Gastric Cancer, Front. Oncol. 11 (2021) 637871. https://doi.org/10.3389/fonc.2021.637871.
[41]
S. Zhang, Y. Liu, J. Chen, H. Shu, S. Shen, Y. Li, X. Lu, X. Cao, L. Dong, J. Shi, Y. Cao, X. Wang, J. Zhou, Y. Liu, L. Chen, J. Fan, G. Ding, Q. Gao, Autoantibody signature in hepatocellular carcinoma using seromics, J Hematol Oncol. 13 (2020) 85. https://doi.org/10.1186/s13045-020-00918-x.
[42]
P. Zaenker, D. Prentice, M. Ziman, Tropomyosin autoantibodies associated with checkpoint inhibitor myositis, OncoImmunology. 9 (2020) 1804703. https://doi.org/10.1080/2162402X.2020.1804703.
[43]
A.H. Rowley, S.C. Baker, D. Arrollo, L.J. Gruen, T. Bodnar, N. Innocentini, M. Hackbart, Y.E. Cruz-Pulido, K.M. Wylie, K.-Y.A. Kim, S.T. Shulman, A Protein Epitope Targeted by the Antibody Response to Kawasaki Disease, The Journal of Infectious Diseases. 222 (2020) 158–168. https://doi.org/10.1093/infdis/jiaa066.
[44]
J. Pan, L. Yu, Q. Wu, X. Lin, S. Liu, S. Hu, C. Rosa, D. Eichinger, I. Pino, H. Zhu, J. Qian, Y. Huang, Integration of IgA and IgG Autoantigens Improves Performance of Biomarker Panels for Early Diagnosis of Lung Cancer, Molecular & Cellular Proteomics. 19 (2020) 490–500. https://doi.org/10.1074/mcp.RA119.001905.
[45]
I. Osman, K.M. Giles, Y. Qian, M. Wind-Rotolo, J. Loffredo, T. Hulett, J.S. Weber, H. Zhong, Using autoantibody signatures to predict immunotherapy discontinuation in melanoma patients., JCO. 38 (2020) 3069–3069. https://doi.org/10.1200/JCO.2020.38.15_suppl.3069.
[46]
E.J. Needham, O. Stoevesandt, E.P. Thelin, H. Zetterberg, E.R. Zanier, F.A. Nimer, N.J. Ashton, J.G. Outtrim, V.F. Newcombe, H.S. Mousa, J. Simren, K. Blennow, Z. Yang Z, P.J. Hutchinson, F. Piehl, A.E. Helmy, M.J. Taussig, K.K. Wang, J.L. Jones, D.K. Menon, A.J. Coles, Complex Autoantibody Responses Occur Following Moderate to Severe Traumatic Brain Injury, Neurology, 2020. https://doi.org/10.1101/2020.07.24.20161786.
[47]
A. Ma, L. Wen, J. Yin, Y. Hu, X. Yue, J. Li, X. Dong, Y. Gupta, R.J. Ludwig, S. Krauss-Etschmann, G. Riemekasten, F. Petersen, X. Yu, Serum Levels of Autoantibodies Against Extracellular Antigens and Neutrophil Granule Proteins Increase in Patients with COPD Compared to Non-COPD Smokers, COPD. Volume 15 (2020) 189–200. https://doi.org/10.2147/COPD.S235903.
[48]
S. Longobardi, C. Georgescu, C. Lawrence, C. Moya, J. Wren, J.A. James, K.L. Sivils, A.D. Farris, Novel shared antibody specificities in anti-Ro/ La antibody negative Sjögren’s Syndrome, The Journal of Immunology. 204 (2020) 218.20-218.20. https://doi.org/10.4049/jimmunol.204.Supp.218.20.
[49]
H.-Z. Ling, S.-Z. Xu, R.-X. Leng, J. Wu, H.-F. Pan, Y.-G. Fan, B. Wang, Y.-R. Xia, Q. Huang, Z.-W. Shuai, D.-Q. Ye, Discovery of new serum biomarker panels for systemic lupus erythematosus diagnosis, Rheumatology. 59 (2020) 1416–1425. https://doi.org/10.1093/rheumatology/kez634.
[50]
Y. Li, C. Li, S. Guo, W. Guo, H. Jiang, H. Li, S. Tao, Longitudinal serum autoantibody repertoire profiling identifies surgery-associated biomarkers in lung adenocarcinoma, EBioMedicine. 53 (2020) 102674. https://doi.org/10.1016/j.ebiom.2020.102674.
[51]
S.S. Kim, S. Shen, S. Miyauchi, P.D. Sanders, I. Franiak-Pietryga, L. Mell, J.S. Gutkind, E.E.W. Cohen, J.A. Califano, A.B. Sharabi, B Cells Improve Overall Survival in HPV-Associated Squamous Cell Carcinomas and Are Activated by Radiation and PD-1 Blockade, Clinical Cancer Research. 26 (2020) 3345–3359. https://doi.org/10.1158/1078-0432.CCR-19-3211.
[52]
C.N. Gruber, R.S. Patel, R. Trachtman, L. Lepow, F. Amanat, F. Krammer, K.M. Wilson, K. Onel, D. Geanon, K. Tuballes, M. Patel, K. Mouskas, T. O’Donnell, E. Merritt, N.W. Simons, V. Barcessat, D.M. Del Valle, S. Udondem, G. Kang, S. Gangadharan, G. Ofori-Amanfo, U. Laserson, A. Rahman, S. Kim-Schulze, A.W. Charney, S. Gnjatic, B.D. Gelb, M. Merad, D. Bogunovic, Mapping Systemic Inflammation and Antibody Responses in Multisystem Inflammatory Syndrome in Children (MIS-C), Cell. 183 (2020) 982-995.e14. https://doi.org/10.1016/j.cell.2020.09.034.
[53]
I.S. Dhande, Y. Zhu, S.C. Kneedler, A.S. Joshi, M.J. Hicks, S.E. Wenderfer, M.C. Braun, P.A. Doris, Stim1 Polymorphism Disrupts Immune Signaling and Creates Renal Injury in Hypertension, JAHA. 9 (2020) e014142. https://doi.org/10.1161/JAHA.119.014142.
[54]
I.S. Dhande, S.C. Kneedler, Y. Zhu, A.S. Joshi, M.J. Hicks, S.E. Wenderfer, M.C. Braun, P.A. Doris, Natural genetic variation in Stim1 creates stroke in the spontaneously hypertensive rat, Genes Immun. 21 (2020) 182–192. https://doi.org/10.1038/s41435-020-0097-5.
[55]
S. Ye, L. Ma, R. Zhang, F. Liu, P. Jiang, J. Xu, H. Cao, X. Du, F. Lin, L. Cheng, X. Zhou, Z. Shi, Y. Liu, Y. Huang, Z. Wang, C. Li, Plasma proteomic and autoantibody profiles reveal the proteomic characteristics involved in longevity families in Bama, China, Clin Proteom. 16 (2019) 22. https://doi.org/10.1186/s12014-019-9242-4.
[56]
K.J. Lastwika, J. Kargl, Y. Zhang, X. Zhu, E. Lo, D. Shelley, J.J. Ladd, W. Wu, P. Kinahan, S.N.J. Pipavath, T.W. Randolph, M. Shipley, P.D. Lampe, A.M. Houghton, Tumor-derived Autoantibodies Identify Malignant Pulmonary Nodules, Am J Respir Crit Care Med. 199 (2019) 1257–1266. https://doi.org/10.1164/rccm.201804-0628OC.
[57]
M.F. Gowen, K.M. Giles, D. Simpson, J. Tchack, H. Zhou, U. Moran, Z. Dawood, A.C. Pavlick, S. Hu, M.A. Wilson, H. Zhong, M. Krogsgaard, T. Kirchhoff, I. Osman, Baseline antibody profiles predict toxicity in melanoma patients treated with immune checkpoint inhibitors, J Transl Med. 16 (2018) 82. https://doi.org/10.1186/s12967-018-1452-4.
[58]
J.M. Chung, Y. Jung, Y.P. Kim, J. Song, S. Kim, J.Y. Kim, M. Kwon, J.H. Yoon, M.-D. Kim, J. Lee, D.-Y. Chung, S.Y. Lee, J. Kang, H.C. Kang, Identification of the Thioredoxin-Like 2 Autoantibody as a Specific Biomarker for Triple-Negative Breast Cancer, J Breast Cancer. 21 (2018) 87. https://doi.org/10.4048/jbc.2018.21.1.87.
[59]
H.D. Bremer, N. Landegren, R. Sjöberg, Å. Hallgren, S. Renneker, E. Lattwein, D. Leonard, M.-L. Eloranta, L. Rönnblom, G. Nordmark, P. Nilsson, G. Andersson, I. Lilliehöök, K. Lindblad-Toh, O. Kämpe, H. Hansson-Hamlin, ILF2 and ILF3 are autoantigens in canine systemic autoimmune disease, Sci Rep. 8 (2018) 4852. https://doi.org/10.1038/s41598-018-23034-w.
[60]
J. Wang, J. You, L. Wang, H. Wang, T. Tian, W. Wang, L. Jia, C. Jiang, PTMA, a new identified autoantigen for oral submucous fibrosis, regulates oral submucous fibroblast proliferation and extracellular matrix, Oncotarget. 8 (2017) 74806–74819. https://doi.org/10.18632/oncotarget.20419.
[61]
S. Gupta, S. Mukherjee, P. Syed, N.G. Pandala, S. Choudhary, V.A. Singh, N. Singh, H. Zhu, S. Epari, S.B. Noronha, A. Moiyadi, S. Srivastava, Evaluation of autoantibody signatures in meningioma patients using human proteome arrays, Oncotarget. 8 (2017) 58443–58456. https://doi.org/10.18632/oncotarget.16997.
[62]
S. Gupta, K.P. Manubhai, S. Mukherjee, S. Srivastava, Serum Profiling for Identification of Autoantibody Signatures in Diseases Using Protein Microarrays, in: D.W. Greening, R.J. Simpson (Eds.), Serum/Plasma Proteomics, Springer New York, New York, NY, 2017: pp. 303–315. https://doi.org/10.1007/978-1-4939-7057-5_21.
[63]
B.K. Chung, B.T. Guevel, G.M. Reynolds, D.B.R.K. Gupta Udatha, E.K.K. Henriksen, Z. Stamataki, G.M. Hirschfield, T.H. Karlsen, E. Liaskou, Phenotyping and auto-antibody production by liver-infiltrating B cells in primary sclerosing cholangitis and primary biliary cholangitis, Journal of Autoimmunity. 77 (2017) 45–54. https://doi.org/10.1016/j.jaut.2016.10.003.
[64]
L. Yang, J. Wang, J. Li, H. Zhang, S. Guo, M. Yan, Z. Zhu, B. Lan, Y. Ding, M. Xu, W. Li, X. Gu, C. Qi, H. Zhu, Z. Shao, B. Liu, S.-C. Tao, Identification of Serum Biomarkers for Gastric Cancer Diagnosis Using a Human Proteome Microarray, Molecular & Cellular Proteomics. 15 (2016) 614–623. https://doi.org/10.1074/mcp.M115.051250.
[65]
M. Ogishi, H. Yotsuyanagi, K. Moriya, K. Koike, Delineation of autoantibody repertoire through differential proteogenomics in hepatitis C virus-induced cryoglobulinemia, Sci Rep. 6 (2016) 29532. https://doi.org/10.1038/srep29532.
[66]
D.F. Fiorentino, M. Presby, A.N. Baer, M. Petri, K.E. Rieger, M. Soloski, A. Rosen, A.L. Mammen, L. Christopher-Stine, L. Casciola-Rosen, PUF60: a prominent new target of the autoimmune response in dermatomyositis and Sjögren’s syndrome, Ann Rheum Dis. 75 (2016) 1145–1151. https://doi.org/10.1136/annrheumdis-2015-207509.
[67]
P. Syed, S. Gupta, S. Choudhary, N.G. Pandala, A. Atak, A. Richharia, M. Kp, H. Zhu, S. Epari, S.B. Noronha, A. Moiyadi, S. Srivastava, Autoantibody Profiling of Glioma Serum Samples to Identify Biomarkers Using Human Proteome Arrays, Sci Rep. 5 (2015) 13895. https://doi.org/10.1038/srep13895.
[68]
C. Hu, W. Huang, H. Chen, G. Song, P. Li, Q. Shan, X. Zhang, F. Zhang, H. Zhu, L. Wu, Y. Li, Autoantibody Profiling on Human Proteome Microarray for Biomarker Discovery in Cerebrospinal Fluid and Sera of Neuropsychiatric Lupus, PLoS ONE. 10 (2015) e0126643. https://doi.org/10.1371/journal.pone.0126643.
[69]
C.-J. Hu, G. Song, W. Huang, G.-Z. Liu, C.-W. Deng, H.-P. Zeng, L. Wang, F.-C. Zhang, X. Zhang, J.S. Jeong, S. Blackshaw, L.-Z. Jiang, H. Zhu, L. Wu, Y.-Z. Li, Identification of New Autoantigens for Primary Biliary Cirrhosis Using Human Proteome Microarrays, Molecular & Cellular Proteomics. 11 (2012) 669–680. https://doi.org/10.1074/mcp.M111.015529.

Antibody Specificity and Crossreactivity

[1]
T. Hotta, Y. Nariai, N. Kajitani, K. Kadota, R. Maruyama, Y. Tajima, T. Isobe, H. Kamino, T. Urano, Generation of the novel anti-FXYD5 monoclonal antibody and its application to the diagnosis of pancreatic and lung cancer, Biochimie. (2023) S0300908423000020. https://doi.org/10.1016/j.biochi.2023.01.002.
[2]
E. Gomez-Bañuelos, Y. Yu, J. Li, K.S. Cashman, M. Paz, M.I. Trejo-Zambrano, R. Bugrovsky, Y. Wang, A.S. Chida, C.A. Sherman-Baust, D.P. Ferris, D.W. Goldman, E. Darrah, M. Petri, I. Sanz, F. Andrade, Affinity maturation generates pathogenic antibodies with dual reactivity to DNase1L3 and dsDNA in systemic lupus erythematosus, Nat Commun. 14 (2023) 1388. https://doi.org/10.1038/s41467-023-37083-x.
[3]
T.V. Lanz, R.C. Brewer, P.P. Ho, J.-S. Moon, K.M. Jude, D. Fernandez, R.A. Fernandes, A.M. Gomez, G.-S. Nadj, C.M. Bartley, R.D. Schubert, I.A. Hawes, S.E. Vazquez, M. Iyer, J.B. Zuchero, B. Teegen, J.E. Dunn, C.B. Lock, L.B. Kipp, V.C. Cotham, B.M. Ueberheide, B.T. Aftab, M.S. Anderson, J.L. DeRisi, M.R. Wilson, R.J.M. Bashford-Rogers, M. Platten, K.C. Garcia, L. Steinman, W.H. Robinson, Clonally Expanded B Cells in Multiple Sclerosis Bind EBV EBNA1 and GlialCAM, Nature. (2022) 1–12. https://doi.org/10.1038/s41586-022-04432-7.
[4]
C. Castrillon, L. Simoni, T. Van Den Broek, C. Van Der Poel, E.H. Akama-Garren, M. Ma, M.C. Carroll, Complex subsets but redundant clonality after B cells egress from spontaneous germinal centers, Immunology, 2022. https://doi.org/10.1101/2022.06.21.496939.
[5]
T.K. MacLachlan, S. Price, J. Cavagnaro, L. Andrews, D. Blanset, M.E. Cosenza, M. Dempster, E. Galbreath, A.M. Giusti, K.M. Heinz-Taheny, R. Fleurance, E. Sutter, M.W. Leach, Classic and evolving approaches to evaluating cross reactivity of mAb and mAb-like molecules – A survey of industry 2008–2019, Regulatory Toxicology and Pharmacology. 121 (2021) 104872. https://doi.org/10.1016/j.yrtph.2021.104872.
[6]
Y.C. Kim, J. Lee, J.N. An, J.H. Kim, Y.-W. Choi, L. Li, S.H. Kwon, M.-Y. Lee, B. Lee, J.-G. Jeong, S.-S. Yu, C.S. Lim, Y.S. Kim, S. Kim, S.H. Yang, J.P. Lee, Renoprotective effects of a novel cMet agonistic antibody on kidney fibrosis, Sci Rep. 9 (2019) 13495. https://doi.org/10.1038/s41598-019-49756-z.
[7]
A. Venkataraman, K. Yang, J. Irizarry, M. Mackiewicz, P. Mita, Z. Kuang, L. Xue, D. Ghosh, S. Liu, P. Ramos, S. Hu, D. Bayron Kain, S. Keegan, R. Saul, S. Colantonio, H. Zhang, F.P. Behn, G. Song, E. Albino, L. Asencio, L. Ramos, L. Lugo, G. Morell, J. Rivera, K. Ruiz, R. Almodovar, L. Nazario, K. Murphy, I. Vargas, Z.A. Rivera-Pacheco, C. Rosa, M. Vargas, J. McDade, B.S. Clark, S. Yoo, S.G. Khambadkone, J. De Melo, M. Stevanovic, L. Jiang, Y. Li, W.Y. Yap, B. Jones, A. Tandon, E. Campbell, G.T. Montelione, S. Anderson, R.M. Myers, J.D. Boeke, D. Fenyö, G. Whiteley, J.S. Bader, I. Pino, D.J. Eichinger, H. Zhu, S. Blackshaw, A toolbox of immunoprecipitation-grade monoclonal antibodies to human transcription factors, Nat Methods. 15 (2018) 330–338. https://doi.org/10.1038/nmeth.4632.
[8]
P. Ramos-López, J. Irizarry, I. Pino, S. Blackshaw, Antibody Specificity Profiling Using Protein Microarrays, in: J. Rockberg, J. Nilvebrant (Eds.), Epitope Mapping Protocols, Springer New York, New York, NY, 2018: pp. 223–229. https://doi.org/10.1007/978-1-4939-7841-0_14.
[9]
N. Washburn, R. Meccariello, S. Hu, M. Hains, N. Bhatnagar, H. Sarvaiya, B. Kapoor, J. Schaeck, I. Pino, A. Manning, J.C. Lansing, C.J. Bosques, High-resolution physicochemical characterization of different intravenous immunoglobulin products, PLoS ONE. 12 (2017) e0181251. https://doi.org/10.1371/journal.pone.0181251.
[10]
E. Sterner, M.L. Peach, M.C. Nicklaus, J.C. Gildersleeve, Therapeutic Antibodies to Ganglioside GD2 Evolved from Highly Selective Germline Antibodies, Cell Reports. 20 (2017) 1681–1691. https://doi.org/10.1016/j.celrep.2017.07.050.
[11]
J.S. Jeong, L. Jiang, E. Albino, J. Marrero, H.S. Rho, J. Hu, S. Hu, C. Vera, D. Bayron-Poueymiroy, Z.A. Rivera-Pacheco, L. Ramos, C. Torres-Castro, J. Qian, J. Bonaventura, J.D. Boeke, W.Y. Yap, I. Pino, D.J. Eichinger, H. Zhu, S. Blackshaw, Rapid Identification of Monospecific Monoclonal Antibodies Using a Human Proteome Microarray, Molecular & Cellular Proteomics. 11 (2012) O111.016253. https://doi.org/10.1074/mcp.O111.016253.

Protein Interactomics

[1]
S. Yamada, T. Ko, M. Ito, T. Sassa, S. Nomura, H. Okuma, M. Sato, T. Imasaki, S. Kikkawa, B. Zhang, T. Yamada, Y. Seki, K. Fujita, M. Katoh, M. Kubota, S. Hatsuse, M. Katagiri, H. Hayashi, M. Hamano, N. Takeda, H. Morita, S. Takada, M. Toyoda, M. Uchiyama, M. Ikeuchi, K. Toyooka, A. Umezawa, Y. Yamanishi, R. Nitta, H. Aburatani, I. Komuro, TEAD1 trapping by the Q353R–Lamin A/C causes dilated cardiomyopathy, Sci. Adv. 9 (2023) eade7047. https://doi.org/10.1126/sciadv.ade7047.
[2]
M. Potez, S. Snedal, C. She, J. Kim, K. Thorner, T.H. Tran, M.C. Ramello, D. Abate-Daga, J.K.C. Liu, Use of phage display biopanning as a tool to design CAR-T cells against glioma stem cells, Front. Oncol. 13 (2023) 1124272. https://doi.org/10.3389/fonc.2023.1124272.
[3]
H. Li, F. Liu, H. Kuang, H. Teng, S. Chen, S. Zeng, Q. Zhou, Z. Li, D. Liang, Z. Li, L. Wu, WDR73 Depletion Destabilizes PIP4K2C Activity and Impairs Focal Adhesion Formation in Galloway–Mowat Syndrome, Biology. 11 (2022) 1397. https://doi.org/10.3390/biology11101397.
[4]
H.M. Kang, D.H. Kim, M. Kim, Y. Min, B. Jeong, K.H. Noh, D.Y. Lee, H.-S. Cho, N.-S. Kim, C.-R. Jung, J.H. Lim, FBXL17/spastin axis as a novel therapeutic target of hereditary spastic paraplegia, Cell Biosci. 12 (2022) 110. https://doi.org/10.1186/s13578-022-00851-1.
[5]
L. Zhou, Y. Ge, Y. Fu, B. Wu, Y. Zhang, L. Li, C.-P. Cui, S. Wang, L. Zhang, Global Screening of LUBAC and OTULIN Interacting Proteins by Human Proteome Microarray, Front. Cell Dev. Biol. 9 (2021) 686395. https://doi.org/10.3389/fcell.2021.686395.
[6]
L. Zhang, J. Zhou, M. Xu, G. Yuan, Exploration of the Hsa-miR-1587–Protein Interaction and the Inhibition to CASK, IJMS. 22 (2021) 10716. https://doi.org/10.3390/ijms221910716.
[7]
X. Wan, L. Zhu, L. Zhao, L. Peng, J. Xiong, W. Yang, J. Yuan, F. Liang, K. Zhang, K. Chen, hPER3 promotes adipogenesis via hHSP90AA1-mediated inhibition of Notch1 pathway, Cell Death Dis. 12 (2021) 301. https://doi.org/10.1038/s41419-021-03584-0.
[8]
G. Song, E.M. Lee, J. Pan, M. Xu, H.-S. Rho, Y. Cheng, N. Whitt, S. Yang, J. Kouznetsova, C. Klumpp-Thomas, S.G. Michael, C. Moore, K.-J. Yoon, K.M. Christian, A. Simeonov, W. Huang, M. Xia, R. Huang, M. Lal-Nag, H. Tang, W. Zheng, J. Qian, H. Song, G. Ming, H. Zhu, An Integrated Systems Biology Approach Identifies the Proteasome as A Critical Host Machinery for ZIKV and DENV Replication, Genomics, Proteomics & Bioinformatics. 19 (2021) 108–122. https://doi.org/10.1016/j.gpb.2020.06.016.
[9]
T. Reiter, S. Pajenda, D. O’Connell, C. Lynch, S. Kapps, H. Agis, A. Schmidt, L. Wagner, N. Leung, W. Winnicki, Renal Expression of Light Chain Binding Proteins, Front. Med. 7 (2021) 609582. https://doi.org/10.3389/fmed.2020.609582.
[10]
A.M. Haapalainen, R. Daddali, M. Hallman, M. Rämet, Human CPPED1 belongs to calcineurin‐like metallophosphoesterase superfamily and dephosphorylates PI3K‐AKT pathway component PAK4, J Cell Mol Med. 25 (2021) 6304–6317. https://doi.org/10.1111/jcmm.16607.
[11]
S.-Y. Kim, H.J. Kim, H.J. Kim, C.-H. Kim, Non-Thermal Plasma Induces Antileukemic Effect Through mTOR Ubiquitination, Cells. 9 (2020) 595. https://doi.org/10.3390/cells9030595.
[12]
G. Song, L. Chen, B. Zhang, Q. Song, Y. Yu, C. Moore, T.-L. Wang, I.-M. Shih, H. Zhang, D.W. Chan, Z. Zhang, H. Zhu, Proteome-wide Tyrosine Phosphorylation Analysis Reveals Dysregulated Signaling Pathways in Ovarian Tumors, Molecular & Cellular Proteomics. 18 (2019) 448–460. https://doi.org/10.1074/mcp.RA118.000851.
[13]
T. Cao, L. Lyu, H. Jia, J. Wang, F. Du, L. Pan, Z. Li, A. Xing, J. Xiao, Y. Ma, Z. Zhang, A Two-Way Proteome Microarray Strategy to Identify Novel Mycobacterium tuberculosis-Human Interactors, Front. Cell. Infect. Microbiol. 9 (2019) 65. https://doi.org/10.3389/fcimb.2019.00065.
[14]
F.-L. Wu, Y. Liu, H.-N. Zhang, H.-W. Jiang, L. Cheng, S.-J. Guo, J.-Y. Deng, L.-J. Bi, X.-E. Zhang, H.-F. Gao, S.-C. Tao, Global Profiling of PknG Interactions Using a Human Proteome Microarray Reveals Novel Connections with CypA, Proteomics. 18 (2018) 1800265. https://doi.org/10.1002/pmic.201800265.
[15]
Y. Wang, X. Weng, L. Wang, M. Hao, Y. Li, L. Hou, Y. Liang, T. Wu, M. Yao, G. Lin, Y. Jiang, G. Fu, Z. Hou, X. Meng, J. Lu, J. Wang, HIC1 deletion promotes breast cancer progression by activating tumor cell/fibroblast crosstalk, Journal of Clinical Investigation. 128 (2018) 5235–5250. https://doi.org/10.1172/JCI99974.
[16]
M. Liu, Y. Ru, Y. Gu, J. Tang, T. Zhang, J. Wu, F. Yu, Y. Yuan, C. Xu, J. Wang, H. Shi, Disruption of Ssp411 causes impaired sperm head formation and male sterility in mice, Biochimica et Biophysica Acta (BBA) – General Subjects. 1862 (2018) 660–668. https://doi.org/10.1016/j.bbagen.2017.12.005.
[17]
G. Guo, S. Ye, S. Xie, L. Ye, C. Lin, M. Yang, X. Shi, F. Wang, B. Li, M. Li, C. Chen, L. Zhang, H. Zhang, X. Xue, The cytomegalovirus protein US31 induces inflammation through mono-macrophages in systemic lupus erythematosus by promoting NF-κB2 activation, Cell Death Dis. 9 (2018) 104. https://doi.org/10.1038/s41419-017-0122-4.
[18]
Y. Feng, C.-S. Chen, J. Ho, D. Pearce, S. Hu, B. Wang, P. Desai, K.S. Kim, H. Zhu, 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 (2018) 10958–10966. https://doi.org/10.1021/acs.analchem.8b02513.
[19]
S.-W. Choi, H.-H. Park, S. Kim, J.M. Chung, H.-J. Noh, S.K. Kim, H.K. Song, C.-W. Lee, M.J. Morgan, H.C. Kang, Y.-S. Kim, PELI1 Selectively Targets Kinase-Active RIP3 for Ubiquitylation-Dependent Proteasomal Degradation, Molecular Cell. 70 (2018) 920-935.e7. https://doi.org/10.1016/j.molcel.2018.05.016.
[20]
Y. Bao, F. Yang, B. Liu, T. Zhao, Z. Xu, Y. Xiong, S. Sun, L. Qu, L. Wang, Angiopoietin-like protein 3 blocks nuclear import of FAK and contributes to sorafenib response, Br J Cancer. 119 (2018) 450–461. https://doi.org/10.1038/s41416-018-0189-4.
[21]
N. Washburn, R. Meccariello, S. Hu, M. Hains, N. Bhatnagar, H. Sarvaiya, B. Kapoor, J. Schaeck, I. Pino, A. Manning, J.C. Lansing, C.J. Bosques, High-resolution physicochemical characterization of different intravenous immunoglobulin products, PLoS ONE. 12 (2017) e0181251. https://doi.org/10.1371/journal.pone.0181251.
[22]
E. Cox, W. Hwang, I. Uzoma, J. Hu, C.M. Guzzo, J. Jeong, M.J. Matunis, J. Qian, H. Zhu, S. Blackshaw, Global Analysis of SUMO-Binding Proteins Identifies SUMOylation as a Key Regulator of the INO80 Chromatin Remodeling Complex, Molecular & Cellular Proteomics. 16 (2017) 812–823. https://doi.org/10.1074/mcp.M116.063719.
[23]
Y. Wang, R. An, G.K. Umanah, H. Park, K. Nambiar, S.M. Eacker, B. Kim, L. Bao, M.M. Harraz, C. Chang, R. Chen, J.E. Wang, T.-I. Kam, J.S. Jeong, Z. Xie, S. Neifert, J. Qian, S.A. Andrabi, S. Blackshaw, H. Zhu, H. Song, G. Ming, V.L. Dawson, T.M. Dawson, A nuclease that mediates cell death induced by DNA damage and poly(ADP-ribose) polymerase-1, Science. 354 (2016) aad6872. https://doi.org/10.1126/science.aad6872.
[24]
H. Li, S. Edie, D. Klinedinst, J.S. Jeong, S. Blackshaw, C.L. Maslen, R.H. Reeves, Penetrance of Congenital Heart Disease in a Mouse Model of Down Syndrome Depends on a Trisomic Potentiator of a Disomic Modifier, Genetics. 203 (2016) 763–770. https://doi.org/10.1534/genetics.116.188045.
[25]
J.S. Ainscough, G.F. Gerberick, I. Kimber, R.J. Dearman, Interleukin-1β Processing Is Dependent on a Calcium-mediated Interaction with Calmodulin, Journal of Biological Chemistry. 290 (2015) 31151–31161. https://doi.org/10.1074/jbc.M115.680694.
[26]
T.M. Ma, B.D. Paul, C. Fu, S. Hu, H. Zhu, S. Blackshaw, H. Wolosker, S.H. Snyder, Serine Racemase Regulated by Binding to Stargazin and PSD-95, Journal of Biological Chemistry. 289 (2014) 29631–29641. https://doi.org/10.1074/jbc.M114.571604.
[27]
J.-G. Jung, A. Stoeck, B. Guan, R.-C. Wu, H. Zhu, S. Blackshaw, I.-M. Shih, T.-L. Wang, Notch3 Interactome Analysis Identified WWP2 as a Negative Regulator of Notch3 Signaling in Ovarian Cancer, PLoS Genet. 10 (2014) e1004751. https://doi.org/10.1371/journal.pgen.1004751.
[28]
Q. Fan, L.-Z. Huang, X.-J. Zhu, K.-K. Zhang, H.-F. Ye, Y. Luo, X.-H. Sun, Y. Lu, Identification of proteins that interact with alpha A-crystallin using a human proteome microarray, Molecular Vision. (2014).
[29]
R.-P. Deng, X. He, S.-J. Guo, W.-F. Liu, Y. Tao, S.-C. Tao, Global identification of O -GlcNAc transferase (OGT) interactors by a human proteome microarray and the construction of an OGT interactome, Proteomics. 14 (2014) 1020–1030. https://doi.org/10.1002/pmic.201300144.
[30]
Y. Chen, L.-N. Yang, L. Cheng, S. Tu, S.-J. Guo, H.-Y. Le, Q. Xiong, R. Mo, C.-Y. Li, J.-S. Jeong, L. Jiang, S. Blackshaw, L.-J. Bi, H. Zhu, S.-C. Tao, F. Ge, Bcl2-associated Athanogene 3 Interactome Analysis Reveals a New Role in Modulating Proteasome Activity, Molecular & Cellular Proteomics. 12 (2013) 2804–2819. https://doi.org/10.1074/mcp.M112.025882.
[31]
Y. Huang, J.S. Jeong, J. Okamura, M. Sook-Kim, H. Zhu, R. Guerrero-Preston, E.A. Ratovitski, Global tumor protein p53/p63 interactome: Making a case for cisplatin chemoresistance, Cell Cycle. 11 (2012) 2367–2379. https://doi.org/10.4161/cc.20863.

Enzymatic assays

[1]
S.-H. Kim, Y.-S. Cho, Y. Kim, J. Park, S.-M. Yoo, J. Gwak, Y. Kim, Y. Gwon, T. Kam, Y.-K. Jung, Endolysosomal impairment by binding of amyloid beta or MAPT/Tau to V-ATPase and rescue via the HYAL-CD44 axis in Alzheimer disease, Autophagy. (2023) 1–20. https://doi.org/10.1080/15548627.2023.2181614.
[2]
T.V. Lanz, R.C. Brewer, P.P. Ho, J.-S. Moon, K.M. Jude, D. Fernandez, R.A. Fernandes, A.M. Gomez, G.-S. Nadj, C.M. Bartley, R.D. Schubert, I.A. Hawes, S.E. Vazquez, M. Iyer, J.B. Zuchero, B. Teegen, J.E. Dunn, C.B. Lock, L.B. Kipp, V.C. Cotham, B.M. Ueberheide, B.T. Aftab, M.S. Anderson, J.L. DeRisi, M.R. Wilson, R.J.M. Bashford-Rogers, M. Platten, K.C. Garcia, L. Steinman, W.H. Robinson, Clonally expanded B cells in multiple sclerosis bind EBV EBNA1 and GlialCAM, Nature. 603 (2022) 321–327. https://doi.org/10.1038/s41586-022-04432-7.
[3]
H. Jiang, C.Y. Chiang, Z. Chen, S. Nathan, G. D’Agostino, J.A. Paulo, G. Song, H. Zhu, S.B. Gabelli, P.A. Cole, Enzymatic analysis of WWP2 E3 ubiquitin ligase using protein microarrays identifies autophagy-related substrates, Journal of Biological Chemistry. 298 (2022) 101854. https://doi.org/10.1016/j.jbc.2022.101854.
[4]
M.J. Cabello-Lobato, M. Jenner, M. Cisneros-Aguirre, K. Brüninghoff, Z. Sandy, I.C. da Costa, T.A. Jowitt, C.M. Loch, S.P. Jackson, Q. Wu, H.D. Mootz, J.M. Stark, M.J. Cliff, C.K. Schmidt, Microarray screening reveals two non-conventional SUMO-binding modules linked to DNA repair by non-homologous end-joining, Nucleic Acids Research. 50 (2022) 4732–4754. https://doi.org/10.1093/nar/gkac237.
[5]
Y. Yan, A. Narayan, S. Cho, Z. Cheng, J.O. Liu, H. Zhu, G. Wang, B. Wharram, A. Lisok, M. Brummet, H. Saeki, T. Huang, K. Gabrielson, E. Gabrielson, L. Cope, Y.M. Kanaan, A. Afsari, T. Naab, H.G. Yfantis, S. Ambs, M.G. Pomper, S. Sukumar, V.F. Merino, CRYβB2 enhances tumorigenesis through upregulation of nucleolin in triple negative breast cancer, Oncogene. 40 (2021) 5752–5763. https://doi.org/10.1038/s41388-021-01975-3.
[6]
L.J. Crawford, D.C. Campbell, J.J. Morgan, M.A. Lawson, J.M. Down, D. Chauhan, R.M. McAvera, T.C. Morris, C. Hamilton, A. Krishnan, K. Rajalingam, A.D. Chantry, A.E. Irvine, The E3 ligase HUWE1 inhibition as a therapeutic strategy to target MYC in multiple myeloma, Oncogene. 39 (2020) 5001–5014. https://doi.org/10.1038/s41388-020-1345-x.
[7]
J. Chen, C. Sagum, M.T. Bedford, Protein domain microarrays as a platform to decipher signaling pathways and the histone code, Methods. 184 (2020) 4–12. https://doi.org/10.1016/j.ymeth.2019.08.007.
[8]
I. Uzoma, J. Hu, E. Cox, S. Xia, J. Zhou, H.-S. Rho, C. Guzzo, C. Paul, O. Ajala, C.R. Goodwin, J. Jeong, C. Moore, H. Zhang, P. Meluh, S. Blackshaw, M. Matunis, J. Qian, H. Zhu, Global Identification of Small Ubiquitin-related Modifier (SUMO) Substrates Reveals Crosstalk between SUMOylation and Phosphorylation Promotes Cell Migration, Molecular & Cellular Proteomics. 17 (2018) 871–888. https://doi.org/10.1074/mcp.RA117.000014.
[9]
G. Song, H.-S. Rho, J. Pan, P. Ramos, K.-J. Yoon, F.A. Medina, E.M. Lee, D. Eichinger, G. Ming, J.L. Muñoz-Jordan, H. Tang, I. Pino, H. Song, J. Qian, H. Zhu, Multiplexed Biomarker Panels Discriminate Zika and Dengue Virus Infection in Humans, Molecular & Cellular Proteomics. 17 (2018) 349–356. https://doi.org/10.1074/mcp.RA117.000310.
[10]
Z. Xu, X. Li, S. Zhou, W. Xie, J. Wang, L. Cheng, S. Wang, S. Guo, Z. Xu, X. Cao, M. Zhang, B. Yu, H. Narimatsu, S. Tao, Y. Zhang, Systematic identification of the protein substrates of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase-T1/T2/T3 using a human proteome microarray, Proteomics. 17 (2017) 1600485. https://doi.org/10.1002/pmic.201600485.
[11]
J. Hu, J. Neiswinger, J. Zhang, H. Zhu, J. Qian, Systematic Prediction of Scaffold Proteins Reveals New Design Principles in Scaffold-Mediated Signal Transduction, PLoS Comput Biol. 11 (2015) e1004508. https://doi.org/10.1371/journal.pcbi.1004508.
[12]
E. Cox, I. Uzoma, C. Guzzo, J.S. Jeong, M. Matunis, S. Blackshaw, H. Zhu, Identification of SUMO E3 Ligase-Specific Substrates Using the HuProt Human Proteome Microarray, in: A. Posch (Ed.), Proteomic Profiling, Springer New York, New York, NY, 2015: pp. 455–463. https://doi.org/10.1007/978-1-4939-2550-6_32.
[13]
Y.-I. Lee, D. Giovinazzo, H.C. Kang, Y. Lee, J.S. Jeong, P.-T. Doulias, Z. Xie, J. Hu, M. Ghasemi, H. Ischiropoulos, J. Qian, H. Zhu, S. Blackshaw, V.L. Dawson, T.M. Dawson, Protein Microarray Characterization of the S-Nitrosoproteome, Molecular & Cellular Proteomics. 13 (2014) 63–72. https://doi.org/10.1074/mcp.M113.032235.
[14]
M.K. Tarrant, H.-S. Rho, Z. Xie, Y.L. Jiang, C. Gross, J.C. Culhane, G. Yan, J. Qian, Y. Ichikawa, T. Matsuoka, N. Zachara, F.A. Etzkorn, G.W. Hart, J.S. Jeong, S. Blackshaw, H. Zhu, P.A. Cole, Regulation of CK2 by phosphorylation and O-GlcNAcylation revealed by semisynthesis, Nat Chem Biol. 8 (2012) 262–269. https://doi.org/10.1038/nchembio.771.

Nucleic Acid Binding

[1]
D. Sun, Y. Wang, N. Sun, Z. Jiang, Z. Li, L. Wang, F. Yang, W. Li, LncRNA DANCR counteracts premature ovarian insufficiency by regulating the senescence process of granulosa cells through stabilizing the interaction between p53 and hNRNPC, J Ovarian Res. 16 (2023) 41. https://doi.org/10.1186/s13048-023-01115-3.
[2]
Q.W. Chen, Q.Q. Cai, Y. Yang, S. Dong, Y.Y. Liu, Z.Y. Chen, C.L. Kang, B. Qi, Y.W. Dong, W. Wu, L.P. Zhuang, Y.H. Shen, Z.Q. Meng, X.Z. Wu, LncRNA BC promotes lung adenocarcinoma progression by modulating IMPAD1 alternative splicing, Clinical & Translational Med. 13 (2023). https://doi.org/10.1002/ctm2.1129.
[3]
D. Van Simaeys, A. De La Fuente, S. Zilio, A. Zoso, V. Kuznetsova, O. Alcazar, P. Buchwald, A. Grilli, J. Caroli, S. Bicciato, P. Serafini, RNA aptamers specific for transmembrane p24 trafficking protein 6 and Clusterin for the targeted delivery of imaging reagents and RNA therapeutics to human β cells, Nat Commun. 13 (2022) 1815. https://doi.org/10.1038/s41467-022-29377-3.
[4]
M.J. Cabello-Lobato, M. Jenner, M. Cisneros-Aguirre, K. Brüninghoff, Z. Sandy, I.C. da Costa, T.A. Jowitt, C.M. Loch, S.P. Jackson, Q. Wu, H.D. Mootz, J.M. Stark, M.J. Cliff, C.K. Schmidt, Microarray screening reveals two non-conventional SUMO-binding modules linked to DNA repair by non-homologous end-joining, Nucleic Acids Research. 50 (2022) 4732–4754. https://doi.org/10.1093/nar/gkac237.
[5]
Q. Wang, S. Yi, Z. Du, X. Huang, J. Xu, Q. Cao, G. Su, A. Kijlstra, P. Yang, The Rs12569232 SNP Association with Vogt-Koyanagi-Harada Disease and Behcet’s Disease is Probably Mediated by Regulation of Linc00467 Expression, Ocular Immunology and Inflammation. 29 (2021) 1464–1470. https://doi.org/10.1080/09273948.2020.1745244.
[6]
B. Yu, L. Qu, T. Wu, B. Yan, X. Kan, X. Zhao, L. Yang, Y. Li, M. Liu, L. Tian, Y. Sun, Q. Li, A Novel LncRNA, AC091729.7 Promotes Sinonasal Squamous Cell Carcinomas Proliferation and Invasion Through Binding SRSF2, Front. Oncol. 9 (2020) 1575. https://doi.org/10.3389/fonc.2019.01575.
[7]
E. Panatta, A.M. Lena, M. Mancini, A. Smirnov, A. Marini, R. Delli Ponti, T. Botta‐Orfila, G.G. Tartaglia, A. Mauriello, X. Zhang, G.A. Calin, G. Melino, E. Candi, Long non‐coding RNA uc.291 controls epithelial differentiation by interfering with the ACTL6A/BAF complex, EMBO Reports. 21 (2020) e46734. https://doi.org/10.15252/embr.201846734.
[8]
L. Liu, T. Li, G. Song, Q. He, Y. Yin, J.Y. Lu, X. Bi, K. Wang, S. Luo, Y.-S. Chen, Y. Yang, B.-F. Sun, Y.-G. Yang, J. Wu, H. Zhu, X. Shen, Insight into novel RNA-binding activities via large-scale analysis of lncRNA-bound proteome and IDH1-bound transcriptome, Nucleic Acids Research. 47 (2019) 2244–2262. https://doi.org/10.1093/nar/gkz032.
[9]
C.L. Kang, B. Qi, Q.Q. Cai, L.S. Fu, Y. Yang, C. Tang, P. Zhu, Q.W. Chen, J. Pan, M.H. Chen, X.Z. Wu, LncRNA AY promotes hepatocellular carcinoma metastasis by stimulating ITGAV transcription, Theranostics. 9 (2019) 4421–4436. https://doi.org/10.7150/thno.32854.
[10]
M. Qin, G. Wei, X. Sun, Circ-UBR5: An exonic circular RNA and novel small nuclear RNA involved in RNA splicing, Biochemical and Biophysical Research Communications. 503 (2018) 1027–1034. https://doi.org/10.1016/j.bbrc.2018.06.112.
[11]
S.A. McClymont, P.W. Hook, A.I. Soto, X. Reed, W.D. Law, S.J. Kerans, E.L. Waite, N.J. Briceno, J.F. Thole, M.G. Heckman, N.N. Diehl, Z.K. Wszolek, C.D. Moore, H. Zhu, J.A. Akiyama, D.E. Dickel, A. Visel, L.A. Pennacchio, O.A. Ross, M.A. Beer, A.S. McCallion, Parkinson-Associated SNCA Enhancer Variants Revealed by Open Chromatin in Mouse Dopamine Neurons, The American Journal of Human Genetics. 103 (2018) 874–892. https://doi.org/10.1016/j.ajhg.2018.10.018.
[12]
G. Barry, J.A. Briggs, D.W. Hwang, S.P. Nayler, P.R.J. Fortuna, N. Jonkhout, F. Dachet, J.L.V. Maag, P. Mestdagh, E.M. Singh, L. Avesson, D.C. Kaczorowski, E. Ozturk, N.C. Jones, I. Vetter, L. Arriola-Martinez, J. Hu, G.R. Franco, V.M. Warn, A. Gong, M.E. Dinger, F. Rigo, L. Lipovich, M.J. Morris, T.J. O’Brien, D.S. Lee, J.A. Loeb, S. Blackshaw, J.S. Mattick, E.J. Wolvetang, The long non-coding RNA NEAT1 is responsive to neuronal activity and is associated with hyperexcitability states, Sci Rep. 7 (2017) 40127. https://doi.org/10.1038/srep40127.
[13]
B. Fan, K.-Y. Lu, F.X. Reymond Sutandy, Y.-W. Chen, K. Konan, H. Zhu, C.C. Kao, C.-S. Chen, A Human Proteome Microarray Identifies that the Heterogeneous Nuclear Ribonucleoprotein K (hnRNP K) Recognizes the 5′ Terminal Sequence of the Hepatitis C Virus RNA, Molecular & Cellular Proteomics. 13 (2014) 84–92. https://doi.org/10.1074/mcp.M113.031682.
[14]
G. Barry, J.A. Briggs, D.P. Vanichkina, E.M. Poth, N.J. Beveridge, V.S. Ratnu, S.P. Nayler, K. Nones, J. Hu, T.W. Bredy, S. Nakagawa, F. Rigo, R.J. Taft, M.J. Cairns, S. Blackshaw, E.J. Wolvetang, J.S. Mattick, The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicing, Mol Psychiatry. 19 (2014) 486–494. https://doi.org/10.1038/mp.2013.45.
[15]
C.J. Donnelly, P.-W. Zhang, J.T. Pham, A.R. Haeusler, N.A. Mistry, S. Vidensky, E.L. Daley, E.M. Poth, B. Hoover, D.M. Fines, N. Maragakis, P.J. Tienari, L. Petrucelli, B.J. Traynor, J. Wang, F. Rigo, C.F. Bennett, S. Blackshaw, R. Sattler, J.D. Rothstein, RNA Toxicity from the ALS/FTD C9ORF72 Expansion Is Mitigated by Antisense Intervention, Neuron. 80 (2013) 415–428. https://doi.org/10.1016/j.neuron.2013.10.015.
[16]
S. Hu, Z. Xie, A. Onishi, X. Yu, L. Jiang, J. Lin, H. Rho, C. Woodard, H. Wang, J.-S. Jeong, S. Long, X. He, H. Wade, S. Blackshaw, J. Qian, H. Zhu, Profiling the Human Protein-DNA Interactome Reveals ERK2 as a Transcriptional Repressor of Interferon Signaling, Cell. 139 (2009) 610–622. https://doi.org/10.1016/j.cell.2009.08.037.

Small Molecule Profiling

[1]
W.-J. Zhou, H.-L. Yang, J. Mei, K.-K. Chang, H. Lu, Z.-Z. Lai, J.-W. Shi, X.-H. Wang, K. Wu, T. Zhang, J. Wang, J.-S. Sun, J.-F. Ye, D.-J. Li, J.-Y. Zhao, L.-P. Jin, M.-Q. Li, Fructose-1,6-bisphosphate prevents pregnancy loss by inducing decidual COX-2 + macrophage differentiation, Sci. Adv. 8 (2022) eabj2488. https://doi.org/10.1126/sciadv.abj2488.
[2]
M. Zhang, B. Lian, R. Zhang, Y. Guo, J. Zhao, S. He, Y. Bai, N. Wang, Y. Lin, X. Wang, Q. Liu, X. Xu, Emodin Ameliorates Intestinal Dysfunction by Maintaining Intestinal Barrier Integrity and Modulating the Microbiota in Septic Mice, Mediators of Inflammation. 2022 (2022) 1–16. https://doi.org/10.1155/2022/5026103.
[3]
G. Wang, X. Li, N. Li, X. Wang, S. He, W. Li, W. Fan, R. Li, J. Liu, S. Hou, Icariin alleviates uveitis by targeting peroxiredoxin 3 to modulate retinal microglia M1/M2 phenotypic polarization, Redox Biology. 52 (2022) 102297. https://doi.org/10.1016/j.redox.2022.102297.
[4]
D. Wang, F. Liu, W. Yang, Y. Sun, X. Wang, X. Sui, J. Yang, Q. Wang, W. Song, M. Zhang, Z. Xiao, T. Wang, Y. Wang, Y. Luo, Meldonium Ameliorates Hypoxia-Induced Lung Injury and Oxidative Stress by Regulating Platelet-Type Phosphofructokinase-Mediated Glycolysis, Front. Pharmacol. 13 (2022) 863451. https://doi.org/10.3389/fphar.2022.863451.
[5]
D. Lee, E. Lee, S. Jang, K. Kim, E. Cho, S.-J. Mun, W. Son, H.-I. Jeon, H.K. Kim, Y.J. Jeong, Y. Lee, J.E. Oh, H.H. Yoo, Y. Lee, S.-J. Min, C.-S. Yang, Discovery of Mycobacterium tuberculosis Rv3364c-Derived Small Molecules as Potential Therapeutic Agents to Target SNX9 for Sepsis, J. Med. Chem. 65 (2022) 386–408. https://doi.org/10.1021/acs.jmedchem.1c01551.
[6]
J. Kim, A.Y. Sim, S. Barua, J.Y. Kim, J.E. Lee, Unbound IRF2 to IRF2BP2 mediates KLF4 signaling leading to anti-inflammatory phenotype of microglia, In Review, 2022. https://doi.org/10.21203/rs.3.rs-2232738/v1.
[7]
Q. Guo, Y.-C. Zhang, W. Wang, Y.-Q. Wang, Y. Liu, Z. Yang, M.-M. Zhao, N. Feng, Y.-H. Wang, X.-W. Zhang, H. Yang, T.-T. Liu, L.-Y. Shi, X.-M. Shi, D. Liu, P.-F. Tu, K.-W. Zeng, Deoxyhypusine hydroxylase as a novel pharmacological target for ischemic stroke via inducing a unique post-translational hypusination modification, Pharmacological Research. 176 (2022) 106046. https://doi.org/10.1016/j.phrs.2021.106046.
[8]
C. Gu, Y. Wang, L. Zhang, L. Qiao, S. Sun, M. Shao, X. Tang, P. Ding, C. Tang, Y. Cao, Y. Zhou, M. Guo, R. Wei, N. Li, Y. Xiao, J. Duan, Y. Yang, AHSA1 is a promising therapeutic target for cellular proliferation and proteasome inhibitor resistance in multiple myeloma, J Exp Clin Cancer Res. 41 (2022) 11. https://doi.org/10.1186/s13046-021-02220-1.
[9]
Q. Gao, H. Deng, Z. Yang, Q. Yang, Y. Zhang, X. Yuan, M. Zeng, M. Guo, W. Zeng, X. Jiang, B. Yu, Sodium danshensu attenuates cerebral ischemia–reperfusion injury by targeting AKT1, Front. Pharmacol. 13 (2022) 946668. https://doi.org/10.3389/fphar.2022.946668.
[10]
P. Zhang, W. Tao, C. Lu, L. Fan, Q. Jiang, C. Yang, E. Shang, H. Cheng, C. Che, J. Duan, M. Zhao, Bruceine A induces cell growth inhibition and apoptosis through PFKFB4/GSK3β signaling in pancreatic cancer, Pharmacological Research. 169 (2021) 105658. https://doi.org/10.1016/j.phrs.2021.105658.
[11]
Y. Xu, C. Liu, X. Han, X. Jia, Y. Li, C. Liu, N. Li, L. Liu, P. Liu, X. Jiang, W. Wang, X. Wang, Y. Li, M. Chen, J. Luo, X. Zuo, J. Han, L. Wang, Y. Du, Y. Xu, J.-D. Jiang, B. Hong, S. Si, E17241 as a Novel ABCA1 (ATP-Binding Cassette Transporter A1) Upregulator Ameliorates Atherosclerosis in Mice, ATVB. 41 (2021). https://doi.org/10.1161/ATVBAHA.120.314156.
[12]
X. Wang, Y. Chen, J. Zhu, Z. Yang, X. Gong, R. Hui, G. Huang, J. Jin, A comprehensive screening method for investigating the potential binding targets of doxorubicin based on protein microarray, European Journal of Pharmacology. 896 (2021) 173896. https://doi.org/10.1016/j.ejphar.2021.173896.
[13]
J. Qian, S. Yin, L. Ye, Z. Wang, S. Shu, Z. Mou, M. Xu, N. Chattipakorn, Z. Liu, G. Liang, An Indole-2-Carboxamide Derivative, LG4, Alleviates Diabetic Kidney Disease Through Inhibiting MAPK-Mediated Inflammatory Responses, JIR. Volume 14 (2021) 1633–1645. https://doi.org/10.2147/JIR.S308353.
[14]
X. Chen, Y. Zhao, W. Luo, S. Chen, F. Lin, X. Zhang, S. Fan, X. Shen, Y. Wang, G. Liang, Celastrol induces ROS-mediated apoptosis via directly targeting peroxiredoxin-2 in gastric cancer cells, Theranostics. 10 (2020) 10290–10308. https://doi.org/10.7150/thno.46728.
[15]
J.M. Coll, Herpesvirus Infection Induces both Specific and Heterologous Antiviral Antibodies in Carp, Front. Immunol. 9 (2018) 39. https://doi.org/10.3389/fimmu.2018.00039.
[16]
C. Azevedo, J. Singh, N. Steck, A. Hofer, F.A. Ruiz, T. Singh, H.J. Jessen, A. Saiardi, Screening a Protein Array with Synthetic Biotinylated Inorganic Polyphosphate To Define the Human PolyP-ome, ACS Chem. Biol. 13 (2018) 1958–1963. https://doi.org/10.1021/acschembio.8b00357.
[17]
H. Zhang, L. Yang, J. Ling, D.M. Czajkowsky, J.-F. Wang, X.-W. Zhang, Y.-M. Zhou, F. Ge, M. Yang, Q. Xiong, S.-J. Guo, H.-Y. Le, S.-F. Wu, W. Yan, B. Liu, H. Zhu, Z. Chen, S. Tao, Systematic identification of arsenic-binding proteins reveals that hexokinase-2 is inhibited by arsenic, Proc. Natl. Acad. Sci. U.S.A. 112 (2015) 15084–15089. https://doi.org/10.1073/pnas.1521316112.
[18]
Y.P. Kim, D. Park, J.J. Kim, W.-J. Choi, S.H. Lee, S.Y. Lee, S. Kim, J.M. Chung, J. Jeon, B.D. Lee, J.-H. Shin, Y. Lee, H. Cho, J.-M. Lee, H.C. Kang, Effective Therapeutic Approach for Head and Neck Cancer by an Engineered Minibody Targeting the EGFR Receptor, PLoS ONE. 9 (2014) e113442. https://doi.org/10.1371/journal.pone.0113442.

Reviews

[1]
N. Yao, J. Pan, X. Chen, P. Li, Y. Li, Z. Wang, T. Yao, L. Qian, D. Yi, Y. Wu, Discovery of potential biomarkers for lung cancer classification based on human proteome microarrays using Stochastic Gradient Boosting approach, J Cancer Res Clin Oncol. (2023). https://doi.org/10.1007/s00432-023-04643-z.
[2]
L.H. Carlton, R. McGregor, N.J. Moreland, Human antibody profiling technologies for autoimmune disease, Immunol Res. (2023). https://doi.org/10.1007/s12026-023-09362-8.
[3]
N. Bizzaro, L. Cinquanta, R. Tozzoli, Autoantibody profiling in autoimmune rheumatic diseases: How research may translate into clinical practice, in: Translational Autoimmunity, Elsevier, 2023: pp. 149–168. https://doi.org/10.1016/B978-0-323-85831-1.00008-5.
[4]
G.M. Aparna, K.K.R. Tetala, Recent Progress in Development and Application of DNA, Protein, Peptide, Glycan, Antibody, and Aptamer Microarrays, Biomolecules. 13 (2023) 602. https://doi.org/10.3390/biom13040602.
[5]
H. Qi, J. Xue, D. Lai, A. Li, S. Tao, Current advances in antibody‐based serum biomarker studies: From protein microarray to phage display, Proteomics Clinical Apps. 16 (2022) 2100098. https://doi.org/10.1002/prca.202100098.
[6]
L. Cinquanta, M. Infantino, N. Bizzaro, Detecting Autoantibodies by Multiparametric Assays: Impact on Prevention, Diagnosis, Monitoring, and Personalized Therapy in Autoimmune Diseases, The Journal of Applied Laboratory Medicine. 7 (2022) 137–150. https://doi.org/10.1093/jalm/jfab132.
[7]
S. Bérubé, T. Kobayashi, A. Wesolowski, D.E. Norris, I. Ruczinski, W.J. Moss, T.A. Louis, A pre‐processing pipeline to quantify, visualize, and reduce technical variation in protein microarray studies, Proteomics. 22 (2022) 2100033. https://doi.org/10.1002/pmic.202100033.
[8]
S. Bérubé, T. Kobayashi, A. Wesolowski, D.E. Norris, I. Ruczinski, W.J. Moss, T.A. Louis, A Bayesian Hierarchical Model for Signal Extraction from Protein Microarrays, Bioinformatics, 2022. https://doi.org/10.1101/2022.02.16.480698.
[9]
X. Zhang, M. Liu, X. Zhang, Y. Wang, L. Dai, Autoantibodies to tumor-associated antigens in lung cancer diagnosis, in: Advances in Clinical Chemistry, Elsevier, 2021: pp. 1–45. https://doi.org/10.1016/bs.acc.2020.08.005.
[10]
S. Mukherjee, K. Sundfeldt, C.A.K. Borrebaeck, M.E. Jakobsson, Comprehending the Proteomic Landscape of Ovarian Cancer: A Road to the Discovery of Disease Biomarkers, Proteomes. 9 (2021) 25. https://doi.org/10.3390/proteomes9020025.
[11]
T.K. MacLachlan, S. Price, J. Cavagnaro, L. Andrews, D. Blanset, M.E. Cosenza, M. Dempster, E. Galbreath, A.M. Giusti, K.M. Heinz-Taheny, R. Fleurance, E. Sutter, M.W. Leach, Classic and evolving approaches to evaluating cross reactivity of mAb and mAb-like molecules – A survey of industry 2008–2019, Regulatory Toxicology and Pharmacology. 121 (2021) 104872. https://doi.org/10.1016/j.yrtph.2021.104872.
[12]
S. Li, G. Song, Y. Bai, N. Song, J. Zhao, J. Liu, C. Hu, Applications of Protein Microarrays in Biomarker Discovery for Autoimmune Diseases, Front. Immunol. 12 (2021) 645632. https://doi.org/10.3389/fimmu.2021.645632.
[13]
P.V. Belousov, Analysis of the Repertoires of Circulating Autoantibodies’ Specificities as a Tool for Identification of the Tumor-Associated Antigens: Current Problems and Solutions, Biochemistry Moscow. 86 (2021) 1225–1242. https://doi.org/10.1134/S0006297921100060.
[14]
G.-D. Syu, S.-C. Wang, G. Ma, S. Liu, D. Pearce, A. Prakash, B. Henson, L.-C. Weng, D. Ghosh, P. Ramos, D. Eichinger, I. Pino, X. Dong, J. Xiao, S. Wang, N. Tao, K.S. Kim, P.J. Desai, H. Zhu, Development and application of a high-content virion display human GPCR array, Nat Commun. 10 (2019) 1997. https://doi.org/10.1038/s41467-019-09938-9.
[15]
Y. Feng, C.-S. Chen, J. Ho, D. Pearce, S. Hu, B. Wang, P. Desai, K.S. Kim, H. Zhu, 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 (2018) 10958–10966. https://doi.org/10.1021/acs.analchem.8b02513.
[16]
S. Gupta, K.P. Manubhai, S. Mukherjee, S. Srivastava, Serum Profiling for Identification of Autoantibody Signatures in Diseases Using Protein Microarrays, in: D.W. Greening, R.J. Simpson (Eds.), Serum/Plasma Proteomics, Springer New York, New York, NY, 2017: pp. 303–315. https://doi.org/10.1007/978-1-4939-7057-5_21.
[17]
S. Liu, H. Zhang, J. Dai, S. Hu, I. Pino, D.J. Eichinger, H. Lyu, H. Zhu, Characterization of monoclonal antibody’s binding kinetics using oblique-incidence reflectivity difference approach, MAbs. 7 (2015) 110–119. https://doi.org/10.4161/19420862.2014.985919.