Meta-analysis of microarray-derived data from PACAP-deficient adrenal gland in vivo and PACAP-treated chromaffin cells identifies distinct classes of PACAP-regulated genes

Abstract

Initial PACAP-regulated transcriptomes of PACAP-treated cultured chromaffin cells, and the adrenal gland of wild-type versus PACAP-deficient mice, have been assembled using microarray analysis. These were compared to previously acquired PACAP-regulated transcriptome sets from PC12 cells and mouse central nervous system, using the same microarray platform. The Ingenuity Pathways Knowledge Base was then employed to group regulated transcripts into common first and second messenger regulatory clusters. The purpose of our meta-analysis was to identify sets of genes regulated distinctly or in common by the neurotransmitter/neurotrophin PACAP in specific physiological contexts. Results suggest that PACAP participates in both the basal differentiated expression, and the induction upon physiological stimulation, of distinct sets of transcripts in neuronal and endocrine cells. PACAP in both developmental and acute regulatory paradigms acts on target genes also regulated by either TNFalpha or TGFbeta, two first messengers acting on transcription mainly through NFkappaB and Smads, respectively.

Pituitary Adenylate Cyclase-Activating Polypeptide and Its Receptors: 20 Years after the Discovery

“…Microarray studies have provided a comprehensive view of the genes activated by PACAP in PC12 cells (Vaudry et al, 2002b;Grumolato et al, 2003b;Ishido and Masuo, 2004;Eiden et al, 2008;Ravni et al, 2008). Many of the known genes and proteins regulated by PACAP are associated with neuritogenesis [i.e., DISC1-binding zinc-finger protein or early growth response 1 Ravni et al, 2008)], hormone secretion [i.e., selenoprotein T (Grumolato et al, 2003a(Grumolato et al, , 2008], cell growth [i.e., growth arrest specific 1 or cyclin B2 (Vaudry et al, 2002b)], and cell survival [i.e., caspase3 or serum/glucocorticoid regulated kinase (Lebon et al, 2006;Ravni et al, 2006aRavni et al, , 2008Samal et al, 2007)]. It should be pointed out, however, that during differentiation, PACAP probably synergizes with other growth factors to induce the full functional phenotype of neuroendocrine cells (Lazarovici and Fink, 1999;Hashimoto et al, 2000a;Sakai et al, 2001;Vaudry and Taupenot, 2002;Beaujean et al, 2003;Greene and Angelastro, 2005).…”

Acute Response of the Hippocampal Transcriptome Following Mild Traumatic Brain Injury After Controlled Cortical Impact in the Rat

“…A first-messenger network analysis was conducted using IPA to identify candidate upstream regulators of the CCI-induced transcripts altered in expression following mCCI, using internal quality and post hoc bioinformatic controls established for transcriptome analysis in our earlier studies, and adapted for the Affymetrix Rat 2.0 ST Array (Ait-Ali et al 2010;Chen et al 2006;Eiden et al 2008;Samal et al 2007;Samal and Eiden 2008). Of the dataset of 193 upregulated 1 transcripts uploaded into the IPA tool, 190 were recognized by IPA and used as gene target molecules in the IPA first-messenger network analysis.…”

Neuropeptides, Growth Factors, and Cytokines: A Cohort of Informational Molecules Whose Expression Is Up-Regulated by the Stress-Associated Slow Transmitter PACAP in Chromaffin Cells

“…We noticed in our previous studies that secretory proteins known to be present, and in some cases induced by PACAP, in primary chromaffin cells were neither expressed, nor induced by PACAP in the PC12 cell line (Vaudry et al 2002; Samal et al 2007; Eiden et al 2008; Ghzili et al 2008). The PC12 cell response to PACAP is a compound one—the initial phase of growth arrest and neurite extension takes the cells to a neuronal phenotype, followed by terminal differentiated into a final neurochemical phenotype (Rausch et al 1988).…”

“…Linear amplification of RNA was performed (Amino Allyl MessageAmp II aRNA Amplification Kit, Ambion, Austin, TX) prior to labeling with Cy3 and Cy5 fluorescent dyes (GE Healthcare UK, Chalfont, Buckinghamshire, England), and microarray hybridization to oligonucleotides arrays consisting of the Qiagen mouse MV3 oligo set with oligonucleotide length generally ~70 nucleotides. General methods for data extraction, normalization, and filtration for quality and dye bias have been summarized in detail previously (Samal et al 2007). Here data from three microarrays were analyzed in the NCI mAdb microarray databasing system after standard deArray M-value correction with allowed quality ratio of 0.3.…”