Human Chromosome 11q13 Research Articles

A 6-Mb contig-based comparative gene and linkage map of the rat schwannoma tumor suppressor region at 10q32.3

Frequent genetic aberrations of malignant schwannomas induced by the alkylating agent N-ethyl- N-nitrosourea in hybrids from inbred BD rat strains include allelic imbalances of the telomeric 20 Mb of chromosome 5 ( Dis-2) and of the telomeric 5 Mb of chromosome 10q32 ( Dis-1) in 59 and 94% of the tumors, respectively. The Dis-1 minimal loss of heterozygosity consensus region extends from D10Rat4 to the telomere and harbors a putative tumor suppressor gene(s). We constructed a 6-Mb BAC/PAC contig containing more than 70 known genes, 18 mapped microsatellites, and further ESTs/reference RNAs. A continuous block of strongly conserved synteny with mouse chromosome 11E2 and human chromosome 17q25.3 was found. Combining the sequence information from the rat and closely related syntenic regions of different mammalian species produces nearly complete gene maps as a basis for a positional candidate approach and gives insight into mammalian genomic evolution.

Hsp47 a novel collagen binding serpin chaperone, autoantigen and therapeutic target

Hsp47 was originally discovered as a cell surface collagen binding protein, colligin, and was later shown to be an endoplasmic reticulum (ER) resident protein with collagen binding properties in chick fibroblasts. Hsp47 has been termed J6, gp46, CB48 and CBP2 in various other organisms and has been mapped to human chromosome 11q13.5 a known "hot spot" in a number of human cancers. Hsp47 has been shown to be constitutively expressed with collagens; it is heat inducible and binds to both helical and non-helical forms of collagens. Hsp47 binds closely to procollagen in the ER, but dissociates from it in the cis-Golgi to allow fibril formation. Hsp47 is over-expressed in many fibrotic diseases including: glomerulosclerosis, pulmonary fibrosis, liver cirrhosis, cicatricial pemphigoid, epidermolysis bullosa acquista and keloids. Hsp47 is associated with fibrosis following myocardial infarction and has been localized in artherosclerotic arteries. Among a number of rheumatoid conditions, Hsp47 manifests properties of an autoantigen and in some cancers appears to be a biomarker. The unique properties of Hsp47 in modulating collagen production and its location to the cell membrane in many forms of cancer have designated Hsp47 as a potential biomarker and/or therapeutic target for a number of conditions and diseases.

Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition

BackgroundThe selection of markers in association studies can be informed through the use of haplotype blocks. Recent reports have determined the genomic architecture of chromosomal segments through different haplotype block definitions based on linkage disequilibrium (LD) measures or haplotype diversity criteria. The relative applicability of distinct block definitions to association studies, however, remains unclear. We compared different block definitions in 6.1 Mb of chromosome 17q in 189 unrelated healthy individuals. Using 137 single nucleotide polymorphisms (SNPs), at a median spacing of 15.5 kb, we constructed haplotype block maps using published methods and additional methods we have developed. Haplotype tagging SNPs (htSNPs) were identified for each map.ResultsBlocks were found to be shorter and coverage of the region limited with methods based on LD measures, compared to the method based on haplotype diversity. Although the distribution of blocks was highly variable, the number of SNPs that needed to be typed in order to capture the maximum number of haplotypes was consistent.ConclusionFor the marker spacing used in this study, choice of block definition is not important when used as an initial screen of the region to identify htSNPs. However, choice of block definition has consequences for the downstream interpretation of association study results.

Congenital generalized lipodystrophy: profile of the disease and gender differences in two siblings

Congenital generalized Lipodystrophy (BSCL) or Berardinelli-Seip syndrome (Mendelian inheritance in man, catalog no. 269700) is a rare autosomal recessive syndrome characterized by paucity of body fat since birth and insulin resistance. The pathophysiology of this condition is unclear, but defects in insulin function and impaired adipogenesis have been described as important factors in the etiology of the disease. Recently, two gene loci have been identified to harbor the mutations causing this disorder: BSCL1 mapped to human chromosome 9q34 (1, 2) and BSCL2 mapped to human chromosome 11q13 (1, 3). This report describes the natural history of the disease in two siblings (female and male) of Lebanese origin who have mutations in the BSCL2 locus (669delGTATC).

Long-range comparison of human and mouse Sprr loci to identify conserved noncoding sequences involved in coordinate regulation

Mammalian epidermis provides a permeability barrier between an organism and its environment. Under homeostatic conditions, epidermal cells produce structural proteins, which are cross-linked in an orderly fashion to form a cornified envelope (CE). However, under genetic or environmental stress, specific genes are induced to rapidly build a temporary barrier. Small proline-rich (SPRR) proteins are the primary constituents of the CE. Under stress the entire family of 14 Sprr genes is upregulated. The Sprr genes are clustered within the larger epidermal differentiation complex on mouse chromosome 3, human chromosome 1q21. The clustering of the Sprr genes and their upregulation under stress suggest that these genes may be coordinately regulated. To identify enhancer elements that regulate this stress response activation of the Sprr locus, we utilized bioinformatic tools and classical biochemical dissection. Long-range comparative sequence analysis identified conserved noncoding sequences (CNSs). Clusters of epidermal-specific DNaseI-hypersensitive sites (HSs) mapped to specific CNSs. Increased prevalence of these HSs in barrier-deficient epidermis provides in vivo evidence of the regulation of the Sprr locus by these conserved sequences. Individual components of these HSs were cloned, and one was shown to have strong enhancer activity specific to conditions when the Sprr genes are coordinately upregulated.

KIF27 is one of orthologs for Drosophila Costal-2

Signals of Hedgehog family proteins (SHH, IHH and DHH) are transduced through Patched family receptors (PTCH1 and PTCH2) and Smoothened (SMO) to GLI family transcription factors (GLI1, GLI2 and GLI3). SHH plays a key role in development and progression of pancreatic cancer, gastric cancer, basal cell carcinoma, and brain tumors. Drosophila Costal-2 (Cos2) is implicated in the Hedgehog pathway through the interaction with Smoothened (Smo), Cubitus interruptus (Ci), Fused (Fu), and microtubule; however, mammalian ortholog of Drosophila Cos2 remained to be identified. Here we identified and characterized human ortholog of Drosophila Cos2 by using bioinformatics. Full-length Drosophila Cos2 was most homologous to human KIF27, followed by mouse Kif7, and other KIF family members. KIF27 gene at human chromosome 9q22.1 and KIF7 gene at human chromosome 15q26.1 were paralogs within the human genome. Phylogenetic analysis revealed that KIF27, Kif7, KIF4A, KIF4B and KIF21A constitute the KIF27 subfamily among mammalian Kinesin family. Drosophila Cos2 protein consists of Kinesin motor (KISc) domain, Ci-binding domain, and Smo-binding domain. KIF27 itself shared the common domain structure with Drosophila Cos2, while other members of KIF27 subfamily shared partial domain structure with Drosophila Cos2. These facts indicate that KIF27 is one of mammalian orthologs for Drosophila Cos2.

Characterization of the loricrin (LOR) gene as a positional candidate for the PSORS4 psoriasis susceptibility locus

Psoriasis is a chronic inflammatory disease of the skin with both genetic and environmental risk factors. Non-parametric linkage analyses have mapped many susceptibility loci on different chromosomes. We mapped one of these loci, PSORS4, on human chromosome 1q21. Using the linkage disequilibrium approach, we refined the critical region to a specific genomic interval of about 100 Kb which contains only the loricrin (LOR) gene. Here we report a genetic and functional study of this gene to verify its involvement in psoriasis pathogenesis. We document low expression of LOR in psoriatic skin of patients selected from families in which the disease was segregating with the PSORS4 locus. Re-sequencing of the entire gene in a subset of patients revealed the existence of novel polymorphisms able to influence the protein structure, as shown by molecular modelling studies. However, no evidence for genetic association was detected in a large cohort of Italian nuclear families. This rules out the LOR gene as a candidate for the PSORS4 locus.

Characterization of human FOXN4 gene in silico

Forkhead-box (FOX) superfamily genes are implicated in carcinogenesis through gene amplification, retroviral integration and chromosomal translocation. FOX superfamily genes within the human genome are classified into 17 or 18 families, designated FOX# (# is alphabet A-Q or R). FOXN1, FOXN2 (HTLF), FOXN3 (CHES1), FOXN4, FOXN5 (FOXR1) and FOXN6 (FOXR2) genes constitute the FOXN gene family. Here, we characterized human FOXN4 gene by using bioinformatics. FOXN4 gene at human chromosome 12q24.12 was found to encode three isoforms. FOXN4 isoform 1 (representative transcript), encoding a 518-aa protein, consists of exons 1-10. FOXN4 isoform 2 (NM_ 213596.1), encoding a 337-aa protein, consists of exons 1, 2, 7v, 8-10. FOXN4 isoform 3, encoding a 314-aa protein, consists of exons 1-5, 7-10. Codon 205-518 of isoform 1 was conserved in isoforms 2 and 3. FOXN4 mRNA was expressed in testis, embryonic stem (ES) cells, uterus tumors, and leiomyosarcoma. FOXN4 was most homologous to FOXN1 among human FOXN family members. FOXN4 and FOXN1 showed 41.3% total-amino-acid identity. FOX domain (codon 192-305 of FOXN4) was well conserved among mammalian FOXN family members. FN14 domain (codon 367-456 of FOXN4) was identified as the novel domain conserved among FOXN4 and FOXN1 orthologs. FOXN4 and FOXN1 orthologs were found to share the common domain structure, consisting of FOX and FN14 domains. This is the first report on comprehensive characterization of the human FOXN4 gene as well as on identification of the FN14 domain.

Identification and characterization of ARHGAP27 gene in silico

ARHGAP1, ARHGAP2, ARHGAP3, ARHGAP4, ARHGAP5, ARHGAP6, ARHGAP7 (DLC1), ARHGAP8, ARHGAP9, ARHGAP10, ARHGAP12, ARHGAP13 (SRGAP1), ARHGAP14 (SRGAP2), ARHGAP15, ARHGAP17 (RICH1), ARHGAP18, ARHGAP19, ARHGAP20, ARHGAP21, ARHGAP22, ARHGAP23, ARHGAP24, ARHGAP25, ARHGAP26, STARD13 (DLC2), HA-1, GMIP, PARG1, RACGAP1, PIK3R1, PIK3R2, and FNBP2 genes encode Rho/Rac/Cdc42-like GTPase activating (RhoGAP) proteins. Here, we characterized human ARHGAP27 gene by using bioinformatics. Complete coding sequence of ARHGAP27 isoform 1, encoding a full-length 889-aa protein, was determined by assembling exon 1 (nucleotide position 143440-144096 of AC091132.16) and most part of FLJ43547 cDNA (nucleotide position 69-3628 of AK125535.1). Complete coding sequence of ARHGAP27 isoform 2, encoding an N-terminally truncated 548-aa protein, was derived from FLJ43547 cDNA. ARHGAP27 isoform 1 consists of exons 1-17, while ARHGAP27 isoform 2 consists of exons 1B, and 2-17. ARHGAP27 gene encoded two isoforms due to alternative splicing of alternative promoter type. ARHGAP27 mRNA was expressed in germinal center B cell, spleen, chronic lymphocytic leukemia, pancreatic cancer, and lung cancer. LOC303583 (NM_ 198759.1) was the representative rat Arhgap27 cDNA. Human ARHGAP27 showed 84.3% total-amino-acid identity with rat Arhgap27, and 39.0% total-amino-acid identity with human ARHGAP12. ARHGAP27 and ARHGAP12 shared the common-domain structure, consisting of SH3, WW, PH, and RhoGAP domains. ARHGAP27 gene was located at human chromosome 17q21, while ARHGAP12 gene was located at human chromosome 10p11. ARHGAP family genes are cancer-associated genes, because their genetic alterations lead to carcinogenesis through the dysregulation of Rho/Rac/ Cdc42-like GTPases. This is the first report on identification and characterization of the ARHGAP27 gene.

Late Breaking Science Abstracts

### A New Apolipoprotein Influencing Plasma Triglyceride Levels in Humans and Mice Len Pennacchio, Lawrence Berkeley National Laboratory, Berkeley, CA; Michael Olivier, Medical College of Wisconsin, Milwaukee, WI; Jaroslav A Hubacek, Jonathan C Cohen, UT Southwestern Medical Center, Dallas, TX; David R Cox, Stanford Human Genome Center, Palo Alto, CA; Jamilla Fruchart, Pasteur Institute, Lille, France; Ronald M Krauss, Edward M Rubin, Lawrence Berkeley National Laboratory, Berkeley, CA The apolipoprotein gene cluster on human chromosome 11q23 (apoAI/CIII/AIV) represents a well-studied region that influences a variety of plasma lipid parameters and atherosclerosis susceptibility in humans. To facilitate the identification of evolutionarily conserved sequences with potential function near this cluster, we determined the sequence of ∼200 kbp of orthologous mouse DNA and compared the mouse and human sequences. The presence of a stretch of inter-species sequence conservation approximately 30 kbp proximal to the apoAI/CIII/AIV gene cluster, led us to an interval that upon further analysis was shown to encode a new member (apoAV) of the chromosome 11 apolipoprotein gene cluster. ApoAV transcripts were identified predominantly in liver tissue from mice and humans. To assess the function of apoAV, we generated mice over-expressing a human apoAV transgene as well as apoAV knockout mice. We observed dramatic but opposite effects on plasma triglyceride in these two groups of animals; a 3-fold decrease in plasma triglycerides in the apoAV transgenics and a 4-fold increase in the knockout mice. To explore the relationship between apoAV and lipid parameters in humans, several single nucleotide polymorphisms (SNPs) across the apoAV locus were identified and genotyped in two independent patient populations of normo-lipidemics. A common haplotype was found to be significantly associated with increased plasma triglycerides in the two large independent studies each employing different study designs. These findings in humans and mice illustrate the utility of comparative sequence analysis as a means to prioritize regions of the genome for further …

Characterization of human TMEM16G gene in silico.

TMEM16A, TMEM16B, TMEM16C, TMEM16D, TMEM16E, TMEM16F and TP53I5 are TMEM16 family eight-transmembrane proteins with N- and C-terminal tails facing the cytoplasm. TMEM16A gene at human chromosome 11q13.3 is amplified in head and neck tumors, and TMEM16E gene at human chromosome 11p14.3 is mutated in gnathodiaphyseal dysplasia (GDD). Ngep cDNA (NM_207031.1) is derived from mouse Tmem16g gene. Here, we characterized human TMEM16G gene by using bioinformatics. TMEM16G gene, consisting of 25 exons, was located at human chromosome 2q37.3. Intra-species comparative genomics revealed that the PASK-PPP1R7-TMEM16G-HDLBP-NEDD5 locus was the unique region without paralogous region. TMEM16G mRNA was preferentially expressed in normal prostate and prostate cancer. Complete coding sequence of TMEM16G cDNA was determined by assembling 25 exons of TMEM16G gene. Human TMEM16G gene was found to encode 932-amino-acid TMEM16G protein with TM16H1, TM16H2 and TM16H3 domains. Comparative proteomics revealed that T844N amino-acid substitution occurred in human TMEM16G during evolution. TMHMM2 program predicted that mouse Tmem16g and artificial human TMEM16G (844T) were eight-transmembrane proteins, but that wild-type human TMEM16G (844N) was a seven-transmembrane protein. These facts indicate that amino-acid substitution at codon 844 of human TMEM16G resulted in the mis-folding of the eighth transmembrane helix. Human TMEM16G with altered membrane topology might show functional divergence compared with other members of the TMEM16 family.

Identification and characterization of human FOXK1 gene in silico

Forkhead-box (FOX) family transcription factors are implicated in carcinogenesis and embryogenesis. Here, we identified and characterized the human FOXK1 gene by using bioinformatics. Complete coding sequence of human FOXK1 cDNA was determined by assembling CB959941 EST, AW206906 EST, and 5'-truncated FLJ16099 (AK122663.1) cDNA. FOXK1 gene, consisting of nine exons, was mapped to human chromosome 7p22.1. Mouse Foxk1 (NM_199068.1) was an aberrant cDNA with frame shifts due to multiple insertions and deletions, while mouse IMAGE6853263 (BC060238.1) was a Foxk1 cDNA with a frame shift due to two base deletions. Complete coding sequence of mouse Foxk1 cDNA was determined by inserting CA nucleotides between nucleotide position 1628 and 1629 of BC060238.1. Foxk1 gene, consisting of nine exons, was mapped to mouse chromosome 5G2. Because interleukin enhancer-binding factor 1 (ILF1) gene at human chromosome 17q25.3 was the paralog of FOXK1 gene, ILF1 gene was designated the FOXK2 gene. Xenopus BC046369.1 cDNA was Foxk2 ortholog rather than Foxk1 ortholog. Human FOXK1 (733 aa) showed 88.7% total amino-acid identity with mouse Foxk1 (719 aa), 48.7% total amino-acid identity with human FOXK2, and 47.5% total amino-acid identity with Xenopus Foxk2. Forkhead associated (FHA) domain and FOX domain were conserved among human FOXK1, FOXK2, mouse FoxK1, and Xenopus Foxk2. At least 42 FOX family genes, including FOXK1, FOXN5 (FOXR1) and FOXN6 (FOXR2), have been identified within the human genome.

Characterisation of the NUCKS gene on human chromosome 1q32.1 and the presence of a homologous gene in different species

The NUCKS gene is located on human chromosome 1q32.1 and consists of seven exons and six introns. The gene lacks a TATA box but contains two Inr elements, two GC boxes, and one consensus-binding site for E2F-1. NUCKS is expressed in all human adult and foetal tissues investigated, and has all the features of being a housekeeping gene. Both data searches and Western immunoblotting experiments show that a homologous protein is present in fish, amphibians, and birds but not in insects and yeast, suggesting that NUCKS is a vertebrate specific gene. In all the species investigated, the protein contains several consensus phosphorylation sites for cyclin-dependent kinases and CK-2, and we have shown that the fish protein (like mammalian NUCKS) indeed is a substrate for CDK1 and CK-2 in vitro. The NUCKS protein is also conserved with respect to a DNA-binding domain previously characterised in mammals, and two putative bipartite nuclear localisation signals.

Post-transcriptional Regulation of Endothelial Nitric-oxide Synthase by an Overlapping Antisense mRNA Transcript

Endothelial nitric-oxide synthase (eNOS) mRNA levels are abnormal in diseases of the cardiovascular system, but changes in gene expression cannot be accounted for by transcription alone. We found evidence for the existence of an antisense mRNA (sONE) that is derived from a transcription unit (NOS3AS) on the opposite DNA strand from which the human eNOS (NOS3) mRNA is transcribed at human chromosome 7q36. The genes are oriented in a tail-to-tail configuration, and the mRNAs encoding sONE and eNOS are complementary for 662 nucleotides. The mRNA for sONE could be detected in a variety of cell types, both in vivo and in vitro, but not vascular endothelial cells. In contrast, expression of eNOS is highly restricted to vascular endothelium. Most surprisingly, interrogation of transcriptional events across NOS3/NOS3AS genomic regions, using single- and double-stranded probes for nuclear run-off analyses and chromatin immunoprecipitation-based assessments of RNA polymerase II distribution, indicated that NOS3 and NOS3AS gene transcription did not correlate with steady-state mRNA levels. We found strong evidence supporting a role for NOS3AS in the post-transcriptional regulation of NOS3 expression. RNA interference-mediated inhibition of sONE expression in vascular smooth muscle cells increased eNOS expression. Overexpression of sONE in endothelial cells blunted eNOS expression. Finally, the histone deacetylase inhibitor trichostatin A is known to regulate the expression of eNOS via a post-transcriptional mechanism. We found that trichostatin A treatment of vascular endothelial cells increased expression of sONE mRNA levels prior to the observed decrease in eNOS mRNA expression. Taken together, these results indicate that an antisense mRNA (sONE) participates in the post-transcriptional regulation of eNOS and provide a newer model for endothelial cell-specific gene expression.

Germ-line mutation of Foxn5 gene in mouse lineage

Amplified region (amplicon) around MLL gene is closely linked to the 11q23.3 commonly deleted region of neuroblastoma, which includes cancer-associated genes such as PHLDB1 (LL5A), BCL9L, FOXN5 (FOXR1), CBL, MFRP, and PVRL1 (Nectin) genes. FOXN6 (FOXR2) gene at human chromosome Xp11.21 is generated due to retrotransposition of ancestral Foxn5 gene during evolution. FOXN5 and FOXN6 orthologs share the common domain structure consisting of FN56 and Forhead-box (FOX) domains. Here, we identified and characterized mouse Foxn5 gene by using bioinformatics. Mouse Foxn5, consisting of six exons, was located within mouse genome sequences AC122428.4 and AC125129.5. Foxn5 locus at mouse chromosome 9B was synthenic to rat chromosome 8q22 and human chromosome 11q23.3. Mouse Foxn5 (180 aa) was C-terminally truncated compared with rat Foxn5 and human FOXN5. Mouse 'Foxn5' protein without FOX domain was generated due to a frame shift introduced by germ-line one-base deletion within exon 3. Mouse Foxn5 mRNA was expressed in embryonic germ cells and fertilized eggs. Germ-line mutation of Foxn5 gene in the mouse lineage might lead to divergent scenario of early embryogenesis between mouse and rat through the deregulation of Foxn5 target genes in mouse early embryos, and explain the difficulty in manipulation of rat embryonic stem (ES) cells based on the mouse equivalent system. This is the first report on identification and characterization of mouse Foxn5 gene as well as on species specific germ-line mutation of the Fox family gene.

Identification and characterization of human DFNA5L, mouse Dfna5l, and rat Dfna5l genes in silico

An evolutionary recombination hotspot around the GSDML-GSDM locus at human chromosome 17q21 is closely linked to an oncogenomic recombination hotspot around the PPP1R1B-STARD3-TCAP-PNMT-PERLD1 (MGC9753)-ERBB2-C17orf37 (MGC14832)-GRB7 locus at human chromosome 17q12. Here, we identified DFNA5L (GSDMDC1) gene related to GSDM and GSDML genes by using bioinformatics. Human DFNA5L gene at chromosome 8q24.3 was linked to ZC3HDC3, PP3856, EEF1D, and TIGD5 genes. NM_024736.4 (AK127941.1), AK022212.1, BC008904.2, and BC069000.1 cDNAs were derived from human DFNA5L gene. BC008904.2 was the representative human DFNA5L cDNA, while NM_024736.4 was an aberrant human DFNA5L cDNA with frame shifts due to the retention of introns 1, 3, 4, 5 and 8. Human DFNA5L mRNA was expressed in placenta, pancreatic cancer, prostate cancer, melanoma, salivary gland tumor, Jarkat T cells, and Ramos B cells. Complete coding sequence of rat Dfna5l cDNA was determined by assembling 11 exons of rat Dfna5l gene within AC120830.4 genome sequence, and that of mouse Dfna5l cDNA was derived from 1810036L03 (NM_026960.1). Exon-intron boundaries were conserved among human DFNA5L and rodent Dfna5l genes. Human DFNA5L (484 aa) showed 59.5% total-amino-acid identity with rat Dfna5l (488 aa), and 58.7% total-amino-acid identity with mouse Dfna5l (487 aa). DFNA5L orthologs were DNFA5 (GSDM) domain containing DFNA5 DC or GSDMDC proteins with Coiled-coil and Leucine zipper domains. Human DFNA5L, GSDM, GSDML, MLZE, DFNA5 and their mammalian orthologs were found to constitute the DFNA5 DC (GSDMDC) family. Because DFNA5 and MLZE are cancer-associated genes, DFNA5L, GSDM, and GSDML are predicted cancer associated genes.

Role of Protein Phosphatase Type 1 in Contractile Functions: Myosin Phosphatase

Role of Protein Phosphatase Type 1 in Contractile Functions: Myosin Phosphatase

S100 proteins in the epidermis.

The S100 proteins comprise a family of 21 low molecular weight (9-13 kDa) proteins that are characterized by the presence of two calcium-binding EF-hand motifs. Fourteen S100 protein genes are located within the epidermal differentiation complex on human chromosome 1q21 and 13 S100 proteins (S100A2, S100A3, S100A4, S100A6, S100A7, S100A8, S100A9, S100A10, S100A11, S100A12, S100A15, S100B, and S100P) are expressed in normal and/or diseased epidermis. S100 proteins exist in cells as anti-parallel hetero- and homodimers and upon calcium binding interact with target proteins to regulate cell function. S100 proteins are of interest as mediators of calcium-associated signal transduction and undergo changes in subcellular distribution in response to extracellular stimuli. They also function as chemotactic agents and may play a role in the pathogenesis of epidermal disease, as selected S100 proteins are markedly overexpressed in psoriasis, wound healing, skin cancer, inflammation, cellular stress, and other epidermal states.

Association of protein kinase C alpha (PRKCA) gene with multiple sclerosis in a UK population

Twin, family and adoption studies suggest that susceptibility to multiple sclerosis is substantially mediated by genetic factors. Linkage to human chromosome 17q, homologous to a locus linked to experimental animal models of multiple sclerosis, has been widely replicated and the region likely to harbour a multiple sclerosis susceptibility gene has recently been refined to a 2.5 Mb region of 17q22-24. The candidate multiple sclerosis susceptibility gene, protein kinase C alpha (PRKCA), maps within this interval and association with 35 single-nucleotide polymorphism (SNP) markers, spanning the gene with a median spacing of 7.8 kb, was tested using a case-control approach. Single-marker genotype and estimated haplotype frequencies were compared in UK unrelated cases with multiple sclerosis (n = 184) and healthy controls (n = 340) in order to investigate association with susceptibility to disease. A haplotype of two SNPs mapping to the proximal region of the gene showed evidence for association with susceptibility (Bonferroni-corrected P value = 1.1 x 10(-5)). These findings suggest that further investigation of the PRKCA gene is warranted, particularly in cohorts with evidence of linkage to 17q22. Most of the SNPs investigated in this study were intronic and screening to identify disease-associated functional mutations is now required. Our results suggest that the promoter and proximal gene region should be not only included but prioritized in any screening strategy.

Refining the DFNB17 interval in consanguineous Indian families.

We previously mapped the DFNB17 locus to a 3-4 cM interval on human chromosome 7q31 in a large consanguineous Indian family with congenital profound sensorineural hearing loss. To further refine this interval, 30 new highly polymorphic markers and 8 SNPs were analyzed against the pedigree. Re-analysis in the original DFNB 17 family and additional data from a second unrelated consanguineous family with congenital deafness found to map to the interval, limited the area of shared homozygosity-by-descent (HBD) to approximately 4 megabase (Mb) between markers D7S2453 and D7S525. Nineteen known genes and over 20 other cDNAs have been identified in the refined DFNB 17 interval, including the SLC26A4 gene. We have analyzed 4 other cochlear-expressed genes that map to the DFNB17 interval as candidate genes. Analysis of coding and splice site regions of these cochlear expressed genes did not reveal any disease causing mutations. Further study of other candidate genes is currently underway.