Mono- and biallelic variant effects on disease at biobank scale

Identifying causal factors for Mendelian and common diseases is an ongoing challenge in medical genetics¹. Population bottleneck events, such as those that occurred in the history of the Finnish population, enrich some homozygous variants to higher frequencies, which facilitates the identification of variants that cause diseases with recessive inheritance^2,3. Here we examine the homozygous and heterozygous effects of 44,370 coding variants on 2,444 disease phenotypes using data from the nationwide electronic health records of 176,899 Finnish individuals. We find associations for homozygous genotypes across a broad spectrum of phenotypes, including known associations with retinal dystrophy and novel associations with adult-onset cataract and female infertility. Of the recessive disease associations that we identify, 13 out of 20 would have been missed by the additive model that is typically used in genome-wide association studies. We use these results to find many known Mendelian variants whose inheritance cannot be adequately described by a conventional definition of dominant or recessive. In particular, we find variants that are known to cause diseases with recessive inheritance with significant heterozygous phenotypic effects. Similarly, we find presumed benign variants with disease effects. Our results show how biobanks, particularly in founder populations, can broaden our understanding of complex dosage effects of Mendelian variants on disease.

Application of machine learning to identify top determinants of fibrofatty plaque burden by CCTA in humans with psoriasis

Introduction

Fibrofatty plaque burden (FFB) is a high-risk, vulnerable plaque feature comprised of an atheromatous core and fibrous cap with increased risk of coronary artery disease (CAD) [1]. Psoriasis (PSO) is a chronic inflammatory disease linked with atherosclerotic risk and premature cardiovascular disease, driven in part by vulnerable plaque rupture [2,3]. Machine learning (ML) previously showed the prognostic value of FFB in predicting 5-year risk of cardiac-related mortality in patients with CAD [4]. Whether ML can predict FFB in psoriasis is understudied.

Purpose

To use ML to identify top determinants of FFB by CCTA in PSO.

Methods

320 consecutive participants with psoriasis were recruited as part of an ongoing cohort study, of whom 307 had FFB analyzed with coronary computed tomography angiography (CCTA) and quantified by QAngio CT (Medis, The Netherlands). 140 out of 182 potential determinants were subjected to ML algorithms analyzed by random forest and validated by 5-fold cross validation to select the top determinants based on R-square criteria. Lipid concentration and size were measured by nuclear magnetic resonance (NMR) and sdLDL-C was calculated by Sampson's formula.

Results

The top 21 determinants of FFB at baseline were grouped into 3 categories: cardiometabolic risk factors (BMI, sex, DBP, mean arterial pressure, exercise, heart rate, glucose, anxiety, psoriasis disease duration), clinical measurements (basophils, platelets, hemoglobin, RBC, alkaline phosphatase, ALT, creatinine, neutrophil-to-lymphocyte ratio), and lipoproteins (LDL particle size, apolipoprotein A1, apolipoprotein B-to-A1 ratio, calculated sdLDL-C).

Conclusion

ML confirmed that FFB strongly correlates with cardiometabolic risk factors, clinical measurements, and lipoproteins. Further investigations into these top determinants of FFB over time may provide insight into potential therapeutic interventions that decrease cardiovascular risk in patients with chronic inflammatory diseases and should be validated in larger studies.

Funding Acknowledgement

Type of funding sources: Public Institution(s). Main funding source(s): This study was supported by the National Heart, Lung and Blood Institute (NHLBI) IntramuralResearch Program (ZIA-HL-06193). This research was made possible through the NIH MedicalResearch Scholars Program, a public-private partnership supported jointly by the NIH andcontributions to the Foundation for the NIH from the Doris Duke Charitable Foundation,Genentech, the American Association for Dental Research, the Colgate-Palmolive Company, andother private donors.

Effect of a home-based resistance exercise program in elderly participants with osteoporosis: a randomized controlled trial

The effectiveness of home-based resistance exercise in elder participants with osteoporosis remains unclear. This study demonstrates the beneficial effects of this mode of exercise on improving physical function, increasing confidence in exercise, and reducing fear of falling.

INTRODUCTION

This study aims to evaluate the effect of a home-based resistance exercise (HBRE) program versus control on physical function, exercise self-efficacy, falling efficacy, and health-related quality of life (HRQOL).

METHODS

This randomized controlled trial included 72 elderly participants with osteoporosis. Participants in the intervention group received a 12-week HBRE program, and the control group received usual care. The primary outcome was physical function, including muscle strength and balance ability; secondary outcomes were exercise self-efficacy, falling efficacy, and HRQOL. Within-group and between-group changes in outcome were evaluated by t-test and rank-sum test.

RESULTS

A total of 68 subjects were included in the final analysis. Improvement in physical function was significantly greater in the HBRE group compared with controls. On a psychological level, exercise self-efficacy and falling efficacy improved significantly in the HBRE group; no significant change was observed in the control group. Most of the dimensions of HRQOL demonstrated improvements as well. The adherence was 85.29%, with no adverse events related to the exercise.

CONCLUSION

A 12-week HBRE program was safe non-pharmacological therapy for elderly participants with osteoporosis, improving physical function, exercise self-efficacy, reduced fear of falling, and improved HRQOL.

TRIAL REGISTRATION

Chinese Clinical Trial Register: ChiCTR2100051455. Registered 23.09.21. Retrospectively registered.

[Preconception reproductive health and birth outcome cohort in Chongqing: the cohort profile]

Birth cohort is an important platform to study the effect of early-life exposure on health outcome, but large cohorts to investigate the effect of preconception exposure, especially paternal exposure, on reproductive health and birth outcome are limited. The Preconception Reproductive Health and Birth Outcome Cohort (PREBIC) is a prospective birth cohort study which pays equal attention to the contribution of environmental, psychological, behavioral as well as other factors to reproductive health and adverse birth outcomes in both men and women in Chongqing, China. PREBIC started in 2019 and plans to recruit 20 800 reproductive-age couples with child-bearing willingness. Followed up was conducted to understand the conception status of the women within two years. Women in pregnancy would be visited at first, second, third trimesters and after delivery. The offspring would be monitored until 2 years old to understand the incidences of preterm birth, low birth weight, birth defects, neurodevelopmental disorders and other outcomes. Related information and biospecimen collections (including semen, peripheral blood, urine, placenta, umbilical cord, cord blood and oral swab) were scheduled in each period. By January 2022, PREBIC had recruited 8 698 participants from all 38 districts in Chongqing. The goal of PREBIC is to establish one of the largest prospective preconception birth cohorts covering both men and women, which might provide a unique insight to understand the effects of the full reproductive cycle on reproductive health and adverse outcomes, with especial emphasis on preconception exposures.

[Cone-beam CT analysis of external root resorption of maxillary incisors before and after traction of impacted canines]

Objective: To analyze the external root resorption of incisors caused by maxillary canine impaction, and to explore the changes of incisor external root resorption after orthodontic treatment. Methods: Twenty-four patients with impacted maxillary canines leading to external root resorption of incisors treated in Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University from July 2011 to January 2019 were selected. The age ranged from 10 to 14 years [(12.3±1.6) years], including 11 males and 14 females. The maxillary incisors with external root resorption before treatment were included in the resorption group (21 central incisors and 22 lateral incisors), and the maxillary incisors without external root resorption were used as the control group (26 central incisors and 21 lateral incisors). Cone-beam CT was taken before treatment, immediately after treatment and one year after treatment. At the one year follow-up 15 patients were collected (10 central incisors and 12 lateral incisors in the resorption group, while 16 central incisors and 12 lateral incisors in the control group). The root length and tooth volume of maxillary incisors were measured and analyzed before canine traction, after canine traction finished and at the one year follow-up. Results: After the treatment of maxillary impacted canines, the root length and volume of the central and lateral incisors in both resorption group and control group were significantly less than that before treatment (P<0.05). At the one year follow-up, the root length and volume of the incisors (central incisors in the resorption group and the central and lateral incisors in control group) were significantly less than those immediately after impacted canine traction (P<0.05). During the canine traction, the difference of the volume change in lateral incisors between the resorption group [(17±6) mm³] and the control group [(12±5) mm³] was statistically significant (t=2.51, P<0.05). During the one year follow-up period, the difference between the changes of the root length in maxillary central incisors in the resorption group [(0.5±0.4) mm] and in the control group [(0.2±0.1) mm] was statistically significant (t=2.35, P<0.05). Conclusions: For maxillary incisors with external root resorption caused by impacted maxillary canines, the external root resorption could not stop immediately after the treatment of impacted canines. The root resorption in maxillary lateral incisors mainly occured during the traction process, while the root resorption in maxillary central incisors existed during the orthodontic treatment and in the follow-up period.

Cardiopulmonary transit time: A novel PET imaging biomarker of in vivo physiology for risk stratification of heart transplant recipients

BACKGROUND

Myocardial blood flow (MBF) can be quantified using dynamic PET studies. These studies also inherently contain tomographic images of early bolus displacement, which can provide cardiopulmonary transit times (CPTT) as measure of cardiopulmonary physiology. The aim of this study was to assess the incremental prognostic value of CPTT in heart transplant (OHT) recipients.

METHODS

94 patients (age 56 ± 16 years, 78% male) undergoing dynamic 13N-ammonia stress/rest studies were included, of which 68 underwent right-heart catherization. A recently validated cardiac allograft vasculopathy (CAV) score based on PET measures of regional perfusion, peak MBF and left-ventricular (LV) ejection fraction (LVEF) was used to identify patients with no, mild or moderate-severe CAV. Time-activity curves of the LV and right ventricular (RV) cavities were obtained and used to calculate the difference between the LV and RV bolus midpoint times, which represents the CPTT and is expressed in heartbeats. Patients were followed for a median of 2.5 years for the occurrence of major adverse cardiac events (MACE), including cardiovascular death, hospitalization for heart failure or acute coronary syndrome, or re-transplantation.

RESULTS

CPTT was significantly correlated with cardiac filling pressures (r = .434, P = .0002 and r = .439, P = .0002 for right atrial and pulmonary wedge pressure), cardiac output (r = - .315, P = .01) and LVEF (r = - .513, P < .0001). CPTT was prolonged in patients with MACE (19.4 ± 6.0 vs 14.5 ± 3.0 heartbeats, P < .001, N = 15) with CPTT ≥ 17.75 beats showing optimal discriminatory value in ROC analysis. CPTT ≥ 17.75 heartbeats was associated with a 10.1-fold increased risk (P < .001) of MACE and a 7.3-fold increased risk (P < .001) after adjusting for PET-CAV, age, sex and time since transplant.

CONCLUSION

Measurements of cardiopulmonary transit time provide incremental risk stratification in OHT recipients and enhance the value of multiparametric dynamic PET imaging, particularly in identifying high-risk patients.

Delicate Tuning of the Ni/Co Ratio in Bimetal Layered Double Hydroxides for Efficient N2 Electroreduction

Electroreduction of N₂ to NH₃ at ambient conditions using renewable electricity is promising, but developing efficient electrocatalysts is still challenging due to the inertness of N≡N bonds. Layer double hydroxides (LDHs) composed of first-row transition metals with empty d-orbitals are theoretically promising for N₂ electroreduction (NRR) but rarely reported. Herein, hollow NiCo-LDH nanocages with different Ni/Co ratios were prepared, and their electronic structures and atomic arrangements were critical. The synergetic mechanisms of Ni and Co ions were revealed, and the optimized catalytic sites were proposed. Besides, in-situ Raman spectroscopy and ¹⁵ N₂ isotopic labeling studies were applied to detect reaction intermediates and confirm the origin of NH₃ . As a result, high NH₃ yield of 52.8 μg h^-1  mg_cat ^-1 and faradaic efficiency of 11.5 % were obtained at -0.7 V, which are top-ranking among Co/Ni-based NRR electrocatalysts. This work elucidates the structure-activity relationship between LDHs and NRR and is instructive for rational design of LDH-based electrocatalysts.

[Functional characterization of SLC12A1 gene variants in 3 patients with Bartter syndrome type Ⅰ]

Objective: To clarify the molecular basis of patients with Bartter syndrome type I and explore the therapeutic effect of trafficking-defective variations by chemical chaperone 4-Phenylbutyric acid(4-PBA). Methods: The clinical characteristics, laboratory findings and genetic data of 3 patients diagnosed with Bartter syndrome type I who were admitted to Department of Nephrology, Children's Hospital of Nanjing Medical University from 2017 to 2018 were retrospectively analyzed. Wild type and variant SLC12A1 gene constructs were transiently overexpressed in HEK293 cells. Western blotting was used to detect the expression levels of Na⁺-K⁺-2Cl^-cotransporter(NKCC2) protein. Immunofluorescent staining was applied to investigate the subcellular localization of NKCC2 protein. In addition, the effect of the chemical chaperone 4-PBA on the expression and localization of the SLC12A1 gene variants was investigated. Unpaired t test was used for statistical analysis of 4-PBA treatment. Results: All the 3 patients (2 males and 1 female), aged 3.0, 4.0 and 1.2 years, respectively. All patients had antenatal onset with polyhydramnios and were born prematurely. After birth, all patients presented with hypochlorine alkalosis accompanied by hypokalemia and hyponatremia. Sequencing analysis revealed that the 3 patients were homozygotes or compound heterozygotes for variants in the SLC12A1 gene. In HEK293 cells, the surface expression of NKCC2 in 3 variants (p.L463S, p.L479V, p.507-510del) are all lower than in wild type (0.718±0.039, 0.287±0.081, 0.025±0.156 vs. 1.001±0.028, t=5.92, 8.35, 30.49, all P<0.01). Moreover, the total protein expression of p.L479V and p.507-510del group were all lower than that in wild type group (0.630±0.032, 0.043±0.003 vs. 1.000±0.111, t=3.21, 8.65, all P<0.05). 4-PBA treatment increased the mature protein expression level of the p.L463S and p. L479V group in 4-PBA treatment group are all higher than the untreated group (0.459±0.018 vs. 1.123±0.024, 0.053±0.012 vs. 1.256±0.037, t=2.75, 18.35, all P<0.05). Cytoplasmic retention of the L479V and 507-510del variants were observed by immunofluorescent staining. 4-PBA treatment could rescue a number of NKCC2 L479V variants to the membrane. Conclusions: The 3 SLC12A1 variants cause expression or subcellular localization defects of the protein. The findings that plasma membrane expression and activity can be rescued by 4PBA might help to develop novel therapeutic strategy for Bartter syndrome type Ⅰ.

A systematic study of mosaicism in heritable thoracic aortic aneurysm and dissection

Mosaicisms are often overlooked in routine molecular diagnosis. Although not common, they are of great significance for accurate diagnosis and genetic counseling. In this study, we systematically evaluated the frequency of mosaicisms in both asymptomatic parents and affected patients with thoracic aortic aneurysm and dissection (TAAD). Next-generation sequencing (NGS) data from 1085 patients was reanalyzed with a more lenient allele frequency to detect potential mosaic variants. In addition, parental mosaicisms were investigated in 80 TAAD families. Finally, a total of six mosaic variants were detected in our cohort. Three of them were identified in symptomatic patients and three were in asymptomatic parents. Notably, a low-level mosaic variant in TGFB2 was detected combined with a causative FBN1 variant in patient AD2001, which might partially explain the clinical heterogeneity in his family. Our study hinted that it is necessary and feasible to implement mosaicism analysis in routine molecular diagnosis.

Microwave vacuum-dried durian flour and its application in biscuits

Durian is one of most popular fruits due to its nutritional values and unique flavor. Durian products have been continuously developed to meet market needs. In this study, durian (Durio zibethinus Murr.) cv. 'Monthong' was subjected to microwave vacuum-drying at 1,200 W to produce durian flour for use in biscuits that are normally made from wheat flour. The microwave treatment induced starch gelatinization to a significant extent. As a result, compared to the wheat flour, the durian flour had lower viscosity, pasting temperature, gelatinization temperatures, and enthalpy of gelatinization but higher water absorption capacity. Dough properties including development time, dough stability, time to breakdown and the phase angle tangent of the durian dough were less than those of the wheat dough. The elastic modulus (G') and viscous modulus (G″) of the durian dough were higher than for the wheat dough. All the tested durian doughs had higher G' values than G″, indicating a viscoelastic structure. Substitution of wheat flour with durian flour should not exceed 50% to obtain reasonable dough properties and baking quality of durian biscuits.

Coupled electronic and magnetic relaxation in Fe1+yTe: direct evidence for the interaction between itinerant carriers and local moments

Iron chalcogenides are of particular interests among iron-based superconductors due to their distinct properties such as high-T_con FeSe monolayer and competing magnetic correlations in Fe_1+yTe. Here we report unusual transport properties observed near the critical composition of Fe_1+yTe (y∼ 0.09) where competing magnetic correlations exist. The resistivity exhibits surprising temperature-dependent relaxation behavior belowT_N, resulting in the increase of resistivity with time for 35 K <T<T_N, but the decrease of resistivity with time for 10 K <T< 35 K. Such resistivity relaxation is intimately coupled to the magnetization relaxation and can be attributed to the glassy magnetic states induced by the competing magnetic orders. These findings demonstrate strong coupling between itinerant carriers and local ordered moments in Fe_1+yTe.

Chronic inflammation in psoriasis promotes visceral adipose tissue association with lipid-rich necrotic core through atherogenic myeloid score

Background/Introduction

Psoriasis is a chronic inflammatory condition associated with adipose dysfunction and high-risk coronary artery disease features, including non-calcified coronary burden (NCB) and lipid-rich necrotic core (LRNC). Visceral adipose tissue (VAT) is a metabolically-active depot that secretes inflammatory and proatherogenic factors, and is associated with increased NCB. Additionally, an atherogenic myeloid score (AMS) comprised of classical monocytes, low-density granulocytes, and platelets was shown to associate with psoriasis severity and NCB.

Purpose

To investigate the relationship between VAT and high-risk plaque features and test whether this relationship was potentially mediated by myeloid cells.

Methods

A cohort of 131 psoriasis patients were included in this study. Atherogenic myeloid score components were calculated using complete blood count data (platelets) and by flow cytometry (monocytes, LDGs). Coronary NCB and LRNC were quantified using QAngio and vascuCAP respectively. VAT was defined as intra-abdominal fat and was quantified using an automated contouring software with abdominal CT scans. Statistical analyses were performed using STATA 12.

Results

The cohort was middle-aged 50 (42–61) (median (IQR)), and predominantly male (61%). High VAT vs low VAT groups differed significantly in their NCB ((0.910±0.279) vs (1.431±0.517)); p&lt;0.001), (mean ± SD). After adjustment for cardiovascular risk factors, VAT associated with the atherogenic myeloid score (β=0.221, p=0.044), with LRNC (β=0.128, p=0.047), and atherogenic myeloid score associated with LRNC (β=0.161, p=0.003). The relationship of VAT to LRNC was partially mediated by atherogenic myeloid score (25.14%, p=0.029) (Figure 1).

Conclusions

VAT associated with LRNC, and this relationship was partially mediated by the atherogenic myeloid score. These findings suggest that bioactive VAT may impart risk on coronary artery disease in part through myeloid cells.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): National Heart, Lung, and Blood Institute Intramural Research Program in Bethesda, Maryland Figure 1. Log-transformed atherogenic myeloid score partially mediates the relationship between VAT and log-transformed LRNC. Adjusted by Framingham Risk Score, PASI score, biologic therapy, statin therapy, type 2 diabetes, hyperlipidemia, and subcutaneous adipose tissue volume. Red arrow: represents indirect effect; Beta: standard regression coefficient.