Regulatory network analysis of Paneth cell and goblet cell enriched gut organoids using transcriptomics approaches.

The epithelial lining of the small intestine consists of multiple cell types, including Paneth cells and goblet cells, that work in cohort to maintain gut health. 3D in vitro cultures of human primary epithelial cells, called organoids, have become a key model to study the functions of Paneth cells and goblet cells in normal and diseased conditions. Advances in these models include the ability to skew differentiation to particular lineages, providing a useful tool to study cell type specific function/dysfunction in the context of the epithelium. Here, we use comprehensive profiling of mRNA, microRNA and long non-coding RNA expression to confirm that Paneth cell and goblet cell enrichment of murine small intestinal organoids (enteroids) establishes a physiologically accurate model. We employ network analysis to infer the regulatory landscape altered by skewing differentiation, and using knowledge of cell type specific markers, we predict key regulators of cell type specific functions: Cebpa, Jun, Nr1d1 and Rxra specific to Paneth cells, Gfi1b and Myc specific for goblet cells and Ets1, Nr3c1 and Vdr shared between them. Links identified between these regulators and cellular phenotypes of inflammatory bowel disease (IBD) suggest that global regulatory rewiring during or after differentiation of Paneth cells and goblet cells could contribute to IBD aetiology. Future application of cell type enriched enteroids combined with the presented computational workflow can be used to disentangle multifactorial mechanisms of these cell types and propose regulators whose pharmacological targeting could be advantageous in treating IBD patients with Crohn's disease or ulcerative colitis.

African swine fever virus infection of porcine aortic endothelial cells leads to inhibition of inflammatory responses, activation of the thrombotic state, and apoptosis.

African swine fever (ASF) is an asymptomatic infection of warthogs and bushpigs, which has become an emergent disease of domestic pigs, characterized by hemorrhage, lymphopenia, and disseminated intravascular coagulation. It is caused by a large icosohedral double-stranded DNA virus, African swine fever virus (ASFV), with infection of macrophages well characterized in vitro and in vivo. This study shows that virulent isolates of ASFV also infect primary cultures of porcine aortic endothelial cells and bushpig endothelial cells (BPECs) in vitro. Kinetics of early and late gene expression, viral factory formation, replication, and secretion were similar in endothelial cells and macrophages. However, ASFV-infected endothelial cells died by apoptosis, detected morphologically by terminal deoxynucleotidyltransferase-mediated dUTP nick end labeling and nuclear condensation and biochemically by poly(ADP-ribose) polymerase (PARP) cleavage at 4 h postinfection (hpi). Immediate-early proinflammatory responses were inhibited, characterized by a lack of E-selectin surface expression and interleukin 6 (IL-6) and IL-8 mRNA synthesis. Moreover, ASFV actively downregulated interferon-induced major histocompatibility complex class I surface expression, a strategy by which viruses evade the immune system. Significantly, Western blot analysis showed that the 65-kDa subunit of the transcription factor NF-kappaB, a central regulator of the early response to viral infection, decreased by 8 hpi and disappeared by 18 hpi. Both disappearance of NF-kappaB p65 and cleavage of PARP were reversed by the caspase inhibitor z-VAD-fmk. Interestingly, surface expression and mRNA transcription of tissue factor, an important initiator of the coagulation cascade, increased 4 h after ASFV infection. These data suggest a central role for vascular endothelial cells in the hemorrhagic pathogenesis of the disease. Since BPECs infected with ASFV also undergo apoptosis, resistance of the natural host must involve complex pathological factors other than viral tropism.

Mechanism of inactivation of NF-kappa B by a viral homologue of I kappa b alpha. Signal-induced release of i kappa b alpha results in binding of the viral homologue to NF-kappa B.

Activation of the nuclear factor kappa B plays a key role in viral pathogenesis, resulting in inflammation and modulation of the immune response. We have previously shown that A238L, an open reading frame from African swine fever virus (ASFV), encoding a protein with 40% homology to porcine I kappa B alpha exerts a potent anti-inflammatory effect in host macrophages, where it down-regulates NF-kappa B-dependent gene transcription and proinflammatory cytokine production. This paper reveals the mechanism of suppression of NF-kappa B activity by A238Lp. A238Lp is synthesized throughout infection as two molecular mass forms of 28 and 32 kDa, and vaccinia-mediated expression of A238L demonstrated that both proteins are produced from a single gene. Significantly, the higher 32-kDa form of A238L, but not the 28-kDa form, interacts directly with RelA, the 65-kDa subunit of NF-kappa B, indicating that the binding is dependent on a post-translational modification. Immunoprecipitation analysis shows the NF-kappa B p65-A238L p32 heterodimer is a separate complex from NF-kappa B-I kappa B alpha, and it resides in the cytoplasm. Moreover, we show that ASFV infection stimulates the NF kappa B signal transduction pathway, which results in the rapid degradation of endogenous I kappa B alpha, although both forms of A238Lp are resistant to stimulus-induced degradation. Using the proteasome inhibitor MG132, we show that when degradation of I kappa B alpha is inhibited, A238Lp binding to NF-kappa B p65 is reduced. The results suggest that the virus exploits its activation of the NF-kappa B pathway to enable its own I kappa B homologue to bind to NF-kappa B p65. Last, we show that synthesis of I kappa B alpha is increased during ASFV infection, indicating RelA-independent transcription of the I kappa B alpha gene.

Differential expression of fibroblast growth factor receptors 1 to 4 and ligand genes in late fetal and early postnatal rat lung.

To characterize fibroblast growth factor (FGF) gene expression in the late fetal (days E18 to E22) and early postnatal lung (days P0 to P28), when the alveolar region undergoes extensive growth and reorganization, we analyzed the expression of four FGF receptors and six ligands. FGF receptor 1 (FGFR1) RNA levels were first low (E18) before rising late in the postnatal period (P28). FGFR2 RNA levels were detected early (at E18) and then increased (E20-P0) before falling (P2) to below later postnatal levels (P6 to P28). FGFR3 RNA levels were low at first (E18) and then increased, with peak levels in the days after birth (P2 to P10). FGFR4 RNA levels, barely detected in fetal lung (E18 to E22), increased at birth (P0) and remained high postnatally (P2 to P28). In fetal lung, FGF2 (basic FGF) RNA expression levels were low and FGF1 (acidic FGF) RNA levels were not detected: low RNA levels of each ligand were detected postnatally (P7 to P28). FGF3 to 5 and FGF7 RNA were not detected in fetal or postnatal lung. With in situ hybridization, predominantly the smooth muscle cells of large vessels expressed FGFR1 and 4 mRNA; the epithelial cells of large airways expressed FGFR1, 2, and 4; and alveolar cells expressed FGFR2, 3, and 4. Analysis of protein expression first identified FGF2 localized to the basement membrane of large airways and branching epithelial buds, to mesenchymal cells associated with buds, to the putative smooth muscle cells of large airways and vessels, and to pleural- and mesenchymal-associated cells (E18). Immediately before birth, this pattern of expression persisted (E20 to E22), with FGF2 also being expressed by putative smooth muscle cells of smaller airways and vessels (E22). After birth (P0 to P28), FGF2 expression remained relatively high in the smooth muscle cells of large and small vessels and in pleural cells; in airway smooth muscle cells and in most cells in the alveolar region, however, although FGF2 expression persisted in some cells, its intensity decreased with time.

Detection of African swine fever virus in infected pig tissues by immunocytochemistry and in sity hybridisation.

The techniques for determining cellular sites of establishment and persistence of African swine fever virus (ASFV) were established in susceptible domestic pigs and the resistant African reservoir hosts, the warthog and bushpig. Detection, both in vitro and in vivo, was achieved by in situ hybridisation and immunocytochemistry, focusing principally on specific probes for vp73, a major capsid protein. Hybridisation of radio-labelled probes for DNA and RNA was relatively insensitive and time consuming whereas hybridisation of non-radioactive DNA probes was quicker and more sensitive. Detection of vp73 protein by immunocytochemistry was as sensitive as non-radioactive DNA hybridisation, offering in addition improved speed, ease and morphology. Both non-radioactive DNA hybridisation and immunocytochemistry were therefore used to detect ASFV DNA and protein in a range of porcine cells infected in vitro with different ASFV isolates. Malta and Malawi isolates infected both alveolar and bone marrow macrophages, but infected negligible numbers of endothelial (< 1%) and kidney cells (IBRS2 cells). Attenuated Uganda isolate, however, infected a high percentage of endothelial cells and IBRS2 cells as well as alveolar and bone marrow macrophages. When used to investigate the cell tropism of ASFV in tissues from pigs infected with the highly virulent Malawi isolate of ASFV, both techniques identified virus principally in cells of the mononuclear phagocytic system. In the lung, double staining revealed that pulmonary intravascular macrophages, but not alveolar macrophages, were infected.

African swine fever: a disease characterized by apoptosis.

The cell tropism, organ distribution and resultant pathology of African swine fever were compared in domestic pigs infected with lethal (Malawi) and sublethal (Malta) isolates of African swine fever virus (ASFV). After infections with both isolates, ASFV was predominantly localized in cells of the mononuclear phagocytic system and was not observed in endothelial cells in lymphoid tissue. More severe tissue destruction and cell depletion, associated with high levels of infected macrophages, were seen in lymphoid tissues from domestic pigs infected with the virulent Malawi isolate compared to the less virulent Malta isolate of ASFV. The abundant lymphocyte death was caused by apoptosis and not necrosis. In the spleen, as early as 3 days post-infection (p.i.), many lymphocytes in the B and T cell areas of the white and red pulp were apoptotic. Apoptosis in the T cells of the periarteriolar lymphoid sheaths in the spleen, however, occurred later, at 5-7 days p.i. In lymph nodes apoptosis was observed in T lymphocytes as early as 4 days p.i. and extended to B lymphocytes in the follicles later in infection. In pigs recovered from infection with the sublethal Malta isolate, virus was found to persist in lymph nodes and tonsils for up to 48 days p.i. and was located in cells, surrounded by apoptotic lymphocytes, in the paracortex of lymph nodes up to 32 days p.i. Taken together, these observations suggest that apoptosis of uninfected lymphocytes was induced by cytokines or apoptotic mediators released from ASFV infected macrophages.

The pathogenesis of African swine fever in the resistant bushpig.

Bushpigs and warthogs are natural reservoir hosts of African swine fever virus (ASFV) in the wild, showing no clinical signs of disease when infected with the same highly virulent isolates of ASFV that induce rapid, haemorrhagic death in domestic pigs. In contrast to domestic pigs, infection of bushpigs with Malawi isolate results in low levels of virus replication and lymphocyte apoptosis within the spleen, and a relatively low spread of virus to other lymphoid tissues. However, at 10 days post-infection, a high degree of apoptosis was seen in B lymphocytes of the B cell follicles in bushpig lymph nodes. Virus infected cells were present amongst the apoptotic B cells of these follicles, suggesting that indirect factors released from ASFV infected macrophages signal surrounding lymphocytes to enter apoptosis. The susceptibility/resistance of domestic pigs/bushpigs to ASFV may serve as a unique veterinary model for the recently emerging haemorrhagic disease of man.

An IkappaB homolog encoded by African swine fever virus provides a novel mechanism for downregulation of proinflammatory cytokine responses in host macrophages.

Cytokines stimulate inflammatory defenses against viral infections. In order to evade host defenses, viruses have developed strategies to counteract antiviral cytokines. African swine fever virus (ASFV) is a large, double-stranded DNA virus that infects macrophages. This study demonstrates that ASFV effectively inhibited phorbol myristic acid-induced synthesis of antiviral, proinflammatory cytokines alpha interferon, tumor necrosis factor alpha, and interleukin-8 in infected macrophages as assessed by enzyme-linked immunosorbent assay and reverse transcriptase PCR. In contrast, levels of mRNA and protein for transforming growth factor beta, an anti-inflammatory cytokine, were increased by ASFV infection, suggesting that ASFV-induced inhibition of cytokine synthesis may be limited to cytokines activated by NFkappaB. An interleukin-8 promoter, containing an NFkappaB enhancer site, driving expression of a luciferase reporter gene was used to show that NFkappaB-dependent transcription was inhibited by the virus and by a cloned ASFV gene, A238L. This gene encodes a protein with homology to IkappaB, the inhibitor of NFkappaB. Electrophoretic mobility shift assay showed that cells expressing the A238L gene inhibited NFkappaB binding to DNA. These results suggest that the A238L gene product interacts with NFkappaB to prevent transcription and downregulate proinflammatory cytokine production. This novel viral evasion strategy encoded in a single IkappaB-like protein may be capable of inhibiting most macrophage NFkappaB-dependent antiviral mechanisms and may provide insights into how ASFV causes a fatal hemorrhagic disease of domestic pigs and a persistent infection in the African warthog, which is its natural permissive host.

Regulation of basic fibroblast growth factor mRNA expression in rat C6 glioma cells.

Multiple basic fibroblast growth factor (bFGF) mRNAs are transcribed in rat brain at 6.0, 3.7, 2.5, 1.8, 1.6, 1.4, and 1.0 kb. These seven transcripts are also seen in Rat-1 fibroblasts and ras-transformed Rat-1 fibroblasts in culture. However, only a single bFGF transcript at 6.0 kb is detectable in the rat astrocytoma cell line, C6, and this mRNA is identical to that seen in a primary culture of cortical astrocytes. C6 glioma cells also transcribe message for FGF receptor 1 (FR1), suggesting possible autocrine growth by these cells. Growth factor activity in a C6 cell lysate was characterized by heparin affinity chromatography and Western blot analysis using an anti-bFGF antibody. Proteins of 18, 21.5, and 22 kDa were detected in C6 cells, indicating that the 6.0-kb mRNA is translated into the three characteristic bFGF proteins. Rat-1 fibroblasts also synthesize bFGF proteins of identical molecular weight. The small transcripts detected in brain probably represent bFGF or FGF-related mRNAs in cell types other than glia, such as fibroblasts, endothelial cells, or neurons. In cultured C6 cells, bFGF protein levels are highest in confluent, quiescent cells, whereas mRNA levels are low. Addition of serum, phorbol ester, or cycloheximide to both C6 cells and fibroblasts induces the level bFGF mRNA transcripts 10-fold after 1-4 h. This rapid induction after cell activation indicates that bFGF is an early response gene. Therefore, even though there are abundant intracellular stores of the factor, the transcriptional activation seen after mitogenic activation of cells implies that de novo bFGF mRNA synthesis is an important part of the mitogenic response.

Eosinophils expressing heparin-binding EGF-like growth factor mRNA localize around lung microvessels in pulmonary hypertension.

In pulmonary hypertension, induced in rats breathing high oxygen at normobaric pressure, vascular cell hypertrophy and hyperplasia thicken the walls of lung microvessels (15-100 microns in diameter). Over a 28-day time course, new contractile cells develop from intimal precursor smooth muscle cells, which include intermediate cells and interstitial fibroblasts. Cell labeling studies in vivo have shown that these cells proliferate more than other vascular cells and that most of this activity occurs between 4 and 7 days of hyperoxia. The growth factors responsible for this proliferation are unknown. In the present study, we investigate the expression of mRNA for the epidermal growth factor (EGF)-related protein, heparin-binding EGF-like growth factor (HB-EGF), a newly discovered mitogen for fibroblasts and smooth muscle cells. Northern analysis shows HB-EGF mRNA levels to be low in normal lung but increased 100-fold by day 7 of hyperoxia. In situ hybridization identifies a select group of cells expressing HB-EGF mRNA. In normal lung, hybridizing cells are randomly distributed in the alveolar wall and space. By day 7, they increase in number and cluster around the microvessels. Histochemical techniques identify cells expressing HB-EGF mRNA as eosinophils.

Differential regulation of the genes encoding platelet-derived growth factor receptor and its ligand in rat lung during microvascular and alveolar wall remodeling in hyperoxia.

The growth factors that operate while the lung remodels in hyperoxia are not known. At the lung periphery, high oxygen levels cause cell hypertrophy and hyperplasia, and this results in a thickening of the alveolar-capillary membrane and the walls of its associated microvessels. The present study examines gene expression of platelet-derived growth factor (PDGF) receptor and its ligand in this region of the lung of rats breathing 87% oxygen and compares this with the levels of expression in normal lung. In similar peripheral lung tissue, the proliferative response of specific cell populations has been assessed by [3H]thymidine incorporation and autoradiography. Normal lung expresses PDGF alpha-receptor subunit transcripts of 6.5 and 4.7 kb and PDGF beta-receptor transcripts of 5.5 and 4.5 kb. PDGF A-chain transcripts of 2.9, 2.3, and 1.7 kb are also expressed, each being at 10-fold higher levels than the single 3.5-kb transcript detected for PDGF B-chain. Within hours of breathing high concentrations of oxygen, mRNA levels change rapidly for the PDGF receptor subunits. These levels return to normal after 1 day and then decline over the next 28 days of exposure. PDGF A-chain mRNA increases 12 to 18 h after exposure, but then returns to normal levels. It is the PDGF B-chain mRNA that responds most to hyperoxia by increasing 10-fold on day 3. This increase immediately precedes the proliferative response on day 4 of microvascular adventitial fibroblasts, precursor smooth muscle cells, and epithelial cells but not smooth muscle cells, which do not proliferate until day 28.

Three forms of rat basic fibroblast growth factor are made from a single mRNA and localize to the nucleus.

The molecular weight of rat basic fibroblast growth factor is predicted to be 18 kDa when the amino acid sequence is read from the single AUG initiation codon found in the cDNA. DNA sequencing upstream of this AUG codon indicated, however, that there was an extended open reading frame. In vitro translation of the rat cDNA for basic FGF gave three proteins of 18.0, 21.5, and 22.0 kDa in equal abundance. The same proteins were produced in vivo by COS cells transfected with the rat cDNA. Deletion of 81 base pairs from the reading frame upstream of the AUG codon resulted in the expression of only one protein observed at 18.0 kDa. These results indicated that the 22.0 and 21.5 kDa forms of rat basic FGF were formed when translation initiates at the alternative upstream non-AUG codons. Rat cell lines and tissues were found to express all three forms of basic FGF protein. The cDNA was used to analyze the subcellular distribution of the different forms of rat basic FGF. Subcellular fractionation and immunofluorescence of transfected COS cells showed that all three forms of the protein localized preferentially in the nucleus. Expression of a truncated cDNA from which 81 base pairs (27 amino acids) of the upstream reading frame had been deleted, showed localization of the smaller form of bFGF alone in the nucleus. These results demonstrated that although the amino acids that were deleted from the N-terminus of rat basic fibroblast growth factor have a sequence characteristic of nuclear localization motifs, they are not obligatory for the transport of the growth factor into the nucleus. Nuclear extracts taken from transfected cells also contained two smaller proteins of 16 and 12 kDa that were detected by Western blot analysis. It is possible that these are proteolytic products of bFGF.

Temporal, differential and regional expression of mRNA for basic fibroblast growth factor in the developing and adult rat brain.

The expression of basic fibroblast growth factor (bFGF) mRNA and bFGF receptor mRNA was investigated in developing rat brain. In embryonic rat brain days 13-21 (E13-E21), an abundant 1.8 kb bFGF mRNA was detected. Expression of 1.8 kb bFGF mRNA was the highest at E17 to E19 and was relatively undetectable 20 days after birth. However, very little mitogenic activity was associated with prenatal brain. On the other hand, multiple bFGF mRNA species of 6.0, 3.7, 2.5, 1.8, 1.6, 1.4 and 1.0 kb were detected in total adult rat brain and a significant amount of mitogenic activity was present. Differential and spatial bFGF mRNA expression was found in different parts of developing rat brain. Embryonic hypothalamus was found to contain the 1.8 kb bFGF mRNA while the 6.0 kb bFGF mRNA transcript was predominant in adult hypothalamus. Adult pituitary and cortex transcribed the lower molecular weight mRNAs but not the 6.0 kb mRNA. Expression of high-affinity bFGF receptor (flg) mRNA was found to be temporally regulated. flg 4.3 kb mRNA expression was high in embryonic rat brain (E13-E19). There appears to be coordinate expression between the 1.8 kb bFGF mRNA and flg. These results suggest that the expression of basic FGF mRNA is complex since it is both temporally and differentially regulated with different species being expressed at different times in development.

Cloning and characterization of the human beta-glucuronidase gene.

We have isolated a cosmid clone that contains GUSB, the human gene encoding beta-glucuronidase. The 21-kb gene contains 12 exons ranging from 85 to 376 bp in length. Exon 6 corresponds to the 153-bp deletion in the shorter of two types of cDNAs reported earlier, supporting the hypothesis that this cDNA arose by alternate splicing leading to exon skipping. The insert contains 4.2 kb of sequence upstream from the first exon and 6 kb 3' of the last exon. The clone expresses human beta-glucuronidase in stably transformed rat XCtk- cells. Comparison of the human gene organization with that recently reported for the murine beta-glucuronidase gene revealed that the intron/exon boundaries are identical. In the splice junctions, the most highly conserved regions are those identified as consensus sequences, and these are at least as highly conserved as bases encoding the translated portion of the gene.

Increased levels of basic fibroblast growth factor (bFGF) following focal brain injury.

Focal injury to the mammalian central nervous system (CNS) results in a cascade of cellular responses - including glial and capillary proliferation and neural sprouting - that contribute to the repair of neural tissue and to the recovery of neurological function. Fibroblast growth factors (FGFs) are heparin-binding polypeptides with potent trophic effects on CNS glia, endothelia, and neurons; both acidic and basic forms are found in the mammalian CNS. We used heparin-affinity chromatography coupled to Balb/c 3T3 mitogenic assay to show a marked increase in levels of bioactive FGFs in tissue surrounding focal cortical lesions of the mature rat brain at one week after injury. Heparin-affinity HPLC showed that this increase was due to a large increase in levels of basic FGF (bFGF), and a much smaller increase in levels of acidic FGF (aFGF) after injury. Increased bFGF bioactivity was paralleled by increased levels of immunoreactive bFGF, as assessed by Western blotting techniques. Increased bFGF levels may play an important role in the cascade of cellular reactions occurring after focal brain injury.

Neurofibrosarcoma as a complication of von Recklinghausen neurofibromatosis.

Neurofibrosarcoma (NFS), which is rare in the general population, occurs with excessive frequency among patients with von Recklinghausen neurofibromatosis (NF-1). Among 693 patients with NF-1 enrolled in the Baylor NF Program, 24 patients (3.5%) developed NFS or one of its variant forms. Nine of the twenty-four patients developed NFS within 3-94 months after enrolling in the Program for other reasons. Focus on these 9 patients alone suggests that the relative risk for patients with NF-1 developing NFS is 10-10,000 times greater than for the general population. Also, in NFS cohorts, patients with NF-1 are almost twice as likely to be under 30 years of age.

Rat liver beta-glucuronidase. cDNA cloning, sequence comparisons and expression of a chimeric protein in COS cells.

A cDNA for rat liver beta-glucuronidase was isolated, its sequence determined and its expression after transfection into COS cells studied. The deduced amino acid sequence of the rat liver clone showed 77% homology with that from the cDNA for human placental beta-glucuronidase and 47% homology with that deduced from the cDNA for Escherichia coli beta-glucuronidase. Several differences were found between the cDNA from rat liver and that previously reported from rat preputial gland. Only one change leads to an amino acid difference in the mature enzyme. A chimeric clone was constructed by using a fragment encoding the first 18 amino acid residues of the signal sequence from the human placental cDNA clone and a fragment from the rat clone encoding four amino acid residues of the signal sequence, all 626 amino acid residues of the mature rat enzyme, and all of the 3' untranslated region. After transfection into COS cells the chimeric clone expressed beta-glucuronidase activity that was specifically immunoprecipitated by antibody to rat beta-glucuronidase. The Mr value of 76,000 of the expressed gene product was characteristic of the glycosylated rat enzyme. It was proteolytically processed in COS cells to Mr 75,000 6 h after metabolic labelling. At least 50% of the expressed enzyme was secreted at 60 h post-transfection, but the secreted enzyme did not undergo proteolytic processing. These results provide evidence that the partial cDNA isolated from a rat liver library contains the complete coding sequence for the mature rat liver enzyme and that the chimeric signal sequence allows normal biosynthesis and processing of the transfected rat liver enzyme in COS cells.