Journal: bioRxiv

Article Title: PAK6 rescues pathogenic LRRK2-mediated ciliogenesis and centrosomal cohesion defects in a mutation-specific manner

doi: 10.1101/2024.04.11.589075

Figure Lengend Snippet: (a) Distribution of PAK6 candidate interactors according to their Z-score retrieved from a Human Proteome Microarray probed with recombinant full-length human PAK6. (b) A GO:BP analysis using gProfiler g:GOSt ( https://biit.cs.ut.ee/gprofiler/gost ) was performed for PAK6 candidate interactors with Z score >2.5 (left) and for PAK6 interactors annotated in PPI web-based tools PINOT, HIPPIE and MIST (PHM) (right). GO:BP terms with 2000 (array) and 1000 (PHM) term size were grouped into semantic categories. (c) Venn diagrams showing overlaps between the primary cilium proteome (GO:0005929, 640 genes) and the experimental (array) PAK6 interactome (left) or the literature-based (PHM) PAK6 interactome (right). (d) Protein network of overlapping PAK6 interactors with the primary cilium proteome (c) (including PAK6) obtained with STRING ( https://string-db.org/cgi/input?sessionId=b1S4T5BW27rz&input_page_show_search=on ); number of nodes: 11, number of edges: 11, average node degree: 2, average local clustering coefficient: 0.591, expected number of edges: 3, PPI enrichment P -value: 0.000502. Blue nodes are ciliary proteins present in the experimental PAK6 interactome (array) and grey nodes are those found in the literature-based PAK6 interactome.

Article Snippet: HuProt TM Human Proteome Microarray v4.0 was purchased from Cambridge Protein Arrays (Babraham Research Campus, Cambridge, UK) and employed to screen PAK6 interactor candidates following manufacturer’s instructions.

Techniques: Microarray, Recombinant

Journal: Molecular & Cellular Proteomics : MCP

Article Title: Identification of Novel Serological Autoantibodies in Takayasu Arteritis Patients Using HuProt Arrays

doi: 10.1074/mcp.RA120.002119

Figure Lengend Snippet: Global analysis of the serum profiling assays on HuProt. A , histogram analysis of signal intensity of all the proteins on HuProt arrays in the serum profiling assays (75 serum samples). Using a cutoff value of 8 SD determined using the control sera, autoantigens recognized by IgG autoantibodies (positives) were identified. B , distribution of positives identified in each of the 75 serum samples, ranging from <100 to >1000. C , boxplot analysis of positives identified in the TAK, healthy, and disease control groups. The median of positive autoantigens (303) identified in the TAK group is significantly higher than that obtained in the healthy group (168). No significant differences were observed between the TAK and disease control groups or between the healthy and disease control groups. AAV, ANCA-associated vasculitis; DC, disease control; HC, healthy control; RA, rheumatoid arthritis; SLE, systemic lupus erythematosus; SS, primary Sjögren's syndrome; TAK, Takayasu arteritis.

Article Snippet: Each HuProt array (CDI Laboratories) is comprised of 20,240 individual purified full-length human proteins as previously described ( ).

Techniques: Control, Immunopeptidomics

Journal: Molecular & Cellular Proteomics : MCP

Article Title: Identification of Novel Serological Autoantibodies in Takayasu Arteritis Patients Using HuProt Arrays

doi: 10.1074/mcp.RA120.002119

Figure Lengend Snippet: Representative images of candidate autoantigens identified in HuProt arrays in phase I. Anti-SPATA7 and -QDPR autoantibodies were observed in the TAK sample ( A ) but not in the disease control ( B ) or healthy control samples ( C ). Green boxes indicate candidate autoantigens; yellow boxes indicate positive control proteins. TAK, Takayasu arteritis.

Article Snippet: Each HuProt array (CDI Laboratories) is comprised of 20,240 individual purified full-length human proteins as previously described ( ).

Techniques: Immunopeptidomics, Control, Positive Control

Journal: Journal of Cellular and Molecular Medicine

Article Title: Human CPPED1 belongs to calcineurin‐like metallophosphoesterase superfamily and dephosphorylates PI3K‐AKT pathway component PAK4

doi: 10.1111/jcmm.16607

Figure Lengend Snippet: CPPED1‐interacting proteins obtained by human proteome microarray. Above‐threshold interactions are listed in order of highest to lowest binding affinity with CPPED1

Article Snippet: The HuProt TM v3.1‐Human Proteome Microarray (Cambridge Protein Arrays Ltd.) was used to identify protein interactions on an immobilized array.

Techniques: Microarray, Binding Assay, Derivative Assay, RNA Binding Assay, Ubiquitin Proteomics, Transduction

Journal: Journal of Cellular and Molecular Medicine

Article Title: Human CPPED1 belongs to calcineurin‐like metallophosphoesterase superfamily and dephosphorylates PI3K‐AKT pathway component PAK4

doi: 10.1111/jcmm.16607

Figure Lengend Snippet: KEGG pathway analysis of CPPED1 binding partners identified by human proteome microarray. Significant terms ( P <.05) are shown

Article Snippet: The HuProt TM v3.1‐Human Proteome Microarray (Cambridge Protein Arrays Ltd.) was used to identify protein interactions on an immobilized array.

Techniques: Binding Assay, Microarray

Journal: Molecular & Cellular Proteomics : MCP

Article Title: Integration of IgA and IgG Autoantigens Improves Performance of Biomarker Panels for Early Diagnosis of Lung Cancer *

doi: 10.1074/mcp.RA119.001905

Figure Lengend Snippet: Examples of IgA-bound autoantigens identified on HuProt arrays in Phase I. A, Anti-human IgA images of BCL7A and MTERF4 obtained with serum samples collected from a LC patient, healthy subject, and LBL patient. IgA-bound autoantibodies were visualized with a Cy3-labeled anti-human IgA secondary antibody on HuProt arrays. In both cases, BCL7A and MTERF4 were specifically recognized by IgA antibodies of a LC patient; no detectable signals were observed with a healthy or LBL serum. B, Box plot analysis of HuProt array profiling of BCL7A (upper panel) and MTERF4 (lower panel) in LC, healthy and LBL.

Article Snippet: HuProt Arrays and Serum Profiling Assays HuProt arrays were manufactured by CDI Laboratories, Inc. Each HuProt array v3.0 is comprised of 20,240 unique human full-length proteins, covering ∼75% of the human proteome.

Techniques: Labeling

Journal: Frontiers in Medicine

Article Title: Follicular dendritic cell differentiation is associated with distinct synovial pathotype signatures in rheumatoid arthritis

doi: 10.3389/fmed.2022.1013660

Figure Lengend Snippet: The FDC mAb CNA.42 recognizes FBXO2. (A) Immunoprecipitation (IP) and characterization of the CNA-42 binding protein. (A-I) Western blotting of total cell lysate (a), negative control (agarose beads only) and the CNA.42-immunoprecipitated proteins (c and d, 1.5 and 6 uls/lane respectively) from tonsillar single cell suspension probed with CNA-42. A single band is detectable at 120 Kd. (A-II) the reactivity of the CNA.42 mAb on the HuProt™ human proteome microarray showing subarray 9-1 of array 1300017931 (used for the CNA.42) with fluorescence detection at 633 nm excitation (a) and 543 nm excitation (b). (a) Staining with biotinylated anti-GST and Streptavidin-647. Rows 1-28 show generic staining of the GST-tagged immobilized human proteins, among them FBXO2 in row 11. (b) Probing with CNA.42 and Cy3 labeled anti-mouse IgM shows one hit, the human protein FBXO2 in the subarray. (A-III) Western blotting of tonsillar lysates with FBXO2 and CNA-42-specific antibodies recognize 120 Kd bands in the lysates [CNA.42 BP = CNA.42 binding protein]. (B) In situ hybridization of FBXO2 mRNA (green) showing intracellular signal in tonsillar CD21 + FDC reticula (red). (C) Western blotting of lysates from the CAN.42 expressing CEM cell line using mAb CAN.42 and anti FBXO2. CEM were untreated or treated either with Accell human FBXO2 siRNA (1 uM), or non-targeting control (NTC). GAPDH is used as a loading control. Compared to untreated cells, densitometric analysis with Image J indicates that FBXO2 siRNA-treated cells expressed 50% (*) and 35% (**) less FBXO2 and CNA.42, respectively.

Article Snippet: CNA.42 specificity was assessed in Cambridge Protein Arrays Ltd., Babraham Research Campus, Cambridge, UK using human proteome arrays (HuProt Ver2).

Techniques: Immunoprecipitation, Binding Assay, Western Blot, Negative Control, Suspension, Microarray, Fluorescence, Staining, Labeling, In Situ Hybridization, Expressing, Control