Enriched biochemical pathways significantly altered in HIV-1Tg rats compared to F344 control rats in the PFC, HIP, and STR.

<p>These pathways were divided into three main groups directly related to immune responses (yellow bars), neurotransmission (blue bars), and neuroplasticity (white bars).</p

Illustration of top two pathways and related genes restored by nicotine in the dorsal striatum (STR) of HIV-1Tg rats.

<p>Restored genes and pathways in saline-treated (HIV_Sal, left panel) and nicotine-treated (HIV_Nic, right panel) HIV-1Tg rats are shown. Compared with saline-treated F344 (F344_Sal) control rats, genes shown in red were increased, those shown in green were decreased in expression, and those in gray showed similar mRNA expression. Cacn, Ca²⁺ channel; CHP, ERK, mitogen-activated protein kinase; IDH, isocitrate dehydrogenase; LETM1, leucine zipper-EF-hand-containing transmembrane protein 1; MDH1, malate dehydrogenase 1, NAD (soluble); PLAA, phospholipase A2, activating protein; PPL2, phospholipase 2; RAP1B, RAS related protein 1b; ROS, reactive oxygen species.</p

Illustration of top two pathways and related genes restored by nicotine in the prefrontal cortex (PFC) of HIV-1Tg rats.

<p>Restored genes and pathways in saline-treated (HIV_Sal, left panel) and nicotine-treated (HIV_Nic, right panel) HIV-1Tg rats are shown. Compared with saline-treated F344 (F344_Sal) control rats, genes shown in red were increased, those shown in green were decreased, and those in gray had similar mRNA expression. APC, adenomatous polyposis coli; AXIN1, Axin-1; EPHB1, Eph receptor B1; Frizzled, frizzled receptor; GNAO1, guanine nucleotide-binding protein G(o) subunit alpha; GPCR, G protein-coupled receptor; GSK, glycogen synthase kinase; JNK, c-Jun N-terminal kinase, LRP5/6, low density lipoprotein receptor-related protein; MAPK8IP2, mitogen-activated protein kinase 8-interacting protein 2; RAC1, ras-related C3 botulinum toxin substrate 1; RHO, rhodopsin; SRC, v-src sarcoma; TCF, transcription factor; WNT5A, wingless-related MMTV integration site 5A; WNT7A, wingless-type MMTV integration site 7A.</p

Pathways significantly restored by nicotine in the prefrontal cortex (PFC), dorsal hippocampus (HIP), and dorsal striatum (STR) of HIV-1Tg rats.

<p>P-value was calculated using Fisher’s exact test, which denotes the probability of overlap between the pathways and the input genes.</p

Transcriptome Sequencing of Gene Expression in the Brain of the HIV-1 Transgenic Rat

<div><p>The noninfectious HIV-1 transgenic (HIV-1Tg) rat was developed as a model of AIDs-related pathology and immune dysfunction by manipulation of a noninfectious HIV-1^gag-pol virus with a deleted 3-kb <i>Sph</i>I<i>-Msc</i>I fragment containing the 3′ -region of <i>gag</i> and the 5′ region of <i>pol</i> into F344 rats. Our previous studies revealed significant behavioral differences between HIV-1Tg and F344 control rats in their performance in the Morris water maze and responses to psychostimulants. However, the molecular mechanisms underlying these behavioral differences remain largely unknown. The primary goal of this study was to identify differentially expressed genes and enriched pathways affected by the <i>gag-pol</i>-deleted HIV-1 genome. Using RNA deep sequencing, we sequenced RNA transcripts in the prefrontal cortex, hippocampus, and striatum of HIV-1Tg and F344 rats. A total of 72 RNA samples were analyzed (i.e., 12 animals per group × 2 strains × 3 brain regions). Following deep-sequencing analysis of 50-bp paired-end reads of RNA-Seq, we used Bowtie/Tophat/Cufflinks suites to align these reads into transcripts based on the Rn4 rat reference genome and to measure the relative abundance of each transcript. Statistical analyses on each brain region in the two strains revealed that immune response- and neurotransmission-related pathways were altered in the HIV-1Tg rats, with brain region differences. Other neuronal survival-related pathways, including those encoding myelin proteins, growth factors, and translation regulators, were altered in the HIV-1Tg rats in a brain region-dependent manner. This study is the first deep-sequencing analysis of RNA transcripts associated the HIV-1Tg rat. Considering the functions of the pathways and brain regions examined in this study, our findings of abnormal gene expression patterns in HIV-1Tg rats suggest mechanisms underlying the deficits in learning and memory and vulnerability to drug addiction and other psychiatric disorders observed in HIV-positive patients.</p> </div

Detected interactions and clusters of enriched pathways in the HIP region in HIV-1 rats.

<p>All pathways identified by IPA software, including both significant and insignificant pathways, are interrelated and can be divided into two functional groups, indicated by circles.</p

Summary of represented genes and enriched biochemical pathways related to neurobehavioral deficits in the HIV-1Tg rat.

<p>Red represents up-regulation, whereas green represents down-regulation in mRNA expression in the PFC¹, HIP², and STR³ of HIV-1Tg rats. Numbers with strikethroughs reflect marginal significance (0.005Table S1). Abbreviations: Aspa = aspartoacylase; Camk2b = calcium/calmodulin-dependent protein kinase II beta; Ccl2 =  chemokine ligand 2; Ccl6 =  chemokine ligand 6; Chrna4 =  neuronal acetylcholine receptor subunit alpha-4; Cldn = Claudin 1; Cnp = 2,3-cyclic-nucleotide 3-phosphodiesterase; Drd4 =  D(4) dopamine receptor; Ephb1 =  EPH receptor B1; Fgf9 =  fibroblast growth factor 9; Fgf13 =  fibroblast growth factor 13; Gabbr2, Gnal = guanine nucleotide binding protein, alpha activating activity polypeptide; Grid1 =  glutamate receptor, ionotropic, delta1; Grin2a = NMDA receptor subunit epsilon-1; HDGF = hepatoma-derived growth factor; Il1rap = interleukin 1 receptor accessory protein; Insr = insulin receptor; Irak4, interleukin-1 receptor-associated kinase 4; Irf5 =  interferon regulatory factor 5; Irf7 =  interferon regulatory factor 7; Mag = myelin-associated glycoprotein; Mbp = myelin-associated glycoprotein; Mog = myelin-oligodendrocyte glycoprotein; Mpz = myelin protein P0; Npm1 =  nucleophosmin; Opalin = oligodendrocytic myelin paranodal and inner loop protein; PDGFb = platelet-derived growth factor beta polypeptide; Ppm1l = protein phosphatase 1L; Ppp1r14a = protein phosphatase 1 regulatory subunit 14A; Ppp2ca = serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform; Rl39 =  ribosomal protein L39; Rpl13 =  ribosomal protein L13; Rpl35 =  ribosomal protein L35; Rpl37 =  ribosomal protein L37; Rps8 =  ribosomal protein S8; Rps19 =  ribosomal protein S19; Rps24 =  ribosomal protein S24; Rtp4 =  receptor transporter protein 4; Slc1a7 =  glutamate transporter, member 7; Wnt5a = wingless-type MMTV integration site family, 5A; Wnt5b = wingless-type MMTV integration site family, 5B.</p

Percentage of mapped reads onto the regions of exons, introns, 5′ -UTRs, 3′ -UTRs, and 10-kb transcribed region upstream and downstream from coding regions in the PFC, STR, and HIP of HIV-1Tg and F344 rats.

<p>Percentage of mapped reads onto the regions of exons, introns, 5′ -UTRs, 3′ -UTRs, and 10-kb transcribed region upstream and downstream from coding regions in the PFC, STR, and HIP of HIV-1Tg and F344 rats.</p

Illustration of top two pathways and related genes restored by nicotine in the dorsal hippocampus (HIP) of HIV-1Tg rats.

<p>Restored genes and pathways in saline-treated (HIV_Sal, left panel) and nicotine-treated (HIV_Nic, right panel) HIV-1Tg rats are shown. Compared with saline-treated F344 (F344_Sal) control rats, genes shown in red were increased, those shown in green were decreased, and those in gray had similar mRNA expression. AKT, v-akt murine thymoma viral oncogene homolog; CABP1, calcium-binding protein 1;Cacn, Ca²⁺ channel; CALM, calmodulin; CALM3, calmodulin 3; CAMK, calcium/calmodulin-dependent protein kinase; CREB, cAMP-responsive element-binding protein; BDNF, brain-derived neurotrophic factor; ERK, mitogen-activated protein kinase; G(olf), guanine nucleotide-binding protein complex, olfactory type; GNAL, guanine nucleotide-binding protein, alpha stimulating, olfactory type; GPX, glutathione peroxidase; GSH, glutathione; GSR, glutathione reductase; GST, glutathione-S-transferase; GSSG, glutathione disulfide; NTRK2, neurotrophic tyrosine kinase receptor, type 2; PKA, protein kinase A; PLCH1, phospholipase C, eta 1; POLR2C, polymerase (RNA) II polypeptide C; ROH, reduction product of reactive oxygen species; ROS, reactive oxygen species.</p

Comparison of the number of transcripts identified in the three brain regions in HIV-1Tg (A) and F344 (B) rats.

<p>Comparison of the number of transcripts identified in the three brain regions in HIV-1Tg (A) and F344 (B) rats.</p