DNA polymerase θ protects leukemia cells from metabolically induced DNA damage.

Leukemia cells accumulate DNA damage, but altered DNA repair mechanisms protect them from apoptosis. We showed here that formaldehyde generated by serine/1-carbon cycle metabolism contributed to the accumulation of toxic DNA-protein crosslinks (DPCs) in leukemia cells, especially in driver clones harboring oncogenic tyrosine kinases (OTKs: FLT3(internal tandem duplication [ITD]), JAK2(V617F), BCR-ABL1). To counteract this effect, OTKs enhanced the expression of DNA polymerase theta (POLθ) via ERK1/2 serine/threonine kinase-dependent inhibition of c-CBL E3 ligase-mediated ubiquitination of POLθ and its proteasomal degradation. Overexpression of POLθ in OTK-positive cells resulted in the efficient repair of DPC-containing DNA double-strand breaks by POLθ-mediated end-joining. The transforming activities of OTKs and other leukemia-inducing oncogenes, especially of those causing the inhibition of BRCA1/2-mediated homologous recombination with and without concomitant inhibition of DNA-PK-dependent nonhomologous end-joining, was abrogated in Polq-/- murine bone marrow cells. Genetic and pharmacological targeting of POLθ polymerase and helicase activities revealed that both activities are promising targets in leukemia cells. Moreover, OTK inhibitors or DPC-inducing drug etoposide enhanced the antileukemia effect of POLθ inhibitor in vitro and in vivo. In conclusion, we demonstrated that POLθ plays an essential role in protecting leukemia cells from metabolically induced toxic DNA lesions triggered by formaldehyde, and it can be targeted to achieve a therapeutic effect.

Embryo cryopreservation leads to sex-specific DNA methylation perturbations in both human and mouse placentas.

In vitro fertilization (IVF) is associated with DNA methylation abnormalities and a higher incidence of adverse pregnancy outcomes. However, which exposure(s), among the many IVF interventions, contributes to these outcomes remains unknown. Frozen embryo transfer (ET) is increasingly utilized as an alternative to fresh ET, but reports suggest a higher incidence of pre-eclampsia and large for gestational age infants. This study examines DNA methylation in human placentas using the 850K Infinium MethylationEPIC BeadChip array obtained after 65 programmed frozen ET cycles, 82 fresh ET cycles and 45 unassisted conceptions. Nine patients provided placentas following frozen and fresh ET from consecutive pregnancies for a paired subgroup analysis. In parallel, eight mouse placentas from fresh and frozen ET were analyzed using the Infinium Mouse Methylation BeadChip array. Human and mouse placentas were significantly hypermethylated after frozen ET compared with fresh. Paired analysis showed similar trends. Sex-specific analysis revealed that these changes were driven by male placentas in humans and mice. Frozen and fresh ET placentas were significantly different from controls, with frozen samples hypermethylated compared with controls driven by males and fresh samples being hypomethylated compared with controls, driven by females. Sexually dimorphic epigenetic changes could indicate differential susceptibility to IVF-associated perturbations, which highlights the importance of sex-specific evaluation of adverse outcomes. Similarities between changes in mice and humans underscore the suitability of the mouse model in evaluating how IVF impacts the epigenetic landscape, which is valuable given limited access to human tissue and the ability to isolate specific interventions in mice.

Network analysis on psychopathological symptoms, psychological measures, quality of life and COVID-19 related factors in Chinese psychiatric patients in Hong Kong.

BACKGROUND: Psychiatric patients are susceptible to adverse mental health impacts during COVID-19, but complex interplays between psychopathology and pandemic-related variables remain elusive. This study aimed to investigate concomitant associations between psychopathological symptoms, psychological measures and COVID-19 related variables in Chinese psychiatric patients during the peak of fifth pandemic wave in Hong Kong. METHODS: We employed network analysis to investigate inter-relationships among psychopathological symptoms (including depression, anxiety, post-traumatic stress disorder-like [PTSD-like] symptoms, insomnia, psychotic symptoms), cognitive complaints, health-related quality of life, loneliness, resilience and selected pandemic-related factors in 415 psychiatric outpatients between 28 March and 8 April, 2022. Network comparisons between genders, diagnosis (common mental disorders [CMD] vs. severe mental disorders [SMD]), and history of contracting COVID-19 at fifth wave were performed as exploratory analyses. RESULTS: Our results showed that anxiety represented the most central node in the network, as indicated by its highest node strength and expected influence, followed by depression and quality of life. Three comparatively strong connections between COVID-19 and psychopathological variables were observed including: fear of contagion and PTSD-like symptoms, COVID-19 stressor burden and PTSD-like symptoms, and COVID-19 stressor burden and insomnia. Network comparison tests revealed significant network structural difference between participants with history of contracting COVID-19 and those without, but showed no significant difference between genders as well as between CMD and SMD patients. CONCLUSIONS: Our findings suggest the pivotal role of anxiety in psychopathology network of psychiatric patients amidst COVID-19. Pandemic-related variables are critically associated with trauma/stress and insomnia symptoms. Future research is required to elucidate potential network structural changes between pandemic and post-COVID periods.

Prevalence and correlates of depression, anxiety and trauma-like symptoms in Chinese psychiatric patients during the fifth wave of COVID-19 pandemic: a cross-sectional study in Hong Kong.

BACKGROUND: Psychiatric patients are susceptible to adverse mental health outcome during COVID-19 pandemic, but its associated factors are understudied. This observational cross-sectional study aimed to comprehensively examine prevalence and correlates of psychological distress, in terms of depression, anxiety and post-traumatic-stress-disorder (PTSD)-like symptoms, among Chinese adult psychiatric outpatients amidst the peak of fifth COVID-19 wave in Hong-Kong. METHODS: A total of 415 patients (comprising 246 patients with common-mental-disorders [CMD] and 169 with severe-mental-disorders [SMD]) and 399 demographically-matched controls without mental disorders were assessed with self-rated questionnaires between 28-March and 8-April-2022, encompassing illness profile, mental health symptoms, psychosocial measures (loneliness, resilience, coping styles) and COVID-19 related factors. Univariate and multivariable logistic regression analyses were conducted to determine variables associated with moderate-to-severe depressive, anxiety and PTSD-like symptoms among psychiatric patients. RESULTS: Our results showed that CMD patients had the greatest psychological distress relative to SMD patients and controls. Approximately 40-55% CMD patients and 25% SMD patients exhibited moderate-to-severe depression, anxiety and PTSD-like symptoms. Multivariable regression analyses revealed that female gender, lower educational attainment, single marital status, being housewife, more severe insomnia, psychotic-like symptoms and cognitive complaints, self-harm behavior, lower resilience, avoidance coping, never contracting COVID-19 infection, greater fear of contagion, and longer exposure to pandemic-related information were independently associated with depression, anxiety and/or PTSD-like symptoms in psychiatric patients. CONCLUSIONS: Our results affirm increased vulnerability of psychiatric patients toward psychological distress during pandemic. An array of identified correlates facilitates early detection of high-risk psychiatric patients for targeted strategies to minimize pandemic-related negative psychological impact.

Antipsychotic utilization patterns in pregnant women with psychotic disorders: a 16-year population-based cohort study.

Despite growing concern about reproductive safety of antipsychotics, there is a paucity of research specifically assessing prenatal antipsychotic prescribing practices for psychotic disorders. This population-based cohort study identified women aged 15-50 years with diagnosis of psychotic disorders, who delivered their first and singleton child between 2003-2018 in Hong Kong, with an aim to examine temporal trends and predictors of prenatal antipsychotic use as well as antipsychotic utilization patterns before and during pregnancy. Data were retrieved from territory-wide medical-record database of public healthcare services. Of 804 women, 519 (65%) redeemed at least one prescription for antipsychotics during pregnancy. Older age at conception (25-34 years: OR 2.12 [95% CI 1.22-3.67]; 35-50 years: 2.52 [1.38-4.61]; 15-24 years as reference category) and antipsychotic treatment within 12 months pre-pregnancy (24.22 [16.23-36.16]) were significantly associated with prenatal antipsychotic use. Second-generation-antipsychotic (SGA) use during pregnancy increased over 16-year study period, while prenatal first-generation-antipsychotic (FGA) use showed declining trend. Overall antipsychotic and SGA use progressively decreased across pre-pregnancy and trimesters of pregnancy. Further analyses on antipsychotic use trajectories revealed that 87.4% (n = 459) of 529 women receiving antipsychotics in 12-month pre-pregnancy redeemed antipsychotic prescription during pregnancy, and 63.4% (n = 333) continued antipsychotic treatment throughout pregnancy. Only 7.5% of the cohort (n = 60) commenced antipsychotics in pregnancy. This is one of the few studies evaluating real-world prenatal antipsychotic utilization among women with psychotic disorders. Future research delineating risk conferred by illness-related factors and antipsychotic exposure on adverse maternal and fetal outcomes is warranted to facilitate treatment guideline development.

Mortality rates in people with first diagnosis of schizophrenia-spectrum disorders: A 5-year population-based cohort study.

OBJECTIVE: Schizophrenia-spectrum disorder (SSD) is associated with increased premature death, with emerging data suggesting early illness course as a high-risk period for excess mortality. This study aimed to examine mortality rate in patients with incident SSD and differential mortality risk between inpatient-diagnosed and outpatient-diagnosed subsamples within 5 years of first diagnosis. METHOD: This population-based cohort study identified 8826 patients aged 18-39 years receiving first-recorded SSD diagnosis upon service entry, comprising 3877 inpatient-diagnosed and 4949 outpatient-diagnosed patients, between 2006 and 2012 in Hong Kong using a territory-wide medical record database of public health care services. All-cause, natural-cause, and unnatural-cause mortality risks within 5 years after first diagnosis were quantified by standardized mortality ratios (SMRs) relative to the general population. We also directly compared mortality rates between inpatient and outpatient subsamples over 5-year follow-up. RESULTS: SSD patients exhibited markedly elevated all-cause (SMR: 12.28, 95% confidence interval [CI]: [10.83, 13.88]), natural-cause (SMR: 3.76, 95% CI: [2.77, 4.98]) and unnatural-cause (SMR: 20.64, 95% CI: [17.49, 24.20]) mortality during first 5 years of diagnosis. Increased mortality rate was most pronounced in the first year of treatment, especially for unnatural deaths (SMR 32.2, 95% CI: [24.08, 42.22]). Discharged inpatient-diagnosed patients displayed significantly higher all-cause and unnatural-cause mortality rates than outpatient-diagnosed counterparts within first 3 years of treatment, and differential mortality risks on all-cause (adjusted hazard ratio [aHR]: 7.05, 95% CI: [2.02, 24.64]) and unnatural-cause (aHR: 5.15, 95% CI: [1.38, 19.19]) deaths were the highest in the first month of follow-up. CONCLUSIONS: Substantial increase in early mortality risk among people with incident SSD, particularly in the first year of diagnosis and the time shortly after discharge, underscores an urgent need of targeted early intervention for effective suicide prevention and physical health improvement to minimize mortality gap.

Antidepressant utilization patterns and predictors of treatment continuation in pregnant women: A 16-year population-based cohort.

OBJECTIVE: Existing data on prenatal antidepressant prescribing patterns are mostly derived from Western countries, with limited research assessing antidepressant continuation and reinitiation during pregnancy. This study aimed to examine antidepressant prescribing practice among Chinese pregnant women in Hong Kong. METHODS: This population-based study identified women aged 15-50 years who delivered their first and singleton child, and had redeemed at least one antidepressant prescription within 3 months pre-pregnancy and/or during pregnancy between 2003 and 2018, using data from the health-record database of Hong Kong public healthcare services. Antidepressant utilization patterns before and during pregnancy, and factors associated with antidepressant continuation and reinitiation following medication discontinuation were evaluated. RESULTS: Of 466,358 pregnancies, 3019 (0.67%) received antidepressants within 3 months of pre-pregnancy and/or during pregnancy, and 2700 (0.58%) had prenatal antidepressant use. There was a significant rising trend of prenatal antidepressant use over time (0.6% in 2003 to 1.3% in 2018; odds ratio: 1.09, 95% confidence interval = [1.08, 1.10], p < 0.001). A consistent pattern of decreasing overall antidepressant use from 3 months pre-pregnancy to the second trimester was observed, followed by a slight increase in the third trimester. Almost half (n = 949, 49.5%) of 1918 women on antidepressants in 3 months pre-pregnancy continued treatment beyond the first trimester. A total of 8.2% that discontinued antidepressants in 3 months pre-pregnancy or in the first trimester reinitiated treatment in the later stage of pregnancy. Older age at conception (⩾35 years), recent calendar year of delivery (2015-2018), pre-existing depression/anxiety disorders, longer-term pre-pregnancy antidepressant treatment and pre-pregnancy prescription of other psychotropics were significantly associated with antidepressant continuation. Antidepressant reinitiation was predicted by pre-existing depression/anxiety disorders. CONCLUSIONS: Our results that prenatal antidepressant use is increasingly prevalent and half of pregnant women discontinued antidepressants 3 months before or after conception underscore the need for future research to clarify the risk and benefit of antidepressant continuation versus discontinuation to facilitate development of evidence-based guidelines, so as to optimize maternal and fetal outcomes.

Associations of Serum Uromodulin and Urinary Epidermal Growth Factor with Measured Glomerular Filtration Rate and Interstitial Fibrosis in Kidney Transplantation.

INTRODUCTION: Noninvasive biomarkers that reflect tubular health and allow early recognition of accelerated graft fibrosis development are warranted. Serum uromodulin (sUmod) and urinary epidermal growth factor (uEGF) originate from kidney tubules and may reflect functional nephron mass. The aim of this study was to investigate the associations between sUmod and uEGF with measured glomerular filtration rate (mGFR) and kidney allograft interstitial fibrosis percentage (IF%) score. METHODS: sUmod and uEGF measurements, mGFR by iohexol-clearance and kidney allograft biopsies were obtained from kidney transplant recipients (KTRs) included in the Omega-3 fatty acids in Renal Transplantation (ORENTRA) trial at 8 weeks (baseline) and at 1 year after transplantation (end of study). Associations were analyzed with univariable and multivariable linear regression. RESULTS: Ninety patients at baseline and 48 patients at end of study had complete study variable assessments. uEGF normalized to urinary creatinine (uEGF/Cr) was associated with mGFR both at baseline (standardized ß-coefficient [Std. ß-coeff] = 0.457 [p = <0.001]) and at end of study (Std. ß-coeff = 0.637 [p = <0.001]). sUmod was only associated with mGFR at end of study (Std. ß-coeff = 0.443 [p = 0.002]). uEGF/Cr, sUmod, and mGFR were associated with graft IF% score both at baseline (Std. ß-coeff = -0.349 [p = 0.001], -0.274 [p = 0.009] and -0.289 [p = 0.006], respectively) and at end of study (Std. ß-coeff = -0.365 [p = 0.011], -0.347 [p = 0.016] and -0.405 [p = 0.004], respectively). The results remained largely unchanged in multivariable analysis. CONCLUSION: uEGF/Cr and sUmod were associated with mGFR and graft IF% score. Our results indicate a possible role of uEGF/Cr and sUmod in the follow-up of KTRs.

Life expectancy and years of potential life lost in bipolar disorder: systematic review and meta-analysis.

BACKGROUND: There is increasing research examining excess mortality in people with bipolar disorder using life expectancy and related measures, which quantify the disease impact on survival. However, there has been no meta-analysis to date summarising existing data on life expectancy in those with bipolar disorder. AIMS: To systematically review and quantitatively synthesise estimates of life expectancy and years of potential life lost (YPLL) in people with bipolar disorder. METHOD: We searched Embase, Medline, PsycINFO and Web of Science databases up to 31 March 2021. We generated pooled life expectancy using random-effects models, and derived YPLL summary estimate by calculating averaged values weighted by sample size of individual studies. Subgroup analyses were conducted for gender, geographical region, study period, a given age (set-age) for lifespan estimation and causes of death. The study was registered with PROSPERO (CRD42021241705). RESULTS: Eleven and 13 studies were included in the review for life expectancy (n = 96 601) and YPLL (n = 128 989), respectively. Pooled life expectancy was 66.88 years (95% CI 64.47-69.28; I2 = 99.9%, P < 0.001), was higher in women than men (70.51 (95% CI 68.61-72.41) v. 64.59 (95% CI 61.16-68.03); z = 2.00, P = 0.003) and was lowest in Africa. Weighted average YPLL was 12.89 years (95% CI 12.72-13.07), and was greatest in Africa. More YPLL was observed when lifespan was estimated at birth than at other set-age. YPLLs attributable to natural and unnatural deaths were 5.94 years (95% CI 5.81-6.07) and 5.69 years (95% CI 5.59-5.79), respectively. CONCLUSIONS: Bipolar disorder is associated with substantially shortened life expectancy. Implementation of multilevel, targeted interventions is urgently needed to reduce this mortality gap.

Pre-existing chronic physical morbidity and excess mortality in people with schizophrenia: a population-based cohort study.

PURPOSE: Schizophrenia is associated with increased premature mortality and physical morbidity. This study aimed to examine prevalence of pre-existing chronic physical diseases, and association between physical multimorbidity burden and mortality rates among patients with newly diagnosed schizophrenia. METHODS: This population-based cohort study investigated patients with first-recorded diagnosis of schizophrenia between January 2006 and December 2016, using territory-wide medical-record database of public healthcare service in Hong Kong. Physical morbidities were measured by Charlson Comorbidity Index (CCI), taking into consideration both number and severity of physical diseases, and were grouped into nine broad disease categories for analyses. Physical multimorbidity burden was stratified into three levels according to CCI of 0, 1 or ≥ 2. Cox proportional hazards regression models were used to examine associations of physical multimorbidity with mortality rates. RESULTS: Of the 13,945 patients, 8.6% (n = 1207) had pre-existing physical morbidity. Patients with physical morbidity exhibited elevated all-cause mortality rate relative to those without physical morbidity [adjusted HR 2.38 (95% CI 2.04-2.77)]. Gastrointestinal/liver diseases, diabetes and cardiovascular diseases constituted the three most frequently diagnosed physical morbidities, whereas cancers displayed the highest all-cause mortality rate. An increase in physical multimorbidity burden was associated with increased all-cause mortality rate [CCI = 1: 1.98 (1.64-2.40); CCI ≥ 2: 3.08 (2.51-3.77), CCI = 0 as reference]. CONCLUSION: Schizophrenia patients with pre-existing physical morbidity had two-fold increased risk of premature mortality compared to those without physical morbidity. Physical multimorbidity confers incremental impact on excess mortality. Early detection and intervention of physical morbidity in the initial phase of schizophrenia is necessary to reduce avoidable mortality.

Risk of mortality and complications in patients with schizophrenia and diabetes mellitus: population-based cohort study.

BACKGROUND: Schizophrenia patients have markedly elevated prevalence of diabetes compared with the general population. However, risk of mortality and diabetes-related complications among schizophrenia patients with co-occurring diabetes is understudied. AIMS: We investigated whether schizophrenia increased the risk of overall mortality, complications and post-complication mortality in people with diabetes. METHOD: This population-based, propensity-score matched (1:10) cohort study identified 6991 patients with incident diabetes and pre-existing schizophrenia and 68 682 patients with incident diabetes only between 2001 and 2016 in Hong Kong using a medical record database of public healthcare services. Association between schizophrenia and all-cause mortality was examined with a Cox proportional hazards model. Effect of schizophrenia on first-year complication occurrence following diabetes diagnosis and post-complication mortality rates were evaluated. RESULTS: Schizophrenia was associated with increased all-cause mortality (adjusted hazards ratio [aHR] 1.11, 95% CI 1.05-1.18), particularly among men and older age groups. Schizophrenia patients with diabetes had higher metabolic complication rate (aHR 1.99, 95% CI 1.63-2.42), lower microvascular complication rate (aHR 0.75, 95% CI 0.65-0.86) and comparable macrovascular complication rate (aHR 0.93, 95% CI 0.85-1.03), relative to patients with diabetes only. Among patients with diabetes complications, schizophrenia was associated with elevated all-cause mortality after macrovascular (aHR 1.19, 95% CI 1.04-1.37) and microvascular (aHR 1.33, 95% CI 1.08-1.64) complications. Gender-stratified analyses revealed that a significant effect of schizophrenia on heightened post-complication mortality was observed in men only. CONCLUSIONS: Schizophrenia patients with co-occurring diabetes are at increased risk of excess mortality, including post-complication mortality. Further research identifying effective interventions is warranted to optimise diabetes-related outcomes in this vulnerable population.

A Fully Automated Method for the Determination of Serum Belatacept and Its Application in a Pharmacokinetic Investigation in Renal Transplant Recipients.

BACKGROUND: Belatacept (Nulojix; Bristol-Myers Squibb, New York, NY) is a biological immunosuppressive drug used for the prophylaxis of acute rejection after renal transplantation. Few studies have described belatacept pharmacokinetics, and the effect of therapeutic drug monitoring has not been investigated. We have developed a drug-capture assay (using drug target) to measure belatacept in serum and applied this assay in a pharmacokinetic study in renal transplant recipients. METHODS: CD80 was used to trap belatacept onto streptavidin-coated wells. Captured drug was quantified using Eu-labeled protein A and time-resolved fluorescence. The assay was applied in a pilot pharmacokinetic study in renal transplanted patients receiving belatacept infusions. Belatacept serum concentrations were determined at several time points between belatacept infusions. A simple population pharmacokinetic model was developed to visualize measured and predicted belatacept serum concentrations. RESULTS: The assay range was 0.9-30 mg/L with accuracy within 91%-99% and coefficients of variation ranging from 1.2% to 3.6%. Predilution extended the measurement range to 130 mg/L with an accuracy of 90% and coefficients of variation of 3.8%. Samples were stable during storage at 4°C for 15 days and during 2 freeze-thaw cycles. Belatacept concentrations were determined in a total of 203 serum samples collected during 26 infusion intervals from 5 renal transplant recipients. The population pharmacokinetic model visualized both measured and predicted concentrations. CONCLUSIONS: We have developed an automated, accurate, and precise assay for the determination of belatacept serum concentrations. The assay was successfully applied in a pharmacokinetic study in renal transplant recipients receiving belatacept infusions.

Determination of Tacrolimus Concentration and Protein Expression of P-Glycoprotein in Single Human Renal Core Biopsies.

BACKGROUND: Tacrolimus (TAC) is currently the cornerstone of immunosuppressive protocols for renal transplant recipients. Despite therapeutic whole blood monitoring, TAC is associated with nephrotoxicity, and it has been hypothesized that intrarenal accumulation of TAC and/or its metabolites are involved. As TAC is a substrate of P-glycoprotein (P-gp), the expression and activity of this efflux transporter could influence the levels of TAC in renal tissue. The primary aim of this study was to develop and validate a method for quantification of TAC in tissue homogenates from single human renal core biopsies. The secondary aim was to provide measures of P-gp expression and of the demethylated metabolites of TAC in the same renal biopsy. METHODS: Human renal tissue, with and without clinical TAC exposure, was used for method development and validation. Homogenates were prepared with bead-beating, and concentrations of TAC and its demethylated metabolites were analyzed with liquid chromatography tandem mass spectrometry after protein precipitation. A Western blot method was used for semiquantification of P-gp expression in the homogenates. The final methods were applied to renal core biopsies from 2 transplant patients. RESULTS: The TAC assay showed within- and between-run mean accuracy between 99.7% and 107% and coefficients of variation ≤6.7%. Matrix effects were nonsignificant, and samples were stable for 3 months preanalytically when stored at -80°C. TAC concentrations in the renal core biopsies were 62.6 and 43.7 pg/mg tissue. The methods for measurement of desmethyl-TAC and P-gp expression were suitable for semiquantification in homogenates from renal core biopsies. CONCLUSIONS: These methods may be valuable for the elucidation of the pharmacokinetic mechanisms behind TAC-induced nephrotoxicity in renal transplant recipients.

A signal processing and deep learning framework for methylation detection using Oxford Nanopore sequencing.

Oxford Nanopore sequencing can detect DNA methylations from ionic current signal of single molecules, offering a unique advantage over conventional methods. Additionally, adaptive sampling, a software-controlled enrichment method for targeted sequencing, allows reduced representation methylation sequencing that can be applied to CpG islands or imprinted regions. Here we present DeepMod2, a comprehensive deep-learning framework for methylation detection using ionic current signal from Nanopore sequencing. DeepMod2 implements both a bidirectional long short-term memory (BiLSTM) model and a Transformer model and can analyze POD5 and FAST5 signal files generated on R9 and R10 flowcells. Additionally, DeepMod2 can run efficiently on central processing unit (CPU) through model pruning and can infer epihaplotypes or haplotype-specific methylation calls from phased reads. We use multiple publicly available and newly generated datasets to evaluate the performance of DeepMod2 under varying scenarios. DeepMod2 has comparable performance to Guppy and Dorado, which are the current state-of-the-art methods from Oxford Nanopore Technologies that remain closed-source. Moreover, we show a high correlation (r = 0.96) between reduced representation and whole-genome Nanopore sequencing. In summary, DeepMod2 is an open-source tool that enables fast and accurate DNA methylation detection from whole-genome or adaptive sequencing data on a diverse range of flowcell types.

Prenatal antidepressant use and risk of congenital malformations: A population-based cohort study.

Previous studies examining antidepressants and congenital-malformations were primarily conducted in western countries, and many were constrained by important methodological limitations. This population-based study identified 465,069 women (including 1,705 redeemed ≥1 prescription of antidepressants during first-trimester) aged 15-50 years who delivered their first and singleton child between 2003 and 2018 in a predominantly-Chinese population in Hong Kong, using territory-wide medical-record database of public-healthcare services, and employed propensity-score fine-stratification-weighted logistic-regression analyses to evaluate risk of any major and organ/system-specific congenital-malformations following first-trimester exposure to antidepressants. Major malformation overall was not associated with any antidepressant (weighted-odds-ratio wOR, 0.88 [95 %CI, 0.44-1.76]), specific drug-class, or individual antidepressants. Exposure to any antidepressant was associated with increased risk of cardiac (wOR, 1.82 [95 %CI, 1.07-3.12]) and respiratory anomalies (wOR,4.11 [95 %CI, 1.61-10.45]). Exposure to selective-serotonin-reuptake-inhibitors (SSRI) and multiple-AD-classes were associated with respiratory and cardiac anomalies, respectively. However, these identified associations were not consistently affirmed across sensitivity analyses, precluding firm conclusion. Observed associations of specific cardiac defects with serotonin-norepinephrine-reuptake-inhibitors (SNRI), tricyclic-antidepressants (TCA) and multiple-AD-classes were noted with wide confidence-intervals, suggesting imprecise estimation. Overall, our findings suggest that first-trimester antidepressant exposure was not robustly associated with increased risk of congenital-malformations. Further research clarifying comparative safety of individual antidepressants on specific malformations is warranted.

Single-Cell Omics for Transcriptome CHaracterization (SCOTCH): isoform-level characterization of gene expression through long-read single-cell RNA sequencing.

The advent of long-read single-cell transcriptome sequencing (lr-scRNA-Seq) represents a significant leap forward in single-cell genomics. With the recent introduction of R10 flowcells by Oxford Nanopore, we propose that previous computational methods designed to handle high sequencing error rates are no longer relevant, and that the prevailing approach using short reads to compile "barcode space" (candidate barcode list) to de-multiplex long reads are no longer necessary. Instead, computational methods should now shift focus on harnessing the unique benefits of long reads to analyze transcriptome complexity. In this context, we introduce a comprehensive suite of computational methods named Single-Cell Omics for Transcriptome CHaracterization (SCOTCH). Our method is compatible with the single-cell library preparation platform from both 10X Genomics and Parse Biosciences, facilitating the analysis of special cell populations, such as neurons, hepatocytes and developing cardiomyocytes. We specifically re-formulated the transcript mapping problem with a compatibility matrix and addressed the multiple-mapping issue using probabilistic inference, which allows the discovery of novel isoforms as well as the detection of differential isoform usage between cell populations. We evaluated SCOTCH through analysis of real data across different combinations of single-cell libraries and sequencing technologies (10X + Illumina, Parse + Illumina, 10X + Nanopore_R9, 10X + Nanopore_R10, Parse + Nanopore_R10), and showed its ability to infer novel biological insights on cell type-specific isoform expression. These datasets enhance the availability of publicly available data for continued development of computational approaches. In summary, SCOTCH allows extraction of more biological insights from the new advancements in single-cell library construction and sequencing technologies, facilitating the examination of transcriptome complexity at the single-cell level.

Mortality risk and mood stabilizers in bipolar disorder: a propensity-score-weighted population-based cohort study in 2002-2018.

AIMS: Accumulating studies have assessed mortality risk associated with mood-stabilizers, the mainstay treatment for bipolar disorder (BD). However, existing data were mostly restricted to suicide risk, focused on lithium and valproate and rarely adequately adjusted for potential confounders. This study aimed to assess comparative mortality risk with all, natural and unnatural causes between lithium, valproate and three frequently prescribed second-generation antipsychotics (SGA), with adjustment for important confounders. METHODS: This population-based cohort study identified 8137 patients with first-diagnosed BD, who had exposed to lithium (n = 1028), valproate (n = 3580), olanzapine (n = 797), quetiapine (n = 1975) or risperidone (n = 757) between 2002 and 2018. Data were retrieved from territory-wide medical-record database of public healthcare services in Hong Kong. Propensity-score (PS)-weighting method was applied to optimize control for potential confounders including pre-existing chronic physical diseases, substance/alcohol use disorders and other psychotropic medications. PS-weighted Cox proportional-hazards regression was conducted to assess risk of all-, natural- and unnatural-cause mortality related to each mood-stabilizer, compared to lithium. Three sets of sensitivity analyses were conducted by restricting to patients with (i) length of cumulative exposure to specified mood-stabilizer ≥90 days and its medication possession ratio (MPR) ≥90%, (ii) MPR of specified mood-stabilizer ≥80% and MPR of other studied mood-stabilizers <20% and (iii) monotherapy. RESULTS: Incidence rates of all-cause mortality per 1000 person-years were 5.9 (95% confidence interval [CI]: 4.5-7.6), 8.4 (7.4-9.5), 11.1 (8.3-14.9), 7.4 (6.0-9.2) and 12.0 (9.3-15.6) for lithium-, valproate-, olanzapine-, quetiapine- and risperidone-treated groups, respectively. BD patients treated with olanzapine (PS-weighted hazard ratio = 2.07 [95% CI: 1.33-3.22]) and risperidone (1.66 [1.08-2.55]) had significantly higher all-cause mortality rate than lithium-treated group. Olanzapine was associated with increased risk of natural-cause mortality (3.04 [1.54-6.00]) and risperidone was related to elevated risk of unnatural-cause mortality (3.33 [1.62-6.86]), relative to lithium. The association between olanzapine and increased natural-cause mortality rate was consistently affirmed in sensitivity analyses. Relationship between risperidone and elevated unnatural-cause mortality became non-significant in sensitivity analyses restricted to low MPR in other mood-stabilizers and monotherapy. Valproate- and lithium-treated groups did not show significant differences in all-, natural- or unnatural-cause mortality risk. CONCLUSION: Our data showed that olanzapine and risperidone were associated with higher mortality risk than lithium, and further supported the clinical guidelines recommending lithium as the first-line mood-stabilizer for BD. Future research is required to further clarify comparative mortality risk associated with individual SGA agents to facilitate risk-benefit evaluation of alternative mood-stabilizers to minimize avoidable premature mortality in BD.

Risk of adverse pregnancy, delivery and neonatal outcomes associated with bipolar disorder and prenatal use of mood stabilizers: A population-based cohort study.

Previous research examining bipolar-disorder (BD) and pregnancy/neonatal outcomes yielded mixed results, were mostly derived from Western countries and rarely delineated effect between disorder and mood-stabilizers. This population-based study identified women age 15-50 years who delivered first/singleton child in 2003-2018 in Hong Kong, utilizing territory-wide medical-record database of public healthcare services. Propensity-score weighted logistic-regression analyses adjusted for confounders were employed to examine risk of adverse pregnancy, delivery and neonatal outcomes associated with BD and mood-stabilizers (lithium, anticonvulsants and antipsychotics). Exploratory unadjusted-analyses were conducted to assess risk for congenital-malformations. Of 465,069 women, 302 had BD-diagnosis, including 168 redeemed ≥ 1 prescription of mood-stabilizers during pregnancy (treated-BD) and 134 gestationally-unexposed to mood-stabilizers (untreated-BD). BD was significantly-associated with increased risk of gestational-diabetes (adjusted-odds-ratio: 1.75 [95 % CI: 1.15-2.70]) and maternal somatic hospitalization ≤ 90 days post-discharge from index-delivery (2.12 [1.19-3.90]). In treatment status-stratified analyses, treated-BD women exhibited significantly-increased rate of gestational-diabetes (2.09 [1.21-3.70]) relative to controls (non-BD and gestationally-unexposed to mood-stabilizers). No significant association of BD or mood-stabilizers with other adverse outcomes was observed. Overall, our findings indicate that BD and mood-stabilizers are not associated with most adverse pregnancy, delivery and neonatal outcomes. Further research clarifying comparative safety of individual mood-stabilizing agents on pregnancy/neonatal outcomes is required.

The risk of stroke and post-stroke mortality in people with schizophrenia: A systematic review and meta-analysis study.

Sources of heterogeneity in risk of stroke and mortality risk following acute-stroke in schizophrenia are understudied. We systematically searched four electronic-databases until 1-November-2022, and conducted meta-analysis to synthesize estimates of stroke-risk and post-stroke mortality for schizophrenia patients relative to non-schizophrenia counterparts. Subgroup-analyses and meta-regression models stratified by sex, nature of sample (incident/prevalent), geographical region, study-period and time-frame following stroke were conducted when applicable. Fifteen and 5 studies were included for meta-analysis of stroke-risk (n=18,368,253; 129,095 schizophrenia patients) and all-cause post-stroke mortality (n=289,231; 4,477 schizophrenia patients), respectively. Schizophrenia patients exhibited elevated stroke-risk (relative-risk =1.55[95% CI:1.31-1.84]) relative to non-schizophrenia controls. Schizophrenia was associated with increased stroke-risk in both sexes, study-periods of 1990s and 2000s, and irrespective of nature of sample and geographical regions. Meta-regression revealed regional differences in relative-risk for stroke, but limited by small number of studies. After removal of an outlier study, meta-analysis demonstrated that schizophrenia was associated with increased overall (hazard-ratio=1.37[1.30-1.44]), short-term (≤90 days; 1.29[1.14-1.46]) and longer-term (≥1 year; 1.45[1.32-1.60]) post-stroke mortality rates. Raised post-stroke mortality rate for schizophrenia was observed irrespective of nature of sample, geographical regions and study-periods. Taken together, schizophrenia is associated with increased stroke-risk and post-stroke mortality. Multilevel-interventions are required to reduce these physical-health disparities.