Whole-genome sequencing identifies variants in ANK1, LRRN1, HAS1, and other genes and regulatory regions for stroke in type 1 diabetes.

Individuals with type 1 diabetes (T1D) carry a markedly increased risk of stroke, with distinct clinical and neuroimaging characteristics as compared to those without diabetes. Using whole-exome or whole-genome sequencing of 1,051 individuals with T1D, we aimed to find rare and low-frequency genomic variants associated with stroke in T1D. We analysed the genome comprehensively with single-variant analyses, gene aggregate analyses, and aggregate analyses on genomic windows, enhancers and promoters. In addition, we attempted replication in T1D using a genome-wide association study (N = 3,945) and direct genotyping (N = 3,263), and in the general population from the large-scale population-wide FinnGen project and UK Biobank summary statistics. We identified a rare missense variant on SREBF1 exome-wide significantly associated with stroke (rs114001633, p.Pro227Leu, p-value = 7.30 × 10-8), which replicated for hemorrhagic stroke in T1D. Using gene aggregate analysis, we identified exome-wide significant genes: ANK1 and LRRN1 displayed replication evidence in T1D, and LRRN1, HAS1 and UACA in the general population (UK Biobank). Furthermore, we performed sliding-window analyses and identified 14 genome-wide significant windows for stroke on 4q33-34.1, of which two replicated in T1D, and a suggestive genomic window on LINC01500, which replicated in T1D. Finally, we identified a suggestively stroke-associated TRPM2-AS promoter (p-value = 5.78 × 10-6) with borderline significant replication in T1D, which we validated with an in vitro cell-based assay. Due to the rarity of the identified genetic variants, future replication of the genomic regions represented here is required with sequencing of individuals with T1D. Nevertheless, we here report the first genome-wide analysis on stroke in individuals with diabetes.

Data-driven comorbidity analysis of 100 common disorders reveals patient subgroups with differing mortality risks and laboratory correlates.

The populational heterogeneity of a disease, in part due to comorbidity, poses several complexities. Individual comorbidity profiles, on the other hand, contain useful information to refine phenotyping, prognostication, and risk assessment, and they provide clues to underlying biology. Nevertheless, the spectrum and the implications of the diagnosis profiles remain largely uncharted. Here we mapped comorbidity patterns in 100 common diseases using 4-year retrospective data from 526,779 patients and developed an online tool to visualize the results. Our analysis exposed disease-specific patient subgroups with distinctive diagnosis patterns, survival functions, and laboratory correlates. Computational modeling and real-world data shed light on the structure, variation, and relevance of populational comorbidity patterns, paving the way for improved diagnostics, risk assessment, and individualization of care. Variation in outcomes and biological correlates of a disease emphasizes the importance of evaluating the generalizability of current treatment strategies, as well as considering the limitations that selective inclusion criteria pose on clinical trials.

Whole-exome sequencing identifies novel protein-altering variants associated with serum apolipoprotein and lipid concentrations.

BACKGROUND: Dyslipidemia is a major risk factor for cardiovascular disease, and diabetes impacts the lipid metabolism through multiple pathways. In addition to the standard lipid measurements, apolipoprotein concentrations provide added awareness of the burden of circulating lipoproteins. While common genetic variants modestly affect the serum lipid concentrations, rare genetic mutations can cause monogenic forms of hypercholesterolemia and other genetic disorders of lipid metabolism. We aimed to identify low-frequency protein-altering variants (PAVs) affecting lipoprotein and lipid traits. METHODS: We analyzed whole-exome (WES) and whole-genome sequencing (WGS) data of 481 and 474 individuals with type 1 diabetes, respectively. The phenotypic data consisted of 79 serum lipid and apolipoprotein phenotypes obtained with clinical laboratory measurements and nuclear magnetic resonance spectroscopy. RESULTS: The single-variant analysis identified an association between the LIPC p.Thr405Met (rs113298164) and serum apolipoprotein A1 concentrations (p=7.8×10-8). The burden of PAVs was significantly associated with lipid phenotypes in LIPC, RBM47, TRMT5, GTF3C5, MARCHF10, and RYR3 (p<2.9×10-6). The RBM47 gene is required for apolipoprotein B post-translational modifications, and in our data, the association between RBM47 and apolipoprotein C-III concentrations was due to a rare 21 base pair p.Ala496-Ala502 deletion; in replication, the burden of rare deleterious variants in RBM47 was associated with lower triglyceride concentrations in WES of >170,000 individuals from multiple ancestries (p=0.0013). Two PAVs in GTF3C5 were highly enriched in the Finnish population and associated with cardiovascular phenotypes in the general population. In the previously known APOB gene, we identified novel associations at two protein-truncating variants resulting in lower serum non-HDL cholesterol (p=4.8×10-4), apolipoprotein B (p=5.6×10-4), and LDL cholesterol (p=9.5×10-4) concentrations. CONCLUSIONS: We identified lipid and apolipoprotein-associated variants in the previously known LIPC and APOB genes, as well as PAVs in GTF3C5 associated with LDLC, and in RBM47 associated with apolipoprotein C-III concentrations, implicated as an independent CVD risk factor. Identification of rare loss-of-function variants has previously revealed genes that can be targeted to prevent CVD, such as the LDL cholesterol-lowering loss-of-function variants in the PCSK9 gene. Thus, this study suggests novel putative therapeutic targets for the prevention of CVD.

Association of Coding Variants in Hydroxysteroid 17-beta Dehydrogenase 14 (HSD17B14) with Reduced Progression to End Stage Kidney Disease in Type 1 Diabetes.

BACKGROUND: Rare variants in gene coding regions likely have a greater impact on disease-related phenotypes than common variants through disruption of their encoded protein. We searched for rare variants associated with onset of ESKD in individuals with type 1 diabetes at advanced kidney disease stage. METHODS: Gene-based exome array analyses of 15,449 genes in five large incidence cohorts of individuals with type 1 diabetes and proteinuria were analyzed for survival time to ESKD, testing the top gene in a sixth cohort (n=2372/1115 events all cohorts) and replicating in two retrospective case-control studies (n=1072 cases, 752 controls). Deep resequencing of the top associated gene in five cohorts confirmed the findings. We performed immunohistochemistry and gene expression experiments in human control and diseased cells, and in mouse ischemia reperfusion and aristolochic acid nephropathy models. RESULTS: Protein coding variants in the hydroxysteroid 17-ß dehydrogenase 14 gene (HSD17B14), predicted to affect protein structure, had a net protective effect against development of ESKD at exome-wide significance (n=4196; P value=3.3 × 10-7). The HSD17B14 gene and encoded enzyme were robustly expressed in healthy human kidney, maximally in proximal tubular cells. Paradoxically, gene and protein expression were attenuated in human diabetic proximal tubules and in mouse kidney injury models. Expressed HSD17B14 gene and protein levels remained low without recovery after 21 days in a murine ischemic reperfusion injury model. Decreased gene expression was found in other CKD-associated renal pathologies. CONCLUSIONS: HSD17B14 gene is mechanistically involved in diabetic kidney disease. The encoded sex steroid enzyme is a druggable target, potentially opening a new avenue for therapeutic development.

Differential metabolomic signatures of declining renal function in Types 1 and 2 diabetes.

BACKGROUND: Chronic kidney disease (CKD) shows different clinical features in Types1 (T1D) and 2 diabetes (T2D). Metabolomics have recently provided useful contribution to the identification of biomarkers of CKD progression in either form of the disease. However, no studies have so far compared plasma metabolomics between T1D and T2D in order to identify differential signatures of progression of estimated glomerular filtration rate (eGFR) decline. METHODS: We used two large cohorts of T1D (from Finland) and T2D (from Italy) patients followed up to 7 and 3 years, respectively. In both groups, progression was defined as the top quartile of yearly decline in eGFR. Pooled data from the two groups were analysed by univariate and bivariate random forest (RF), and confirmed by bivariate partial least squares (PLS) analysis, the response variables being type of diabetes and eGFR progression. RESULTS: In progressors, yearly eGFR loss was significantly larger in T2D [-5.3 (3.0), median (interquartile range)mL/min/1.73 m2/year] than T1D [-3.7 (3.1) mL/min/1.73 m2/year ; P = 0.018]. Out of several hundreds, bivariate RF extracted 22 metabolites associated with diabetes type (all higher in T1D than T2D except for 5-methylthioadenosine, pyruvate and ß-hydroxypyruvate) and 13 molecules associated with eGFR progression (all higher in progressors than non-progressors except for sphyngomyelin). Three of the selected metabolites (histidylphenylalanine, leucylphenylalanine, tryptophylasparagine) showed a significant interaction between disease type and progression. Only eight metabolites were common to both bivariate RF and PLS. CONCLUSIONS: Identification of metabolomic signatures of CKD progression is partially dependent on the statistical model. Dual analysis identified molecules specifically associated with progressive renal impairment in both T1D and T2D.

Liver nucleotide biosynthesis is linked to protection from vascular complications in individuals with long-term type 1 diabetes.

Identification of biomarkers associated with protection from developing diabetic complications is a prerequisite for an effective prevention and treatment. The aim of the present study was to identify clinical and plasma metabolite markers associated with freedom from vascular complications in people with very long duration of type 1 diabetes (T1D). Individuals with T1D, who despite having longer than 30 years of diabetes duration never developed major macro- or microvascular complications (non-progressors; NP) were compared with those who developed vascular complications within 25 years from diabetes onset (rapid progressors; RP) in the Scandinavian PROLONG (n = 385) and DIALONG (n = 71) cohorts. The DIALONG study also included 75 healthy controls. Plasma metabolites were measured using gas and/or liquid chromatography coupled to mass spectrometry. Lower hepatic fatty liver indices were significant common feature characterized NPs in both studies. Higher insulin sensitivity and residual ß-cell function (C-peptide) were also associated with NPs in PROLONG. Protection from diabetic complications was associated with lower levels of the glycolytic metabolite pyruvate and APOCIII in PROLONG, and with lower levels of thiamine monophosphate and erythritol, a cofactor and intermediate product in the pentose phosphate pathway as well as higher phenylalanine, glycine and serine in DIALONG. Furthermore, T1D individuals showed elevated levels of picolinic acid as compared to the healthy individuals. The present findings suggest a potential beneficial shunting of glycolytic substrates towards the pentose phosphate and one carbon metabolism pathways to promote nucleotide biosynthesis in the liver. These processes might be linked to higher insulin sensitivity and lower liver fat content, and might represent a mechanism for protection from vascular complications in individuals with long-term T1D.

Effect of pulse waveforms on movement amplitudes and perceived discomfort in electric muscle stimulation in unresolved facial nerve palsy.

Studies on the effects of the pulse waveform used in electrical muscle stimulation on the activations and perceived discomfort of the waveform have been mainly executed on limb muscles with variable results, however, knowledge of these effects on facial muscles is currently lacking. We studied two waveforms, square wave and sinusoidal wavelet, for the activation of the frontalis muscle in 9 individuals with unresolved facial nerve palsy. Both waveforms produced a movement that was greater in amplitude compared with the maximal voluntary movement of the affected side in 8 participants and at least as great as the healthy side's maximal voluntary movement in 4 participants. Both waveforms were equally successful in producing movements, and there was no significant difference in perceived discomfort ratings between the two waveforms. These findings will be useful for the future development of neuroprosthetic applications for reanimating facial muscles using electrical stimulation. Trial registration: ClinicalTrials.gov NCT03496025, registration date March 19, 2018.

Genome-Wide Association Study of Diabetic Kidney Disease Highlights Biology Involved in Glomerular Basement Membrane Collagen.

BACKGROUND: Although diabetic kidney disease demonstrates both familial clustering and single nucleotide polymorphism heritability, the specific genetic factors influencing risk remain largely unknown. METHODS: To identify genetic variants predisposing to diabetic kidney disease, we performed genome-wide association study (GWAS) analyses. Through collaboration with the Diabetes Nephropathy Collaborative Research Initiative, we assembled a large collection of type 1 diabetes cohorts with harmonized diabetic kidney disease phenotypes. We used a spectrum of ten diabetic kidney disease definitions based on albuminuria and renal function. RESULTS: Our GWAS meta-analysis included association results for up to 19,406 individuals of European descent with type 1 diabetes. We identified 16 genome-wide significant risk loci. The variant with the strongest association (rs55703767) is a common missense mutation in the collagen type IV alpha 3 chain (COL4A3) gene, which encodes a major structural component of the glomerular basement membrane (GBM). Mutations in COL4A3 are implicated in heritable nephropathies, including the progressive inherited nephropathy Alport syndrome. The rs55703767 minor allele (Asp326Tyr) is protective against several definitions of diabetic kidney disease, including albuminuria and ESKD, and demonstrated a significant association with GBM width; protective allele carriers had thinner GBM before any signs of kidney disease, and its effect was dependent on glycemia. Three other loci are in or near genes with known or suggestive involvement in this condition (BMP7) or renal biology (COLEC11 and DDR1). CONCLUSIONS: The 16 diabetic kidney disease-associated loci may provide novel insights into the pathogenesis of this condition and help identify potential biologic targets for prevention and treatment.

Metabolomic Profile Predicts Development of Microalbuminuria in Individuals with Type 1 Diabetes.

Elevated urinary albumin excretion (microalbuminuria) is an early marker of diabetic nephropathy, but there is an unmet need for better biomarkers that capture the individuals at risk with higher accuracy and earlier than the current markers do. We performed an untargeted metabolomic study to assess baseline differences between individuals with type 1 diabetes who either developed microalbuminuria or remained normoalbuminuric. A total of 102 individuals progressed to microalbuminuria during a median follow-up of 3.2 years, whereas 98 sex-, age- and body mass index (BMI) matched non-progressors remained normoalbuminuric during a median follow-up of 7.1 years. Metabolomic screening identified 1,242 metabolites, out of which 111 differed significantly between progressors and non-progressors after adjustment for age of diabetes onset, baseline glycosylated hemoglobin A1c (HbA1c), and albumin excretion rate (AER). The metabolites that predicted development of microalbumiuria included several uremic toxins and carnitine metabolism related molecules. Iterative variable selection indicated erythritol, 3-phenylpropionate, and N-trimethyl-5-aminovalerate as the best set of variables to predict development of microalbuminuria. A metabolomic index based on these metabolites improved the prediction of incident microalbuminuria on top of the clinical variables age of diabetes onset, baseline HbA1c and AER (ROCAUC = 0.842 vs 0.797), highlighting their ability to predict early-phase diabetic nephropathy.

Confirmation of GLRA3 as a susceptibility locus for albuminuria in Finnish patients with type 1 diabetes.

Urinary albumin excretion is an early sign of diabetic kidney disease, affecting every third individual with diabetes. Despite substantial estimated heritability, only variants in the GLRA3 gene have been genome-wide significantly associated (p-value < 5 × 10-8) with diabetic albuminuria, in Finnish individuals with type 1 diabetes; However, replication attempt in non-Finnish Europeans with type 1 diabetes showed nominally significant association in the opposite direction, suggesting a population-specific effect, but simultaneously leaving the finding controversial. In this study, the association between the common rs10011025 variant in the GLRA3 locus, and albuminuria, was confirmed in 1259 independent Finnish individuals with type 1 diabetes (p = 0.0013), and meta-analysis of all Finnish individuals yielded a genome-wide significant association. The association was particularly pronounced in subjects not reaching the treatment target for blood glucose levels (HbA1c > 7%; N = 2560, p = 1.7 × 10-9). Even though further studies are needed to pinpoint the causal variants, dissecting the association at the GLRA3 locus may uncover novel molecular mechanisms for diabetic albuminuria irrespective of population background.

Emotional responses of clients to veterinarian communication style during a vaccination visit in companion animal practice.

OBJECTIVE To study the effects of veterinarian communication (ie, the information provided and gaze and body direction) and vaccination style on the emotions and physiologic reactions experienced by clients and on clients' evaluation of the expertise and trustworthiness of the veterinarian. DESIGN Simulation study. PARTICIPANTS 20 small animal clients. PROCEDURES Participants were shown 12 videos of a female veterinarian in which she first provided information about puppy vaccination and then performed the procedure. The veterinarian's behavior varied regarding the information provided about the vaccination (ie, scarce, factual, or emotional), her gaze and body direction (ie, direct or 30° averted), and her vaccination style (ie, routine or emotional). While the participants watched the videos, their corrugator supercilii muscle activity (corrugator supercilii muscles are activated when frowning) and skin conductance activity were measured. Participants also rated the emotions they experienced (ie, valence and arousal) and assessed the veterinarian's behavior (ie, expertise and trustworthiness). RESULTS Overall, emotional information, a direct gaze and body direction, and an emotional vaccination style were associated with more pleasant emotions and higher ratings of the expertise and trustworthiness of the veterinarian's behavior by clients. CONCLUSIONS AND CLINICAL RELEVANCE Results suggested that through certain behavioral actions, veterinarians may positively affect the emotions and feelings experienced by clients during veterinary clinic visits, even in the case of vaccination visits, which can be considered routine visits from the viewpoint of the veterinarian.

Exploration of a haloarchaeon, Halostagnicola larsenii, isolated from rock pit sea water, West Coast of Maharashtra, India, for the production of bacteriorhodopsin.

AIMS: The aim of the present investigation was to isolate haloarchaea from rock pit sea water, West Coast of India and to explore their potential in the production of bacteriorhodopsin (BR) which converts light energy into electrical energy. METHODS AND RESULTS: Haloarchaeal strains were isolated from rock pit sea water samples collected from Rock garden, Malvan, West Coast of India. Based on morphological, physiological and biochemical characteristics, and 16S rRNA gene sequencing, all the 11 strains were identified as Halostagnicola larsenii. All the strains require at least 1·5 mol l(-1) NaCl for growth; grow optimally in the range of 3·5-5·2 mol l(-1) NaCl. BR was detected in all the strains ranging from 0·035 to 0·258 g l(-1) . All 11 strains showed conversion of light energy into electrical energy in the range of 0·7-44·2 mV, when exposed to sunlight. CONCLUSIONS: A haloarchaeon, Hst. larsenii is isolated from rock pit sea water and demonstrated to have BR that converted light energy into electrical energy. SIGNIFICANCE AND IMPACT OF THE STUDY: The present investigation is presumably the first report of the isolation of Hst. larsenii from low salinity environment and its potential in production of BR. The haloarchaeon could be explored for the generation of electrical energy.

The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera.

Previous studies have reported that chromosome synteny in Lepidoptera has been well conserved, yet the number of haploid chromosomes varies widely from 5 to 223. Here we report the genome (393 Mb) of the Glanville fritillary butterfly (Melitaea cinxia; Nymphalidae), a widely recognized model species in metapopulation biology and eco-evolutionary research, which has the putative ancestral karyotype of n=31. Using a phylogenetic analyses of Nymphalidae and of other Lepidoptera, combined with orthologue-level comparisons of chromosomes, we conclude that the ancestral lepidopteran karyotype has been n=31 for at least 140 My. We show that fusion chromosomes have retained the ancestral chromosome segments and very few rearrangements have occurred across the fusion sites. The same, shortest ancestral chromosomes have independently participated in fusion events in species with smaller karyotypes. The short chromosomes have higher rearrangement rate than long ones. These characteristics highlight distinctive features of the evolutionary dynamics of butterflies and moths.

Challenges in monoclonal antibody-based therapies.

Therapeutic monoclonal antibodies (mAbs) are the fastest growing class of new therapeutic molecules. They hold great promises for the treatment of a variety of diseases, including chronic inflammatory diseases and cancer. However, the current manufacturing and purification processes cause limitations in the production capacity of therapeutic antibodies, leading to an increase in cost. Genetic delivery of therapeutic monoclonal antibodies by in vivo production offers a new potential solution to these problems. Firstly, therapeutic efficacy can be improved by maintaining stable therapeutic, non-toxic levels within the blood circulation over a long period of time. Repeated high-dose bolus injections could be avoided, thereby reducing the possibility of side-effects. Secondly, the high cost of manufacturing and purification of the therapeutic antibodies could be reduced, making an in vivo/ex vivo mAb gene transfer an economically viable and attractive option. In general, three approaches can be used for the stable long-term expression and secretion of therapeutic antibodies in vivo: 1) direct in vivo administration of integrating vectors carrying a mAb gene, 2) grafting of ex vivo genetically modified autologous cells, and 3) implantation of an encapsulated antibody producing heterologous or autologous cells. This paper describes the key factors and problems associated with the current antibody-based immunotherapies and reviews prospects for genetic in vivo delivery of therapeutic antibodies.

Improving safety of gene therapy.

Gene therapy has progressed from early clinical trials to first commercial gene therapy drugs. While there is a long history with the side-effects and adverse effects of pharmaceutical drugs, drugs based on gene delivery have presented new challenges for researchers, clinicians and regulatory authorities. On the path from early pre-clinical research to final commercial products, gene therapy tools and production methods have undergone tremendous changes to improve safety and efficacy. Deletion of adenovirus replication genes E1 and E3 has progressed to gutless adenoviruses with all viral genes removed; similarly evolution of lentiviral vectors has progressed from first generation viruses to safer third generation self-inactivating vectors. Improved chromatographic methods have eased the purification of viruses and delivery reservoirs, such as collagen or silicon collars for cardiovascular gene transfer have decreased systemic leakage of viruses; together with tissue-specific promoters and imaging of the biodistribution of viral particles, gene therapy specificity and safety can be improved even further. This review will introduce gene delivery vectors used in gene therapy and highlight key approaches used to improve their safety.

Laparoscopic sutured closure with mesh reinforcement of incisional hernias.

BACKGROUND: This study reports medium-term outcomes of laparoscopic incisional hernia repair. STUDY DESIGN: Laparoscopic repair was performed on 721 patients with ventral hernia. After adhesiolysis the defect was closed with no. 1 polyamide suture or loop. This was followed by reinforcement with intraperitoneal onlay repair with a bilayered mesh. RESULTS: Laproscopic repair of ventral hernia was performed on 613 females and 108 males. Of these, 185 (25.7%) were recurrent incisional hernias of which 93 had undergone previous open hernioplasty. The remaining 92 patients had previously undergone sutured repair. The average operating time was 95 min (range 60-115 min). Conversion rate was 1%. The average hospital stay was 2 days (range 1-6 days). The commonest complication was seroma formation at the incisional hernia site. Full-thickness bowel injury occurred in two patients. The mean follow-up period was 4.2 years (range 3 months to 10 years). Recurrence was noted in four (0.55%) patients. CONCLUSION: Laparoscopic repair is well-tolerated and can be accomplished with minimum morbidity in ventral hernias.

Laparoscopic distal pancreatectomy: results of a prospective non-randomized study from a tertiary center.

BACKGROUND: Though laparoscopic distal pancreatectomy for benign conditions was first described in the early 1990s, it has not become as popular as other laparoscopic surgeries. Published literature on this topic consists of several case reports and a handful of small series. We present our experience, which, to the best of our knowledge, is the largest series reported to date. METHODS: Since 1998, 22 patients have undergone distal pancreatectomy at our institute. The technique of distal pancreatosplenectomy, as well as spleen-preserving distal pancreatectomy, is described. RESULTS: Four males and 18 females in the age range of 12-69 years underwent operation. Splenic preservation was possible in 7 patients. The tumor diameter ranged from 2.1 cm to 7.4 cm. The mean operating time was 215 min. The mean length of incision required for specimen retrieval was 3.4 cm. All patients were started on a liquid diet on the first postoperative day. The median hospital stay was 4 days. One patient developed a pancreatic fistula that was managed conservatively. At the end of an average follow-up of 4.6 years, no recurrence has been reported. CONCLUSIONS: Laparoscopic distal pancreatectomy is a safe procedure, with minimal morbidity, rapid recovery, and short hospital stay. In appropriate cases, splenic preservation is feasible.

Palanivelu hydatid system for safe and efficacious laparoscopic management of hepatic hydatid disease.

BACKGROUND: Hydatid disease, being endemic in several areas of the world, is of interest even to surgeons in non-endemic areas because they may encounter the disease due to ease and rapidity of travel as well as immigration. We describe a new device for laparoscopic management of hepatic hydatid disease. METHODS: The special trocar-cannula system--the Palanivelu hydatid system (PHS)--and the technique of operation are described. A total of 75 patients were operated on using this technique. RESULTS: In 83.3% of patients, only evacuation of the hydatid cyst by the PHS was done. In 13.7%, this was followed by left lobectomy because the cysts were large, occupying almost the entire left lobe of the liver. The remnant cavity was dealt with by omentoplasty. The average follow-up period was 5.9 years, during which there were no recurrences. CONCLUSIONS: PHS is successful in preventing spillage, evacuating the contents of hydatid cysts, performing transcystic fenestration, and for dealing with cyst-biliary communications.