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Cai N, Wang X, Zhu H, Hu Y, Zhang X, Wang L. Isotopic insights and integrated analysis for heavy metal levels, ecological risks, and source apportionment in river sediments of the Qinghai-Tibet Plateau. ENVIRONMENTAL RESEARCH 2024; 251:118626. [PMID: 38467358 DOI: 10.1016/j.envres.2024.118626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/02/2024] [Accepted: 03/04/2024] [Indexed: 03/13/2024]
Abstract
The research was carried out to examine the pollution characteristics, ecological risk, and origins of seven heavy metals (Hg, As, Pb, Cu, Cd, Zn, and Ni) in 51 sediment samples gathered from 8 rivers located on the Qinghai-Tibet Plateau (QTP) in China. The contents of Hg and Cd were 5.0 and 1.1 times higher than their background values, respectively. The mean levels of other measured heavy metals were below those found naturally in the local soil. The enrichment factor showed that the study area exhibited significantly enriched Hg with 70.6% sampling sites. The Cd contents at 19.6% of sampling sites were moderately enriched. The other sampling sites were at a less enriched level. The sediments of all the rivers had a medium level of potential ecological risk. Hg was the major ecological risk factor in all sampling sites, followed by Cd. The findings from the positive matrix factorization (PMF) analysis shown agricultural activities, industrial activities, traffic emissions, and parent material were the major sources. The upper, middle, and low reaches of the Quanji river had different Hg isotope compositions, while sediments near the middle reaches were similar to the δ202Hg of the industrial source. At the upstream sampling sites, the Hg isotope content was very close to the background level. The results of this research can establish a strong scientific sound to improve the safety of the natural circumstances of rivers on the QTP.
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Huang L, Tang S, Rietkerk J, Appadurai V, Krebs MD, Schork AJ, Werge T, Zuber V, Kendler K, Cai N. Polygenic Analyses Show Important Differences Between Major Depressive Disorder Symptoms Measured Using Various Instruments. Biol Psychiatry 2024; 95:1110-1121. [PMID: 38056704 PMCID: PMC11139567 DOI: 10.1016/j.biopsych.2023.11.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 11/06/2023] [Accepted: 11/26/2023] [Indexed: 12/08/2023]
Abstract
BACKGROUND Symptoms of major depressive disorder (MDD) are commonly assessed using self-rating instruments like the Patient Health Questionnaire-9 (PHQ-9) (current symptoms) and the Composite International Diagnostic Interview Short-Form (CIDI-SF) (worst-episode symptoms). We performed a systematic comparison between them for their genetic architecture and utility in investigating MDD heterogeneity. METHODS Using data from the UK Biobank (n = 41,948-109,417), we assessed the single nucleotide polymorphism heritability and genetic correlation (rg) of both sets of MDD symptoms. We further compared their rg with non-MDD traits and used Mendelian randomization to assess whether either set of symptoms has more genetic sharing with non-MDD traits. We also assessed how specific each set of symptoms is to MDD using the metric polygenic risk score pleiotropy. Finally, we used genomic structural equation modeling to identify factors that explain the genetic covariance between each set of symptoms. RESULTS Corresponding symptoms reported through the PHQ-9 and CIDI-SF have low to moderate genetic correlations (rg = 0.43-0.87), and this cannot be fully attributed to different severity thresholds or the use of a skip structure in the CIDI-SF. Both Mendelian randomization and polygenic risk score pleiotropy analyses showed that PHQ-9 symptoms are more associated with traits that reflect general dysphoria, whereas the skip structure in the CIDI-SF allows for the identification of heterogeneity among likely MDD cases. Finally, the 2 sets of symptoms showed different factor structures in genomic structural equation modeling, reflective of their genetic differences. CONCLUSIONS MDD symptoms assessed using the PHQ-9 and CIDI-SF are not interchangeable; the former better indexes general dysphoria, while the latter is more informative about within-MDD heterogeneity.
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Zhao H, Liu Y, Cai N, Liao X, Tang L, Wang Y. Endocannabinoid Hydrolase Inhibitors: Potential Novel Anxiolytic Drugs. Drug Des Devel Ther 2024; 18:2143-2167. [PMID: 38882045 PMCID: PMC11179644 DOI: 10.2147/dddt.s462785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 05/27/2024] [Indexed: 06/18/2024] Open
Abstract
Over the past decade, the idea of targeting the endocannabinoid system to treat anxiety disorders has received increasing attention. Previous studies focused more on developing cannabinoid receptor agonists or supplementing exogenous cannabinoids, which are prone to various adverse effects due to their strong pharmacological activity and poor receptor selectivity, limiting their application in clinical research. Endocannabinoid hydrolase inhibitors are considered to be the most promising development strategies for the treatment of anxiety disorders. More recent efforts have emphasized that inhibition of two major endogenous cannabinoid hydrolases, monoacylglycerol lipase (MAGL) and fatty acid amide hydrolase (FAAH), indirectly activates cannabinoid receptors by increasing endogenous cannabinoid levels in the synaptic gap, circumventing receptor desensitization resulting from direct enhancement of endogenous cannabinoid signaling. In this review, we comprehensively summarize the anxiolytic effects of MAGL and FAAH inhibitors and their potential pharmacological mechanisms, highlight reported novel inhibitors or natural products, and provide an outlook on future directions in this field.
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Zhang SY, Ma XJ, Zhu XX, Cai N. Exploring predictive markers for liver failure post-hepatectomy in hepatocellular carcinoma patients. World J Gastrointest Surg 2024; 16:1482-1484. [PMID: 38817295 PMCID: PMC11135300 DOI: 10.4240/wjgs.v16.i5.1482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/09/2024] [Accepted: 04/17/2024] [Indexed: 05/23/2024] Open
Abstract
This letter to the editor addresses the study titled "Predictive value of NLR, Fib4, and APRI in the occurrence of liver failure after hepatectomy in patients with hepatocellular carcinoma" by Kuang et al in the World Journal of Gastrointestinal Surgery. The study acknowledges the comprehensive patient data analysis while suggesting that there is a need for further discussion on the clinical applicability of these markers across diverse patient populations. This letter recommends prospective studies for validation and considers the influence of confounding factors. This finding underscores the significance of this study in improving hepatocellular carcinoma management.
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Xu F, Wang B, Hu J, Cai N, Han L, Jiang M, Zhao Y, Zhu B. Optimization of benzene exposure risk assessment: An integrated approach utilizing internal and external concentrations with a focus on biomarkers S-PMA & t, t-MA. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171719. [PMID: 38490405 DOI: 10.1016/j.scitotenv.2024.171719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 03/17/2024]
Abstract
In the majority of occupational settings within China, the concentrations of benzene are observed to fall markedly below the demarcated detection thresholds. Employing traditional risk assessment models, the presence of exceptionally low airborne benzene exposure concentrations may infuse heightened degrees of uncertainty. Consequently, the necessity arises to investigate risk assessment methodologies more apt for the prevalent exposure environment among employees. In the present study, a pharmacokinetic model premised on urinary benzene metabolites (S-PMA and t, t-MA) was employed to ascertain a more precise daily airborne benzene exposure concentration per individual. This value was integrated into the linear multistage model as the 'internal exposure concentration'. In conjunction with the U.S National Environmental Protection Agency's (EPA) inhalation risk assessment model predicated on the external exposure concentration, the Singapore Ministry of Manpower's (MOM) model, and the linear multistage (LMS) model, the carcinogenic and non-carcinogenic effects of benzene were evaluated for 1781 benzene-exposed employees across 76 enterprises in Jiangsu Province. Findings suggest that in the linear multilevel model assessment, the cancer risk levels based on t, t-MA and S-PMA were higher in the printing and recording media reproduction industry, automobile manufacturing industry, general equipment manufacturing industry and the furniture manufacturing industry (median 2.842 × 10-4, 2.819 × 10-4, 2.809 × 10-4, and 2.678 × 10-4), which align more consistently with the actual benzene exposure circumstances of each industry's study participants, with overall risk levels calculated by the linear multistage model exceeding those of the EPA inhalation risk assessment model and the MOM model. This implies that the linear multistage model of internal exposure, based on the reciprocal of benzene biomarkers S-PMA and t, t-MA for airborne benzene exposure, presents enhanced sensitivity and suitability for the current occupational health risk assessment of workers. Without doubt, biomarker-based benzene exposure risk assessment emerges as the optimal choice.
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Xu C, Wang Q, Du C, Chen L, Zhou Z, Zhang Z, Cai N, Li J, Huang C, Ma T. Histone deacetylase-mediated silencing of PSTPIP2 expression contributes to aristolochic acid nephropathy-induced PANoptosis. Br J Pharmacol 2024; 181:1452-1473. [PMID: 38073114 DOI: 10.1111/bph.16299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 11/21/2023] [Accepted: 11/29/2023] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND AND PURPOSE Aristolochic acid nephropathy (AAN) is a progressive kidney disease caused by using herbal medicines. Currently, no therapies are available to treat or prevent aristolochic acid nephropathy. Histone deacetylase (HDAC) plays a crucial role in the development and progression of renal disease. We tested whether HDAC inhibitors could prevent aristolochic acid nephropathy and determined the underlying mechanism. EXPERIMENTAL APPROACH HDACs expression in the aristolochic acid nephropathy model was examined. The activation of PANoptosis of mouse kidney and renal tubular epithelial cell were assessed after exposure to HDAC1 and HDAC2 blockade. Kidney-specific knock-in of proline-serine-threonine-phosphatase-interacting protein 2 (PSTPIP2) mice were used to investigate whether PSTPIP2 affected the production of PANoptosome. KEY RESULTS Aristolochic acid upregulated the expression of HDAC1 and HDAC2 in the kidneys. Notably, the HDAC1 and HDAC2 specific inhibitor, romidepsin (FK228, depsipeptide), suppressed aristolochic acid-induced kidney injury, epithelial cell pyroptosis, apoptosis and necroptosis (PANoptosis). Moreover, romidepsin upregulated PSTPIP2 in renal tubular epithelial cells, which was enhanced by aristolochic acid treatment. Conditional knock-in of PSTPIP2 in the kidney protected against aristolochic acid nephropathy. In contrast, the knockdown of PSTPIP2 expression in PSTPIP2-knock-in mice restored kidney damage and PANoptosis. PSTPIP2 function was determined in vitro using PSTPIP2 knockdown or overexpression in mouse renal tubular epithelial cells (mTECs). Additionally, PSTPIP2 was found to regulate caspase 8 in aristolochic acid nephropathy. CONCLUSION AND IMPLICATIONS HDAC-mediated silencing of PSTPIP2 may contribute to aristolochic acid nephropathy. Hence, HDAC1 and HDAC2 specific inhibitors or PSTPIP2 could be valuable therapeutic agents for preventing aristolochic acid nephropathy.
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Wang L, Mizumoto S, Zhang R, Zhang Y, Liu Y, Cheng W, Li X, Dan M, Zhang C, Gao X, Wang J, Han J, Jiao L, Wang Y, Jin Q, Yang L, Li C, Li S, Zhu J, Jiang H, Nishimura G, Yamada T, Yamada S, Cai N, Qiang R, Guo L. Identification of a novel LFNG variant in a Chinese fetus with spondylocostal dysostosis and a systematic review. J Hum Genet 2024:10.1038/s10038-024-01248-3. [PMID: 38565611 DOI: 10.1038/s10038-024-01248-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/04/2024]
Abstract
Spondylocostal dysostosis (SCDO) encompasses a group of skeletal disorders characterized by multiple segmentation defects in the vertebrae and ribs. SCDO has a complex genetic etiology. This study aimed to analyze and identify pathogenic variants in a fetus with SCDO. Copy number variant sequencing and whole exome sequencing were performed on a Chinese fetus with SCDO, followed by bioinformatics analyses, in vitro functional assays and a systematic review on the reported SCDO cases with LFNG pathogenic variants. Ultrasound examinations in utero exhibited that the fetus had vertebral malformation, scoliosis and tethered cord, but rib malformation was not evident. We found a novel homozygous variant (c.1078 C > T, p.R360C) within the last exon of LFNG. The variant was predicted to cause loss of function of LFNG by in silico prediction tools, which was confirmed by an in vitro assay of LFNG enzyme activity. The systematic review listed a total of 20 variants of LFNG in SCDO. The mutational spectrum spans across all exons of LFNG except the last one. This study reported the first Chinese case of LFNG-related SCDO, revealing the prenatal phenotypes and expanding the mutational spectrum of the disorder.
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Zhang R, Cui D, Song C, Ma X, Cai N, Zhang Y, Feng M, Cao Y, Chen L, Qiang R. Evaluating the efficacy of a long-read sequencing-based approach in the clinical diagnosis of neonatal congenital adrenocortical hyperplasia. Clin Chim Acta 2024; 555:117820. [PMID: 38307397 DOI: 10.1016/j.cca.2024.117820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/04/2024]
Abstract
Congenital adrenal hyperplasia (CAH) is a group of autosomal recessive disorders predominantly characterized by impaired corticosteroid synthesis. Clinical phenotypes include hypoadrenocorticism, electrolyte disturbances, abnormal gonadal development, and short stature, of which severe hyponadrenocorticism and salt wasting can be life-threatening. Genetic analysis can help in the clinical diagnosis of CAH. However, the 21-OHD-causing gene CYP21A2 is arranged in tandem with the highly homologous CYP21A1P pseudogene, making it difficult to determine the exact genotypes using the traditional method of multiplex ligation-dependent probe amplification (MLPA) plus Sanger sequencing or next-generation sequencing (NGS). We applied a long-read sequencing-based approach termed comprehensive analysis of CAH (CACAH) to 48 newborns with CAH that were diagnosed by clinical features and the traditional MLPA plus Sanger sequencing method for retrospective analysis, to evaluate its efficacy in the clinical diagnosis of neonatal CAH. Compared with the MLPA plus Sanger sequencing method, CACAH showed 100 % consistency in detecting SNV/indel variants located in exons and exon-intron boundary regions of CAH-related genes. It can directly determine the cis-trans relationship without the need to analyze parental genotypes, which reduces the time to diagnosis. Moreover, CACAH was able to distinguish different CYP21A1P/CYP21A2 and TNXA/TNXB chimeras, and detect additional variants (CYP21A2 variants c.-121C > T, c.*13G > A, c.*52C > T, c.*440C > T, c.*443 T > C, and TNXB variants c.12463 + 2 T > C, c.12204 + 5G > A). We also identified the TNXB variant c.11435_11524 + 30del alone instead of as a part of the TNXA/TNXB-CH-1 chimera in two newborns, which might be introduced by gene conversion. All of these characteristics enabled clinicians to better explain the phenotype of subjects and manage them more effectively. CACAH has a great advantage over the traditional MLPA and Sanger sequencing methods, showing substantial potential in the genetic diagnosis and screening of neonatal CAH.
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Zhang G, Li S, Wei S, Ge S, Cai N, Zhao Y. Multimodal Composition Example Mining for Composed Query Image Retrieval. IEEE TRANSACTIONS ON IMAGE PROCESSING : A PUBLICATION OF THE IEEE SIGNAL PROCESSING SOCIETY 2024; 33:1149-1161. [PMID: 38300775 DOI: 10.1109/tip.2024.3359062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Composed query image retrieval task aims to retrieve the target image in the database by a query that composes two different modalities: a reference image and a sentence declaring that some details of the reference image need to be modified and replaced by new elements. Tackling this task needs to learn a multimodal embedding space, which can make semantically similar targets and queries close but dissimilar targets and queries as far away as possible. Most of the existing methods start from the perspective of model structure and design some clever interactive modules to promote the better fusion and embedding of different modalities. However, their learning objectives use conventional query-level examples as negatives while neglecting the composed query's multimodal characteristics, leading to the inadequate utilization of the training data and suboptimal construction of metric space. To this end, in this paper, we propose to improve the learning objective by constructing and mining hard negative examples from the perspective of multimodal fusion. Specifically, we compose the reference image and its logically unpaired sentences rather than paired ones to create component-level negative examples to better use data and enhance the optimization of metric space. In addition, we further propose a new sentence augmentation method to generate more indistinguishable multimodal negative examples from the element level and help the model learn a better metric space. Massive comparison experiments on four real-world datasets confirm the effectiveness of the proposed method.
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Du C, Xu C, Jia P, Cai N, Zhang Z, Meng W, Chen L, Zhou Z, Wang Q, Feng R, Li J, Meng X, Huang C, Ma T. PSTPIP2 ameliorates aristolochic acid nephropathy by suppressing interleukin-19-mediated neutrophil extracellular trap formation. eLife 2024; 13:e89740. [PMID: 38314821 PMCID: PMC10906995 DOI: 10.7554/elife.89740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 02/04/2024] [Indexed: 02/07/2024] Open
Abstract
Aristolochic acid nephropathy (AAN) is a progressive kidney disease caused by herbal medicines. Proline-serine-threonine phosphatase-interacting protein 2 (PSTPIP2) and neutrophil extracellular traps (NETs) play important roles in kidney injury and immune defense, respectively, but the mechanism underlying AAN regulation by PSTPIP2 and NETs remains unclear. We found that renal tubular epithelial cell (RTEC) apoptosis, neutrophil infiltration, inflammatory factor, and NET production were increased in a mouse model of AAN, while PSTPIP2 expression was low. Conditional knock-in of Pstpip2 in mouse kidneys inhibited cell apoptosis, reduced neutrophil infiltration, suppressed the production of inflammatory factors and NETs, and ameliorated renal dysfunction. Conversely, downregulation of Pstpip2 expression promoted kidney injury. In vivo, the use of Ly6G-neutralizing antibody to remove neutrophils and peptidyl arginine deiminase 4 (PAD4) inhibitors to prevent NET formation reduced apoptosis, alleviating kidney injury. In vitro, damaged RTECs released interleukin-19 (IL-19) via the PSTPIP2/nuclear factor (NF)-κB pathway and induced NET formation via the IL-20Rβ receptor. Concurrently, NETs promoted apoptosis of damaged RTECs. PSTPIP2 affected NET formation by regulating IL-19 expression via inhibition of NF-κB pathway activation in RTECs, inhibiting RTEC apoptosis, and reducing kidney damage. Our findings indicated that neutrophils and NETs play a key role in AAN and therapeutic targeting of PSTPIP2/NF-κB/IL-19/IL-20Rβ might extend novel strategies to minimize Aristolochic acid I-mediated acute kidney injury and apoptosis.
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Meng X, Navoly G, Giannakopoulou O, Levey DF, Koller D, Pathak GA, Koen N, Lin K, Adams MJ, Rentería ME, Feng Y, Gaziano JM, Stein DJ, Zar HJ, Campbell ML, van Heel DA, Trivedi B, Finer S, McQuillin A, Bass N, Chundru VK, Martin HC, Huang QQ, Valkovskaya M, Chu CY, Kanjira S, Kuo PH, Chen HC, Tsai SJ, Liu YL, Kendler KS, Peterson RE, Cai N, Fang Y, Sen S, Scott LJ, Burmeister M, Loos RJF, Preuss MH, Actkins KV, Davis LK, Uddin M, Wani AH, Wildman DE, Aiello AE, Ursano RJ, Kessler RC, Kanai M, Okada Y, Sakaue S, Rabinowitz JA, Maher BS, Uhl G, Eaton W, Cruz-Fuentes CS, Martinez-Levy GA, Campos AI, Millwood IY, Chen Z, Li L, Wassertheil-Smoller S, Jiang Y, Tian C, Martin NG, Mitchell BL, Byrne EM, Awasthi S, Coleman JRI, Ripke S, Sofer T, Walters RG, McIntosh AM, Polimanti R, Dunn EC, Stein MB, Gelernter J, Lewis CM, Kuchenbaecker K. Multi-ancestry genome-wide association study of major depression aids locus discovery, fine mapping, gene prioritization and causal inference. Nat Genet 2024; 56:222-233. [PMID: 38177345 PMCID: PMC10864182 DOI: 10.1038/s41588-023-01596-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 10/26/2023] [Indexed: 01/06/2024]
Abstract
Most genome-wide association studies (GWAS) of major depression (MD) have been conducted in samples of European ancestry. Here we report a multi-ancestry GWAS of MD, adding data from 21 cohorts with 88,316 MD cases and 902,757 controls to previously reported data. This analysis used a range of measures to define MD and included samples of African (36% of effective sample size), East Asian (26%) and South Asian (6%) ancestry and Hispanic/Latin American participants (32%). The multi-ancestry GWAS identified 53 significantly associated novel loci. For loci from GWAS in European ancestry samples, fewer than expected were transferable to other ancestry groups. Fine mapping benefited from additional sample diversity. A transcriptome-wide association study identified 205 significantly associated novel genes. These findings suggest that, for MD, increasing ancestral and global diversity in genetic studies may be particularly important to ensure discovery of core genes and inform about transferability of findings.
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Dahl A, Thompson M, An U, Krebs M, Appadurai V, Border R, Bacanu SA, Werge T, Flint J, Schork AJ, Sankararaman S, Kendler KS, Cai N. Phenotype integration improves power and preserves specificity in biobank-based genetic studies of major depressive disorder. Nat Genet 2023; 55:2082-2093. [PMID: 37985818 PMCID: PMC10703686 DOI: 10.1038/s41588-023-01559-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/18/2023] [Indexed: 11/22/2023]
Abstract
Biobanks often contain several phenotypes relevant to diseases such as major depressive disorder (MDD), with partly distinct genetic architectures. Researchers face complex tradeoffs between shallow (large sample size, low specificity/sensitivity) and deep (small sample size, high specificity/sensitivity) phenotypes, and the optimal choices are often unclear. Here we propose to integrate these phenotypes to combine the benefits of each. We use phenotype imputation to integrate information across hundreds of MDD-relevant phenotypes, which significantly increases genome-wide association study (GWAS) power and polygenic risk score (PRS) prediction accuracy of the deepest available MDD phenotype in UK Biobank, LifetimeMDD. We demonstrate that imputation preserves specificity in its genetic architecture using a novel PRS-based pleiotropy metric. We further find that integration via summary statistics also enhances GWAS power and PRS predictions, but can introduce nonspecific genetic effects depending on input. Our work provides a simple and scalable approach to improve genetic studies in large biobanks by integrating shallow and deep phenotypes.
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An U, Pazokitoroudi A, Alvarez M, Huang L, Bacanu S, Schork AJ, Kendler K, Pajukanta P, Flint J, Zaitlen N, Cai N, Dahl A, Sankararaman S. Deep learning-based phenotype imputation on population-scale biobank data increases genetic discoveries. Nat Genet 2023; 55:2269-2276. [PMID: 37985819 PMCID: PMC10703681 DOI: 10.1038/s41588-023-01558-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/04/2023] [Indexed: 11/22/2023]
Abstract
Biobanks that collect deep phenotypic and genomic data across many individuals have emerged as a key resource in human genetics. However, phenotypes in biobanks are often missing across many individuals, limiting their utility. We propose AutoComplete, a deep learning-based imputation method to impute or 'fill-in' missing phenotypes in population-scale biobank datasets. When applied to collections of phenotypes measured across ~300,000 individuals from the UK Biobank, AutoComplete substantially improved imputation accuracy over existing methods. On three traits with notable amounts of missingness, we show that AutoComplete yields imputed phenotypes that are genetically similar to the originally observed phenotypes while increasing the effective sample size by about twofold on average. Further, genome-wide association analyses on the resulting imputed phenotypes led to a substantial increase in the number of associated loci. Our results demonstrate the utility of deep learning-based phenotype imputation to increase power for genetic discoveries in existing biobank datasets.
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Cai N, Zhang X, Hu Y, Liu Y. Nontraditional Movement Behavior of Skyrmion in a Circular-Ring Nanotrack. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:2977. [PMID: 37999331 PMCID: PMC10675125 DOI: 10.3390/nano13222977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/16/2023] [Accepted: 11/18/2023] [Indexed: 11/25/2023]
Abstract
Magnetic skyrmions are considered promising candidates for use as information carriers in future spintronic devices. To achieve the development of skyrmion-based spintronic devices, a reasonable and feasible nanotrack is essential. In this paper, we conducted a study on the current-driven skyrmion movement in a circular-ring-shaped nanotrack. Our results suggest that the asymmetry of the inside and outside boundary of the circular ring changed the stable position of the skyrmion, causing it to move like the skyrmion Hall effect when driven by currents. Moreover, the asymmetric boundaries have advantages in enhancing or weakening the skyrmion Hall effect. Additionally, we also compared the skyrmion Hall effect from the asymmetric boundary of circular-ring nanotracks with that from the inhomogeneous Dzyaloshinskii-Moriya interaction. It was found that the skyrmion Hall effect in the circular ring is significantly greater than that caused by the inhomogeneous Dzyaloshinskii-Moriya interaction. These results contribute to our understanding of the skyrmion dynamics in confined geometries and offer an alternative method for controlling the skyrmion Hall effect of skyrmion-based devices.
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Chen X, Shan W, Wu D, Patel SB, Cai N, Li C, Ye S, Liu Z, Hwang S, Zakharov DN, Boscoboinik JA, Wang G, Zhou G. Atomistic mechanisms of water vapor-induced surface passivation. SCIENCE ADVANCES 2023; 9:eadh5565. [PMID: 37910618 PMCID: PMC10619940 DOI: 10.1126/sciadv.adh5565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 09/29/2023] [Indexed: 11/03/2023]
Abstract
The microscopic mechanisms underpinning the spontaneous surface passivation of metals from ubiquitous water have remained largely elusive. Here, using in situ environmental electron microscopy to atomically monitor the reaction dynamics between aluminum surfaces and water vapor, we provide direct experimental evidence that the surface passivation results in a bilayer oxide film consisting of a crystalline-like Al(OH)3 top layer and an inner layer of amorphous Al2O3. The Al(OH)3 layer maintains a constant thickness of ~5.0 Å, while the inner Al2O3 layer grows at the Al2O3/Al interface to a limiting thickness. On the basis of experimental data and atomistic modeling, we show the tunability of the dissociation pathways of H2O molecules with the Al, Al2O3, and Al(OH)3 surface terminations. The fundamental insights may have practical significance for the design of materials and reactions for two seemingly disparate but fundamentally related disciplines of surface passivation and catalytic H2 production from water.
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Shen L, Cai N, Wan S, Chen S. Development and validation of a predictive model for early diagnosis of neonatal acute respiratory distress syndrome based on the Montreux definition. Front Pediatr 2023; 11:1276915. [PMID: 38027256 PMCID: PMC10652555 DOI: 10.3389/fped.2023.1276915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023] Open
Abstract
Objective Based on the Montreux definition, we aim to develop and validate a predictive model for the early diagnosis of neonatal acute respiratory distress syndrome (ARDS). Methods A retrospective analysis of clinical data on 198 neonates with respiratory distress from January 2018 to January 2022 was conducted. Neonates meeting Montreux definition were classified as ARDS group (n = 79), while the rest were non-ARDS group (n = 119). Univariate analysis identified indicators for neonatal ARDS, followed by logistic regression to construct a predictive model for early diagnosis. The ability of predictors and models to predict neonatal ARDS was evaluated using area under the curve (AUC), and model performance was estimated through bootstrap resampling. Results Maternal prenatal fever, abnormal fetal heart beat, meconium-stained amniotic fluid (MSAF), white blood cell (WBC), absolute neutrophil count (ANC), neutrophil percentage (NE%), platelet count (PLT), C-reactive protein (CRP), procalcitonin (PCT), creatine kinase (CK), activated partial thromboplastin time (APTT), serum calcium (Ca) and sodium (Na)exhibited significant differences between the ARDS group and the non-ARDS group (P < 0.05). MSAF (OR=5.037; 95% CI: 1.523-16.657; P < 0.05), ANC (OR = 1.324; 95% CI: 1.172-1.495; P < 0.05), PLT (OR = 0.979; 95% CI: 0.971-0.986; P < 0.05), Ca (OR = 0.020; 95% CI: 0.004-0.088; P < 0.05) emerged as independent risk factors for the development of ARDS. The respective AUC values for MSAF, ANC, PLT, Ca, and the combined prediction models were 0.606, 0.691, 0.808, 0.761 and 0.931. Internal validation showed that the C-index for the model was 0.931. Conclusions Early application of the model combining MSAF, ANC, PLT and Ca may have a good predictive effect on the early diagnosis of neonatal ARDS.
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Zheng C, Cai N, Huang C, Huang Y, Zou J, Zhang G, Fei P. Evaluation of amidated pectin as fat substitutes for minced chicken breast: Physicochemical properties and edible quality. Food Res Int 2023; 173:113371. [PMID: 37803709 DOI: 10.1016/j.foodres.2023.113371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/07/2023] [Accepted: 08/10/2023] [Indexed: 10/08/2023]
Abstract
An investigation was conducted to assess the gelation characteristics of amino acid amidated pectin and its subsequent influence on the quality of minced chicken breast (MCB) when employed as a lipid substitute. Through experimentation, it was evidenced that amidated pectin, such as glycine amidated pectin (AP@Gly), glutamic amidated pectin (AP@Glu), and lysine amidated pectin (AP@Lys), demonstrated superior viscosity and gelation capacity in comparison to their native pectin (PE) counterpart. In contrast to PE, amidated pectin samples exhibited the potential to form high-strength hydrogels under conditions of minimal restriction. Additionally, evaluations conducted on all samples established that MCB samples enriched with pectin and amidated pectin demonstrated superior water retention capability. Before thermal processing, MCB samples fortified with amidated pectin showcased higher hardness and L* values in comparison to PE and the control group. However, upon thermal processing, no significant divergence was found in the chroma and texture profile analysis (TPA) attributes across all MCB samples, and the electronic tongue sensory evaluation was closely aligned with the control group. This evidence substantiates the effectiveness of amidated pectin samples as viable lipid substitutes in MCB products.
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Du C, Cai N, Dong J, Xu C, Wang Q, Zhang Z, Li J, Huang C, Ma T. Uncovering the role of cytoskeleton proteins in the formation of neutrophil extracellular traps. Int Immunopharmacol 2023; 123:110607. [PMID: 37506501 DOI: 10.1016/j.intimp.2023.110607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/23/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023]
Abstract
Neutrophils are a type of lymphocyte involved in innate immune defense. In response to specific stimuli, these phagocytic cells undergo a unique form of cell death, NETosis, during which they release neutrophil extracellular traps (NETs) composed of modified chromatin structures decorated with cytoplasmic and granular proteins. Multiple proteins and pathways have been implicated in the formation of NETs. The cytoskeleton, an interconnected network of filamentous polymers and regulatory proteins, plays a crucial role in resisting deformation, transporting intracellular cargo, and changing shape during movement of eukaryotic cells. It may also have evolved to defend eukaryotic organisms against infection. Recent research focuses on understanding the mechanisms underlying NETs formation and how cytoskeletal networks contribute to this process, by identifying enzymes that trigger NETosis or interact with NETs and influence cellular behavior through cytoskeletal dynamics. An enhanced understanding of the complex relationship between the cytoskeleton and NET formation will provide a framework for future research and the development of targeted therapeutic strategies, and supports the notion that the long-lived cytoskeleton structures may have a lasting impact on this area of research.
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Albert M, Delgado-Herrera L, Paruch J, Gerritsen-van Schieveen P, Kishimoto T, Takusagawa S, Cai N, Fengler J, Raizer J. Pudexacianinium (ASP5354) chloride for ureter visualization in participants undergoing laparoscopic, minimally invasive colorectal surgery. Surg Endosc 2023; 37:7336-7347. [PMID: 37474823 PMCID: PMC10462524 DOI: 10.1007/s00464-023-10193-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 06/01/2023] [Indexed: 07/22/2023]
Abstract
BACKGROUND Intraoperative ureteral injury, a serious complication of abdominopelvic surgeries, can be avoided through ureter visualization. Near-infrared fluorescence imaging offers real-time anatomical visualization of ureters during surgery. Pudexacianinium (ASP5354) chloride is an indocyanine green derivative under investigation for intraoperative ureter visualization during colorectal or gynecologic surgery in adult and pediatric patients. METHODS In this phase 2 study (NCT04238481), adults undergoing laparoscopic colorectal surgery were randomized to receive one intravenous dose of pudexacianinium 0.3 mg, 1.0 mg, or 3.0 mg. The primary endpoint was successful intraoperative ureter visualization, defined as observation of ureter fluorescence 30 min after pudexacianinium administration and at end of surgery. Safety and pharmacokinetics were also assessed. RESULTS Participants received pudexacianinium 0.3 mg (n = 3), 1.0 mg (n = 6), or 3.0 mg (n = 3). Most participants were female (n = 10; 83.3%); median age was 54 years (range 24-69) and median BMI was 29.3 kg/m2 (range 18.7-38.1). Successful intraoperative ureter visualization occurred in 2/3, 5/6, and 3/3 participants who received pudexacianinium 0.3 mg, 1.0 mg, or 3.0 mg, respectively. Median intensity values per surgeon assessment were 1 (mild) with the 0.3-mg dose, 2 (moderate) with the 1.0-mg dose, and 3 (strong) with the 3.0-mg dose. A correlation was observed between qualitative (surgeon's recognition/identification of the ureter during surgery) and quantitative (video recordings of the surgeries after study completion) assessment of fluorescence intensity. Two participants experienced serious adverse events, none of which were drug-related toxicities. One adverse event (grade 1 proteinuria) was related to pudexacianinium. Plasma pudexacianinium concentrations were dose-dependent and the mean (± SD) percent excreted into urine during surgery was 22.3% ± 8.0% (0.3-mg dose), 15.6% ± 10.0% (1.0-mg dose), and 39.5% ± 12.4% (3.0-mg dose). CONCLUSIONS In this study, 1.0 and 3.0 mg pudexacianinium provided ureteral visualization for the duration of minimally invasive, laparoscopic colorectal procedures and was safe and well tolerated.
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Walters RG, Millwood IY, Lin K, Schmidt Valle D, McDonnell P, Hacker A, Avery D, Edris A, Fry H, Cai N, Kretzschmar WW, Ansari MA, Lyons PA, Collins R, Donnelly P, Hill M, Peto R, Shen H, Jin X, Nie C, Xu X, Guo Y, Yu C, Lv J, Clarke RJ, Li L, Chen Z. Genotyping and population characteristics of the China Kadoorie Biobank. CELL GENOMICS 2023; 3:100361. [PMID: 37601966 PMCID: PMC10435379 DOI: 10.1016/j.xgen.2023.100361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 02/09/2023] [Accepted: 06/24/2023] [Indexed: 08/22/2023]
Abstract
The China Kadoorie Biobank (CKB) is a population-based prospective cohort of >512,000 adults recruited from 2004 to 2008 from 10 geographically diverse regions across China. Detailed data from questionnaires and physical measurements were collected at baseline, with additional measurements at three resurveys involving ∼5% of surviving participants. Analyses of genome-wide genotyping, for >100,000 participants using custom-designed Axiom arrays, reveal extensive relatedness, recent consanguinity, and signatures reflecting large-scale population movements from recent Chinese history. Systematic genome-wide association studies of incident disease, captured through electronic linkage to death and disease registries and to the national health insurance system, replicate established disease loci and identify 14 novel disease associations. Together with studies of candidate drug targets and disease risk factors and contributions to international genetics consortia, these demonstrate the breadth, depth, and quality of the CKB data. Ongoing high-throughput omics assays of collected biosamples and planned whole-genome sequencing will further enhance the scientific value of this biobank.
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Ding B, Su X, Zhuang J, Cai N, Ou Y, Jiang H, Jiang H, Hu J. Six Years of Complaints Issued by Patients at a Laser Treatment Center in a Plastic Surgery Hospital. PLASTIC AND RECONSTRUCTIVE SURGERY-GLOBAL OPEN 2023; 11:e5206. [PMID: 37600835 PMCID: PMC10435038 DOI: 10.1097/gox.0000000000005206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 07/07/2023] [Indexed: 08/22/2023]
Abstract
Background Patient complaints can provide valuable feedback regarding the objective deficiencies of medical services. There are few studies on the complaints of patients receiving photoelectric therapy, so this study aims to understand the expectations and requirements of patients by analyzing the complaints of patients receiving photoelectric therapy. Methods The complaints of patients who underwent photoelectric therapy were retrospectively examined. Authors plan to analyze treatment items, complaint contents, appeals, time trend regarding the number of complaints, and economic compensation. Results Fifty-four patients were involved in the study in total, and all of them were included. According to the standardized coding classification of complaints by Reader et al., the number of clinical, management and relationship complaints were 36 (59.02%), 14 (22.95%), and 11 (18.03%), respectively. These were divided among the categories of quality (31.15%), safety (27.87%), institutional issues (22.95%), communication (8.20%), and humaneness/caring (9.84%); with the most common subcategories involving treatment (31.15%) and safety incidents (24.59%). The patients' demands involved 20 cases (32.26%) requesting a refund of their medical expenses, 16 (25.81%) issuing a warning, 15 (24.19%) requesting compensation for loss, 10 (16.13%) requiring free repair or consultation, and 1 (1.61%) demanding an apology. Eventually, financial compensation was provided to the patients in eight of the cases. At a significance level of P = 0.05, even if the number of annual complaints increased over time, the increasing trend was not significant. Conclusions Patient complaints in photoelectric therapy were most commonly clinical in nature. Specifically, quality and safety concerns are the main complaints.
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Huang L, Tang S, Rietkerk J, Appadurai V, Krebs MD, Schork AJ, Werge T, Zuber V, Kendler K, Cai N. Polygenic analyses show important differences between MDD symptoms collected using PHQ9 and CIDI-SF. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.27.23286527. [PMID: 36909638 PMCID: PMC10002792 DOI: 10.1101/2023.02.27.23286527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Symptoms of Major Depressive Disorder (MDD) are commonly assessed using self-rating instruments like the Patient Health Questionnaire 9 (PHQ9, for current symptoms), and the Composite International Diagnostic Interview Short-Form (CIDI-SF, for lifetime worst-episode symptoms). Using data from the UKBiobank, we show that corresponding symptoms endorsed through PHQ9 and CIDI-SF have low to moderate genetic correlations (rG=0.43-0.87), and this cannot be fully attributed to different severity thresholds or the use of a skip-structure in CIDI-SF. Through a combination of Mendelian Randomization (MR) and polygenic prediction analyses, we find that PHQ9 symptoms are more associated with traits which reflect general dysphoria, while the skip-structure in CIDI-SF allows for the identification of heterogeneity among likely MDD cases. This has important implications on factor analyses performed on their respective genetic covariance matrices for the purpose of identification of genetic factors behind MDD symptom dimensions and heterogeneity.
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Wang H, Cai N, Gong S, Zhou J, He T, Wang B, Fu T. Establishment and Optimization of Soil Cd Risk Threshold in Typical Karst Area with Potato Production, China. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2023; 110:34. [PMID: 36592234 DOI: 10.1007/s00128-022-03640-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 10/31/2022] [Indexed: 06/17/2023]
Abstract
The threshold is key to risk assessment of soil cadmium (Cd) pollution. However, there is limited research on the soil Cd risk threshold of potatoes. Soil and potato samples (n = 256) were used to establish and optimize the Cd risk threshold by using relative cumulative frequency, bioconcentration factor, and regression model. The results showed that suggested risk screening values (SRSVs) for soil Cd were divided into 2.465 (pH ≤ 5.5), 2.564 (5.5 < pH ≤ 6.5), 2.778 (6.5 < pH ≤ 7.5), and 4.348 mg kg-1 (pH > 7.5). SRSVs were applied to classify soil Cd risk assessment by collecting soil samples (n = 100). Low-risk areas only comprised 0.98% of the total area using risk screening values (RSVs) (GB15618-2018), and risk areas comprised as much as 99.02%. Low-risk area and risk area comprised 97.75% and 2.25% of the total area based on SRSVs. SRSVs are appropriate for potato production in typical karst areas.
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Border R, Athanasiadis G, Buil A, Schork AJ, Cai N, Young AI, Werge T, Flint J, Kendler KS, Sankararaman S, Dahl AW, Zaitlen NA. Cross-trait assortative mating is widespread and inflates genetic correlation estimates. Science 2022; 378:754-761. [PMID: 36395242 PMCID: PMC9901291 DOI: 10.1126/science.abo2059] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The observation of genetic correlations between disparate human traits has been interpreted as evidence of widespread pleiotropy. Here, we introduce cross-trait assortative mating (xAM) as an alternative explanation. We observe that xAM affects many phenotypes and that phenotypic cross-mate correlation estimates are strongly associated with genetic correlation estimates (R2=74%). We demonstrate that existing xAM plausibly accounts for substantial fractions of genetic correlation estimates and that previously reported genetic correlation estimates between some pairs of psychiatric disorders are congruent with xAM alone. Finally, we provide evidence for a history of xAM at the genetic level using cross-trait even/odd chromosome polygenic score correlations. Together, our results demonstrate that previous reports have likely overestimated the true genetic similarity between many phenotypes.
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Chang S, Fermani F, Lao CL, Huang L, Jakovcevski M, Di Giaimo R, Gagliardi M, Menegaz D, Hennrich AA, Ziller M, Eder M, Klein R, Cai N, Deussing JM. Tripartite extended amygdala-basal ganglia CRH circuit drives locomotor activation and avoidance behavior. SCIENCE ADVANCES 2022; 8:eabo1023. [PMID: 36383658 PMCID: PMC9668302 DOI: 10.1126/sciadv.abo1023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
An adaptive stress response involves various mediators and circuits orchestrating a complex interplay of physiological, emotional, and behavioral adjustments. We identified a population of corticotropin-releasing hormone (CRH) neurons in the lateral part of the interstitial nucleus of the anterior commissure (IPACL), a subdivision of the extended amygdala, which exclusively innervate the substantia nigra (SN). Specific stimulation of this circuit elicits hyperactivation of the hypothalamic-pituitary-adrenal axis, locomotor activation, and avoidance behavior contingent on CRH receptor type 1 (CRHR1) located at axon terminals in the SN, which originate from external globus pallidus (GPe) neurons. The neuronal activity prompting the observed behavior is shaped by IPACLCRH and GPeCRHR1 neurons coalescing in the SN. These results delineate a previously unidentified tripartite CRH circuit functionally connecting extended amygdala and basal ganglia nuclei to drive locomotor activation and avoidance behavior.
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