A Novel ARL3 Gene Mutation Associated With Autosomal Dominant Retinal Degeneration

Despite major progress in the discovery of causative genes, many individuals and families with inherited retinal degenerations (IRDs) remain without a molecular diagnosis. We applied whole exome sequencing to identify the genetic cause in a family with an autosomal dominant IRD. Eye examinations were performed and affected patients were studied with electroretinography and kinetic and chromatic static perimetry. Sequence variants were analyzed in genes (n = 271) associated with IRDs listed on the RetNet database. We applied a stepwise filtering process involving the allele frequency in the control population, in silico prediction tools for pathogenicity, and evolutionary conservation to prioritize the potential causal variant(s). Sanger sequencing and segregation analysis were performed on the proband and other family members. The IRD in this family is expressed as a widespread progressive retinal degeneration with maculopathy. A novel heterozygous variant (c.200A > T) was identified in the ARL3 gene, leading to the substitution of aspartic acid to valine at position 67. The Asp67 residue is evolutionary conserved, and the change p.Asp67Val is predicted to be pathogenic. This variant was segregated in affected members of the family and was absent from an unaffected individual. Two previous reports of a de novo missense mutation in the ARL3 gene, each describing a family with two affected generations, are the only examples to date of autosomal dominant IRD associated with this photoreceptor gene. Our results, identifying a novel pathogenic variant in ARL3 in a four-generation family with a dominant IRD, augment the evidence that the ARL3 gene is another cause of non-syndromic retinal degeneration.

The Opioid Epidemic and Nonmarital Childbearing in the United States, 2000–2016

The United States has experienced a dramatic rise in opioid addiction and opioid overdose deaths in recent years. We investigate the effect of the opioid epidemic at the local level on nonmarital fertility using aggregate- and individual-level analyses. Opioid overdose death rates and prescriptions per capita are used as indicators of the intensity of the opioid epidemic. We estimate area fixed-effects models to test the effect of the opioid epidemic on nonmarital birth rates obtained from vital statistics for 2000–2016. We find an increase in nonmarital birth rates in communities that experienced a rise in opioid overdose deaths and higher prescription rates. Our analyses also show that the local effect of the opioid epidemic is not driven by a reduction in marriage rates and that marital birth rates are unaffected. Individual-level data from the ACS 2008–2016 are then used to further assess the potential causal mechanisms and to test heterogeneous effects by education and race/ethnicity. Our findings suggest that the opioid epidemic increased nonmarital birth rates through social disruptions primarily affecting unmarried women but not through changes in their economic condition.

Polymorphisms in COL2A1 gene in Adolescents with Temporomandibular Disorders

Objectives: Temporomandibular disorder (TMD) is considered a functional disorder with multifactorial aspects. The goal of this study was to investigate if genetic polymorphisms in the COL2A1 gene could be associated with TMD in adolescents. Study design: The case group (TMD-affected) included individuals diagnosed with any of the following TMD subgroups according to the RDC/TMD criteria: myofascial pain, disc displacements and arthralgia. Genomic DNA for molecular analysis was extracted from buccal cells and genetic polymorphisms in COL2A1 were genotyped by real time polymerase chain reactions using the TaqMan assay. Data were analyzed using the Epi Info 3.5.7 and Stata software. Results: 249 subjects were included in this study (148 subjects “affected” by TMD). There were no significant differences between the affected and unaffected individual (p>0.05), for TMD, arthralgia and myofascial pain however, rs2276454 was borderline in the genotype distribution (p=0.07) and was associated with disc displacement (p=0.03) in the allelic distribution. Recessive model showed significant differences between groups for with disc displacement (p=0.02). Conclusions: Genetic polymorphisms in COL2A1 are not associated with myofascial pain, arthralgia or TMD in adolescents but this study provides evidence that rs2276454 is involved in the disc displacement of the temporomandibular joint.

Single-Cell RNA-Seq to Assess Differential Responses to Tnfα in Human Hematopoietic Stem and Progenitor Cells in Myeloproliferative Neoplasm

Somatic mutations in hematopoietic stem and progenitor cells (HSPCs) leading to constitutive activation of thrombopoietin receptor signaling result in myeloproliferative neoplasms (MPN). The most common mutation found in MPN patients occurs in the Janus kinase 2 gene (JAK2V617F). We have previously found that JAK2V617F hematopoietic progenitors are resistant to tumor necrosis factor alpha (TNFα), however this mechanism is not well defined. We hypothesize that resistance to TNFα in JAK2V617F hematopoietic stem and progenitors is a driver of the competitive advantage over non-malignant clones. Here, we used droplet-based single-cell RNA-sequencing to investigate transcriptional profiling in primary human HSPCs. First, we harvested white blood cells from fresh bone marrow aspirates from one MPN patient (Polycythemia Vera with 71% JAK2V617F allele burden) as well as one unaffected individual then sorted Lin-/CD34+/CD38- hematopoietic progenitors. Immediately following sorting, half of the cells were stimulated with TNFα for 4 hours while the other half of cells were used as unstimulated controls. We then utilized the 10X Chromium platform to generate single-cell droplets for the 8,129 total cells from the unaffected individual and 33,299 total cells from the MPN patient. We ran alignment using the CellRanger pipeline then performed analysis using the Seurat package in R. Expression profiles of untreated HSPCs in both normal and MPN cells revealed high expression of genes involved in important pathways for hematopoiesis (Polycomb repressive complexes, chromatin regulation, the ubiquitin proteasome system etc.). Expression of CD34 was confirmed in both MPN and non-MPN cells, though CD34 expression was reduced following TNFα stimulation. Expression of stem (i.e. THY1, ITGA6) and progenitor (i.e. PTPRC) genes were detected within both individuals, which highlights the heterogeneity within Lineage-/CD34+/CD38- cells. Following stimulation with TNFα, we observed expression of genes in canonical pathways downstream of TNF including NF-κB, Mitogen-Activated Protein Kinase (MAPK), and Transforming Growth Factor Beta (TGFβ). Indeed, we observed a baseline level of expression of TGFβ-related genes in both normal and MPN cells. Upon inflammatory stimulation, normal HSPCs upregulated SMAD expression which are involved in the TGFβ pathway. Strikingly, we did not observe an increase in SMAD expression in MPN cells following TNF. This suggests a dampened response via the TGFβ pathway to TNF in MPN cells. Additionally, we found that TNF-stimulated HPSCs from the unaffected individual expressed canonical genes of the TNF pathway that encode for chemokines, cytokines, transcription factors and negative feedback regulators. In normal TNF-stimulated cells, we identified highly expressed genes involved in the caspase cascade, suggesting a robust apoptotic response in normal HPSCs. However, there was a lower expression of caspases in stimulated MPN cells, suggesting a dampened apoptotic response to TNF. One observation that was unique to TNF-stimulated cells from the MPN individual was the expression of glycoproteins involved in angiogenesis and platelet aggregation. Taken together, these data serve as a proof of principle for transcriptional profiling of primary human hematopoietic stem and progenitor cells and that this cell population rapidly and robustly alter their gene expression program upon TNFα stimulation. In conclusion, we show that HSPCs from an MPN patient exhibit a dampened response to TNF compared to normal HSPCs. Specifically, we observed a lower expression of genes involved with apoptosis and TGFβ signaling in MPN cells compared to normal cells following TNF stimulation. The finding of a dampened apoptotic response to TNF is consistent with the hypothesis that JAK2V617F cells gain a selective advantage over normal cells under inflammatory stress. To our knowledge, this is the first report of single-cell RNA-seq analysis on primary human HSPCs following FACS and inflammatory stimulation. Disclosures Fleischman: incyte: Speakers Bureau.

Pasture condition and milk production by grazing dairy cows as affected by daily herbage-allowance restriction

Daily herbage allowance is recognised as the main tool to control pasture utilisation and milk production per cow. The aim of the present study was to evaluate the long-term effects of daily herbage allowance (DHA) on pasture characteristics and milk production of dairy cows. Forty-four dairy cows were randomly assigned to one of four treatments in a 2 × 2 factorial design by considering two levels of DHA (20 and 30 kg DM/cow.day) and two types of supplements (high-moisture maize and maize silage) over a 77-day period. Pre- and post-grazing herbage masses, vertical distribution of herbage mass, species density, botanical and chemical composition, sward depletion and changes in morphological components of the pasture were measured. The effect of DHA on soil compaction was evaluated on the basis of the penetration resistance. Milk production and composition levels, bodyweights and body condition scores were recorded. Post-grazing residual declined as the level of DHA decreased, while grazing efficiency increased from 39.8% to 44.8%. We found no effects of DHA on any pasture characteristics, pasture regrowth or soil compaction. Low-DHA conditions induced a faster sward-height reduction, while the herbage mass remained unaffected. Individual milk production decreased with DHA. However, milk outputs per hectare increased by 2772 L/ha. Milk composition, bodyweight and body condition score were not affected by DHA. The results showed that DHA restriction decreases milk production per cow while increasing both herbage utilisation and milk production per hectare, without affecting long-term pasture condition.

A cost analysis of a cancer genetic service model in the UK

Background: Technological advances in DNA sequencing have made gene testing fast and more affordable. Evidence of cost-effectiveness of genetic service models is essential for successful translation, but remain sparse in the literature. In particular there is a lack of cost data related to genetic services. Methods: A detailed micro-costing of 28 pathways relating to breast and/or ovarian cancer and gene testing for the BRCA1 and BRCA2 genes (termed ′BRCA testing′) was carried out. These data were combined with patient-level data from a Royal Marsden Cancer Genetics Service audit during which BRCA testing was offered to individuals at ≥10% risk of having a mutation. Results: The average cost across all pathways was &pound2,222.68 (range &pound376.47- &pound13,531.24). The average pathway cost for a person with cancer was &pound1897.71 compared to &pound2,403.22 for a person without cancer. Of the women seen during audit period, 38% were affected with breast and/or ovarian cancer and 62% were unaffected but concerned about their family history. Conclusion: There is considerable variation in the costs of different gene testing pathways. Improved cost-efficiency could be achieved by increasing the proportion of cancer patients tested, because the pathway cost of an unaffected individual in whom testing has already been performed in a relative with cancer is considerably less.

Assessment of Liquid Microbead Arrays for the Screening of Newborns for Spinal Muscular Atrophy

Background: Spinal muscular atrophy is a common neurodegenerative disorder that has recently been considered for inclusion in the next generation of newborn screening regimens. We sought to validate liquid microbead arrays for the identification of affected individuals by direct DNA analysis. Methods: Assays were created to detect the homozygous deletions in exon 7 of the SMN1 gene found in approximately 95% of affected individuals by use of 2 different microbead chemistries on the Luminex 200: MultiCode-PLx and Tag-It. A series of 367 blood spots including 164 from affected individuals, 46 from known carriers, and 157 from unaffected individuals were then analyzed with each assay. Results: The MultiCode-PLx assay required 4.2 h to perform and provided correct identification of all 164 samples from affected individuals. Correct exclusion was also made for all 46 carrier and 157 unaffected individual samples. The Tag-It assay required 6.8 h, detected all samples from affected individuals, and excluded all but 1 (99.5%) of the samples from carriers and unaffected individuals. Neither method was sensitive to increasing copy numbers of the SMN2 gene. Conclusions: Both methods showed high sensitivity and specificity for the detection of patients with spinal muscular atrophy. For both methods, ample DNA was extracted from all blood spots for analysis, and SMN2 copy numbers did not interfere. Liquid bead arrays represent a robust method for DNA analysis in newborn screening laboratories.

Bernard-Soulier Syndrome Caused by a Dinucleotide Deletion and Reading Frameshift in the Region Encoding the Glycoprotein Ibα Transmembrane Domain

We investigated the molecular genetic and biosynthetic basis of Bernard-Soulier syndrome in a severely affected white woman. Flow cytometric analysis showed a severe deficiency of glycoprotein (GP) Ib, GP IX, and GP V on the surface of her platelets. Similarly, GP Ibα was undetectable by immunoblot analysis of platelet lysates. Surprisingly, a large quantity of a 70-kD protein (which probably represents a GP Ibα degradation product) was found in the patient's plasma in much greater quantities than in the plasma of an unaffected individual. To analyze the molecular lesion responsible for the disorder, we amplified and sequenced gene segments corresponding to the entire coding regions of the GP Ibα, GP Ibβ, and GP IX genes. The patient was homozygous for a specific GP Ibα allele that contained two tandem VNTR repeats in the region encoding the macroglycopeptide (C variant) and three differences from the published GP Ibα gene sequence. Two mutations were unlikely to be involved in the disorder: the substitution of a single base (T → C) in the second nucleotide of exon 2, which is in the 5′ untranslated region of the GP Ibα transcript, and a silent mutation in the third base of the codon for Arg342 (A → G) that does not change the amino acid sequence. The third mutation was a deletion of the last two bases of the codon for Tyr492 (TAT). This mutation causes a frameshift that alters the GP Ibα amino acid sequence, beginning within its transmembrane region. The mutant polypeptide contains 81 novel amino acids and is 38 amino acids shorter than its wild-type counterpart. The new sequence changes the hydrophobic nature of the transmembrane domain and greatly decreases the net positive charge of what had been the cytoplasmic domain. The deletion mutation was introduced into the GP Ibα cDNA, alone and in combination with the 5′ mutation, and expressed in Chinese hamster ovary (CHO) cells. The deletion alone severely reduced GP Ibα expression on the cell surface. Expression was not decreased further by addition of the 5′ mutation, confirming that the deletion was the cause of the Bernard-Soulier phenotype. Stable cell lines expressing the mutant polypeptide secreted large amounts of the polypeptide into the medium, suggesting that the mutant anchors poorly in the plasma membrane. Nevertheless, a fraction of the mutant was able to associate with GP Ibβ, as demonstrated by their coimmunoprecipitation with a GP Ibβ antibody.

Bernard-Soulier Syndrome Caused by a Dinucleotide Deletion and Reading Frameshift in the Region Encoding the Glycoprotein Ibα Transmembrane Domain

We investigated the molecular genetic and biosynthetic basis of Bernard-Soulier syndrome in a severely affected white woman. Flow cytometric analysis showed a severe deficiency of glycoprotein (GP) Ib, GP IX, and GP V on the surface of her platelets. Similarly, GP Ibα was undetectable by immunoblot analysis of platelet lysates. Surprisingly, a large quantity of a 70-kD protein (which probably represents a GP Ibα degradation product) was found in the patient's plasma in much greater quantities than in the plasma of an unaffected individual. To analyze the molecular lesion responsible for the disorder, we amplified and sequenced gene segments corresponding to the entire coding regions of the GP Ibα, GP Ibβ, and GP IX genes. The patient was homozygous for a specific GP Ibα allele that contained two tandem VNTR repeats in the region encoding the macroglycopeptide (C variant) and three differences from the published GP Ibα gene sequence. Two mutations were unlikely to be involved in the disorder: the substitution of a single base (T → C) in the second nucleotide of exon 2, which is in the 5′ untranslated region of the GP Ibα transcript, and a silent mutation in the third base of the codon for Arg342 (A → G) that does not change the amino acid sequence. The third mutation was a deletion of the last two bases of the codon for Tyr492 (TAT). This mutation causes a frameshift that alters the GP Ibα amino acid sequence, beginning within its transmembrane region. The mutant polypeptide contains 81 novel amino acids and is 38 amino acids shorter than its wild-type counterpart. The new sequence changes the hydrophobic nature of the transmembrane domain and greatly decreases the net positive charge of what had been the cytoplasmic domain. The deletion mutation was introduced into the GP Ibα cDNA, alone and in combination with the 5′ mutation, and expressed in Chinese hamster ovary (CHO) cells. The deletion alone severely reduced GP Ibα expression on the cell surface. Expression was not decreased further by addition of the 5′ mutation, confirming that the deletion was the cause of the Bernard-Soulier phenotype. Stable cell lines expressing the mutant polypeptide secreted large amounts of the polypeptide into the medium, suggesting that the mutant anchors poorly in the plasma membrane. Nevertheless, a fraction of the mutant was able to associate with GP Ibβ, as demonstrated by their coimmunoprecipitation with a GP Ibβ antibody.