Sini Junttila

Alternate pathways for Bcl6-mediated regulation of B cell to plasma cell differentiation

The transcription factor Bcl6 regulates germinal center formation and differentiation of B cells into high‐affinity antibody‐producing plasma cells. The direct double‐negative regulatory circuit between Bcl6 and Blimp‐1 is well established. We now reveal alternative mechanisms for Bcl6‐mediated regulation of B‐cell differentiation to plasma cells and show with DT40 cells that Bcl6 directly promotes the expression of Bach2, a known suppressor of Blimp‐1. Moreover, Bcl6 suppresses Blimp‐1 expression through direct binding to the IRF4 gene, as well as by promoting the expression of MITF, a known suppressor of IRF4. We also provide evidence that Bcl6 is needed for the expression of AID and UNG, the indispensable proteins for somatic hypermutation and class‐switch recombination, and UNG appears to be a direct Bcl6 target. Our findings reveal a complex regulatory network in which Bcl6 acts as a key element dictating the transition of DT40 B cells to plasma cells.

Differential Promoter Methylation of Macrophage Genes Is Associated With Impaired Vascular Growth in Ischemic Muscles of Hyperlipidemic and Type 2 Diabetic Mice Genome-Wide Promoter Methylation Study

RATIONALE Hyperlipidemia and type 2 diabetes mellitus (T2DM) severely impair adaptive vascular growth responses in ischemic muscles. This is largely attributed to dysregulated gene expression, although details of the changes are unknown. OBJECTIVE To define the role of promoter methylation in adaptive vascular growth in hyperlipidemia (LDLR(-/-)ApoB(100/100)) and T2DM (IGF-II/LDLR(-/-)ApoB(100/100)) mouse models of hindlimb ischemia. METHODS AND RESULTS Unilateral hindlimb ischemia was induced by ligating femoral artery. Perfusion was assessed using ultrasound, and capillary and arteriole parameters were assessed using immunohistochemistry. Genome-wide methylated DNA sequencing was performed with DNA isolated from ischemic muscle, tissue macrophages (Mϕs), and endothelial cells. Compared with the controls, hyperlipidemia and T2DM mice showed impaired perfusion recovery, which was associated with impaired angiogenesis and arteriogenesis. Genome-wide proximal promoter DNA methylation analysis suggested differential patterns of methylation in Mϕ genes in ischemic muscles. Classically activated M1-Mϕ gene promoters, including Cfb, Serping1, and Tnfsf15, were significantly hypomethylated, whereas alternatively activated M2-Mϕ gene promoters, including Nrp1, Cxcr4, Plxnd1, Arg1, Cdk18, and Fes, were significantly hypermethylated in Mϕs isolated from hyperlipidemia and T2DM ischemic muscles compared with controls. These results combined with mRNA expression and immunohistochemistry showed the predominance of proinflammatory M1-Mϕs, compared with anti-inflammatory and proangiogenic M2-Mϕs in hyperlipidemia and T2DM ischemic muscles. CONCLUSIONS We found significant promoter hypomethylation of genes typical for proinflammatory M1-Mϕs and hypermethylation of anti-inflammatory, proangiogenic M2-Mϕ genes in hyperlipidemia and T2DM ischemic muscles. Epigenetic alterations modify Mϕ phenotype toward proinflammatory M1 as opposed to anti-inflammatory, proangiogenic, and tissue repair M2 phenotype, which may contribute to the impaired adaptive vascular growth under these pathological conditions.

Whole transcriptome characterization of the effects of dehydration and rehydration on Cladonia rangiferina, the grey reindeer lichen

BackgroundLichens are symbiotic organisms with a fungal and an algal or a cyanobacterial partner. Lichens inhabit some of the harshest climates on earth and most lichen species are desiccation-tolerant. Lichen desiccation-tolerance has been studied at the biochemical level and through proteomics, but the underlying molecular genetic mechanisms remain largely unexplored. The objective of our study was to examine the effects of dehydration and rehydration on the gene expression of Cladonia rangiferina.ResultsSamples of C. rangiferina were collected at several time points during both the dehydration and rehydration process and the gene expression intensities were measured using a custom DNA microarray. Several genes, which were differentially expressed in one or more time points, were identified. The microarray results were validated using qRT-PCR analysis. Enrichment analysis of differentially expressed transcripts was also performed to identify the Gene Ontology terms most associated with the rehydration and dehydration process.ConclusionsOur data identify differential expression patterns for hundreds of genes that are modulated during dehydration and rehydration in Cladonia rangiferina. These dehydration and rehydration events clearly differ from each other at the molecular level and the largest changes to gene expression are observed within minutes following rehydration. Distinct changes are observed during the earliest stage of rehydration and the mechanisms not appear to be shared with the later stages of wetting or with drying. Several of the most differentially expressed genes are similar to genes identified in previous studies that have investigated the molecular mechanisms of other desiccation-tolerant organisms. We present here the first microarray experiment for any lichen species and have for the first time studied the genetic mechanisms behind lichen desiccation-tolerance at the whole transcriptome level.

Characterization of a transcriptome from a non-model organism, Cladonia rangiferina, the grey reindeer lichen, using high-throughput next generation sequencing and EST sequence data

BackgroundLichens are symbiotic organisms that have a remarkable ability to survive in some of the most extreme terrestrial climates on earth. Lichens can endure frequent desiccation and wetting cycles and are able to survive in a dehydrated molecular dormant state for decades at a time. Genetic resources have been established in lichen species for the study of molecular systematics and their taxonomic classification. No lichen species have been characterised yet using genomics and the molecular mechanisms underlying the lichen symbiosis and the fundamentals of desiccation tolerance remain undescribed. We report the characterisation of a transcriptome of the grey reindeer lichen, Cladonia rangiferina, using high-throughput next-generation transcriptome sequencing and traditional Sanger EST sequencing data.ResultsAltogether 243,729 high quality sequence reads were de novo assembled into 16,204 contigs and 49,587 singletons. The genome of origin for the sequences produced was predicted using Eclat with sequences derived from the axenically grown symbiotic partners used as training sequences for the classification model. 62.8% of the sequences were classified as being of fungal origin while the remaining 37.2% were predicted as being of algal origin. The assembled sequences were annotated by BLASTX comparison against a non-redundant protein sequence database with 34.4% of the sequences having a BLAST match. 29.3% of the sequences had a Gene Ontology term match and 27.9% of the sequences had a domain or structural match following an InterPro search. 60 KEGG pathways with more than 10 associated sequences were identified.ConclusionsOur results present a first transcriptome sequencing and de novo assembly for a lichen species and describe the ongoing molecular processes and the most active pathways in C. rangiferina. This brings a meaningful contribution to publicly available lichen sequence information. These data provide a first glimpse into the molecular nature of the lichen symbiosis and characterise the transcriptional space of this remarkable organism. These data will also enable further studies aimed at deciphering the genetic mechanisms behind lichen desiccation tolerance.

Linear ubiquitination by LUBEL has a role in Drosophila heat stress response

The HOIP ubiquitin E3 ligase generates linear ubiquitin chains by forming a complex with HOIL‐1L and SHARPIN in mammals. Here, we provide the first evidence of linear ubiquitination induced by a HOIP orthologue in Drosophila. We identify Drosophila CG11321, which we named Linear Ubiquitin E3 ligase (LUBEL), and find that it catalyzes linear ubiquitination in vitro. We detect endogenous linear ubiquitin chain‐derived peptides by mass spectrometry in Drosophila Schneider 2 cells and adult flies. Furthermore, using CRISPR/Cas9 technology, we establish linear ubiquitination‐defective flies by mutating residues essential for the catalytic activity of LUBEL. Linear ubiquitination signals accumulate upon heat shock in flies. Interestingly, flies with LUBEL mutations display reduced survival and climbing defects upon heat shock, which is also observed upon specific LUBEL depletion in muscle. Thus, LUBEL is involved in the heat response by controlling linear ubiquitination in flies.

SAP30L (Sin3A‐associated protein 30‐like) is involved in regulation of cardiac development and hematopoiesis in zebrafish embryos

The Sin3A‐associated proteins SAP30 and SAP30L share 70% sequence identity and are part of the multiprotein Sin3A corepressor complex. They participate in gene repression events by linking members of the complex and stabilizing interactions among the protein members as well as between proteins and DNA. While most organisms have both SAP30 and SAP30L, the zebrafish is exceptional because it only has SAP30L. Here we demonstrate that SAP30L is expressed ubiquitously in embryonic and adult zebrafish tissues. Knockdown of SAP30L using morpholino‐mediated technology resulted in a morphant phenotype manifesting as cardiac insufficiency and defective hemoglobinization of red blood cells. A microarray analysis of gene expression in SAP30L morphant embryos revealed changes in the expression of genes involved in regulation of transcription, TGF‐beta signaling, Wnt‐family transcription factors, and nuclear genes encoding mitochondrial proteins. The expression of the heart‐specific nkx2.5 gene was markedly down‐regulated in SAP30L morphants, and the cardiac phenotype could be partially rescued by nkx2.5 mRNA. In addition, changes were detected in the expression of genes known to be important in hemoglobin synthesis and erythropoiesis. Our results demonstrate that SAP30L regulates several transcriptional pathways in zebrafish embryos and is involved in the development of cardiac and hematopoietic systems. J. Cell. Biochem. 113: 3843–3852, 2012.

Retene causes multifunctional transcriptomic changes in the heart of rainbow trout (Oncorhynchus mykiss) embryos

Fish are particularly sensitive to aryl hydrocarbon receptor (AhR)-mediated developmental toxicity. The molecular mechanisms behind these adverse effects have remained largely unresolved in salmonids, and for AhR-agonistic polycyclic aromatic hydrocarbons (PAHs). This study explored the cardiac transcriptome of rainbow trout (Oncorhynchus mykiss) eleuteroembryos exposed to retene, an AhR-agonistic PAH. The embryos were exposed to retene (nominal concentration 32 μg/L) and control, their hearts were collected before, at and after the onset of the visible signs of developmental toxicity, and transcriptomic changes were studied by microarray analysis. Retene up- or down-regulated 122 genes. The largest Gene Ontology groups were signal transduction, transcription, apoptosis, cell growth, cytoskeleton, cell adhesion/mobility, cardiovascular development, xenobiotic metabolism, protein metabolism, lipid metabolism and transport, and amino acid metabolism. Together these findings suggest that retene affects multiple signaling cascades in the heart of rainbow trout embryos, and potentially disturbs processes related to cardiovascular development and function.

Effect of ciprofloxacin exposure on DNA repair mechanisms in Campylobacter jejuni

Ciprofloxacin resistance is common both among animal and human Campylobacter jejuni isolates. Resistant isolates are shown to persist even without selection pressure. To obtain further insight on effects of ciprofloxacin exposure on C. jejuni we compared transcriptional responses of both C. jejuni wild-type strain 81-176 (ciprofloxacin MIC 0.125 mg l(-1)) and its intermediate ciprofloxacin-resistant variant P3 (Asp90→Asn in GyrA) in the absence and presence of ciprofloxacin. Further, we sequenced the genome of P3 and compared the sequence with that of wild-type 81-176. One hour of exposure to 8 mg l(-1) of ciprofloxacin did not decrease the viability of the parent strain 81-176. Transcriptional analysis revealed that ciprofloxacin exposure caused changes in the expression of genes involved in DNA replication and repair. While in the wild-type the exposure caused downregulation of several genes involved in the control of DNA replication and recombination, the genes controlling nucleotide excision repair and DNA modification were upregulated in both the wild-type and P3. In addition, we observed that ciprofloxacin exposure caused upregulation of genes responsible for damage recognition in base excision repair in P3. In contrast, without ciprofloxacin exposure, DNA repair mechanisms were substantially downregulated in P3. The genome sequence of P3 compared to that of the 81-176 parental strain had three non-synonymous substitutions and a deletion, revealing that the resistant variant had maintained genetic integrity. In conclusion, enhanced DNA repair mechanisms under ciprofloxacin exposure might explain maintenance of genomic integrity in ciprofloxacin-resistant variant P3.

IRF4 Deficiency Leads to Altered BCR Signalling Revealed by Enhanced PI3K Pathway, Decreased SHIP Expression and Defected Cytoskeletal Responses

The graded expression of transcription factor interferon regulatory factor 4 (IRF4) regulates B cell development and is critical for plasma cell differentiation. However, the mechanisms, by which IRF4 elicits its crucial tasks, are largely unknown. To characterize the molecular targets of IRF4 in B cells, we established an IRF4‐deficient DT40 B cell line. We found that in the absence of IRF4, the expression of several molecules involved in BCR signalling was altered. For example, the expression of B cell adaptor for PI3K (BCAP) was upregulated, whereas the SHIP (SH2‐containing Inositol 5?‐Phosphatase) expression was downregulated. These molecular unbalances were accompanied by increased BCR‐induced calcium signalling, attenuated B cell linker protein (BLNK) and ERK activity and enhanced activity of PI3K/protein kinase B (Akt) pathway. Further, the IRF4‐deficient cells showed dramatically diminished cytoskeletal responses to anti‐IgM cross‐linking. Our results show that IRF4 has an important role in the regulation of BCR signalling and help to shed light on the molecular mechanisms of B cell development and germinal centre response.

Complete Genome Sequence of Escherichia coli 81009, a Representative of the Sequence Type 131 C1-M27 Clade with a Multidrug-Resistant Phenotype

ABSTRACT The sequence type 131 (ST131)-H30 clone is responsible for a significant proportion of multidrug-resistant extraintestinal Escherichia coli infections. Recently, the C1-M27 clade of ST131-H30, associated with blaCTX-M-27, has emerged. The complete genome sequence of E. coli isolate 81009 belonging to this clone, previously used during the development of ST131-specific monoclonal antibodies, is reported here.