👤 Steven A Wall

Familial hypercholesterolemia (FH) is a genetic disorder driven in part by mutations in three genes that encode components of the cholesterol pathway: LDLR, APOB, and PCSK9. However, the majority of FH genetics has been performed in individuals of European descent. Here, we leveraged a cohort of 300 patients from the Mexican FH registry to understand how rare, high liability alleles and common variants might contribute to shaping individual risk. Using a combination of whole exome and of short- and long-read whole genome sequencing, we report three key findings. First, we observed that rare pathogenic point mutations and structural variants in all known FH genes, together with variants in APOE, CREB3L3, and PLIN1, contribute to a molecular FH diagnosis in 67% of families, including novel gene-disruptive copy number variants (CNVs) which arose in a native American background. Second, ancestry-adjusted polygenic risk score analysis identified a significant liability for coronary artery disease, hypertension, LDL, HDL, and Type 2 Diabetes. The polygenic signal for LDL was present in patients with rare, pathogenic FH mutations and was more prominent in individuals bereft of a molecular FH diagnosis. Finally, we report both a whole-gene duplication and common, non-coding variants in a novel locus, PDZK1, which contribute to the genetic burden of FH, a finding we replicated in the UK Biobank (UKB). Together, our analyses illustrate the value of genetic studies in non-European populations and reinforce the notion that individual risk to disease can arise from both rare, large effect alleles (alone or in combination across genes) and common variants that increase the mutational burden of a biological system. Show less

BACKGROUNDHypoactive sexual desire disorder (HSDD) is characterized by a persistent deficiency of sexual fantasies and desire for sexual activity, causing marked distress and interpersonal difficulty. It is the most prevalent female sexual health problem globally, affecting approximately 10% of women, but has limited treatment options. Melanocortin 4 receptor (MC4R) agonists have emerged as a promising therapy for women with HSDD, through unknown mechanisms. Studying the pathways involved is crucial for our understanding of normal and abnormal sexual behavior.METHODSUsing psychometric, functional neuroimaging, and hormonal analyses, we conducted a randomized, double-blinded, placebo-controlled, crossover clinical study to assess the effects of MC4R agonism compared with placebo on sexual brain processing in 31 premenopausal heterosexual women with HSDD.RESULTSMC4R agonism significantly increased sexual desire for up to 24 hours after administration compared with placebo. During functional neuroimaging, MC4R agonism enhanced cerebellar and supplementary motor area activity and deactivated the secondary somatosensory cortex, specifically in response to visual erotic stimuli, compared with placebo. In addition, MC4R agonism enhanced functional connectivity between the amygdala and the insula during visual erotic stimuli compared with placebo.CONCLUSIONThese data suggest that MC4R agonism enhanced sexual brain processing by reducing self-consciousness, increasing sexual imagery, and sensitizing women with HSDD to erotic stimuli. These findings provide mechanistic insight into the action of MC4R agonism in sexual behavior and are relevant to the ongoing development of HSDD therapies and MC4R agonist development more widely.TRIAL REGISTRATIONClinicalTrials.gov NCT04179734.FUNDINGThis is an investigator-sponsored study funded by AMAG Pharmaceuticals Inc., the Medical Research Council (MRC) (MR/T006242/1), and the National Institute for Health Research (NIHR) (CS-2018-18-ST2-002 and RP-2014-05-001). Show less

The U937 cell line is widely employed as a research tool. It has a complex karyotype. A PICALM-MLLT10 fusion gene formed by the recurrent t(10;11) translocation is present, and the myeloid common deleted region at 20q12 has been lost from its near-triploid karyotype. We carried out a detailed investigation of U937 genome reorganisation including the chromosome 20 rearrangements and other complex rearrangements. SNP array, G-banding and Multicolour FISH identified chromosome segments resulting from unbalanced and balanced rearrangements. The organisation of the abnormal chromosomes containing these segments was then reconstructed with the strategic use of targeted metaphase FISH. This provided more accurate karyotype information for the evolving karyotype. Rearrangements involving the homologues of a chromosome pair could be differentiated in most instances. Centromere capture was demonstrated in an abnormal chromosome containing parts of chromosomes 16 and 20 which were stabilised by joining to a short section of chromosome containing an 11 centromere. This adds to the growing number of examples of centromere capture, which to date have a high incidence in complex karyotypes where the centromeres of the rearranged chromosomes are identified. There were two normal copies of one chromosome 20 homologue, and complex rearrangement of the other homologue including loss of the 20q12 common deleted region. This confirmed the previously reported loss of heterozygosity of this region in U937, and defined the rearrangements giving rise to this loss. Centromere capture, stabilising chromosomes pieced together from multiple segments, may be a common feature of complex karyotypes. However, it has only recently been recognised, as this requires deliberate identification of the centromeres of abnormal chromosomes. The approach presented here is invaluable for studying complex reorganised genomes such as those produced by chromothripsis, and provides a more complete picture than can be obtained by microarray, karyotyping or FISH studies alone. One major advantage of SNP arrays for this process is that the two homologues can usually be distinguished when there is more than one rearrangement of a chromosome pair. Tracking the fate of each homologue and of highly repetitive DNA regions such as centromeres helps build a picture of genome evolution. Centromere- and telomere-containing elements are important to deducing chromosome structure. This study confirms and highlights ongoing evolution in cultured cell lines. Show less

T-cell lymphoblastic lymphoma/T-cell acute lymphoblastic leukemia (T-LBL/T ALL) is an aggressive hematological malignancy arising from malignant transformation of T-cell progenitors with poor prognosis in adult patients. Outcomes are particularly dismal in the relapsed/refractory setting, and therapeutic options are limited in this context. Genomic profiling has shown frequent aberrations in the JAK-STAT pathway, including recurrent mutations in Show less

We performed a comprehensive assessment of rare inherited variation in autism spectrum disorder (ASD) by analyzing whole-genome sequences of 2,308 individuals from families with multiple affected children. We implicate 69 genes in ASD risk, including 24 passing genome-wide Bonferroni correction and 16 new ASD risk genes, most supported by rare inherited variants, a substantial extension of previous findings. Biological pathways enriched for genes harboring inherited variants represent cytoskeletal organization and ion transport, which are distinct from pathways implicated in previous studies. Nevertheless, the de novo and inherited genes contribute to a common protein-protein interaction network. We also identified structural variants (SVs) affecting non-coding regions, implicating recurrent deletions in the promoters of DLG2 and NR3C2. Loss of nr3c2 function in zebrafish disrupts sleep and social function, overlapping with human ASD-related phenotypes. These data support the utility of studying multiplex families in ASD and are available through the Hartwell Autism Research and Technology portal. Show less

This study investigated the dietary effect of steam-pelleted rapeseed (RS) diets with different inclusion levels on the fatty acid composition of chicken meat and the expression of lipid metabolism-related genes in the liver. Experimental diets included 6 different wheat-soybean meal based diets either in nonpelleted or steam-pelleted form supplemented with 80, 160, and 240 g RS/kg feed and one nonpelleted wheat-soybean meal based diet without RS supplementation as the control. These diets were fed to newly hatched broiler chickens (Ross 308) for 34 days. Compared to the control diet, steam-pelleted diets containing 160 or 240 g/kg RS significantly increased the content of omega-3 long chain polyunsaturated fatty acids (n-3 LC-PUFA) in the breast and drumstick, while their meat yields were not affected. Moreover, the mRNA levels of fatty acid desaturase 1 (FADS1) and acyl-coenzyme A oxidase 1 (ACOX1) in their livers increased. Therefore, steam-pelleted diets with 160 or 240 g/kg RS can be used to increase the n-3 LC-PUFA content in chicken meat without compromising meat yield. Show less

Genotyping by high-resolution melting analysis of small amplicons is homogeneous and simple. However, this approach can be limited by physical and chemical components of the system that contribute to intersample melting variation. It is challenging for this method to distinguish homozygous G::C from C::G or A::T from T::A base-pair neutral variants, which comprise approximately 16% of all human single nucleotide polymorphisms (SNPs). We used internal oligonucleotide calibrators and custom analysis software to improve small amplicon (42-86 bp) genotyping on the LightScanner. Three G/C (PAH c.1155C>G, CHK2 c.1-3850G>C and candidate gene BX647987 c.261+22,290C>G) and three T/A (CPS1 c.3405-29A>T, OTC c.299-8T>A and MSH2 c.1511-9A>T) human single nucleotide variants were analyzed. Calibration improved homozygote genotyping accuracy from 91.7 to 99.7% across 1105 amplicons from 141 samples for five of the six targets. The average T(m) standard deviations of these targets decreased from 0.067 degrees C before calibration to 0.022 degrees C after calibration. We were unable to generate a small amplicon that could discriminate the BX647987 c.261+22,290C>G (rs1869458) SNP, despite reducing standard deviations from 0.086 degrees C to 0.032 degrees C. Two of the sites contained symmetric nearest neighbors adjacent to the SNPs. Unexpectedly, we were able to distinguish these homozygotes by T(m) even though current nearest neighbor models predict that the two homozygous alleles would be identical. Show less

The aim of this study was to examine the expression of the RBM5 tumor suppressor, in relation to RBM6 and RBM10, to obtain a better understanding of the potential role played by these RBM5-related factors in the regulation of RBM5 tumor-suppressor activity. Paired non-tumor and tumor samples were obtained from 73 breast cancer patients. RNA and protein expression were examined by semi-quantitative reverse transcription-polymerase chain reaction and immunoblot, respectively. Data were analyzed using various statistical methods to test for correlations amongst the RBM5-related factors, and between the factors and various pathological parameters. Most notably, RBM5, RBM10v1, and HER2 protein expression levels were elevated in tumor tissue (P < 0.0001). RBM5 and RBM10v1 protein expression were significantly positively correlated (P < 0.001), as were RBM5 and HER2 protein expression (P < 0.01), in both non-tumor and tumor tissue, whereas RBM10v1 and HER2 protein expression were only marginally correlated, in non-tumor tissue (P < 0.05). Interestingly, RBM5 and RBM10v1 protein expression were both deregulated in relation to RNA expression in tumor tissue. RBM10v2 and RBM6 RNA were highly significantly positively correlated in relation to various factors relating to poor prognosis (P < 0.0001). To our knowledge, this study is the first to examine RBM5 expression at both the RNA and protein level in primary breast tumor tissue, and the first to examine expression of all RBM5-related factors in a comprehensive manner. The results provide a graphic illustration that RBM5-related factors are significantly differentially expressed in breast cancer, and suggest complex inter-related regulatory networks involving alternative splicing, oncogenic expression, and tissue-specific function. Show less

We have studied a possible role of T cell sensitization to eye muscle antigens in patients with thyroid-associated ophthalmology (TAO). Peripheral blood mononuclear cell (PBMC) proliferation in response to crude porcine orbital tissue antigens, partially purified porcine eye muscle membrane proteins and predicted epitopic fragments of the recombinant 64 kDa protein 1D, was determined in patients with TAO and thyroid autoimmunity without eye disease. When membrane and cytosol fractions were used as antigen PBMC from 43% of patients with TAO but only 12.5% of normal subjects were responsive to a crude orbital connective tissue membrane fraction, although this difference was not significant. We were unable to demonstrate specific recognition of partially purified eye muscle membrane fractions; although most of the fractions tested were occasionally recognized by T cells from patients with ophthalmopathy, this was also the case for patients with autoimmune thyroid disease without ophthalmopathy and normal subjects. We did not clearly identify epitopic sequences within the 1D protein, most of the predicted peptides tested being recognized not only by T cells from a small proportion of patients with TAO, but also by those from some patients with autoimmune thyroid disease without ophthalmopathy and normal subjects. It is noteworthy however that approximately 22% of TAO patients, but no normal subjects, were positive to one or more of three peptides, suggesting that reactivity to the 1D protein may play a role in the pathogenesis of the eye disorder in some patients with TAO. The inconsistent and generally low T cell responses to crude and purified antigens noted in a few patients with TAO could be explained by low numbers of specifically sensitized lymphocytes in peripheral blood. Show less