bluuebunny/crossref_metadata_2025 huggingface dataset:
Multi-ancestry population attributable risk assessment of common genetic variation in Alzheimer’s and Parkinson’s diseases
Authors: Jones Lietsel , Cerquera-Cleves Catalina , Schuh Artur FS , Makarious Mary B , Iwaki Hirotaka , Nalls Mike A. , Noyce Alastair J ,   Global Parkinson’s Genetics Program (GP2), Blauwendraat Cornelis , Singleton Andrew , Mata Ignacio , Bandres-Ciga Sara
Published: September 2024

Multiple scientific studies, mostly performed within European populations, have unraveled many of the genetic factors associated with Alzheimer’s disease (AD) and Parkinson’s disease (PD) etiologies, improving our understanding of the molecular pathways implicated in the pathogenesis of these conditions. However, there is increasing evidence that the genetic architecture of these diseases differs across ancestral populations. This raises concerns about the efficacy of therapeutic interventions crafted around genetic targets prevalent only in European ancestry populations. Such interventions neglect potentially distinctive etiological profiles, including Latino, Black/African American, and East Asian populations. In the current study, we explore Population Attributable Risk (PAR) in AD and PD etiologies and assess the proportion of disease attributed to specific genetic factors across diverse populations. Leveraging data from genome-wide association studies across four ancestries, we explore distinct and universal therapeutic targets across diverse populations. Multi-ancestral genetics research is critical to the development of successful therapeutics and treatments for neurodegenerative diseases. By offering insights into genetic disparities, we aim to inform more inclusive and effective therapeutic strategies, advancing personalized healthcare.
Comprehensive Sequencing of Environmental RNA from Japanese Medaka at Various Size Fractions and Comparison with Skin RNA
Authors: Hiki Kyoshiro , Jo Toshiaki S.
Published: September 2024

Environmental RNA (eRNA) is emerging as a non-invasive tool for assessing the health of macro-organisms, but key information on its origin and particle sizes remains unclear. In this study, we performed comprehensive RNA-sequencing of eRNA (> 13 Gb/sample) collected from tank water containing Japanese medaka (Oryzias latipes), using sequential filtration through filters with pore sizes of 10, 3, and 0.4 μm. Fish skin RNA was also sequenced to reveal the origin of eRNA. Our results showed that the 3−10 μm fraction contained the lowest relative abundance of microbial RNA, the highest amount of medaka eRNA, and the largest number of detected medaka genes (5398 genes), while the 0.4−3 μm fraction had the fewest (972 genes). Only a small number of genes (42 genes) were unique to the 0.4−3 μm fraction. These findings suggest that a 3 μm filter is optimal for eRNA analysis, as it allows for larger filtration volumes while maintaining the relative abundance of macro-organism eRNA. Furthermore, 81% of the genes detected in eRNA overlapped with skin RNA, indicating skin is a major source of fish eRNA.

Synopsis

The 3 µm filter is recommended to maximize the detection of eRNA from macro-organisms while reducing the relative abundance of microbial RNA.

TOC Art
GDF3 promotes adipose tissue macrophage-mediated inflammation via altered chromatin accessibility during aging
Authors: Jang In Hwa , Kruglov Victor , Cholensky Stephanie H. , Smith Declan M. , Carey Anna , Bai Suxia , Nottoli Timothy , Bernlohr David A. , Camell Christina D.
Published: September 2024

Age-related susceptibility to sepsis and endotoxemia is poorly defined, although hyperactivation of the immune system and the expansion of the visceral adipose as an immunological reservoir are underlying features. Macrophages from older organisms exhibit substantial changes, including chronic NLRP3 inflammasome activation, genomic remodeling and a dysfunctional, amplified inflammatory response upon new exposure to pathogen. However, the mechanisms by which old macrophages maintain their inflammatory phenotype during endotoxemia remains elusive. We previously identifiedGdf3, a TGFβ superfamily cytokine, as a top-regulated gene by age and the NLRP3 inflammasome in adipose tissue macrophages (ATMs). Here, we demonstrate that endotoxemia increases inflammatory (CD11c+) ATMs in aGdf3-dependent manner in old mice. Lifelong systemic or myeloid-specific deletion ofGdf3leads to reduced endotoxemia- induced inflammation, with decreased CD11c+ATMs and inflammatory cytokines, and protection from hypothermia. Moreover, acute blockade ofGdf3using JQ1, a BRD4 inhibitor, phenocopies old mice with lifelongGdf3-deficiency. We show that GDF3 promotes the inflammatory phenotype in ATMs by phosphorylating SMAD2/3. Mechanistically, the differential chromatin landscape of ATMs from old mice with or without myeloid-drivenGdf3indicates that GDF3- SMAD2/3 signaling axis shifts the chromatin accessibility of ATMs towards an inflammatory state during aging. Furthermore, pharmaceutical inhibition of SMAD3 with a specific inhibitor of SMAD3 (SIS3) mimicsGdf3deletion. SIS3 reduces endotoxemia-mediated inflammation with fewer CD11c+ATMs and less severe hypothermia in old, but not young mice, as well as reduced mortality. In human adipose tissue, age positively correlates withGDF3level, while inflammation correlates with pSMAD2/3 level. Overall, these results highlight the importance of GDF3-SMAD2/3 axis in driving inflammation in older organisms and identify this signaling axis as a promising therapeutic target for mitigating endotoxemia-related inflammation in the aged.
Mapping genomic regions associated with temperature stress in the wheat pathogenZymoseptoria tritici
Authors: Stapley Jessica , Zhong Ziming , McDonald Bruce A.
Published: September 2024

Climate change can alter interactions between plants and their pathogens, which could adversely affect crop production. To better understand the molecular mechanisms underlying the responses of pathogenic fungal to temperature stress, we conducted a quantitative trait loci (QTL) mapping study in the wheat pathogenZymoseptoria triticito identify genomic regions associated with colony growth and melanisation at three temperatures (10°C, 18°C, 27°C). We then identified likely candidate genes for thermal adaptation within these intervals by combining information regarding gene function, GO annotation enrichment, transcriptional profile, and results from previous genome wide association studies (GWAS) investigating responses to climate, temperature and thermal adaptation. The QTL mapping, conducted for two separate crosses involving four Swiss parents, found significant QTL uniquely associated with traits measured in high and low temperatures. These intervals contained many genes known to regulate responses to temperature stress, including heat shock proteins (HSPs) and proteins involved in the mitogen-activated protein kinase (MAPK) pathways, and were enriched for genes with a zinc ion binding GO annotation. We highlight the most promising candidate genes for thermal adaptation, including an ammonium transporter gene, a stress response factor (Whi1) and two MAPK pathway genes -SSk2andOpy2. Future validation work on these candidate genes could provide novel insight into the molecular mechanisms underlying temperature adaptation in this important wheat pathogen.
Hydrogels with Independently Controlled Adhesion Ligand Mobility and Viscoelasticity Increase Cell Adhesion and Spreading
Authors: Moghaddam Abolfazl Salehi , Dunne Katelyn , Breyer Wendy , Wu Yingjie , Pashuck E. Thomas
Published: September 2024

A primary objective in designing hydrogels for cell culture is recreating the cell-matrix interactions found within human tissues. Identifying the most important biomaterial features for these interactions is challenging because it is difficult to independently adjust variables such as matrix stiffness, stress relaxation, the mobility of adhesion ligands and the ability of these ligands to support cellular forces. In this work we designed a hydrogel platform consisting of interpenetrating polymer networks of covalently crosslinked poly(ethylene glycol) (PEG) and self-assembled peptide amphiphiles (PA). We can tailor the storage modulus of the hydrogel by altering the concentration and composition of each network, and we can tune the stress relaxation half-life through the non-covalent bonding in the PA network. Ligand mobility can be adjusted independently of the matrix mechanical properties by attaching the RGD cell adhesion ligand to either the covalent PEG network, the dynamic PA network, or both networks at once. Interestingly, our findings show that endothelial cell adhesion formation and spreading is maximized in soft, viscoelastic gels in which RGD adhesion ligands are present on both the covalent PEG and non-covalent PA networks. The dynamic nature of cell adhesion domains, coupled with their ability to exert substantial forces on the matrix, suggests that having different presentations of RGD ligands which are either mobile or are capable of withstanding significant forces are needed mimic different aspects of complex cell-matrix adhesions. By demonstrating how different presentations of RGD ligands affect cell behavior independently of viscoelastic properties, these results contribute to the rational design of hydrogels that facilitate desired cell-matrix interactions, with the potential of improvingin vitromodels and regenerative therapies.
ELLA: Modeling Subcellular Spatial Variation of Gene Expression within Cells in High-Resolution Spatial Transcriptomics
Authors: Wang Jade Xiaoqing , Zhou Xiang
Published: September 2024

Spatial transcriptomic technologies are becoming increasingly high-resolution, enabling precise measurement of gene expression at the subcellular level. Here, we introduce a computational method called subcellular expression localization analysis (ELLA), for modeling the subcellular localization of mRNAs and detecting genes that display spatial variation within cells in high-resolution spatial transcriptomics. ELLA creates a unified cellular coordinate system to anchor diverse cell shapes and morphologies, utilizes a nonhomogeneous Poisson process to model spatial count data, leverages an expression gradient function to characterize subcellular expression patterns, and produces effective control of type I error and high statistical power. We illustrate the benefits of ELLA through comprehensive simulations and applications to four spatial transcriptomics datasets from distinct technologies, where ELLA not only identifies genes with distinct subcellular localization patterns but also associates these patterns with unique mRNA characteristics. Specifically, ELLA shows that genes enriched in the nucleus exhibit an abundance of long noncoding RNAs or protein-coding mRNAs, often characterized by longer gene lengths. Conversely, genes containing signal recognition peptides, encoding ribosomal proteins, or involved in membrane related activities tend to enrich in the cytoplasm or near the cellular membrane. Furthermore, ELLA reveals dynamic subcellular localization patterns during the cell cycle, with certain genes showing decreased nuclear enrichment in the G1 phase while others maintain their enrichment patterns throughout the cell cycle. Overall, ELLA represents a calibrated, powerful, robust, scalable, and versatile tool for modeling subcellular spatial expression variation across diverse high-resolution spatial transcriptomic platforms.
Extracellular phase separation mediates storage and release of thyroglobulin in the thyroid follicular lumen
Authors: Yao Yihan , Erkamp Nadia , Sneideris Tomas , Yang Xiqiao , Scrutton Rob , Schneider Matthias M. , Fischer Charlotte M. , Schoenmakers Erik , Schoenmakers Nadia , Knowles Tuomas P.J.
Published: September 2024

Thyroid hormones are produced by the thyroid gland and are essential for regulating metabolism, growth and development. Maintenance of circulating thyroid hormone levels within an appropriate range is thus a prerequisite for health.In vivo, this objective is, at least in part, facilitated through an extracellular storage depot of thyroglobulin, the glycoprotein precursor for thyroid hormones, in the thyroid follicular lumen. The molecular basis for how soluble thyroglobulin molecules form such dense depot assemblies remains elusive. Here, we describein vitrobiophysical analysis of thyroglobulin phase behaviour, suggesting that thyroglobulin is prone to undergoing ionic strength-dependent phase separation, leading to the formation of liquid-like condensates. Fluorescence photobleaching measurements further show that these condensates age as a function of time to form reversible gel-like high density storage depots of thyroglobulin. Immunofluorescence experiments on mouse and human thyroid folliclesex vivoreveal that spherical globules of Tg protein dense phase are present in the follicular lumen, consistent with the idea that Tg undergoes phase separation. These findings reveal a molecular mechanism for the last-come-first-served process of thyroglobulin storage and release, suggesting a role for extracellular phase separation in thyroid hormone homeostasis by providing organizational and architectural specificity without requiring membrane-mediated confinement.
Robotic Visible-Light Optical Coherence Tomography Visualizes Segmental Schlemm’s Canal Anatomy and Segmental Pilocarpine Response
Authors: Fang Raymond , Zhang Pengpeng , Kim Daniel , Kweon Junghun , Sun Cheng , Huang Alex S. , Zhang Hao F.
Published: September 2024

Purpose

To use robotic visible-light OCT (vis-OCT) to study circumferential segmental Schlemm’s canal (SC) anatomy in mice after topical pilocarpine administration.

Methods

Anterior segment imaging was performed using a vis-OCT sample arm attached to a 6-degree-of-freedom robotic arm to maintain normal (perpendicular) laser illumination aimed at SC around the limbus. Sixteen mice were studied for repeatability testing and to study aqueous humor outflow (AHO) pathway response to topical drug. Pharmaceutical-grade pilocarpine (1%; n = 5) or control artificial tears (n = 9) were given, and vis-OCT imaging was performed before and 15 minutes after drug application. After SC segmentation, SC areas and volumes were measured circumferentially in control- and drug-treated eyes.

Results

Circumferential vis-OCT provided high-resolution imaging of the anterior segment and AHO pathways, including SC. Segmental SC anatomy was visualized with the average cross-sectional area greatest temporal (3971 ± 328 µm2) and the least nasal (2727 ± 218 µm2; p = 0.018). After pilocarpine administration, the iris became flatter, and SC became larger (pilocarpine: 26.8 ± 5.0% vs. control: 8.9 ± 4.6% volume increase; p = 0.030). However, the pilocarpine alteration was segmental as well, with a greater increase observed superior (pilocarpine: 31.6 ± 8.9% vs. control: 1.8 ± 5.7% volume increase; p = 0.023) and nasal (pilocarpine: 41.1 ± 15.3% vs. control: 13.9 ± 4.5% volume increase; p = 0.045).

Conclusion

High-resolution circumferential non-invasive imaging using AS-OCT of AHO pathways is possible in living animals with robotic control. Segmental SC anatomy was seen at baseline and was consistent with the known segmental nature of trabecular AHO. Segmental SC anatomical response to a muscarinic agonist was seen as well. Segmental glaucoma drug response around the circumference of AHO pathways is a novel observation that may explain the variable patient response to glaucoma treatments.
Microbial Degradation of Contaminants of Emerging Concern by Pseudomonas putida in Wastewater Treatment Plants
Authors: Lyu Boyu , Manna Bharat , Zhou Xueyang , Leung Ivanhoe K. H. , Singhal Naresh
Published: September 2024

Contaminants of Emerging Concern (CECs) are a class of contaminants that are commonly found in urban wastewater treatment plants (WWTP) at low concentrations. These compounds include antibiotic drugs, personal care products, and industrial chemicals, which are widely used in modern society. Although they provide undeniable benefits in our daily lives, their accumulation in the environment poses a significant risk to human health and the ecosystem. Due to the incomplete removal of these compounds by traditional WWTPs, there is a need to understand the interactions between microbes and CECs to develop effective solutions to this environmental challenge.Pseudomonas putidais a bacterium commonly found in water-related habitats, including freshwater streams, forests, and WWTPs. It is known for its ability to degrade various organic compounds, making it a suitable model for understanding the linkages between bacterial enzymes and CECs found in WWTPs. In this study, isolatedPseudomonas putidastrain KT2440 was cultured in lab-scale reactors to mimic the WWTP environment. The degradation of this isolated strain towards different groups of CECs were studied over a 24-hour period using liquid chromatography with tandem mass spectrometry (LC-MS/MS). Mass spectrometry-based quantitative proteomics was also performed at different sampling points to establish a linkage between the enzyme expression profile of this strain and its degradation of CECs via bioinformatics analysis. The results of this study demonstrated thatPseudomonas putidaKT2440 is capable of degrading atrazine, acetamiprid, carbendazim, diclofenac acid, erythromycin, and sulfamethazine at lab scale. At the 20-hour time point, the enzyme expression profile indicated a high protein abundance of various oxidoreductases that could explain the observed CEC degradation.The study’s findings provide important insights into the potential of Pseudomonas putida as a bioremediation agent for CECs in WWTPs. The degradation of CECs byPseudomonas putidaKT2440 is a significant contribution to the bioremediation process, and its enzyme expression profile can serve as a case study for more complex interactions of microbes and CECs in real WWTPs. Furthermore, this study supports the potential ofPseudomonas putidaas a promising strain for various bioremediation applications. Finally, this study’s results can help develop more efficient and effective methods for removing CECs from wastewater, which can contribute to the protection of public health and the environment.
Generation of a PARPi-sensitive homozygous BRCA1-methylated OVCAR8 cell line using targeted CRISPR gene editing
Authors: Nesic Ksenija , Beard Sally , Xu Lijun , Kondrashova Olga , Vandenberg Cassandra J , Rubin Alan F. , Zhang Fan , Dobrovic Alexander , Waddell Nicola , Scott Clare L. , Shield-Artin Kristy , Wakefield Matthew J.
Published: September 2024

Up to 17% of high grade serous ovarian carcinomas (HGSOC) harbour BRCA1 promoter methylation (meBRCA1), making them susceptible to treatment with targeted PARP inhibitor (PARPi) therapy. Unfortunately, meBRCA1 loss can be acquired following PARPi or platinum chemotherapy, resulting in BRCA1 re–expression and PARPi resistance. Our understanding of meBRCA1 stability in HGSOC is currently limited, in part due to a paucity of pre–clinical models with homozygous meBRCA1. Herein, we describe the generation of a several OVCAR8 cell line derivatives containing landing pad constructs, for future functional studies, and representing various BRCA1 states, including a homozygous meBRCA1 variant. Our PARPi resistant OVCAR8 has two methylated BRCA1 copies and one unmethylated copy, enabling BRCA1 expression. CRISPR–Cas9 gene editing was used to delete copies of the BRCA1 gene in landing pad–containing clones of this cell line (A6 and H4). We produced one variant with deletion of all BRCA1 copies (H4–53), and another with two copies deleted and only a single methylated gene copy remaining (A6–30 – validated further using nanopore long–read sequencing). These both lacked BRCA1 gene expression and were sensitive to PARPi treatment. The A6–30 line was transplanted into immunocompromised mice to generate a xenograft model that retained homozygous meBRCA1 and demonstrated some response to PARPi in vivo. Thus, using CRISPR gene editing we have created several novel isogenic HGSOC cell line models, including one with homozygous meBRCA1, that will support future studies of meBRCA1 stability and PARPi resistance.
Americans in rural areas are less likely to receive stress management counseling from physicians: a national repeated cross-sectional study of the 2018 and 2019 National Ambulatory Medical Care Survey
Authors: Ira Stephanie Marie , Gillette Chris
Published: September 2024

Stress is a significant contributor to suicide ideation and attempts. This paper (1) describes the frequency of clinic visits in which physicians record stress management counseling; and (2) identifies visit-, physician-, and patient-related predictors of stress management counseling. We conducted a secondary analysis of the 2018 and 2019 National Ambulatory Medical Care Survey (NAMCS) clinic visit datasets. We identified clinic-, patient-, and physician-related predictors of stress management counseling. All analyses used weighted adjustment to account for the complex survey design. The weighted sample included 1,495,326,615 visits (unweighted (n=14,175) in 2018-2019. Combined, 1.32 per 100 visits (95% CI=0.72-1.92) included stress management counseling. Stress management counseling was less likely to occur when the visit occurred in a rural area (OR=0.22, 95% CI=0.09-0.53), among other characteristics. Stress management counseling rarely occurs during physician office visits in rural areas, despite rural areas suffering disproportionately worse health outcomes than urban areas.
Molecular Diagnosis of Heart Allograft Rejection Using Intra-Graft Targeted Gene Expression Profiling: the heart HistoMX system
Authors: Giarraputo Alessia , Coutance Guillaume , Patel Jignesh K. , Fedrigo Marny , Aubert Olivier , Dagobert Jessy , Mezine Fariza , Robin Blaise , Rouvier Philippe , Varnous Shaida , Van Huyen Jean Paul Duong , Bruneval Patrick , Angelini Annalisa , Kobashigawa Jon , Loupy Alexandre
Published: September 2024

Background and aims

Tissular gene expression profiling has the potential to refine the diagnosis of cardiac allograft rejection. Contrary to whole-transcriptome approaches, targeted molecular profiling applicable to formalin-fixed paraffin-embedded (FFPE) endomyocardial biopsies (EMB) can be easily implemented in clinical practice. We aimed to develop and validate the first rejection molecular diagnostic system dedicated to heart transplantation (HTx).

Methods

An international multicenter study was designed, building a deep phenotyped cohort of HTx recipients recruited between 2011 and 2021 at 4 referral centers. Detailed donors, recipients, clinical, immunological, biological, and histological parameters were collected. EMBs were graded according to international working formulations. Tissue gene expression was analyzed on FFPE-EMB using the consensus Banff Human Organ Transplant gene set. Molecular classifiers of antibody-mediated (AMR) and acute cellular rejection (ACR) were built. Discrimination and calibration were assessed in the development and validation sets (NCT06436027).

Results

A total of 591 biopsies were included: 188 AMR (pAMR1(I+): n=51; pAMR1(H+): n=58; pAMR2-3: n=79), 289 ACR (1R n=174; 2-3R n=115) and 114 matched non-rejection cases. Biopsies were split in a derivation (n=476) and a validation set (n=115). AMR top significant transcripts were related to the IFN-gamma inducible pathway, endothelial activation, and monocyte-macrophage recruitment. ACR was characterized by transcripts related to T-cell receptor, CD3 receptor activation, and CD28 signaling. ACR and AMR molecular rejection models were strongly associated with the pathology severity of rejection and accurately identified rejection in the derivation (ROC-AUC: AMR=0.831, ACR:=0.837) and validation sets (ROC-AUC: AMR=0.812; ACR=0.849). Calibration was adequate. The robustness of the molecular classifiers were reinforced by various sensitivity analyzes. An automated report was developed to enhance the reproducibility and clinical applicability of the molecular analysis.

Conclusions

In this study, the first tissue-based rejection molecular diagnostic system applicable to FFPE- EMB and dedicated to heart transplantation rejection was developed and internally validated. This tool has the potential to refine the diagnosis of rejection.
Intravenous streptokinase for myocardial infarction: a reanalysis of the historical cumulative evidence using Trial Sequential Analysis
Authors: Boesen Kim , Gluud Christian
Published: September 2024

Introduction

Cumulative meta-analysis of intravenous streptokinase for myocardial infarction has been used as a text-book example to show how the megatrials GISSI and ISIS-II were redundant and wasteful. We decided to reanalyse the dataset with Trial Sequential Analysis to account for statistical heterogeneity and the risk of bias of the historical trials to reassess whether GISSI and ISIS-II were justified or redundant.

Methods

We extracted data from overviews published in 1982 and 1985 and trial reports on mortality outcomes. For the five largest trials conducted before GISSI and ISIS-II, we also extracted information on the used comparator, randomisation, blinding, dropout proportions, and the use of intention-to-treat analyses. We did random-effects cumulative meta-analyses with Trial Sequential Analysis considering diversity.

Results

The largest trials conducted before GISSI and ISIS-II had serious methodological differences and high risks of bias making a cumulative meta-analysis invalid by today’s standards of evidence synthesis. The Trial Sequential Analysis showed that the monitoring boundary for a mortality benefit of streptokinase was reached during the ISAM trial. However, both GISSI and ISIS-II were launched before the ISAM trial was published. Focusing only on the cumulative assessment, the megatrials were potentially futile. Sensitivity analyses corroborated these results.

Conclusion

Our Trial Sequential Analysis of the historical dataset of streptokinase for myocardial infarction found that conclusive evidence favouring streptokinase was established after the megatrials were launched. However, considering the methodological differences and risks of bias, such cumulative meta-analysis seems invalid. Accordingly, the megatrials were not wasteful.
Subcortical imaging-derived phenotypes are associated with the risk of Parkinson’s disease: A Mendelian Randomization Study
Authors: Chen Zhichun , Liu Jun , You Yong
Published: September 2024

Background

The abnormalities of subcortical structures, such as putamen and caudate, play a key role in the occurrence of Parkinson’s disease (PD); however, whether and how imaging-derived phenotypes (IDPs) in subcortical structures are causally associated with the risk of PD remain poorly understood.

Methods

The causal associations between subcortical IDPs from UK biobank and risk of PD were evaluated with bidirectional two-sample Mendelian randomization (MR) studies.

Results

Totally five subcortical IDPs were found to be causally associated with the risk of PD. Among these IDPs, IDP 168 (Global volume of subcortical gray matter, OR = 1.38 [1.16, 1.63],P= 1.82 x 10−4), IDP 214 (Right putamen volume, OR = 1.31 [1.15, 1.50],P= 7.71 x 10−5) and IDP 1441 (T2* signal in right caudate, OR = 1.21 [1.09, 1.35],P= 5.23 x 10−4) were found to be associated with increased risk of PD. In contrast, IDP 1358 (Mean intensity in right caudate, OR = 0.72 [0.62, 0.85),P= 6.77 x 10−5) and IDP 1344 (Mean intensity in left caudate, OR = 0.76 [0.65, 0.88],P= 3.23 x 10−4) were associated with reduced risk of PD.

Conclusions

The specific imaging features of the caudate and putamen are causally associated with altered risk of developing PD, thereby providing new insights into the development of novel predictive imaging biomarkers and therapies for PD patients.
Neanderthal-derived variants shape craniofacial enhancer activity at a human disease locus
Authors: Uttley Kirsty , Jüllig Hannah J , De Angelis Carlo , Auer Julia MT , Ozga Ewa , Bengani Hemant , Long Hannah K
Published: September 2024

Facial appearance is one of the most variable morphological traits in humans, influenced by both rare and common genetic variants that can impact facial form between individuals and in disease. Deletion of an enhancer cluster 1.45 megabases upstream of theSOX9gene (EC1.45) results in Pierre Robin sequence, a human craniofacial disorder characterised by underdevelopment of the lower jaw and frequently associated with cleft palate. We reasoned that single nucleotide variants in EC1.45 may cause more subtle alterations to facial morphology. Here, we took advantage of recent human evolution, and the distinct morphology of the Neanderthal lower jaw, to investigate the impact of three Neanderthal-derived single nucleotide variants on EC1.45 function and jaw development. Utilising a dual enhancer-reporter system in zebrafish, we observed enhanced Neanderthal regulatory activity relative to the human orthologue during a specific developmental window. At this same stage, we show that EC1.45 appears to be selectively active in neural crest- derived progenitor cells which lie in close apposition with and are transcriptionally related to precartilaginous condensations that contribute to craniofacial skeletal development. To examine the potential consequences of increasedSOX9expression in this specific cellular population during jaw development, we overexpressed human SOX9 specifically in EC1.45-active cells and observed an increase in the volume of developing cartilaginous precursors. Taken together, our work implicates Neanderthal-derived variants in increased regulatory activity for a disease- associated enhancer with the potential to impact craniofacial skeletal development and jaw morphology across recent hominin evolution.
Complex genetic variation in nearly complete human genomes
Authors: Logsdon Glennis A. , Ebert Peter , Audano Peter A. , Loftus Mark , Porubsky David , Ebler Jana , Yilmaz Feyza , Hallast Pille , Prodanov Timofey , Yoo DongAhn , Paisie Carolyn A. , Harvey William T. , Zhao Xuefang , Martino Gianni V. , Henglin Mir , Munson Katherine M. , Rabbani Keon , Chin Chen-Shan , Gu Bida , Ashraf Hufsah , Austine-Orimoloye Olanrewaju , Balachandran Parithi , Bonder Marc Jan , Cheng Haoyu , Chong Zechen , Crabtree Jonathan , Gerstein Mark , Guethlein Lisbeth A , Hasenfeld Patrick , Hickey Glenn , Hoekzema Kendra , Hunt Sarah E , Jensen Matthew , Jiang Yunzhe , Koren Sergey , Kwon Youngjun , Li Chong , Li Heng , Li Jiaqi , Norman Paul J , Oshima Keisuke K. , Paten Benedict , Phillippy Adam M. , Pollock Nicholas R , Rausch Tobias , Rautiainen Mikko , Scholz Stephan , Song Yuwei , Soylev Arda , Sulovari Arvis , Surapaneni Likhitha , Tsapalou Vasiliki , Zhou Weichen , Zhou Ying , Zhu Qihui , Zody Michael C. , Mills Ryan E. , Devine Scott E. , Shi Xinghua , Talkowski Mike E , Chaisson Mark J.P. , Dilthey Alexander T , Konkel Miriam K. , Korbel Jan O. , Lee Charles , Beck Christine R. , Eichler Evan E. , Marschall Tobias
Published: September 2024

Diverse sets of complete human genomes are required to construct a pangenome reference and to understand the extent of complex structural variation. Here, we sequence 65 diverse human genomes and build 130 haplotype-resolved assemblies (130 Mbp median continuity), closing 92% of all previous assembly gaps and reaching telomere-to-telomere (T2T) status for 39% of the chromosomes. We highlight complete sequence continuity of complex loci, including the major histocompatibility complex (MHC), SMN1/SMN2, NBPF8, and AMY1/AMY2, and fully resolve 1,852 complex structural variants (SVs). In addition, we completely assemble and validate 1,246 human centromeres. We find up to 30-fold variation in α-satellite high-order repeat (HOR) array length and characterize the pattern of mobile element insertions into α-satellite HOR arrays. While most centromeres predict a single site of kinetochore attachment, epigenetic analysis suggests the presence of two hypomethylated regions for 7% of centromeres. Combining our data with the draft pangenome reference significantly enhances genotyping accuracy from short-read data, enabling whole-genome inference to a median quality value (QV) of 45. Using this approach, 26,115 SVs per sample are detected, substantially increasing the number of SVs now amenable to downstream disease association studies.
Nucleosome placement and polymer mechanics explain genomic contacts on 100kbp scales
Authors: Corrette John , Li Jiachun , Shao Hanjuan , Veerasubramanian Praveen Krishna , Spakowitz Andrew , Downing Timothy L. , Allard Jun
Published: September 2024

The 3d organization of the genome — in particular, which two regions of DNA are in contact with each other — plays a role in regulating gene expression. Several factors influence genome 3d organization. Nucleosomes (where∼100 basepairs of DNA wrap around histone proteins) also bend, twist and compactify chromosomal DNA, altering its polymer mechanics. How much does the positioning of nucleosomes between gene loci influence contacts between those gene loci? And, to what extent is polymer mechanics responsible for this? To address this question, we combine a stochastic polymer mechanics model of chromosomal DNA including twists and wrapping induced by nucleosomes with two data-driven pipelines. The first estimates nucleosome positioning from ATACseq data in regions of high accessibility. Most of the genome is low-accessibility, so we combine this with a novel image analysis method that estimates the distribution of nucleosome spacing from electron microscopy data. There are no free parameters in the biophysical model. We apply this method to IL6, IL15, CXCL9, and CXCL10, inflammatory marker genes in macrophages, before and after immune stimulation, and compare the predictions with contacts measured by conformation capture experiments (4C-seq). We find that within a 500 kilo-basepairs genomic region, polymer mechanics with nucleosomes can explain 71% of close contacts. These results suggest that, while genome contacts on 100kbp-scales are multifactorial, they may be amenable to mechanistic, physical explanation. Our work also highlights the role of nucleosomes, not just at the loci of interest, but between them, and not just the total number of nucleosomes, but their specific placement. The method generalizes to other genes, and can be used to address whether a contact is under active regulation by the cell (e.g., a macrophage during inflammatory stimulation). Importantly, our findings suggest that gene function may have evolved through selective pressures that co-opted contact-mediated regulatory mechanisms reliant largely on polymer mechanics.
Context-Dependent Modulations in Acoustic Features of Zebra Finch Distance Calls: Insights from a Novel Goal-Directed Vocalization Paradigm
Authors: Safarcharati Zohreh , Bahramani Amirreza , Mokari Amjad Pouya , Ravanbakhsh Mahsa , Raoufy Mohammad Reza , Khademian Mahdi
Published: September 2024

Songbirds are renowned for their complex vocal communication abilities; among them, zebra finches (Taeniopygia guttata) are a key species for studying vocal learning and communication. Zebra finches use various calls with different meanings, including the distance call, which is used for long-distance contact. Whether these calls are static with fixed meanings or flexible remains an open question. In this study we aimed to answer this question by designing a novel behavioral paradigm, in which we trained food-restricted zebra finches to use distance calls for food request. Nine out of ten birds learned this association and used their distance calls to obtain food when they were hungry. We then introduced a visually-separated audience and compared the distance calls used for food requests with those used for communication between birds. Results revealed significant acoustic differences in power, pitch, and other spectral characteristics between the distance calls uttered in these two contexts. Our findings suggest that zebra finches can use their distance call for different goals and also acoustically modulate it based on the context. Therefore, it demonstrates a level of vocal control thought to be exclusive to songs. This study enhances our understanding of vocal flexibility and its role in vocal communication.
Molecular Mechanisms Underlying the Spectral Shift in Zebrafish Cone Opsins
Authors: Chi L. América , Pandey Shubham Kumar , Kolodziejczyk Wojciech , Lund-Andersen Peik , Barnes Jonathan E. , Kapusta Karina , Patel Jagdish Suresh
Published: September 2024

Visual pigments are essential for converting light into electrical signals during vision. Composed of an opsin protein and a retinal-based chromophore, pigments in vertebrate rods (Rh1) and cones (Rh2) have different spectral sensitivities, with distinct peak absorption wavelengths determined by the shape and composition of the chromophore binding pocket. Despite advances in understanding Rh1 pigments such as bovine rhodopsin, the molecular basis of spectral shifts in Rh2 cone opsins has been less studied, particularly the E122Q mutation, which accounts for about half of the observed spectral shift in these pigments. In this study, we employed molecular modeling and quantum mechanical techniques to investigate the molecular mechanisms behind the spectral difference in blue-shifted Rh2-1 (absorption peak = 467 nm, 122Q) and green-shifted Rh2-4 (absorption peak = 505 nm, 122E) zebrafish cone opsins. We modeled the pigments 3D structures based on their sequences and conducted all-atom molecular dynamics simulations totaling 2 microseconds. Distance analysis of the trajectories identified three key sites: E113, E181, and E122. The E122Q mutation, previously known, validates our findings, while E181 and E113 are newly identified contributors. Structural analysis revealed key features with differing values that explain the divergent spectral sensitivities of Rh2-1 and Rh2-4: 1) chromophore atom fluctuations and C5-C6 torsion angle, 2) binding pocket volume, 3) hydration patterns, and 4) E113-chromophore interaction stability. Quantum mechanics further confirms the critical role of residue E181 in Rh2-1 and E122 in Rh2-4 for their spectral behavior. Our study provides new insights into the molecular determinants of spectral shifts in cone opsins, and we anticipate that it will serve as a starting point for a broader understanding of the functional diversity of visual pigments.
Dynamic transcriptional and epigenetic changes define postnatal tendon growth
Authors: Dingwall Heather L. , Grinstein Mor , Capellini Terence D. , Galloway Jenna L.
Published: September 2024

Tendons are dynamic structures that efficiently transmit forces and enable movement. From birth, tendons undergo dramatic changes from a principally cellular tissue to a hypocellular one characterized by a dense and highly ordered extracellular matrix. During this time, tendon cells change morphology from rounded to stellate in appearance and their proliferative rates decline. There is also significant expansion and maturation of the extracellular matrix (ECM) as tendons grow in length and diameter and alter their biomechanical properties to sustain increased physical activities. Surprisingly, for such an important stage of tendon maturation, we understand very little about the transcriptional and epigenetic regulators that direct these processes. Here, we present a roadmap of genes that are differentially regulated during the early neonatal and postnatal time period. We find differentially expressed genes fall into specific transcriptional modules, representing expression increases, decreases, or gene sets undergoing dynamic changes over postnatal time. By pairing our transcriptomic data with epigenetic data, we were able to perform an integrative analysis of the datasets and further define modules with highly correlated changes in gene expression and chromatin accessibility. From this analysis, several new pathways emerge. Among them, we focus on Yap1, a transcriptional co-activator of the Hippo signaling pathway. We observe accessible regions near to differentially expressed genes, containing motifs for TEAD, the transcription factor that binds Yap to regulate transcription. Conditional loss ofYap1at postnatal stages results in altered expression ofCol1a1and disrupted matrix organization and density, suggesting that Yap is important for refining tendon ECM maturation. Together, our analyses identify a regulator of matrix maturation and provides a rich dataset with which to interrogate transcriptional networks and pathways during this poorly understood time in tendon growth.
Designing realistic regulatory DNA with autoregressive language models
Authors: Lal Avantika , Garfield David , Biancalani Tommaso , Eraslan Gokcen
Published: September 2024

Cis-regulatory elements (CREs), such as promoters and enhancers, are DNA sequences that regulate the expression of genes. The activity of a CRE is influenced by the order, composition, and spacing of sequence motifs that are bound by proteins called transcription factors (TFs). Synthetic CREs with specific properties are needed for biomanufacturing as well as for many therapeutic applications including cell and gene therapy. Here, we present regLM, a framework to design synthetic CREs with desired properties, such as high, low, or cell type–specific activity, using autoregressive language models in conjunction with supervised sequence-to-function models. We used our framework to design synthetic yeast promoters and cell type–specific human enhancers. We demonstrate that the synthetic CREs generated by our approach are not only predicted to have the desired functionality but also contain biological features similar to experimentally validated CREs. regLM thus facilitates the design of realistic regulatory DNA elements while providing insights into thecis-regulatory code.
AGAPduplicons associate with structural diversity at Chromosome 10q11.22
Authors: Fornezza Stefania , Delvecchio Vincenza Simona , Harvey William T. , Dishuck Philip C. , Eichler Evan E. , Giannuzzi Giuliana
Published: September 2024

The 10q11.22 chromosomal region is a duplication-rich interval of the human genome and one of the last to be fully assembled. It carries copy number–variable genes associated with intellectual disability, bipolar disorder, and obesity. In this study, we characterized the structural diversity at this locus by analyzing 64 haploid assemblies produced by the Human Pangenome Reference Consortium. We identified 11 alternative haplotypes that differ in the copy number and/or orientation of large genomic segments, ranging from hundreds of kilobase pairs (kbp) to over one megabase pair (Mbp). We uncovered a 2.4 Mbp size difference between the shortest and longest haplotypes. Breakpoint analysis revealed that genomic instability results from nonallelic homologous recombination between segmental duplication (SD) pairs with varying similarity (94.4%–99.6%). Nonetheless, these pairs generally recombine at positions where their identity is higher (>99.6%). Recurrent inversions occur with different breakpoints within the same inverted SD pair. Inversion polymorphisms shuffle the entire SD arrangement, creating new predispositions to copy-number variations. The SD architecture is associated with a catarrhine-specific subgroup of theAGAPgene family, which likely triggered the accumulation of SDs at this locus over the past 25 million years of human evolution. Our results reveal extensive structural diversity and genomic instability at the 10q11.22 locus, and expand the general understanding of the mutational mechanisms behind SD-mediated rearrangements.
Absorbing discretization effects with a massive renormalization scheme: The charm-quark mass
Authors: Del Debbio L. , Erben F. , Flynn J. M. , Mukherjee R. , Tsang J. T. ,   RBC and UKQCD Collaborations
Published: September 2024

We present the first numerical implementation of the massive symmetric-momentum-subtraction (mSMOM) renormalization scheme and use it to calculate the charm-quark mass. Based on ensembles with three flavors of dynamical domain-wall fermions with lattice spacings in the range 0.11–0.08 fm, we demonstrate that the mass scale which defines the mSMOM scheme can be chosen such that the extrapolation has significantly smaller discretization effects than the SMOM scheme. Converting our results to the MS¯ scheme we obtain m¯c(3  GeV)=1.008(13)  GeV and m¯c(m¯c)=1.292(12)  GeV.

Published by the American Physical Society
2024
Odd-parity nucleon electromagnetic transitions in lattice QCD
Authors: Stokes Finn M. , Owen Benjamin J. , Kamleh Waseem , Leinweber Derek B.
Published: September 2024

The parity-expanded variational analysis (PEVA) technique enables the isolation of opposite-parity eigenstates at finite momentum. The approach has been used to perform the first lattice QCD calculations of excited-baryon form factors. In particular, these calculations show that the low-lying odd-parity nucleon excitations are described well by constituent quark models at moderate u and d quark masses approaching the strange quark mass. Herein, we extend the PEVA technique to establish a formalism for the determination of odd-parity nucleon electromagnetic transition form factors in lattice QCD. The formalism is implemented in the first calculation of the helicity amplitudes for transitions from the ground state nucleon to the first two odd-parity excitations. Through a comparison with constituent quark-model calculations of these amplitudes, these new results give important insight into the structure of these excitations. This work is a critical step towards confronting experimental electroproduction amplitudes for the N*(1535) and N*(1650) resonances with lattice QCD calculations.

Published by the American Physical Society
2024
Cosmology of dark energy radiation
Authors: Berghaus Kim V. , Karwal Tanvi , Miranda Vivian , Brinckmann Thejs
Published: September 2024

In this work, we quantify the cosmological signatures of dark energy radiation—a novel description of dark energy, which proposes that the dynamical component of dark energy is comprised of a thermal bath of relativistic particles sourced by thermal friction from a slowly rolling scalar field. For a minimal model with particle production emerging from first principles, we find that the abundance of radiation sourced by dark energy can be as large as ΩDER=0.03, exceeding the bounds on relic dark radiation by three orders of magnitude. Although the background and perturbative evolution of dark energy radiation are distinct from Quintessence, we find that current and near-future cosmic microwave background and supernova data will not distinguish these models of dark energy. We also find that our constraints on all models are dominated by their impact on the expansion rate of the Universe. Considering extensions that allow the dark radiation to populate neutrinos, axions, and dark photons, we evaluate the direct detection prospects of a thermal background comprised of these candidates consistent with cosmological constraints on dark energy radiation. Our study indicates that a resolution of ∼6  meV is required to achieve sensitivity to relativistic neutrinos compatible with dark energy radiation in a neutrino capture experiment on tritium. We also find that dark matter axion experiments lack sensitivity to a relativistic thermal axion background, even if enhanced by dark energy radiation, and dedicated search strategies are required to probe new parameter space. We derive constraints arising from a dark photon background from oscillations into visible photons, and find that viable parameter space can be explored with the late dark energy radiation experiment.

Published by the American Physical Society
2024
Nucleon-to-
Δ
Axial and Pseudoscalar Transition Form Factors
Authors: Chen Chen , Fischer Christian S. , Roberts Craig D.
Published: September 2024

A symmetry-preserving approach to the calculation of baryon properties in relativistic quantum field theory is used to predict all form factors associated with nucleon-to-Δ axial and pseudoscalar transition currents, thereby unifying them with many additional properties of these and other baryons. The new parameter-free predictions can serve as credible benchmarks for use in analyzing existing and anticipated data from worldwide efforts focused on elucidation of ν properties.

Published by the American Physical Society
2024