Biomedical subjects

Roland G Roberts

Publications and source records attributed to Roland G Roberts.

10 recordsLinked to original sources

PubMed2006

Mutation, selection, and evolution of the Crohn disease susceptibility gene CARD15.

Three common mutations in the CARD15 (NOD2) gene are known to be associated with susceptibility to Crohn disease (CD), and genetic data suggest a gene dosage model with an increased risk of 2-4-fold in heterozygotes and 20-40-fold in homozygotes. However, the discovery of numerous rare variants of CARD15 indicates that some heterozygotes for the common mutations have a rare mutation on the other CARD15 allele, which would support a recessive model for CD. We addressed this issue by screening CARD15 for mutations in 100 CD patients who were heterozygous for one of the three common mutations. We also developed a strategy for evaluating potential disease susceptibility alleles (DSAs) that involves assessing the degree of evolutionary conservation of involved residues, predicted effects on protein structure and function, and genotyping in a large sample of cases and controls. The evolutionary analysis was aided by sequencing the entire coding region of CARD15 in three primates (chimp, gibbon, and tamarin) and aligning the human sequence with these and orthologs from other species. We found that 11 of the 100 CD patients screened had a second potential pathogenic mutation within the exonic and periexonic sequences examined. Assuming that there are no additional pathogenic mutations in noncoding regions, our study suggests that most carriers of the common DSAs are true heterozygotes, and supports previous evidence for a gene dosage model. Four novel nonsynonymous mutations were detected, one of which would produce premature termination of translation c.2686C>T (p.Arg896X). Two potential DSAs--c.2107C>T (p.Arg703Cys) and g.2238T>A (c.74-7T>A)--were significantly associated with CD in the case control sample. Analysis of the evolution of CARD15 revealed strong conservation of the encoded protein, with identity to the human sequence ranging from 99.1% in the chimp to 44.5% in fugu. Higher primates possess an open reading frame (ORF) upstream of the putative initiation site in other species that encodes a further 27 N-terminal amino acids, while four regions of high conservation are observed outside of the known domains of CARD15, indicative of additional residues of functional importance. The strategy developed here may have general application to the assessment of mutation pathogenicity and genetic models in other complex disorders.

Alleles↗

PubMed2005

Bax/Bak-dependent release of DDP/TIMM8a promotes Drp1-mediated mitochondrial fission and mitoptosis during programmed cell death.

Mitochondrial morphology within cells is controlled by precisely regulated rates of fusion and fission . During programmed cell death (PCD), mitochondria undergo extensive fragmentation and ultimately caspase-independent elimination through a process known as mitoptosis . Though this increased fragmentation is due to increased fission through the recruitment of the dynamin-like GTPase Drp1 to mitochondria , as well as to a block in mitochondrial fusion , cellular mechanisms underlying these processes remain unclear. Here, we describe a mechanism for the increased mitochondrial Drp1 levels and subsequent stimulation of mitochondrial fission seen during PCD. We observed Bax/Bak-mediated release of DDP/TIMM8a, a mitochondrial intermembrane space (IMS) protein , into the cytoplasm, where it binds to and promotes the mitochondrial redistribution of Drp1, a mediator of mitochondrial fission. Using both loss- and gain-of-function assays, we also demonstrate that the Drp1- and DDP/TIMM8a-dependent mitochondrial fragmentation observed during PCD is an important step in mitoptosis, which in turn is involved in caspase-independent cell death. Thus, following Bax/Bak-mediated mitochondrial outer membrane permeabilization (MOMP), IMS proteins released comprise not only apoptogenic factors such as cytochrome c involved in caspase activation but also DDP/TIMM8a, which activates Drp1-mediated fission to promote mitochondrial fragmentation and subsequently elimination during PCD.

Amino Acid Sequence↗

PubMed2005

Nesprin-2 is a multi-isomeric protein that binds lamin and emerin at the nuclear envelope and forms a subcellular network in skeletal muscle.

Nesprin-2 is a multi-isomeric, modular protein composed of variable numbers of spectrin-repeats linked to a C-terminal transmembrane domain and/or to N-terminal paired calponin homology (CH) domains. The smaller isoforms of nesprin-2 co-localize with and bind lamin A and emerin at the inner nuclear envelope (NE). In SW-13 cells, which lack lamin A/C, nesprin-2 epitopes and emerin were both mislocalized and formed aggregates in the endoplasmic reticulum (ER). The larger isoforms and other CH-domain-containing isoforms co-localize with heterochromatin within the nucleus and are also present at the outer NE and in multiple cytoplasmic compartments. Nesprin-2 isoforms relocalize during in vitro muscle differentiation of C2C12 myoblasts to the sarcomere of myotubes. Immunogold electron microscopy using antibodies specific for three different epitopes detected nesprin-2 isoforms at multiple locations including intranuclear foci, both membranes of the NE, mitochondria, sarcomeric structures and plasma membrane foci. In adult skeletal muscle, confocal immunolocalization studies demonstrated that nesprin-2 epitopes were present at the Z-line and were also associated with the sarcoplasmic reticulum (SR) in close apposition to SERCA2. These data suggest that nesprin-2 isoforms form a linking network between organelles and the actin cytoskeleton and thus may be important for maintaining sub-cellular spatial organisation. Moreover, its association at the NE with lamin and emerin, the genes mutated in Emery-Dreifuss muscular dystrophy, suggests a mechanism to explain how disruption of the NE leads to muscle dysfunction.

Actin Cytoskeleton↗

PubMed2004

Structural evolution of the BRCA1 genomic region in primates.

Segmental duplications account for up to 6% of the human genome, and the resulting low-copy repeats (LCRs) are known to be associated with more than 20 genomic disorders. Many such duplication events coincided with the burgeoning of the Alu repeat family during the last 50 million years of primate evolution, and it has been suggested that the two phenomena might be causally related. In tracing the evolution of the BRCA1 17q21 region through the primate clade, we discovered the occurrence over the last 40 million years of a complex set of about eight large gene-conversion-mediated rearrangements in the approximately 4 Mb surrounding the BRCA1 gene. These have resulted in the presence of large and probably recombinogenic LCRs across the region, the creation of the NBR2 gene, the duplication of the BRCA1/NBR1 promoter, the bisection of the highly conserved ARF2 gene, and multiple copies of the KIAA0563 gene. The junctions lie within AluS repeats, members of an Alu subfamily which experienced massive expansion during the time that the rearrangements occurred. We present a detailed history of this region over a critical 40 million-year period of genomic upheaval, including circumstantial evidence for a causal link between Alu family expansion and the rearrangement-mediated destruction and creation of transcription units.

ADP-Ribosylation Factors↗

PubMed2004

Multiplex ligation-dependent probe amplification using a completely synthetic probe set.

The recent development of multiplex ligation-dependent probe amplification (MLPA) has provided an efficient and reliable assay for dosage screening of multiple loci in a single reaction. However, a drawback to this method is the time-consuming process of generating a probe set by cloning in single-stranded bacteriophage vectors. We have developed a synthetic probe set to screen for deletions in a region spanning 18.5 Mb within chromosome 3q. In a pilot study, we tested 15 synthetic probes on 4 control samples and on 2 patients previously found to possess a heterozygous deletion in the region 3q26-q28. These synthetic probes detected deletions at all previously known deleted loci. Furthermore, using synthetic probes, the variability of results within samples was similar to that reported for commercially available M13-derived probes. Our results demonstrate that this novel approach to MLPA provides a generic solution to the difficulties of probe development by cloning; such synthetically generated probes may be used to screen a large number of loci in a single reaction. We conclude that the use of synthetic probes for MLPA is a rapid, robust, and efficient alternative for research (and potentially diagnostic) deletion and duplication screening of multiple genomic loci.

Chromosome Deletion↗

PubMed2003

Interaction of the deafness-dystonia protein DDP/TIMM8a with the signal transduction adaptor molecule STAM1.

The Mohr-Tranebjaerg-Jensen deafness-dystonia-optic atrophy protein DDP/TIMM8a is translated on cytoplasmic ribosomes but targeted ultimately to the mitochondrial intermembrane space, where it is involved in mitochondrial protein import. STAM1 is a cytoplasmic signal-transducing adaptor molecule implicated in cytokine signaling. We report here a direct interaction between DDP and STAM1, identified by yeast two-hybrid screening and confirmed by co-immunoprecipitation, fusion protein "pull downs," and nuclear redistribution assays. DDP coordinates Zn(2+), and Zn(2+) was found to stimulate the DDP-STAM1 interaction in vitro. Endogenous STAM1 localizes predominantly to early endosomes, and we found no evidence that STAM1 is imported into mitochondria in vitro. Thus, the DDP-STAM1 interaction likely occurs in the cytoplasm or at the mitochondrial outer membrane. The DDP-STAM1 interaction requires a coiled-coil region in STAM1 that overlaps with the immunoreceptor tyrosine-based activation motif (ITAM), a region previously shown to be important for interaction with Jak2/3 and hepatocyte growth factor-regulated tyrosine kinase substrate (Hrs). Thus, DDP binding may alter the interactions of STAM1 with several cytoplasmic proteins involved in cell signaling and endosomal trafficking.

Amino Acid Sequence↗

PubMed2003

Loss of a single amino acid from dystrophin resulting in Duchenne muscular dystrophy with retention of dystrophin protein.

Almost all of the thousands of pathogenic mutations which have been described in the dystrophin gene either reduce protein production or remove large regions of the protein. This has severely limited the use of mutational information for the functional dissection of the dystrophin protein and increases the value of rare subtle mutations. We report a 3-bp deletion which removes a single highly conserved residue (glutamic acid 3367) adjacent to the dystrophin ZZ domain. This results in a phenotype of Duchenne muscular dystrophy with substantial retention of a presumably functionally compromised dystrophin protein. Two missense mutations (both affecting nearby residues) have been previously reported to result in this unusual combination of severe phenotype and high protein level. We discuss the functional implications of this and other mutations in the light of the predicted structure of the region. The pathogenicity of E3367del serves to emphasise the functional importance of this region of the dystrophin protein.

Amino Acid Sequence↗

PubMed2003

The dystrophin lymphocyte promoter revisited: 4.5-megabase intron, or artifact?

The human dystrophin gene has seven generally recognised promoters and one, the so-called lymphocyte promoter, whose status remains uncertain. We re-evaluated this promoter in the light of recently available human and mouse genome sequences, and attempted to compare its activity in lymphocytes with that of the muscle promoter. We find that the lymphocyte promoter lies immediately adjacent to the chronic granulomatous disease gene, CYBB, approximately 4.5 megabases upstream of dystrophin exon 2. This makes the supposed lymphocyte dystrophin primary transcript 7 megabases in size, with an expected transcription time in excess of 2 days. We also find that lymphocyte promoter use in peripheral blood lymphocytes is negligible compared to that of the muscle promoter in the same tissue. Together with the presence in the intron of a sense-strand multi-exon gene, and lack of conserved linkage in the mouse, we propose that the lymphocyte promoter is not a biologically significant part of the dystrophin gene.

Animals↗

PubMed2002

The 3'-untranslated region of the dystrophin gene - conservation and consequences of loss.

The 3'-untranslated region (3'UTR) of some vertebrate dystrophin genes shows an extraordinary degree and extent of conservation (better than that of many coding regions), a phenomenon that remains unexplained. We examine novel sequence and mutational data to explore the possible reasons for this. We show that loss of the human dystrophin 3'UTR is sufficient to cause Becker muscular dystrophy with pronounced reduction in dystrophin protein levels. The acquisition of dystrophin 3'UTR sequence from an amphibian and a cartilaginous fish allows us to refine previously identified functionally constrained regions which might account for the observed phenotype. These comprise (a) the open reading frame encoding the ancestral 'alternative' amphipathic C-terminal alpha-helix, normally removed from adult dystrophin by inclusion of a poorly conserved frameshifting penultimate exon, and (b) two highly conserved untranslated regions ('Lemaire A', 350 nucleotides and 'Lemaire D', 250 nucleotides) separated by a non-conserved 700-2000-nucleotide spacer. We consider the possibility that the 3'UTR may represent a significant target for pathogenic mutations.

3' Untranslated Regions↗

PubMed2002

The nesprins are giant actin-binding proteins, orthologous to Drosophila melanogaster muscle protein MSP-300.

Nesprin-1 and nesprin-2 (also known as Syne-1 and Syne-2,) are large ( approximately 3300-residue) vertebrate proteins associated with emerin and lamin A at the nuclear envelope of muscle cells and other cell types. We show that the previously described nesprins are short isoforms of giant proteins comprising an actin-binding amino-terminus connected to a carboxy-terminal klarsicht-related transmembrane domain by a massive ( approximately 6000-8000 amino acid) spectrin-like rod domain, making full-length nesprin-1, at one megadalton, the largest non-titin protein hitherto described in humans. We find that MSP-300, a 7000-residue Drosophila melanogaster protein whose disruption results in defects of muscle development, corresponds to the N-terminal two-thirds of the Drosophila nesprin ortholog. A nesprin-like protein is also encoded by the nematode genome. Moreover, we demonstrate that the larger isoforms of nesprin-1, like MSP-300, are localized to the sarcomeric Z-line of both skeletal and cardiac muscle. The recognition that a characteristic muscle-specific mutant phenotype in the fly results from a disruption of its nesprin ortholog reinforces the candidacy of the human proteins for involvement in genetic diseases of skeletal and cardiac muscle.

Amino Acid Sequence↗