Cellular-resolution gene expression profiling in the neonatal marmoset brain reveals dynamic species- and region-specific differences.

Precise spatiotemporal control of gene expression in the developing brain is critical for neural circuit formation, and comprehensive expression mapping in the developing primate brain is crucial to understand brain function in health and disease. Here, we developed an unbiased, automated, large-scale, cellular-resolution in situ hybridization (ISH)-based gene expression profiling system (GePS) and companion analysis to reveal gene expression patterns in the neonatal New World marmoset cortex, thalamus, and striatum that are distinct from those in mice. Gene-ontology analysis of marmoset-specific genes revealed associations with catalytic activity in the visual cortex and neuropsychiatric disorders in the thalamus. Cortically expressed genes with clear area boundaries were used in a three-dimensional cortical surface mapping algorithm to delineate higher-order cortical areas not evident in two-dimensional ISH data. GePS provides a powerful platform to elucidate the molecular mechanisms underlying primate neurobiology and developmental psychiatric and neurological disorders.

Digital gene atlas of neonate common marmoset brain.

Interest in the common marmoset (Callithrix jacchus) as a primate model animal has grown recently, in part due to the successful demonstration of transgenic marmosets. However, there is some debate as to the suitability of marmosets, compared to more widely used animal models, such as the macaque monkey and mouse. Especially, the usage of marmoset for animal models of human cognition and mental disorders, is still yet to be fully explored. To examine the prospects of the marmoset model for neuroscience research, the Marmoset Gene Atlas (https://gene-atlas.bminds.brain.riken.jp/) provides a whole brain gene expression atlas in the common marmoset. We employ in situ hybridization (ISH) to systematically analyze gene expression in neonate marmoset brains, which allows us to compare expression with other model animals such as mouse. We anticipate that these data will provide sufficient information to develop tools that enable us to reveal marmoset brain structure, function, cellular and molecular organization for primate brain research.

BTBD3 controls dendrite orientation toward active axons in mammalian neocortex.

Experience-dependent structural changes in the developing brain are fundamental for proper neural circuit formation. Here, we show that during the development of the sensory cortex, dendritic field orientation is controlled by the BTB/POZ domain-containing 3 (BTBD3). In developing mouse somatosensory cortex, endogenous Btbd3 translocated to the cell nucleus in response to neuronal activity and oriented primary dendrites toward active axons in the barrel hollow. Btbd3 also directed dendrites toward active axon terminals when ectopically expressed in mouse visual cortex or normally expressed in ferret visual cortex. BTBD3 regulation of dendrite orientation is conserved across species and cortical areas and shows how high-acuity sensory function may be achieved by the tuning of subcellular polarity to sources of high sensory activity.

A case report of a spontaneous gastrointestinal stromal tumor (GIST) occurring in a F344 rat.

We report a case of gastrointestinal stromal tumor (GIST) that developed in a male F344 rat at week 101 of an experiment in a carcinogenicity study. Macroscopically, the primary tumor, which measured 1 cm in diameter, involved the submucosal tissue of the forestomach at the lesser curvature extending to the glandular stomach and esophagus. Histopathologically, the tumor was composed of neoplastic cells with small- to medium-sized spindle-shaped single nuclei and fibrillary cytoplasm lacking distinct cell borders. It invaded extensively into the tunica muscularis and subserosa, further extending to the lamina propria mucosa and serosal surface. A few densely proliferating portions showed a tendency to storiform pattern. Metastatic tumor nodules were found in the liver, spleen, and femur bone marrow, with multiple nodules, up to 1 cm in diameter, apparent in the liver. Immunohistochemically, diffuse, but weak cytoplasmic immunoreactivity for KIT was evident, and most neoplastic cells also exhibited strong immunoreactivity for a -smooth muscle actin and vimentin. Sparse nuclear S-100-immunoreactive cells were further observed, but none of neoplastic cells were immunoreactive for CD34, caldesmon, desmin, cytokeratin, or synaptophysin. Collectively, these features meet the criteria for a GIST, with limited potential for differentiation to smooth muscle and neural cells.

Methacarn fixation--effects of tissue processing and storage conditions on detection of mRNAs and proteins in paraffin-embedded tissues.

In this study, we examined suitable conditions for tissue fixation with methacarn and ethanol dehydration and storage of paraffin-embedded tissues (PETs) on gene expression analysis. With fixation and dehydration of rat liver tissues for up to 16 h (overnight) and 1 week, respectively, at 4 degrees C, integrity of extracted total RNAs and polypeptides did not vary, the former integrity being constantly lower than that with unfixed frozen tissue, while protein yield was slightly reduced with increasing dehydration. Retained expression levels of mRNAs and proteins were mostly unaffected by the period of fixation but slightly fluctuated with the length of dehydration. When PETs were stored for up to 12 months, integrity of both total RNAs and polypeptides was retained at 4 degrees C but reduced at room temperature. Reduced expression levels of mRNAs and proteins were also noted by storage at room temperature after 12 and 3 months, respectively. However, neither tissue processing nor storage affected variability in either mRNA or protein levels among samples. Thus, the results suggest that, for gene expression analysis, tissues can be fixed with methacarn and dehydrated for at least 1 day and 1 week, respectively, and PETs can be stored for at least 12 months, but a temperature of 4 degrees C is preferable.

Effects of TNFalpha on the growth and sensitivity to cytosine arabinoside of blast progenitors in acute myelogenous leukemia with special reference to the role of NF-kappaB.

Leukemic blasts in acute myelogenous leukemia (AML) are derived from a minor population of cells called blast progenitors. Hematopoietic growth factors (HGFs) stimulate their growth and simultaneously sensitize them to cytosine arabinoside (Ara-C), a cell-cycle-specific cytotoxic drug. Since tumor necrosis factor alpha (TNFalpha) modifies HGF activities, we examined the effects of TNFalpha in combination with HGFs on in vitro growth and Ara-C sensitivity of AML blast progenitors in patient samples. TNFalpha variably affected HGF-supported colony formation and the self-renewal of blast progenitors. However, the combination of TNFalpha with IL-3 uniformly rendered blast progenitors more resistant to Ara-C irrespective of whether TNFalpha suppressed or augmented IL-3-supported growth, indicating that TNFalpha regulates the Ara-C sensitivity of leukemic progenitors independently of their cell cycle status. Since nuclear factor-kappaB (NF-kappaB) is activated by TNFalpha and induces expression of prosurvival genes, effects of the antisense oligodeoxynucleotides to NF-kappaB subunits, p65 and p50, were examined. Antisense oligodeoxynucleotides sensitized HL60 cells to Ara-C but rendered leukemic progenitors in patient samples even more resistant to Ara-C in the presence of TNFalpha and IL-3 in combination, indicating that NF-kappaB is involved in the Ara-C sensitivity of leukemic blast progenitors but may exert opposite dual functions, namely protection from and induction of apoptosis, under different conditions.

Analysis of gene expression patterns during glucocorticoid-induced apoptosis using oligonucleotide arrays.

To determine the genes responsible for mediating the effects of glucocorticoids (GCs) on leukemic cells, transcriptional changes in GC-sensitive human pre-B leukemia 697 cells during GC-induced apoptosis were monitored using oligonucleotide microarrays. To circumvent the challenge of recovering mRNAs from dying cells, we compared the pattern of gene expression with that of 697 cells protected from apoptosis by transfection with bcl-2. Of the 12,000 genes examined for their response to GC, 93 genes were induced and 28 genes were repressed, many of which are known to be implicated in signal transduction, growth arrest, and transcription. These included the signal transduction-related genes encoding SOCS1, SOCS2, FKBP51, DSCR1, p56lck, and four protein kinase phosphatases. Growth arrest-related genes encoding p19(INK4d) and several Myc inhibitors were induced in response to the GC treatment. Anti-proliferative- or apoptosis-related genes encoding BTG1, BTG2, and granzyme A were also found to be transcriptionally up-regulated by GC. In addition, the regulation of genes encoding the glucocorticoid receptor and steroid receptor coactivator-1 suggested autoregulation of a GC-mediated signaling pathway.