by Keyword: Phosphorylation

Andrés-Benito, P, Iñigo-Marco, I, Brullas, M, Carmona, M, del Rio, JA, Fernández-Irigoyen, J, Santamaría, E, Povedano, M, Ferrer, I, (2023). Proteostatic modulation in brain aging without associated Alzheimer's disease-and age-related neuropathological changes Aging-Us 15, 3295-3330

(Phospho)proteomics of old-aged subjects without cognitive or behavioral symptoms, and without AD-neuropathological changes and lacking any other neurodegenerative alteration will increase understanding about the physiological state of human brain aging without associate neurological deficits and neuropathological lesions.(Phospho)proteomics using conventional label-free- and SWATH-MS (Sequential window acquisition of all theoretical fragment ion spectra mass spectrometry) has been assessed in the frontal cortex (FC) of individuals without NFTs, senile plaques (SPs) and age-related co-morbidities classified by age (years) in four groups; group 1 (young, 30-44); group 2 (middle-aged: MA, 45-52); group 3 (early-elderly, 64-70); and group 4 (late-elderly, 75-85).Protein levels and deregulated protein phosphorylation linked to similar biological terms/functions, but involving different individual proteins, are found in FC with age. The modified expression occurs in cytoskeleton proteins, membranes, synapses, vesicles, myelin, membrane transport and ion channels, DNA and RNA metabolism, ubiquitin-proteasome-system (UPS), kinases and phosphatases, fatty acid metabolism, and mitochondria. Dysregulated phosphoproteins are associated with the cytoskeleton, including microfilaments, actin-binding proteins, intermediate filaments of neurons and glial cells, and microtubules; membrane proteins, synapses, and dense core vesicles; kinases and phosphatases; proteins linked to DNA and RNA; members of the UPS; GTPase regulation; inflammation; and lipid metabolism. Noteworthy, protein levels of large clusters of hierarchically-related protein expression levels are stable until 70. However, protein levels of components of cell membranes, vesicles and synapses, RNA modulation, and cellular structures (including tau and tubulin filaments) are markedly altered from the age of 75. Similarly, marked modifications occur in the larger phosphoprotein clusters involving cytoskeleton and neuronal structures, membrane stabilization, and kinase regulation in the late elderly.Present findings may increase understanding of human brain proteostasis modifications in the elderly in the subpopulation of individuals not having AD neuropathological change and any other neurodegenerative change in any telencephalon region.

JTD Keywords: (phospho)proteomics, cortex, cytoskeleton, hippocampus, kinases, membranes, mitochondria, mitochondrial-function, pathological process, phosphoproteome analysis, phosphorylation, proteome, quantitative proteomics, synapsis, tau-protein, therapeutic target, (phospho)proteomics, Brain aging, Cytoskeleton, Kinases, Membranes, Mitochondria, Neurodegenerative diseases, Proteome, Synapsis

Andrés-Benito, P, Carmona, M, Pirla, MJ, Torrejón-Escribano, B, del Rio, J, Ferrer, I, (2023). Dysregulated Protein Phosphorylation as Main Contributor of Granulovacuolar Degeneration at the First Stages of Neurofibrillary Tangles Pathology Neuroscience 518, 119-140

The hippocampus of cases with neurofibrillary tangles (NFT) pathology classified as stages I–II, III–IV, and V–VI without comorbidities, and middle-aged (MA) individuals with no NFT pathology, were examined to learn about the composition of granulovacuolar degeneration (GVD). Our results confirm the presence of CK1-?, p38-P Thr180/Tyr182, SAPK/JNK-P Thr183/Thr185, GSK-3?/?-P Tyr279/Tyr216, and GSK-3? Ser9 in the cytoplasmic granules in a subset of neurons of the CA1 and CA2 subfields of the hippocampus. Also, we identify the presence of PKA ?/?-P Thr197, SRC-P Tyr416, PAK1-P Ser199/Ser204, CAMK2A-P Tyr197, and PKCG-P Thr655 in cytoplasmic granules in cases with NFT pathology, but not in MA cases. Our results also confirm the presence of ?-catenin-P Ser45/Thr41, IRE?-P Ser274, eIF2?-P Ser51, TDP-43-P Ser403-404 (but absent TDP-43), and ubiquitin in cytoplasmic granules. Other components of the cytoplasmic granules are MAP2-P Thr1620/1623, MAP1B-P Thr1265, ADD1-P Ser726, and ADD1/ADD1-P Ser726/Ser713, in addition to several tau species including 3Rtau, 4Rtau, and tau-P Ser262. The analysis of GVD at progressive stages of NFT pathology reveals the early appearance of phosphorylated kinases and proteins in cytoplasmic granules at stages I–II, before the appearance of pre-tangles and NFTs. Most of these granules are not surrounded by LAMP1-positive membranes. Markers of impaired ubiquitin-protesome system, abnormal reticulum stress response, and altered endocytic and autophagic pathways occur in a subpopulation of neurons containing cytoplasmic granules, and they appear later. These observations suggest early phosphorylation of kinases leading to their activation, and resulting in the abnormal phosphorylation of various substrates, including tau, as a main alteration at the first stages of GVD. © 2021 The Author(s)

JTD Keywords: alzheimer's disease, alzheimers association guidelines, alzheimer’s disease, brain aging, cyclin-dependent kinase-5, granulovacuolar degeneration, kinases, national institute, neuropathologic assessment, p38 kinase, progressive supranuclear palsy, protein phosphorylation, tau, tau pathology, up-regulation, upstream activator, Alzheimer's disease, Brain aging, Glycogen-synthase kinase-3, Granulovacuolar degeneration, Kinases, Protein phosphorylation, Tau

Andres-Benito, P, Flores, A, Busquet-Areny, S, Carmona, M, Ausin, K, Cartas-Cejudo, P, Lachen-Montes, M, Del Rio, JA, Fernandez-Irigoyen, J, Santamaria, E, Ferrer, I, (2023). Deregulated Transcription and Proteostasis in Adult mapt Knockout Mouse International Journal Of Molecular Sciences 24, 6559

Transcriptomics and phosphoproteomics were carried out in the cerebral cortex of B6.Cg-Mapttm1(EGFP)Klt (tau knockout: tau-KO) and wild-type (WT) 12 month-old mice to learn about the effects of tau ablation. Compared with WT mice, tau-KO mice displayed reduced anxiety-like behavior and lower fear expression induced by aversive conditioning, whereas recognition memory remained unaltered. Cortical transcriptomic analysis revealed 69 downregulated and 105 upregulated genes in tau-KO mice, corresponding to synaptic structures, neuron cytoskeleton and transport, and extracellular matrix components. RT-qPCR validated increased mRNA levels of col6a4, gabrq, gad1, grm5, grip2, map2, rab8a, tubb3, wnt16, and an absence of map1a in tau-KO mice compared with WT mice. A few proteins were assessed with Western blotting to compare mRNA expression with corresponding protein levels. Map1a mRNA and protein levels decreased. However, β-tubulin III and GAD1 protein levels were reduced in tau-KO mice. Cortical phosphoproteomics revealed 121 hypophosphorylated and 98 hyperphosphorylated proteins in tau-KO mice. Deregulated phosphoproteins were categorized into cytoskeletal (n = 45) and membrane proteins, including proteins of the synapses and vesicles, myelin proteins, and proteins linked to membrane transport and ion channels (n = 84), proteins related to DNA and RNA metabolism (n = 36), proteins connected to the ubiquitin-proteasome system (UPS) (n = 7), proteins with kinase or phosphatase activity (n = 21), and 22 other proteins related to variegated pathways such as metabolic pathways, growth factors, or mitochondrial function or structure. The present observations reveal a complex altered brain transcriptome and phosphoproteome in tau-KO mice with only mild behavioral alterations.

JTD Keywords: computational platform, conformational-changes, cytoskeleton, disease, expression, isoforms, mechanisms, mice, phosphoproteomics, phosphorylation, synapse, tau-ko, tauopathies, transcriptomics, Tau-ko, Tau-protein, Transcriptomics

Gomila AMJ, Pérez-Mejías G, Nin-Hill A, Guerra-Castellano A, Casas-Ferrer L, Ortiz-Tescari S, Díaz-Quintana A, Samitier J, Rovira C, De la Rosa MA, Díaz-Moreno I, Gorostiza P, Giannotti MI, Lagunas A, (2022). Phosphorylation disrupts long-distance electron transport in cytochrome c Nature Communications 13, 7100

It has been recently shown that electron transfer between mitochondrial cytochrome c and the cytochrome c1 subunit of the cytochrome bc1 can proceed at long-distance through the aqueous solution. Cytochrome c is thought to adjust its activity by changing the affinity for its partners via Tyr48 phosphorylation, but it is unknown how it impacts the nanoscopic environment, interaction forces, and long-range electron transfer. Here, we constrain the orientation and separation between cytochrome c1 and cytochrome c or the phosphomimetic Y48pCMF cytochrome c, and deploy an array of single-molecule, bulk, and computational methods to investigate the molecular mechanism of electron transfer regulation by cytochrome c phosphorylation. We demonstrate that phosphorylation impairs long-range electron transfer, shortens the long-distance charge conduit between the partners, strengthens their interaction, and departs it from equilibrium. These results unveil a nanoscopic view of the interaction between redox protein partners in electron transport chains and its mechanisms of regulation.© 2022. The Author(s).

JTD Keywords: apoptosis, binding, cardiolipin, complex, dynamics, force, respiration, structural basis, tyrosine phosphorylation, Histone chaperone activity

Astro, V, Ramirez-Calderon, G, Pennucci, R, Caroli, J, Saera-Vila, A, Cardona-Londono, K, Forastieri, C, Fiacco, E, Maksoud, F, Alowaysi, M, Sogne, E, Falqui, A, Gonzalez, F, Montserrat, N, Battaglioli, E, Mattevi, A, Adamo, A, (2022). Fine-tuned KDM1A alternative splicing regulates human cardiomyogenesis through an enzymatic-independent mechanism Iscience 25, 104665

The histone demethylase KDM1A is a multi- faceted regulator of vital developmental processes, including mesodermal and cardiac tube formation during gastrulation. However, it is unknown whether the fine-tuning of KDM1A splicing isoforms, already shown to regulate neuronal maturation, is crucial for the specification and maintenance of cell identity during cardiogenesis. Here, we discovered a temporal modulation of ubKDM1A and KDM1A+2a during human and mice fetal cardiac development and evaluated their impact on the regulation of cardiac differentiation. We revealed a severely impaired cardiac differentiation in KDM1A(-/-) hESCs that can be rescued by re-expressing ubKDM1A or catalytically impaired ubKDM1A-K661A, but not by KDM1A+2a or KDM1A+2a-K661A. Conversely, KDM1A+2a(-/-) hESCs give rise to functional cardiac cells, displaying increased beating amplitude and frequency and enhanced expression of critical cardiogenic markers. Our findings prove the existence of a divergent scaffolding role of KDM1A splice variants, independent of their enzymatic activity, during hESC differentiation into cardiac cells.

JTD Keywords: cell biology, molecular mechanism of gene regulation, omics, Bhlh transcription factor, Corest, Differentiation, Dna, Embryonic stem-cells, Heart, Lsd1, Phosphorylation, Proteins, Stem cells research, Swirm domain

Mesquida-Veny, F, Martinez-Torres, S, Del Rio, JA, Hervera, A, (2022). Nociception-Dependent CCL21 Induces Dorsal Root Ganglia Axonal Growth via CCR7-ERK Activation Frontiers In Immunology 13, 880647

While chemokines were originally described for their ability to induce cell migration, many studies show how these proteins also take part in many other cell functions, acting as adaptable messengers in the communication between a diversity of cell types. In the nervous system, chemokines participate both in physiological and pathological processes, and while their expression is often described on glial and immune cells, growing evidence describes the expression of chemokines and their receptors in neurons, highlighting their potential in auto- and paracrine signalling. In this study we analysed the role of nociception in the neuronal chemokinome, and in turn their role in axonal growth. We found that stimulating TRPV1(+) nociceptors induces a transient increase in CCL21. Interestingly we also found that CCL21 enhances neurite growth of large diameter proprioceptors in vitro. Consistent with this, we show that proprioceptors express the CCL21 receptor CCR7, and a CCR7 neutralizing antibody dose-dependently attenuates CCL21-induced neurite outgrowth. Mechanistically, we found that CCL21 binds locally to its receptor CCR7 at the growth cone, activating the downstream MEK-ERK pathway, that in turn activates N-WASP, triggering actin filament ramification in the growth cone, resulting in increased axonal growth.

JTD Keywords: axonal growth, ccl21, ccr7, mek-erk, Actin dynamics, Axonal growth, Ccl21, Ccr7, Cell-migration, Central-nervous-system, Chemokine, Ligands, Mek-erk, Microglia, Neurons, Neuropathic pain, Nociception, Phosphorylation, Regeneration

Ferrer, I, Andres-Benito, P, Ausin, K, Cartas-Cejudo, P, Lachen-Montes, M, del Rio, JA, Fernandez-Irigoyen, J, Santamaria, E, (2022). Dysregulated Brain Protein Phosphorylation Linked to Increased Human Tau Expression in the hTau Transgenic Mouse Model International Journal Of Molecular Sciences 23, 6427

Altered protein phosphorylation is a major pathologic modification in tauopathies and Alzheimer's disease (AD) linked to abnormal tau fibrillar deposits in neurofibrillary tangles (NFTs) and pre-tangles and beta-amyloid deposits in AD. hTau transgenic mice, which express 3R and less 4R human tau with no mutations in a murine knock-out background, show increased tau deposition in neurons but not NFTs and pre-tangles at the age of nine months. Label-free (phospho)proteomics and SWATH-MS identified 2065 proteins in hTau and wild-type (WT) mice. Only six proteins showed increased levels in hTau; no proteins were down-regulated. Increased tau phosphorylation in hTau was detected at Ser199, Ser202, Ser214, Ser396, Ser400, Thr403, Ser404, Ser413, Ser416, Ser422, Ser491, and Ser494, in addition to Thr181, Thr231, Ser396/Ser404, but not at Ser202/Thr205. In addition, 4578 phosphopeptides (corresponding to 1622 phosphoproteins) were identified in hTau and WT mice; 64 proteins were differentially phosphorylated in hTau. Sixty proteins were grouped into components of membranes, membrane signaling, synapses, vesicles, cytoskeleton, DNA/RNA/protein metabolism, ubiquitin/proteasome system, cholesterol and lipid metabolism, and cell signaling. These results showed that over-expression of human tau without pre-tangle and NFT formation preferentially triggers an imbalance in the phosphorylation profile of specific proteins involved in the cytoskeletal-membrane-signaling axis.

JTD Keywords: cytoskeleton, htau, membrane, phosphorylation, synapsis, tau, Aggregation, Alzheimers-disease, Animal-models, Cytoskeleton, Htau, Membrane, Mice, Networks, Pathology, Phosphoproteome analysis, Phosphorylation, Synapsis, Tau, Tauopathies, Tauopathy

Ferrer, I, Andrés-Benito, P, Ausín, K, Pamplona, R, del Rio, JA, Fernández-Irigoyen, J, Santamaría, E, (2021). Dysregulated protein phosphorylation: A determining condition in the continuum of brain aging and Alzheimer's disease Brain Pathology 31, e12996

Tau hyperphosphorylation is the first step of neurofibrillary tangle (NFT) formation. In the present study, samples of the entorhinal cortex (EC) and frontal cortex area 8 (FC) of cases with NFT pathology classified as stages I–II, III–IV, and V–VI without comorbidities, and of middle-aged (MA) individuals with no NFT pathology, were analyzed by conventional label-free and SWATH-MS (sequential window acquisition of all theoretical fragment ion spectra mass spectrometry) to assess the (phospho)proteomes. The total number of identified dysregulated phosphoproteins was 214 in the EC, 65 of which were dysregulated at the first stages (I–II) of NFT pathology; 167 phosphoproteins were dysregulated in the FC, 81 of them at stages I–II of NFT pathology. A large percentage of dysregulated phosphoproteins were identified in the two regions and at different stages of NFT progression. The main group of dysregulated phosphoproteins was made up of components of the membranes, cytoskeleton, synapses, proteins linked to membrane transport and ion channels, and kinases. The present results show abnormal phosphorylation of proteins at the first stages of NFT pathology in the elderly (in individuals clinically considered representative of normal aging) and sporadic Alzheimer's disease (sAD). Dysregulated protein phosphorylation in the FC precedes the formation of NFTs and SPs. The most active period of dysregulated phosphorylation is at stages III–IV when a subpopulation of individuals might be clinically categorized as suffering from mild cognitive impairment which is a preceding determinant stage in the progression to dementia. Altered phosphorylation of selected proteins, carried out by activation of several kinases, may alter membrane and cytoskeletal functions, among them synaptic transmission and membrane/cytoskeleton signaling. Besides their implications in sAD, the present observations suggest a molecular substrate for “benign” cognitive deterioration in “normal” brain aging.

JTD Keywords: (phospho)proteomics, alzheimer's disease, amyloid-beta, association guidelines, brain aging, cytoskeleton, frontal-cortex, kinases, lipid rafts, membranes, national institute, neuropathologic assessment, pathological process, protein phosphorylation, synapse pathology, synapses, tau, tau pathology, (phospho)proteomics, Age-related tauopathy, Alzheimer's disease, Brain aging, Cytoskeleton, Kinases, Membranes, Protein phosphorylation, Synapses, Tau

Zañudo, JGT, Mao, PP, Alcon, C, Kowalski, K, Johnson, GN, Xu, GT, Baselga, J, Scaltriti, M, Letai, A, Montero, J, Albert, R, Wagle, N, (2021). Cell line-specific network models of er breast cancer identify potential pi3kainhibitor resistance mechanisms and drug combinations Cancer Research 81, 4603-4617

Durable control of invasive solid tumors necessitates identifying therapeutic resistance mechanisms and effective drug combinations. In this work, we used a network-based mathematical model to identify sensitivity regulators and drug combinations for the PI3Ka inhibitor alpelisib in estrogen receptor positive (ER) PIK3CAmutant breast cancer. The model-predicted efficacious combination of alpelisib and BH3 mimetics, for example, MCL1 inhibitors, was experimentally validated in ER breast cancer cell lines. Consistent with the model, FOXO3 downregulation reduced sensitivity to alpelisib, revealing a novel potential resistance mechanism. Cell line-specific sensitivity to combinations of alpelisib and BH3 mimetics depended on which BCL2 family members were highly expressed. On the basis of these results, newly developed cell line-specific network models were able to recapitulate the observed differential response to alpelisib and BH3 mimetics. This approach illustrates how network-based mathematical models can contribute to overcoming the challenge of cancer drug resistance.

JTD Keywords: activation, akt, feedback, foxo, leads, p27(kip1), phosphorylation, reveals, transcription factors, Dependent kinase inhibitor

Ferrer, Isidro, García, M. A., González, I. L., Lucena, D. D., Villalonga, A. R., Tech, M. C., Llorens, F., Garcia-Esparcia, P., Martinez-Maldonado, A., Mendez, M. F., Escribano, B. T., Serra, J. J. B., Sabido, E., de la Torre Gómez, C., del Rio, J. A., (2018). Aging-related tau astrogliopathy (ARTAG): Not only tau phosphorylation in astrocytes Brain Pathology 28, (6), 965–985

Aging-related tau astrogliopathy (ARTAG) is defined by the presence of two types of tau-bearing astrocytes: thorn-shaped astrocytes (TSAs) and granular/fuzzy astrocytes in the brain of old-aged individuals. The present study is focused on TSAs in rare forms of ARTAG with no neuronal tau pathology or restricted to entorhinal and transentorhinal cortices, to avoid bias from associated tauopathies. TSAs show 4Rtau phosphorylation at several specific sites and abnormal tau conformation, but they lack ubiquitin and they are not immunostained with tau-C3 antibodies which recognize truncated tau at Asp421. Astrocytes in ARTAG have atrophic processes, reduced glial fibrillary acidic protein (GFAP) and increased superoxide dismutase 2 (SOD2) immunoreactivity. Gel electrophoresis and western blotting of sarkosyl-insoluble fractions reveal a pattern of phospho-tau in ARTAG characterized by two bands of 68 and 64 kDa, and several middle bands between 35 and 50 kDa which differ from what is seen in AD. Phosphoproteomics of dissected vulnerable regions identifies an increase of phosphorylation marks in a large number of proteins in ARTAG compared with controls. GFAP, aquaporin 4, several serine-threonine kinases, microtubule associated proteins and other neuronal proteins are among the differentially phosphorylated proteins in ARTAG thus suggesting a hyper-phosphorylation background that affects several molecules, including many kinases and proteins from several cell compartments and various cell types. Finally, present results show for the first time that tau seeding is produced in neurons of the hippocampal complex, astrocytes, oligodendroglia and along fibers of the corpus callosum, fimbria and fornix following inoculation into the hippocampus of wild type mice of sarkosyl-insoluble fractions enriched in hyper-phosphorylated tau from selected ARTAG cases. These findings show astrocytes as crucial players of tau seeding in tauopathies.

JTD Keywords: ARTAG, Kinases, Phosphorylation, Seeding, Tau, Thorn-shaped astrocytes

Garcia-Esparcia, P., Koneti, A., Rodríguez-Oroz, M. C., Gago, B., del Rio, J. A., Ferrer, Isidro, (2018). Mitochondrial activity in the frontal cortex area 8 and angular gyrus in Parkinson's disease and Parkinson's disease with dementia Brain Pathology 28, (1), 43-57

Altered mitochondrial function is characteristic in the substantia nigra in Parkinson's disease (PD). Information about mitochondria in other brain regions such as the cerebral cortex is conflicting mainly because most studies have not contemplated the possibility of variable involvement depending on the region, stage of disease progression and clinical symptoms such as the presence or absence of dementia. RT-qPCR of 18 nuclear mRNAs encoding subunits of mitochondrial complexes and 12 mRNAs encoding energy metabolism-related enzymes; western blotting of mitochondrial proteins; and analysis of enzymatic activities of complexes I, II, II, IV and V of the respiratory chain were assessed in frontal cortex area 8 and the angular gyrus of middle-aged individuals (MA), and those with incidental PD (iPD), long-lasting PD with parkinsonism without dementia (PD) and long-lasting PD with dementia (PDD). Up-regulation of several genes was found in frontal cortex area 8 in PD when compared with MA and in the angular gyrus in iPD when compared with MA. Marked down-regulation of genes encoding mitochondrial subunits and energy metabolism-related enzymes occurs in frontal cortex but only of genes coding for energy metabolism-related enzymes in the angular gyrus in PDD. Significant decrease in the protein expression levels of several mitochondrial subunits encoded by these genes occurs in frontal cortex area 8 and angular gyrus in PDD. Moreover, expression of MT-ND1 which is encoded by mitochondrial DNA is also reduced in PDD. Reduced enzymatic activity of complex III in frontal cortex area 8 and angular gyrus is observed in PD, but dramatic reduction in the activity of complexes I, II, II and IV in both regions characterizes PDD. Dementia in the context of PD is linked to region-specific deregulation of genomic genes encoding subunits of mitochondrial complexes and to marked reduction in the activity of mitochondrial complexes I, II, III and IV.

JTD Keywords: Cerebral cortex, Dementia, Energy metabolism, Incidental PD, Mitochondria, Oxidative phosphorylation, Parkinson disease, PDD, Respiratory chain

Ansoleaga, B., Garcia-Esparcia, Paula, Llorens, Franc, Hernández-Ortega, Karina, Carmona Tech, Margarita, Antonio del Rio, José, Zerr, Inga, Ferrer, Isidro, (2016). Altered mitochondria, protein synthesis machinery, and purine metabolism are molecular contributors to the pathogenesis of Creutzfeldt–Jakob disease Journal of Neuropathology & Experimental Neurology , 75, (8), 755-769

Neuron loss, synaptic decline, and spongiform change are the hallmarks of sporadic Creutzfeldt–Jakob disease (sCJD), and may be related to deficiencies in mitochondria, energy metabolism, and protein synthesis. To investigate these relationships, we determined the expression levels of genes encoding subunits of the 5 protein complexes of the electron transport chain, proteins involved in energy metabolism, nucleolar and ribosomal proteins, and enzymes of purine metabolism in frontal cortex samples from 15 cases of sCJD MM1 and age-matched controls. We also assessed the protein expression levels of subunits of the respiratory chain, initiation and elongation translation factors of protein synthesis, and localization of selected mitochondrial components. We identified marked, generalized alterations of mRNA and protein expression of most subunits of all 5 mitochondrial respiratory chain complexes in sCJD cases. Expression of molecules involved in protein synthesis and purine metabolism were also altered in sCJD. These findings point to altered mRNA and protein expression of components of mitochondria, protein synthesis machinery, and purine metabolism as components of the pathogenesis of CJD.

JTD Keywords: Creutzfeldt–Jakob disease, Electron transport chain, Mitochondria, Oxidative phosphorylation, Protein synthesis, Purine.

Llorens, Franc, Hummel, Manuela, Pastor, Xavier, Ferrer, Anna, Pluvinet, Raquel, Vivancos, Ana, Castillo, Ester, Iraola, Susana, Mosquera, Ana M., Gonzalez, Eva, Lozano, Juanjo, Ingham, Matthew, Dohm, Juliane C., Noguera, Marc, Kofler, Robert, Antonio del Rio, Jose, Bayes, Monica, Himmelbauer, Heinz, Sumoy, Lauro, (2011). Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis BMC Genomics 12, 326

Background: Epidermal Growth Factor (EGF) is a key regulatory growth factor activating many processes relevant to normal development and disease, affecting cell proliferation and survival. Here we use a combined approach to study the EGF dependent transcriptome of HeLa cells by using multiple long oligonucleotide based microarray platforms (from Agilent, Operon, and Illumina) in combination with digital gene expression profiling (DGE) with the Illumina Genome Analyzer. Results: By applying a procedure for cross-platform data meta-analysis based on RankProd and GlobalAncova tests, we establish a well validated gene set with transcript levels altered after EGF treatment. We use this robust gene list to build higher order networks of gene interaction by interconnecting associated networks, supporting and extending the important role of the EGF signaling pathway in cancer. In addition, we find an entirely new set of genes previously unrelated to the currently accepted EGF associated cellular functions. Conclusions: We propose that the use of global genomic cross-validation derived from high content technologies (microarrays or deep sequencing) can be used to generate more reliable datasets. This approach should help to improve the confidence of downstream in silico functional inference analyses based on high content data.

JTD Keywords: Gene-expression measurements, Quality-control maqc, Cancer-cell-lines, Real-time pcr, Oligonucleotide microarrays, Phosphorylation dynamics, In-vivo, Networks, Signal, Technologies