Evidence for multiple tumor suppressor genes on chromosome arm 8p in supraglottic laryngeal cancer

Loss of heterozygosity studies of a variety of human tumors suggest that there are several tumor suppressor genes on chromosome arm 8p. To localize these genes more precisely, we utilized polymerase chain reaction amplification of microsatellite repeat polymorphisms and examined the allelic loss patterns of 17 marker loci on 8p in a population of 59 supraglottic laryngeal squamous cell carcinomas. Twenty-three of these tumors (39%) had an allelic loss at one or more of the markers examined. The allelic loss patterns of these tumors support the presence of at least three different tumor suppressor genes on 8p: one in 8p23, one in 8p22–23, and another in 8p21. Genes Chromosom Cancer 16:164–169 (1996). © 1996 Wiley-Liss, Inc.     

Linkage studies suggest a possible locus for developmental dyslexia on chromosome 1p.

Eight extended dyslexic families with at least four affected individuals were genotyped with twelve genetic markers spanning the Rh (rhesus factor) locus. Eleven of these markers were located on the short arm and the other was on the long arm of chromosome 1. Five theoretically derived phenotypes were used in the linkage analyses: 1) phonemic awareness; 2) phonological decoding; 3) rapid automatized naming; 4) single word reading; and 5) vocabulary. In addition, a lifetime diagnosis of dyslexia was used as a phenotype. Both parametric and non-parametric genetic analyses were completed. The results supported the importance of a putative locus on 1p. In addition, two-locus analyses assuming the interaction between a 1p locus and a 6p locus, previously shown to be of interest for dyslexia, were conducted. As a result, the nonparametric linkage (NPL) scores for rapid automatized naming and phonological decoding were significantly increased. In particular, the NPL scores for rapid automatized naming exceeded 5.0 for certain markers. These results provide strong evidence for separate but jointly acting contributions of the 1p and 6p loci to the reading impairments associated with rapid naming and suggestive evidence for a similar mechanism involving phonological decoding.     

Mild developmental delay in terminal chromosome 6p deletion

Deletions involving the short arm of chromosome 6 are relatively rare. Although features of this condition are variable, common findings include developmental delay, ocular abnormalities, hearing loss, and cardiac defects. In an effort to define further the clinical variability of this condition, we report a 6-year-old female with a de novo terminal deletion of chromosome 6 at band 6p24, with mild gross motor delays and normal cognition.     

Selective expression of a subset of neuronal genes in oligodendroglioma with chromosome 1p loss

Gliomas are classified based mainly on microscopic resemblance to their presumed glial origin such as astrocyte and oligodendrocyte. However, more objective diagnostic criteria are indispensable for the precise treatment of patients. For instance, loss of the short arm of chromosome 1 (1p) in oligodendrogliomas is recognized as an important marker for better response to chemotherapy and longer survival of the patients. To gain insight into their molecular biological background and to identify genes characterizing each subgroup, we investigated gene expression profile of the 4 glioma subsets, oligodendroglioma with and without 1p loss, diffuse astrocytoma and glioblastoma using DNA microarray. Remarkably, most of the genes showing distinctive expression in oligodendroglioma with 1p loss were also highly expressed in normal brain tissues and had neuron-related function, which included MYT1L, INA, RIMS2, SNAP97 and SNCB. Histological analysis also demonstrated that MYT1L, which were abundantly expressed in normal neuron, were certainly present in tumor cells. These results suggest that oligodendroglioma, especially with 1p loss, has more or less neuronal characteristics although oligodendroglioma is thought to originate form glial lineage cell. With further pathological studies, those neuron-related genes might be good diagnostic markers for oligodendroglioma of better prognosis as well.     

Lupus susceptibility genes on human chromosome 1

During the past five years, there has been an intense interest in studying candidate susceptibility genes for systemic lupus erythematosus (SLE). Many such studies have been focused on candidates located on chromosome 1, demonstrating association of certain genetic variants with SLE. Some of the tested candidate genes were chosen because they encode molecules with relevant immunological functions that may play a role in the pathogenesis of SLE. More recently, the identification of genomic segments linked to SLE has suggested novel positional candidate genes. Thus far, there is considerable evidence supporting that multiple genes on this chromosome contribute to the development and expression of SLE. This review highlights the genetic loci located on chromosome 1 that have recently been associated with SLE. These include loci encoding the tumor necrosis factor receptor 2 (TNFR2), complement component C1q, Fcgamma receptors, T cell receptor zeta chain, interleukin-10 (IL-10), poly (ADP-ribose) polymerase (PARP), and HRES-1.     

Triplications of chromosome 1p36.3, including the genes GABRD and SKI,are associated with a developmental disorder and a facial gestalt

Triplication of chromosomal region 1p36.3 is a rare genomic rearrangement. In this report, we delineate the phenotypic spectrum associated with 1p36.3 triplications. We describe four patients with microtriplications of variable size, but with a strong phenotypic overlap, and compare them to previously described patients with an isolated triplication or duplication of this region. The 1p36.3 triplication syndrome is associated with a distinct phenotype, characterized by global developmental delay, moderate intellectual disability, seizures, behavioral problems, and specific facial dysmorphic features, including ptosis, hypertelorism, and arched eyebrows. The de novo occurrence of these microtriplications demonstrates the reduced reproductive fitness associated with this genotype, in contrast to 1p36.3 duplications which are mostly inherited and can be associated with similar facial features but with a less severe developmental phenotype. The shared triplicated region encompasses four disease-related genes of which GABRD and SKI are most likely to contribute to the phenotype.     

Higher expression of miR-150-5p promotes tumorigenesis by suppressing LKB1 in non-small cell lung cancer

Lung cancer is one of the most malignant tumors that can form in the human. MicroRNAs (MiRNAs) play significant role in tumor progression. Human lung cancer tissues and cell lines were used to determine miR-150-5p respectively, and Liver Kinase B1 (LKB1) expression using quantitative real-time PCR (qRT-PCR). The data analysis website Kaplan-Meier Plotter (database obtained from The Cancer Genome Atlas) was used to perform a survival analysis with LKB1 levels. Using the appropriate assays, the function of miR-150-5p was also detected in cellular proliferation, migration and cell apoptosis as well as cell cycle. Results revealed that miR-150-5p was upregulated in non-small cell lung cancer (NSCLC) tissue and cell lines. In NSCLC, miR-150-5p promoted cellular proliferation and migration, but decreased cellular apoptosis. Conversely, miR-150-5p inhibition suppressed cellular growth. These results further revealed a network of cellular signaling for miR-150-5p to target LKB1. Ectopic expression of LKB1 can mitigate the tumor-promoting function of miR-150-5p. Collectively, these results indicated that miR-150-5p may promote lung cancer by inhibiting the suppressor gene LKB1 in NSCLC.     

Localization of human U1 small nuclear RNA genes to band p36.3 of chromosome 1 by in situ hybridization

Ul small nuclear RNA (Ul snRNA) is encoded by a large family of genes (30–125 copies/haploid genome) which are transcribed by RNA polymerase II. Ul snRNA is thought to function in gene splicing. Since the Ul genes were found to be >20 kb apart by analyzing genomic phage clones, the chromosomal location of Ul genes in the human genome was determined using Southern filter analysis of DNA isolated from human-rodent somatic cell hybrids and by in situ hybridization. Human DNA digested with PvuII and probed with a Ul-specific probe, pD2, show several major hybridizing fragments. Of these, two human PvuII fragments of 1.4 kb and 2.4 kb had unique mobilities compared to mouse fragments. In a study of 19 cell hybrids, the human-specific Ul fragments segregated with the chromosome 1 markers peptidase C and adenylate kinase 2. All other chromosomes showed>-19% discordancy. An additional 13 karyotyped cell hybrids, analyzed by Southern filter analysis, confirmed the assignment of this class of Ul genes to chromosome 1. Additional digests with MspI and PstI indicated that most Ul genes are located on chromosome 1. To determine if the Ul RNAs are located predominantly at one site or dispersed over chromosome 1, a tritium-labeled Ul probe was hybridized in situ to metaphase chromosomes. The majority of the grains were at band 1p36.3, suggesting that most of the Ul genes are located in this region.A preliminary report of these experiments were presented at the Human Gene Mapping Workshop in Los Angeles, August 20–26, 1983 (1).     

Interstitial microdeletion of chromosome 1p in two siblings

Two half-siblings are described with what we believe to be the second and third cases identified of the microdeletion, del(1)(p32.1p32.3). Both siblings had a tethered cord and had mental retardation, but otherwise their phenotypic presentations were quite different. The sister had failure to thrive, congenital dysplasia of the hip, absent corpus callosum, Chiari I malformation, and syringomyelia. The brother experienced neonatal seizures secondary to a hemorrhagic stroke. He had an accessory thumb, inguinal hernia, cryptorchidism, urinary reflux, and cholelithiasis. Although these children have only delayed development in common with the previously reported case, they help to further define chromosomal deletions in this area of chromosome 1. As yet, no clear phenotypic picture has emerged.     

Association analysis of chromosome 1 migraine candidate genes

Background  

Migraine with aura (MA) is a subtype of typical migraine. Migraine with aura (MA) also encompasses a rare severe subtype Familial Hemiplegic Migraine (FHM) with several known genetic loci. The type 2 FHM (FHM-2) susceptibility locus maps to chromosome 1q23 and mutations in the ATP1A2 gene at this site have recently been implicated. We have previously provided evidence of linkage of typical migraine (predominantly MA) to microsatellite markers on chromosome 1, in the 1q31 and 1q23 regions. In this study, we have undertaken a large genomic investigation involving candidate genes that lie within the chromosome 1q23 and 1q31 regions using an association analysis approach.     

Polymorphisms in DNA repair genes, chromosome aberrations, and lung cancer

We have previously investigated the role of polymorphic chemical metabolizing genes in the susceptibility to the development of lung cancer using 110 primary lung cancer patients and 119 matched smoker controls. Together with data from the present study on DNA repair genes, we did not observe significant associations between any single variant genotype for several DNA-repair and chemical-metabolizing genes (XPD [or ERCC2], XRCC1, XRCC3, GSTM1, GSTT1, MPO, and mEH [or EPHX1]) and lung cancer. In the present study, we have further evaluated a nested group of 79 patients and 69 matched controls, and observed that increased chromosome aberrations (CAs) were associated with variant DNA-repair genotypes among both the patient and the control groups, with a significant increase for individuals having the XPD Lys/Gln + Gln/Gln genotypes (P = 0.046). Patients often had significantly increased CAs compared with controls with the same DNA-repair genotype and with similar cigarette smoking habits (< or =40 pack-years or >40 pack-years). Analyses of interactions between the DNA-repair and chemical-metabolizing genes indicated that the most significant interactions were between the repair genotypes and the GSTM1/T1 null genotypes. Significant increases in CA from the interactions were often observed among patients with < or =40 pack-years, but not among those with >40 pack-years. Since some variant DNA-repair genotypes have functional deficits for DNA repair, the association between variant DNA-repair genotypes and increased CAs suggests a risk mechanism for the development of lung cancer, with the DNA-repair genotypes interacting with variant chemical metabolizing genotypes to further increase the risk. The observation that patients had significantly increased CA frequencies compared with controls, irrespective of genotype, suggests that patients have additional factors that contribute to the development of lung cancer.     

Association between genes on chromosome 4p16 and non-syndromic oral clefts in four populations

Isolated cleft lip with or without cleft palate and cleft palate are among the most common human birth defects. Several candidate gene studies on MSX1 have shown significant association between markers in MSX1 and risk of oral clefts, and re-sequencing studies have identified multiple mutations in MSX1 in a small minority of cases, which may account for 1–2% of all isolated oral clefts cases. We explored the 2-Mb region around MSX1, using a marker map of 393 single nucleotide polymorphisms (SNPs) in 297 cleft lip, with or without cleft palate, case–parent trios and 84 cleft palate trios from Maryland, Taiwan, Singapore, and Korea. Both individual markers and haplotypes of two to five SNPs showed several regions yielding statistical evidence for linkage and disequilibrium. Two genes (STK32B and EVC) yielded consistent evidence from cleft lip, with or without cleft palate, trios in all four populations. These two genes plus EVC2 also yielded suggestive evidence for linkage and disequilibrium among cleft palate trios. This analysis suggests that several genes, not just MSX1, in this region may influence risk of oral clefts.