Unknown Genetic Basis Research Articles

The cellular and molecular etiology of the craniofacial defects in the avian ciliopathic mutant talpid2.

talpid2 is an avian autosomal recessive mutant with a myriad of congenital malformations, including polydactyly and facial clefting. Although phenotypically similar to talpid3, talpid2 has a distinct facial phenotype and an unknown cellular, molecular and genetic basis. We set out to determine the etiology of the craniofacial phenotype of this mutant. We confirmed that primary cilia were disrupted in talpid2 mutants. Molecularly, we found disruptions in Hedgehog signaling. Post-translational processing of GLI2 and GLI3 was aberrant in the developing facial prominences. Although both GLI2 and GLI3 processing were disrupted in talpid2 mutants, only GLI3 activator levels were significantly altered in the nucleus. Through additional fine mapping and whole-genome sequencing, we determined that the talpid2 phenotype was linked to a 1.4 Mb region on GGA1q that contained the gene encoding the ciliary protein C2CD3. We cloned the avian ortholog of C2CD3 and found its expression was ubiquitous, but most robust in the developing limbs and facial prominences. Furthermore, we found that C2CD3 is localized proximal to the ciliary axoneme and is important for docking the mother centriole to the ciliary vesicle and cell membrane. Finally, we identified a 19 bp deletion in talpid2 C2CD3 that produces a premature stop codon, and thus a truncated protein, as the likely causal allele for the phenotype. Together, these data provide insight into the cellular, molecular and genetic etiology of the talpid2 phenotype. Our data suggest that, although the talpid2 and talpid3 mutations affect a common ciliogenesis pathway, they are caused by mutations in different ciliary proteins that result in differences in craniofacial phenotype.

Analysis of ELP4, SRPX2, and interacting genes in typical and atypical rolandic epilepsy.

Rolandic epilepsy (RE) and its atypical variants (atypical rolandic epilepsy, ARE) along the spectrum of epilepsy-aphasia disorders are characterized by a strong but largely unknown genetic basis. Two genes with a putative (ELP4) or a proven (SRPX2) function in neuronal migration were postulated to confer susceptibility to parts of the disease spectrum: the ELP4 gene to centrotemporal spikes and SRPX2 to ARE. To reexamine these findings, we investigated a cohort of 280 patients of European ancestry with RE/ARE for the etiological contribution of these genes and their close interaction partners. We performed next-generation sequencing and single-nucleotide polymorphism (SNP)-array based genotyping to screen for sequence and structural variants. In comparison to European controls we could not detect an enrichment of rare deleterious variants of ELP4, SRPX2, or their interaction partners in affected individuals. The previously described functional p.N327S variant in the X chromosomal SRPX2 gene was detected in two affected individuals (0.81%) and also in controls (0.26%), with some preponderance of male patients. We did not detect an association of SNPs in the ELP4 gene with centrotemporal spikes as previously reported. In conclusion our data do not support a major role of ELP4 and SRPX2 in the etiology of RE/ARE.

Next generation sequencing of an australian family to identify the genetic basis of a rare blood group antigen

<h3>Aim</h3> The SARAH red blood cell (RBC) antigen has been described in two families world-wide and has recently been implicated in a case of severe haemolytic disease of the fetus and newborn (HDFN). This study aimed to identify the genetic basis of SARAH. <h3>Methods</h3> DNA samples were collected from nine family members (six SARAH positive) from three generations. Samples were exome sequenced using the Agilent SureSelect All Exon v4 + UTR kit on an Illumina HiSeq2000. Sequence alignment was performed with Illumina CASAVA vl.8.2, mapping to the reference genome HG19. <h3>Results</h3> Sequencing identified 73 782 SNVs common among all family members. SNV filtering excluded SNVs with a NCBI dbSNP ID, non-protein coding SNVs, and SNVs not present in all six positive family members only. Following filtering, one SNV in the Glycophorin A (<i>GYPA)</i> gene was identified. This SNV is not in the 1000 Genomes Project (1000G) or Exome Sequencing Project (ESP6500) databases, further confirming this SNV is novel and of low-frequency. <h3>Discussion</h3> A genetic basis for SARAH was identified by utilising next generation sequencing of related individuals. This approach has application in investigations relating to other rare phenotypes or diseases of unknown genetic basis.

Olfactory impairment in familial ataxias

The main clinical manifestations of the spinocerebellar ataxias (SCAs) result from the involvement of the cerebellum and its connections. Cerebellar activity has been consistently observed in functional imaging studies of...

Phenotype and Polyp Landscape in Serrated Polyposis Syndrome

Serrated polyposis syndrome (SPS), also known as hyperplastic polyposis, is a syndrome of unknown genetic basis defined by the occurrence of multiple serrated polyps in the large intestine and associated with an increased risk of colorectal cancer (CRC). There are a variety of SPS presentations, which may encompass a continuum of phenotypes modified by environmental and genetic factors. To explore the phenotype of SPS, we recorded the histologic and molecular characteristics of multiple colorectal polyps in patients with SPS recruited between 2000 and 2010 from genetics clinics in Australia, New Zealand, Canada, and the United States. Three specialist gastrointestinal pathologists reviewed the polyps, which they classified into conventional adenomas or serrated polyps, with various subtypes, according to the current World Health Organization criteria. Mutations in BRAF and KRAS and mismatch repair protein expression were determined in a subset of polyps. A total of 100 patients were selected for the study, of whom 58 were female and 42 were male. The total polyp count per patient ranged from 6 to 150 (median 30). The vast majority of patients (89%) had polyposis affecting the entire large intestine. From this cohort, 406 polyps were reviewed. Most of the polyps (83%) were serrated polyps: microvesicular hyperplastic polyps (HP) (n=156), goblet cell HP (n=25), sessile serrated adenoma/polyps (SSA/P) (n=110), SSA/P with cytologic dysplasia (n=28), and traditional serrated adenomas (n=18). A further 69 polyps were conventional adenomas. BRAF mutation was mainly detected in SSA/P with dysplasia (95%), SSA/P (85%), microvesicular HP (76%), and traditional serrated adenoma (54%), whereas KRAS mutation was present mainly in goblet cell HP (50%) and in tubulovillous adenoma (45%). Four of 6 SSA/Ps with high-grade dysplasia showed loss of MLH1/PMS2 expression. CRC was diagnosed in 39 patients who were more often found to have a conventional adenoma compared with patients without CRC (P=0.003). Patients with SPS referred to genetics clinics had a pancolonic disease with a high polyp burden and a high rate of BRAF mutation. The occurrence of CRC was associated with the presence of conventional adenoma.

The genetic basis of early T-cell precursor acute lymphoblastic leukaemia

Early T-cell precursor acute lymphoblastic leukaemia (ETP ALL) is an aggressive malignancy of unknown genetic basis. We performed whole-genome sequencing of 12 ETP ALL cases and assessed the frequency of the identified somatic mutations in 94 T-cell acute lymphoblastic leukaemia cases. ETP ALL was characterized by activating mutations in genes regulating cytokine receptor and RAS signalling (67% of cases; NRAS, KRAS, FLT3, IL7R, JAK3, JAK1, SH2B3 and BRAF), inactivating lesions disrupting haematopoietic development (58%; GATA3, ETV6, RUNX1, IKZF1 and EP300) and histone-modifying genes (48%; EZH2, EED, SUZ12, SETD2 and EP300). We also identified new targets of recurrent mutation including DNM2, ECT2L and RELN. The mutational spectrum is similar to myeloid tumours, and moreover, the global transcriptional profile of ETP ALL was similar to that of normal and myeloid leukaemia haematopoietic stem cells. These findings suggest that addition of myeloid-directed therapies might improve the poor outcome of ETP ALL.

A Case Report of Fibular Aplasia, Tibial Campomelia, and Oligosyndactyly (FATCO) Syndrome Associated With Klinefelter Syndrome and Review of the Literature

Limb development is a complex regulated development phenomenon involving multiple genes. Fibular Aplasia, Tibial Campomelia and Oligosyndactyly (FATCO) syndrome (MIM#246570) is a syndrome of unknown genetic basis and inheritance with variable expressivity and penetrance. Its counterpart, Fuhrmann syndrome or Femoral-Fibularaplasia-Campomelia and Oligosyndactyly are a result of defect in the WNT7a gene located on the 3p25. Former is proposed to be a development dysplasia of defective dorso-ventral polarity assignment and distal limb development. Ectrodactyly and fibular a/hypoplasia (EFA, MIM# 113310) share the full phenotypic spectrum of FATCO syndrome, whether they are allelic disorders or represent two variable presentations in the spectrum of the same disorder is not an established fact. We report here one Indian patient with findings of FATCO syndrome with associated Klinefelter syndrome. This is the first such report which is likely to be a co-incidental finding and has implications for genetic counseling. Therapeutic, Level IV.

Hereditary Leukonychia, or Porcelain Nails, Resulting from Mutations in PLCD1

Hereditary leukonychia (porcelain nails or white nails) is a rare nail disorder with an unknown genetic basis. To identify variants in a gene underlying this phenotype, we identified four families of Pakistani origin showing features of hereditary leukonychia. All 20 nails of each affected individual were chalky and white in appearance, consistent with total leukonychia, with no other cutaneous, appendageal, or systemic findings. By using Affymetrix 10K chip, we established linkage to chromosome 3p21.3-p22 with a LOD score (Z) of 5.1. We identified pathogenic mutations in PLCD1 in all four families, which encodes phosphoinositide-specific phospholipase C delta 1 subunit, a key enzyme in phosphoinositide metabolism. We then identified localization of PLCD1 in the nail matrix. It was recently shown that PLCD1 is a component of the human nail plate by proteomic analysis and is localized in the matrix of human nails. Furthermore, mutations detected in PLCD1 resulted in reduced enzymatic activity invitro. Our data show that mutations in PLCD1 underlie hereditary leukonychia, revealing a gene involved in molecular control of nail growth.

Neuronal migration disorders in microcephalic osteodysplastic primordial dwarfism type I/III

Microcephalic osteodysplastic primordial dwarfism (MOPD) is a rare microlissencephaly syndrome, with at least two distinct phenotypic and genetic types. MOPD type II is caused by pericentrin mutations, while types I and III appear to represent a distinct entity (MOPD I/III) with variably penetrant phenotypes and unknown genetic basis. The neuropathology of MOPD I/III is little understood, especially in comparison to other forms of lissencephaly. Here, we report postmortem brain findings in an 11-month-old female infant with MOPD I/III. The cerebral cortex was diffusely pachygyric, with a right parietal porencephalic lesion. Histologically, the cortex was abnormally thick and disorganized. Distinct malformations were observed in different cerebral lobes, as characterized using layer-specific neuronal markers. Frontal cortex was severely disorganized and coated with extensive leptomeningeal glioneuronal heterotopia. Temporal cortex had a relatively normal 6-layered pattern, despite cortical thickening. Occipital cortex was variably affected. The corpus callosum was extremely hypoplastic. Brainstem and cerebellar malformations were also present, as well as old necrotic foci. Findings in this case suggest that the cortical malformation in MOPD I/III is distinct from other forms of pachygyria-lissencephaly.

Familial colorectal cancer type X: clinical, pathological and molecular characterization

Some families fulfilling the Amsterdam Criteria (AC) differ from the Lynch syndrome (LS) in that colorectal cancers (CRC) do not present microsatellite instability (MSI) and DNA mismatch repair gene mutations are not found. These families have been designated as Familial Colorectal Cancer type X (XS) and their genetic basis remains unknown. In families fulfilling AC for LS: 1) To perform MSI testing in CRC and to correlate it with clinical and pathological characteristics and with the mutational analysis in the DNA mismatch repair genes; 2) In cases suggestive of XS, to study the suppressor pathway (SP) of carcinogenesis. 45 patients with CRC, from 41 families fulfilling AC, were included. Clinical and pathological data were recorded. MSI testing was performed with the Bethesda marker panel and mutational analysis in MLH1, MSH2 and MSH6 genes was undertaken by DGGE, MLPA and direct sequencing. To study the SP, loss of heterozigoty was evaluated at the following loci: APC, p53, DCC and SMAD4 genes. 33/41 (80%) and 8/41 (20%) families presented high-grade microsatellite instability (MSI-H) and microsatellite stable (MSS) CRC, respectively. In families suggestive of XS, a smaller number of CRC and less frequent spectrum associated tumors were detected. In comparison with MSI-H CRC, MSS CRC were preferentially located at the distal colon/rectum and less often presented mucous production or lymphocytic infiltrate. In 70% of families with MSI-H CRC, a pathogenic mutation in one of the DNA mismatch repair genes was identified, as opposed to none in the group with MSS CRC. The SP was followed in 2 cases and an alternative one in other two. The remaining 4 cases were noninformative; however, 5/8 (63%) presented allelic losses in the APC gene. 1) Families fulfilling AC and harbouring MSS CRC presented particular characteristics, which reinforce the existence of a new entity, different from LS; 2) The designation of Familial Colorectal Cancer type X seems appropriate to classify an entity whose CRC follow an unclear carcinogenesis pathway and that presents an unknown genetic basis; 3) The designation of LS should be restricted to families with an identified pathogenic DNA mismatch repair gene mutation.

Reticular dysgenesis (aleukocytosis) is caused by mutations in the gene encoding mitochondrial adenylate kinase 2

Human severe combined immunodeficiencies (SCID) are phenotypically and genotypically heterogeneous diseases. Reticular dysgenesis is the most severe form of inborn SCID. It is characterized by absence of granulocytes and almost complete deficiency of lymphocytes in peripheral blood, hypoplasia of the thymus and secondary lymphoid organs, and lack of innate and adaptive humoral and cellular immune functions, leading to fatal septicemia within days after birth. In bone marrow of individuals with reticular dysgenesis, myeloid differentiation is blocked at the promyelocytic stage, whereas erythro- and megakaryocytic maturation is generally normal. These features exclude a defect in hematopoietic stem cells but point to a unique aberration of the myelo-lymphoid lineages. The dramatic clinical course of reticular dysgenesis and its unique hematological phenotype have spurred interest in the unknown genetic basis of this syndrome. Here we show that the gene encoding the mitochondrial energy metabolism enzyme adenylate kinase 2 (AK2) is mutated in individuals with reticular dysgenesis. Knockdown of zebrafish ak2 also leads to aberrant leukocyte development, stressing the evolutionarily conserved role of AK2. Our results provide in vivo evidence for AK2 selectivity in leukocyte differentiation. These observations suggest that reticular dysgenesis is the first example of a human immunodeficiency syndrome that is causally linked to energy metabolism and that can therefore be classified as a mitochondriopathy.

Transcriptome Analysis of a Phenol-Producing Pseudomonas putida S12 Construct: Genetic and Physiological Basis for Improved Production

The unknown genetic basis for improved phenol production by a recombinant Pseudomonas putida S12 derivative bearing the tpl (tyrosine-phenol lyase) gene was investigated via comparative transcriptomics, nucleotide sequence analysis, and targeted gene disruption. We show upregulation of tyrosine biosynthetic genes and possibly decreased biosynthesis of tryptophan caused by a mutation in the trpE gene as the genetic basis for the enhanced phenol production. In addition, several genes in degradation routes connected to the tyrosine biosynthetic pathway were upregulated. This either may be a side effect that negatively affects phenol production or may point to intracellular accumulation of tyrosine or its intermediates. A number of genes identified by the transcriptome analysis were selected for targeted disruption in P. putida S12TPL3. Physiological and biochemical examination of P. putida S12TPL3 and these mutants led to the conclusion that the metabolic flux toward tyrosine in P. putida S12TPL3 was improved to such an extent that the heterologous tyrosine-phenol lyase enzyme had become the rate-limiting step in phenol biosynthesis.

Abnormal Expression of TRAF Adapter Proteins in Waldenstrom's Macroglobulinemia.

Background: Waldenström's Macroglobulinemia (WM) is an incurable low-grade lymphoplasmacytic lymphoma with as yet unknown genetic basis for its pathogenesis. Several TNF family members (CD40L, APRIL and BAFF/BLYS) are known to regulate WM growth and survival. TRAFs are a novel family of adapter proteins that facilitate pro-apoptotic (TACI) or pro-survival/differentiation (CD40, BAFFR, BCMA) receptor signaling mediated by TNF family ligands. Therefore, understanding the TRAF system in WM may yield important clues about WM growth and survival.Methods: WM cell lines (BCWM.1 and WSU-WM), IgM secreting low-grade lymphoma cell lines (MEK1, RL, Namalwa), and primary bone marrow CD19+ selected lymphoplasmacytic cells (LPC) from 20 WM patients and 6 healthy donors were evaluated for TRAF (TRAF 2, 3, 5, 6) expression using semi quantitative RT-PCR and/or western blot analysis.Results: The TNF familiy receptors CD40, BAFFR, BCMA, and TACI were expressed in all cell lines tested as well as in CD19+ selected LPC from WM patients and healthy donors. Moreover, TRAF 2, 3, 5, 6 were expressed in all cell lines by both RT-PCR and western blot analysis. In contrast, we observed loss or abnormally low expression of both TRAF 2 and 5 in 6/20 (30%) patients, whilst TRAF 3 was absent or abnormally low in 3/30 (15%) patients. TRAF 6 was expressed in all patients. Among healthy donors, we observed expression of all TRAF adapter proteins.Conclusion: Up to one third of WM patients demonstrate loss of TRAF 2 and 5 adapter proteins which facilitate signaling through the pro-apoptotic receptor TACI. Ongoing studies including gene sequencing and siRNA knockdown models are delineating a role for TRAF loss in the pathogenesis of WM.

Mutational analysis of the PTH 3′‐untranslated region in parathyroid disorders

Sequence alterations in untranslated regions (UTRs) of genes are important contributors to human diseases, including hereditary thrombophilia, hereditary hyperferritinaemia-cataract and fragile X mental retardation syndromes. Recently, functional studies of the 3'-UTR of the PTH gene, encoding parathyroid hormone, have highlighted it as a potential target for pathogenic mutations in patients with parathyroid dysfunction. Regulation of PTH gene expression occurs in part through protein binding to a specific 26 nucleotide instability element in the 3'-UTR of PTH mRNA, in a sequence-dependent manner. Thus, the PTH 3'-UTR has emerged as an important potential contributor to parathyroid dysfunction. Therefore, we sought to rigorously examine the PTH 3'-UTR in patients with primary and secondary parathyroid disorders, including primary parathyroid hyperplasia, secondary parathyroid hyperplasia, sporadic parathyroid adenoma and familial hypoparathyroidism of unknown genetic basis. Twenty-one parathyroid glands from 14 patients with primary parathyroid hyperplasia, 40 sporadic parathyroid adenomas from 40 patients, 42 parathyroid glands from 29 patients with secondary parathyroid hyperplasia and peripheral blood leucocytes from 24 affected members of eight kindreds with familial hypoparathyroidism of unknown genetic basis were examined for mutations in the 3'-UTR of the PTH gene. No alterations from the normal sequence were detected in any of the 127 samples examined. Based on the absence of identifiable DNA sequence alterations in these forms of parathyroid dysfunction, it is unlikely that mutation of the PTH 3'-UTR contributes frequently to their pathogenesis.

Congenital dyserythropoietic anemias: epidemiology, clinical significance, and progress in understanding their pathogenesis.

The congenital dyserythropoietic anemias (CDAs) comprise a group of rare hereditary disorders of erythropoiesis, characterized by ineffective erythropoiesis as the predominant mechanism of anemia and by distinct morphological abnormalities of the majority of erythroblasts in the bone marrow. The classification in three types as proposed in 1968 is still valid, but there is genetic heterogeneity within each type, and there are additional variants of unknown genetic basis. CDA II is the most frequent, and the nonfamilial type of CDA III the rarest group. The genes of CDA II and CDA III were mapped to chromosome 20 and 15, respectively, and the gene of CDA I on 15q was recently cloned. Therapeutic decision making requires definition of the type, an estimate of individual severity, and presence of or risk for complications. Therapeutic measures include interferon-alpha for CDA I, splenectomy for CDA II, and iron depletion for all individuals at risk for secondary hemochromatosis.

Unraveling the molecular mechanisms of hair and nail genodermatoses.

Inherited hair and nail diseases have long been considered a group of rare and obscure disorders with a largely unknown genetic basis. In the postgenomic era, a large portion of the genes that are responsible for these genetic disorders has been identified, yielding new insights into the complex molecular pathways that regulate the development and biological function of epidermal appendages. This article reviews the recent progress accomplished in this field and discusses the novel clinical and experimental observations in several hair and nail genodermatoses.

Predictive Value of Drosophila

The Drosophila fruitless (fru) mutant analysis of Lisa Ryner et al. ([1][1]) discussed by Wade Roush (Research News, [13 Dec., p. 1836][2]) is an important contribution to our understanding of the largely unknown genetic basis for insect behavior. But the evolutionary implications put forth by Ryner