Alzheimer's Disease Kinome Atlas

AKT COT NDR NIK PAKA PDHK PDK1 PKA PKCA PKCD PKCH PKCI PKD PKG PKN RAF RIPK RSK SGK CAMK1 CAMK2 CAMKK DAPK DMPK IKK MARK MLCK PHK RAD53 AMPK BRSK CHK1 LKB MELK NUAK PAKB PASK QIK SLK CDK CK2 CLK DYRK GSK MAPKAPK NMO BARK2 GRK ERK JNK P38 BUD32 CK1 HAL NAK NEK PEK PIM PLK TLK TTK ULK VRK1 WNK AUR ATM ATR MTOR PRKDC FRAY KHS MLK MOS MSN MST STE11 STE7 TAO IRAK STKR A G C C A M K L K M A C C G M C K R G K P A M R E H T O K K I P E T S T K L T K R L 3xTG PFC F 3xTG PFC M DLPFC Chr F DLPFC Chr M DLPFC Cyt F DLPFC Cyt M DLPFC Nuc F DLPFC Nuc M DLPFC F 3 DLPFC M 3 DLPFC F 2 DLPFC M 2 DLPFC F 1 DLPFC M 1 DLPFC F AD MCI DLPFC M AD MCI DLPFC F MCI CTL DLPFC M MCI CTL APP HPC F APP HPC M APP PFC F APP PFC M APP iAstro M V717I AB WT AB APP iAstro M V717I AB WT APP iAstro M V717I WT AB APP iAstro M V717I WT PS1 iAstro F intr4del AB WT AB PS1 iAstro F intr4del AB WT PS1 iAstro F intr4del WT AB PS1 iAstro F intr4del WT PS1 iAstro M Y115H AB WT AB PS1 iAstro M Y115H AB WT PS1 iAstro M Y115H WT AB PS1 iAstro M Y115H WT APP iNeuro M V717I AB WT AB APP iNeuro M V717I AB WT APP iNeuro M V717I WT AB APP iNeuro M V717I WT PS1 iNeuro F intr4del AB WT AB PS1 iNeuro F intr4del AB WT PS1 iNeuro F intr4del WT AB PS1 iNeuro F intr4del WT PS1 iNeuro M Y115H AB WT AB PS1 iNeuro M Y115H AB WT PS1 iNeuro M Y115H WT AB PS1 iNeuro M Y115H WT Z Score −4 −2 0 2 4 Alzheimer’s Disease Kinome Atlas John Vergis1,, Nicholas Henkel1, Ali Sajid Imami1, Alyssa Wallstrum1, Jacob Wood1, Robert E. McCullumsmith1,2 University of Toledo Department of Neurosciences and Psychiatry, Toledo, OH; 2Promedica, Toledo, OH Abstract Introduction. The lack of treatments and successful clinical trials for Alzheimer’s disease (AD) treatments highlights a need to better understand the pathogenesis of AD. We assessed the serine/threonine subkinome in AD using a functional proteomics approach. AD progression was investigated in postmortem DLPFC brain samples from control, mild cognitive impairment (MCI), and AD subjects; iPSC-derived neuronal and astrocyte cultures from sporadic (late onset) and familial AD cases were also assessed. Methods. We analyzed the active kinomic signature in AD samples using the Pamgene’s PamStation®12 and serine/threonine kinase (STK) reporter chips. We used the Kinome Random Sampling Analyzer (KRSA) package to identify upstream kinases from the kinome array datasets. Results. Female and male AD brain had AKT1 and AMPK1 as hits in early (CTL vs MCI) and late (MCI vs AD) clinical progression. In females, RSK4 was a hit in early and late progression, while PAK5 was only a hit in late progression. In males, PAK5, TAOK3, and RSK4 were hits in the late stage. PAK5, TAOK3, and RSK4 are understudied in AD, and considered “dark” kinases overall due to the paucity of biochemical annotations for their protein targets. Bayesian networks validated the AMPK kinase relevance in AD progression via emergent and newly absent relationships over time. Conclusion. Major changes in STK subkinome revealed insights such as: • Alzheimer’s Disease shows a significantly reduced (p < 0.05) overall phosphorylation signal as compared to control tissues • AMPK may be a clinically relevant target • Dark kinases with increased activity were identified in Alzheimer’s, supporting kinase function elucidation and further understanding of the disease process • This research supports further biomarker discovery and serves as a touchstone for future kinase inhibitor studies • High potential for new drug development in Alzheimer’s Disease to improve patient outcomes and quality of life. DEPARTMENT OF NEUROSCIENCES AND PSYCHIATRY UNIVERSITY OF TOLEDO Subjects Human AD, MCI Postmortem DLPFC FAD Mutant Mice FAD iPSC Neuron & Astrocyte Cultures * 7.0 7.5 8.0 AD CTL Group Mean Signal Overall Signal Data Collection on PamStation®12 kinome array from Pamgene Processing Data Processing & Analysis Kinome Random Sampling Analyzer Analysis 46 Experimental Comparisons: Males vs Females, AD vs MCI, MCI vs CTL, AD vs CTL, APP vs CTL, 3xTG vs CTL, PS1 vs CTL Aβ vs VEH. HPC, PFC, and DPLFC. Design Homogenized samples were pooled by diagnosis and sex for kinome array analyses. Glossary L i g h t K i n a s e s P r e v i o u s l y U n l i n k e d t o A l z h e i m e r ’ s D i s e a s e D a r k K i n a s e s P r e v i o u s l y U n l i n k e d t o A l z h e i m e r ’ s D i s e a s e PAKA (PAK3, PAK5, PAK6) NDR NMO BARK2 BUD32 COT FRAY KHS HAL STE7 STKR STE11 VRK1 (Overwhelmingly found in excitatory and inhibitory neurons) •v3xTG: Triple transgene mouse Alzheimer’s Disease model, carrying APPswe, TauP301L, and PS1M146V. • AB: “Amyloid beta” (A β); upon accumulation represents a hallmark of Alzheimer’s Disease. • AD: Shorthand for Alzheimer’s Disease. • APP: HGNC symbol for the Amyloid-beta precursor protein. •Chr: “Chromatin fraction”, indicating the chromatin subcellular fraction of postmortem DLPFC tissue. •CTL: “Control”. •Cyt: “Cytosolic fraction”, indicating the cytosolic subcellular fraction of postmortem DLPFC tissue. •DLPFC: “Dorsolateral prefrontal cortex”. •F: “Female”. HPC: “Hippocampus”. •iAstro: “iPSCs from FAD patients, differentiated into astrocytes”. • iNeuro: ”iPSCs from FAD patients, differentiated into neurons”. •intr4del: “intron 4 deletion of PS1”. M: “Male” •MCI: “Mild cognitive impairment”, an intermediary stage between healthy brain and Alzheimer’s Disease • Nuc: Shorthand for “nuclear fraction”, indicating the nuclear subcellular fraction of postmortem DLPFC tissue. • PFC: Prefrontal cortex. • PS1: Indicating mutation of the presenilin-1 gene (PSEN1). •V717I: Valine to isoleucine missense at 717th APP Amino Acid. •WT: “Wildtype”. •Y115H: Tyrosine to histidine missense at 115th PSEN1 Amino Acid.