Olli Lohi

VHS domain -- a longshoreman of vesicle lines.

The VHS ( ps‐27, rs and TAM) domain is a 140 residue long domain present in the very NH2‐terminus of at least 60 proteins. Based on their functional characteristics and on recent data on the involvement of VHS in cargo recognition in trans‐Golgi, VHS domains are considered to have a general membrane targeting/cargo recognition role in vesicular trafficking. Structurally, VHS is a right‐handed superhelix of eight helices with charged surface patches probably serving as sites of protein–protein recognition and docking.

Novel activating STAT5B mutations as putative drivers of T-cell acute lymphoblastic leukemia.

Novel activating STAT5B mutations as putative drivers of T-cell acute lymphoblastic leukemia

STAM/EAST/Hbp adapter proteins – integrators of signalling pathways

STAM/EAST/Hbp family of proteins consists of eight members well conserved from yeast to mammals. The basic domain architecture is comprised of an N‐terminal Vps27, Hrs and STAM homology domain, a ubiquitin‐interacting motif and a central Src homology‐3 domain. Vertebrate members also carry an immunoreceptor tyrosine‐based activation motif. STAM/EAST/Hbp proteins become tyrosine‐phosphorylated by a variety of cytokines and growth factors. STAM 1 and STAM 2A are involved in cytokine‐mediated signalling for DNA synthesis and c‐myc induction. EAST and STAM 2A/Hbp play a role in receptor‐mediated endo‐ and exocytosis and probably also in the regulation of actin cytoskeleton. Knockout experiments implicate a role for STAM 1 in neural cell survival. A picture is emerging of STAM/EAST/Hbp proteins acting as integrators of thus far mechanistically disparate cellular signalling events.

DNA-Binding and -Bending Activities of SAP30L and SAP30 Are Mediated by a Zinc-Dependent Module and Monophosphoinositides

ABSTRACT Deacetylation of histones is carried out by a corepressor complex in which Sin3A is an essential scaffold protein. Two proteins in this complex, the Sin3A-associated proteins SAP30L and SAP30, have previously been suggested to function as linker molecules between various corepressors. In this report, we demonstrate new functions for human SAP30L and SAP30 by showing that they can associate directly with core histones as well as naked DNA. A zinc-coordinating structure is necessary for DNA binding, one consequence of which is bending of the DNA. We provide evidence that a sequence motif previously shown to be a nuclear localization signal is also a phosphatidylinositol (PI)-binding element and that binding of specific nuclear monophosphoinositides regulates DNA binding and chromatin association of SAP30L. PI binding also decreases the repression activity of SAP30L and affects its translocation from the nucleus to the cytoplasm. Our results suggest that SAP30L and SAP30 play active roles in recruitment of deacetylating enzymes to nucleosomes, and mediate key protein-protein and protein-DNA interactions involved in chromatin remodeling and transcription.

The zebrafish as a model for paediatric diseases.

The rapid increase in information about genes and their associations with human diseases has highlighted the need for model organisms suitable for genetic manipulation and drug testing. The zebrafish is a valuable vertebrate animal model that offers many advantages, including the relative ease of husbandry and genetic manipulation and the capacity for high‐throughput screens. In this review, we describe the zebrafish as a model for paediatric diseases, with particular emphasis on haematopoietic and infectious diseases.

Deficient activity of mammalian prolyl oligopeptidase on the immunoactive peptide digestion in coeliac disease

Objective. Gliadin digestion-resistant peptides are harmful in coeliac disease (CD), and initiate an autoimmune reaction that cause a cascade of symptoms. The role of the endogenous prolyl oligopeptidase (POP) is still not clear, and its activity over gliadin immunoactive peptides has not been fully established. Our objective was therefore to determine the endogenous POP protein level, tissue distribution and total activity in normal and CD epithelia, to evaluate tissue peptidase activity over gliadin peptides, and compare this with activities of mammalian POP and rat intestinal extracts. Material and methods. POP was assayed in biopsy preparations enzymatically and by Western blot analysis. Distribution was studied by immunohistochemistry using a specific POP antibody. Peptide cleavage was followed by mass spectroscopy-high-performance liquid chromatography (MS-HPLC). Results. There was no difference in POP activity between normal and CD samples, but those from active CD subjects had an even higher ability to degrade the 33-mer peptide than those from treated CD and healthy humans. POP locates intracellularly in epithelia, similarly to dipeptidyl peptidase IV (DPPIV), but the latter is clearly found in normal microvilli but less so in diseased microvilli. Mammalian POP is unable to digest 33-mer peptide, which, conversely, is a POP inhibitor. Rat intestine is more effective than human intestine in cleaving the 33-mer peptide. However, the products are still harmful epitopes. A surplus of POP eliminates 12-mer and 19-mer peptide products. Conclusions. The results rule out a causative role of POP in the pathogenesis of CD and strongly suggest that other peptidases are needed to eliminate gliadin-derived, immunoactive and toxic peptides larger than 33-mer, which is a POP inhibitors.

Phosphoinositides as Regulators of Protein-Chromatin Interactions

Phosphoinositides can promote or reduce the binding of proteins with roles in transcription to chromatin. The molecular function of phospholipids in the nucleus has been only partially elucidated. The upsurge of epigenetic research has contributed to increased interest in nuclear phospholipids, such as phosphoinositides, and their involvement in gene transcription. However, the mechanisms by which phosphoinositides regulate transcription is still unknown at the molecular level. Certain phosphoinositide species can regulate protein-chromatin and protein–nucleic acid interactions, and specific nuclear target proteins link nuclear signaling lipids to gene expression. We propose that a phosphoinositide-mediated detachment of proteins from chromatin is a general biological mechanism that partly underlies the signaling effects of nuclear phosphoinositides.

Expression of small nucleolar RNAs in leukemic cells

PurposeSmall nucleolar RNAs (snoRNAs) direct sequence-specific modifications to ribosomal RNA. We hypothesized that the expression of snoRNAs may be altered in leukemic cells.MethodsThe expression of snoRNAs was analyzed in various leukemic cell lines by massive parallel sequencing (SOLiD). Quantitative real-time PCR (RT-qPCR) was used to validate the expression profiles.ResultsOur results show characteristic differences in the expression patterns of snoRNAs between cell lines representing the main subgroups of leukemia, AML, pre-B-ALL and T-ALL, respectively. In RT-qPCR analyses, several snoRNAs were found to be differentially expressed in T-ALL as compared to pre-B-ALL cell lines.ConclusionssnoRNAs are differentially expressed in various leukemic cell lines and could, therefore, be potentially useful in the classification of leukemia subgroups.

Background radiation and childhood leukemia: A nationwide register-based case-control study.

High doses of ionizing radiation are an established cause of childhood leukemia. However, substantial uncertainty remains about the effect of low doses of radiation, including background radiation and potential differences between genetic subgroups of leukemia have rarely been explored. We investigated the effect of the background gamma radiation on childhood leukemia using a nationwide register‐based case‐control study. For each of the 1,093 cases, three age‐ and gender matched controls were selected (N = 3,279). Conditional logistic regression analyses were adjusted for confounding by Down syndrome, birth weight (large for gestational age), and maternal smoking. Complete residential histories and previously collected survey data of the background gamma radiation in Finland were used to assess the exposure of the study subjects to indoor and outdoor gamma radiation. Overall, background gamma radiation showed a non‐significant association with the OR of childhood leukemia (OR 1.01, 95% CI 0.97, 1.05 for 10 nSv/h increase in average equivalent dose rate to red bone marrow). In subgroup analyses, age group 2–<7 years displayed a larger effect (OR 1.27, 95% CI 1.01, 1.60 for 1 mSv increase in equivalent cumulative dose to red bone marrow). Suggestive difference in OR by genetic subtype was found. Our results provide further support to the notion that low doses of ionizing radiation increase the risk for childhood leukemia, particularly at age 2–<7 years. Our findings suggest a larger effect of radiation on leukemia with high hyperpdiploidy than other subgroups, but this result requires further confirmation.

Transcription-coupled genetic instability marks acute lymphoblastic leukemia structural variation hotspots.

Progression of malignancy to overt disease requires multiple genetic hits. Activation-induced deaminase (AID) can drive lymphomagenesis by generating off-target DNA breaks at loci that harbor highly active enhancers and display convergent transcription. The first active transcriptional profiles from acute lymphoblastic leukemia (ALL) patients acquired here reveal striking similarity at structural variation (SV) sites. Specific transcriptional features, namely convergent transcription and Pol2 stalling, were detected at breakpoints. The overlap was most prominent at SV with recognition motifs for the recombination activating genes (RAG). We present signal feature analysis to detect vulnerable regions and quantified from human cells how convergent transcription contributes to R-loop generation and RNA polymerase stalling. Wide stalling regions were characterized by high DNAse hypersensitivity and unusually broad H3K4me3 signal. Based on 1382 pre-B-ALL patients, the ETV6-RUNX1 fusion positive patients had over ten-fold elevation in RAG1 while high expression of AID marked pre-B-ALL lacking common cytogenetic changes. DOI: http://dx.doi.org/10.7554/eLife.13087.001