bluuebunny/crossref_metadata_2025 huggingface dataset:
Explicit Scale Simulation for analysis of RNA-sequencing with ALDEx2
Authors: Gloor Gregory B. , Nixon Michelle Pistner , Silverman Justin D.
Published: October 2023

In high-throughput sequencing (HTS) studies, sample-to-sample variation in sequencing depth is driven by technical factors, and not by variation in the scale (e.g., total size, microbial load, or total mRNA expression) of the underlying biological systems. Typically a statistical normalization is used to remove unwanted technical variation in the data or the parameters of the model to enable analyses that are reliant on scale; e.g., differential abundance and differential expression analyses. We recently showed that all normalizations make implicit assumptions about the unmeasured system scale and that errors in these assumptions can dramatically increase false positive and false negative rates. We demonstrated that these errors can be mitigated by accounting for uncertainty about scale using ascale model, which we integrated into the ALDEx2 R package. This article provides new insights into those methods, focusing on the application to transcriptomic analysis. Here we provide transcriptomic case studies demonstrating how scale models, rather than traditional normalizations, can reduce false positive and false negative rates in practice while enhancing the transparency and reproducibility of analyses. We show that these scale models replace the need for dual cutoff approaches often used to address the disconnect between practical and statistical significance. We demonstrate the utility of that scale models built based on known housekeeping genes in complex metatranscriptomic datasets. Thus this work provides example and practical guidance on how to incorporate scale into transcriptomic analysis.
Regulating the proinflammatory response to implanted composite biomaterials comprising polylactide and hydroxyapatite by targeting immunometabolism
Authors: Maduka Chima V. , Makela Ashley V. , Ural Evran , Stivers Katlin B. , Kuhnert Maxwell M. , Tundo Anthony , Alhaj Mohammed , Apu Ehsanul Hoque , Ashammakhi Nureddin , Hankenson Kurt D. , Narayan Ramani , Elisseeff Jennifer H. , Contag Christopher H.
Published: October 2023

Composite biomaterials comprising polylactide (PLA) and hydroxyapatite (HA) are applied in bone, cartilage and dental regenerative medicine, where HA confers osteoconductive properties. However, after surgical implantation, adverse immune responses to these composites can occur, which have been attributed to size and morphology of HA particles. Approaches to effectively modulate these adverse immune responses have not been described. PLA degradation products have been shown to alter immune cell metabolism, which drives the inflammatory response. Therefore, we aimed to modulate the inflammatory response to composite biomaterials by regulating glycolytic flux with small molecule inhibitors incorporated into composites comprised of amorphous PLA (aPLA) and HA (aPLA+HA). Inhibition at specific steps in glycolysis reduced proinflammatory (CD86+CD206-) and increased pro-regenerative (CD206+) immune cell populations around implanted aPLA+HA resulting in a pro-regenerative microenvironment. Notably, neutrophil and dendritic cell (DC) numbers along with proinflammatory monocyte and macrophage populations were decreased, and Arginase 1 expression among DCs was increased. Targeting immunometabolism to control the inflammatory response to biomaterial composites, and creating a pro-regenerative microenvironment, is a significant advance in tissue engineering where immunomodulation enhances osseointegration, and angiogenesis, which will lead to improved bone regeneration.
Bayesian inference for copy number intra-tumoral heterogeneity from single-cell RNA-sequencing data
Authors: Qiao PuXue , Kwok Chun Fung , Qian Guoqi , McCarthy Davis J
Published: October 2023

High-resolution molecular characterization of intra-tumoral clonal structure defined by genomic and epigenomic alterations is crucial in understanding the natural history of tumors and advancing cancer treatment strategies. Copy number alterations (CNA) are of notable importance as both drivers and markers of clonal structure that can now be assayed at individual cell resolution. However, specific computational methods are needed for accurate inference of clonal profiles and cell states from sparse and noisy single-cell ’omics data. Here, we develop a new Bayesian model to utilize single-cell RNA sequencing (scRNA-seq) data for automatic analysis of intra-tumoral clonal structure with respect to CNAs, without reliance on prior knowledge. The model clusters cells into sub-tumoral clones while simultaneously identifying CNA events in each clone, jointly modelling input from gene expression and germline single-nucleotide polymorphisms. Unlike previous methods, our approach automatically infers the number of clones present in the tumor. In detailed simulation studies our model frequently achieves very high (>90%) cell clustering accuracy and high (>80%) CN state inference accuracy, even in settings of high variance and sparsity. Overall, our method compares strongly against existing software tools. Application to human metastatic melanoma tumor data demonstrates accurate clustering of tumor and non-tumor cells, and reveals clonal CNA profiles that highlight functional gene expression differences between clones from the same tumor. Our method is implemented in a publicly-available, open-source R package, Chloris.
Mobile DNA is replete with hotspots for the de novo emergence of gene regulation
Authors: Fuqua Timothy , Wagner Andreas
Published: October 2023

DNA mutations that create new gene expression are important raw materials for Darwinian evolution. One potential source of new gene regulation is mobile DNA, which can sometimes drive the expression of genes near its insertion site in a genome through outward-directed promoters. However, we do not know how frequent this ability is, nor how frequently mobile DNA may evolve such promotersde novo. Here we address these questions for the insertion sequence family IS3, the most abundant family of a simple form of prokaryotic mobile DNA. First, we estimate that at least 30% of IS3 sequences harbor outward-directed promoters. Second, we combine high-throughput mutagenesis with a massively parallel reporter assay to show that single point mutations suffice to create outward-directed promoters in all the IS3 sequences we studied. We found that in 5.6% of 18’607 mutant IS3 sequences, promoter activity emerged de novo. Promoters preferentially arise at emergence hotspots in each IS3 sequence. These hotspots overlap with promoter motifs that already exist or are newly created by mutation. One common route to promoter activity is gaining a -10 box downstream of an existing -35 box, which we call “Shiko Emergence.” Overall, we show that mobile DNA has a high latent potential to drive new gene expression. This makes mobile DNA ideal for domestication by its host organism. It also raises intriguing questions about how this potential has evolved.
Quality and sustainability of Ethiopia’s national surgical indicators
Authors: Cook Kayleigh R , Zeleke Zebenay B , Gebrehana Ephrem , Burssa Daniel , Yeshanew Bantalem , Michael Atkilt , Tediso Yoseph , Jaraczewski Taylor , Dodgion Chris , Beyene Andualem , Iverson Katherine R
Published: October 2023

In 2015, the Ethiopian Federal Ministry of Health (FMOH) developed the Saving Lives through Safe Surgery (SaLTS) initiative to improve national surgical care. Previous work led to development and implementation of 15 surgical key performance indicators (KPIs) to standardize surgical data practices. The objective of this project is to investigate current practices of KPI data collection and assess quality to improve data management and strengthen surgical systems.

The first portion of the study documented the surgical data collection process including methods, instruments, and effectiveness at 10 hospitals across 2 regions in Ethiopia. Secondly, data for KPIs of focus [1. Surgical Volume, 2. Perioperative Mortality Rate (POMR), 3. Adverse Anesthetic Outcome (AAO), 4. Surgical Site Infection (SSI), and 5. Safe Surgery Checklist (SSC) Utilization] were compared between registries, KPI reporting forms, and the DHIS2 (district health information system) electronic database for a 6-month period (January - June 2022). Quality was assessed based on data completeness and consistency.

The data collection process involved hospital staff recording data elements in registries, quality officers calculating KPIs, completing monthly KPI reporting forms, and submitting data into DHIS2 for the national and regional health bureaus. Data quality verifications revealed discrepancies in consistency at all hospitals, ranging from 1-3 indicators. For all hospitals, average monthly surgical volume was 57 cases, POMR was 0.38% (13/3399), inpatient SSI rate was 0.79% (27/3399), AAO rate was 0.15% (5/3399), and mean SSC utilization monthly was 93% (100% median). Half of the hospitals had incomplete data within the registries, ranging from 2-5 indicators. AAO, SSC, and SSI were commonly missing data in registries. Non-standardized KPI reporting forms contributed significantly to the findings.

Facilitators to quality data collection included continued use of registries from previous interventions and use of a separate logbook to document specific KPIs. Delayed rollout of these indicators in each region contributed to issues in data quality. Barriers involved variable indicator recording from different personnel, data collection tools that generate false positives (i.e. completeness of SSC defined as paper form filled out prior to patient discharge) or missing data because of reporting time period (i.e. monthly SSI may miss infections outside of one month), inadequate data elements in registries, and lack of standardized monthly KPI reporting forms. As the FMOH introduces new indicators and changes, we recommend continuous and consistent quality checks and data capacity building, including the use of routinely generated health information for quality improvement projects at the department level.
Beneficial effects of intermittent fasting in NASH and subsequent HCC development are executed by concerted PPARα and PCK1 action in hepatocytes
Authors: Gallage Suchira , Ali Adnan , Barragan Avila Jose Efren , Seymen Nogayhan , Ramadori Pierluigi , Joerke Vera , Zizmare Laimdota , Kosla Jan , Li Xin , Focaccia Enrico , Yousuf Suhail , Sijmonsma Tjeerd , Rahbari Mohammad , Kommoss Katharina S. , Billeter Adrian , Prokosch Sandra , Rothermel Ulrike , Mueller Florian , Hetzer Jenny , Heide Danijela , Machauer Tim , Malek Nisar P. , Longerich Thomas , Rose Adam J. , Roth Susanne , Schwenck Johannes , Trautwein Christoph , Karimi Mohammad M , Heikenwalder Mathias
Published: October 2023

The role and molecular mechanisms of intermittent fasting (IF) in non-alcoholic steatohepatitis (NASH) and its transition to hepatocellular carcinoma (HCC) are unknown. Here, we identified that an IF 5:2 regimen (two non-consecutive days of food deprivation per week), initiated in the active phase of mice, prevents/ameliorates NASH and fibrosis as well as reduces subsequent HCC development without affecting total calorie intake. The timing, length and number of fasting cycles as well as the type of NASH diet were all critical parameters determining the effectiveness of the fasting benefits. Combined proteomic, transcriptomic and metabolomic analyses identified that PPARα and glucocorticoid receptor (GR)-PCK1 act co-operatively as hepatic executors of the fasting response by promoting fatty acid catabolism and gluconeogenesis whilst suppressing anabolic lipogenesis. In line, PPARα targets and PCK1 were reduced in human NASH. Additionally, dynamic [18F]FDG-PET analysisin vivorevealed increased [18F]FDG uptake/retention and enhanced gluconeogenesis in the liver upon fasting (in accordance with PPARα and GR-PCK1 activation) when assessed by compartmental modelling. Hepatocyte-specificGRdeletion only partially abrogated the hepatic fasting response. In contrast, the combined knockdown ofPparaandPck1 in vivoabolished the beneficial outcomes of fasting against inflammation and fibrosis, confirming their causal relationship in integrating systemic signalling in hepatocytes. Notably, PPARα agonist pemafibrate recapitulated key aspects of hepatic fasting signalling at a molecular level. Therefore, IF or pharmacological mimetics of the PPARα and/or GR-PCK1 axis could be a viable intervention against NASH and subsequent liver cancer.

One-Sentence Summary

Intermittent fasting protects against fatty liver disease and liver cancer through concerted PPARα and GR-PCK1 action in hepatocytes.
Dynamic model of carbon dioxide-induced stomatal closure reveals a feedback core for cellular decision-making
Authors: Gan Xiao , Sengottaiyan Palanivelu , Park Kyu Hyong , Assmann Sarah M. , Albert Réka
Published: October 2023

Stomata are pores on plant aerial surfaces, each bordered by a pair of guard cells. They control gas exchange vital for plant survival. Understanding how guard cells respond to environmental signals such as atmospheric carbon dioxide (CO2) levels is not only insightful to fundamental biology but also relevant to real-world issues of crop productivity under global climate change. In the past decade, multiple important signaling elements for stomatal closure induced by elevated CO2have been identified. Yet, there is no comprehensive understanding of high CO2induced stomatal closure. In this work we assemble a cellular signaling network underlying high CO2-induced stomatal closure by integrating evidence from a comprehensive literature analysis. We further construct a Boolean dynamic model of the network, which allowsin silicosimulation of the stomatal closure response to high CO2in wild-typeArabidopsis thalianaplants and in cases of pharmacological or genetic manipulation of network nodes. Our model has a 91% accuracy in capturing known experimental observations. We perform network-based logical analysis and reveal a feedback core of the network, which dictates cellular decisions in closure response to high CO2. Based on these analyses, we predict and experimentally confirm that applying nitric oxide (NO) induces stomatal closure in ambient CO2and causes hypersensitivity to elevated CO2. Moreover, we predict a negative regulatory relationship between NO and the protein phosphatase ABI2 and find experimentally that NO inhibits ABI2 phosphatase activity. The experimental validation of these model predictions demonstrates the effectiveness of network-based modeling and highlights the decision-making role of the feedback core of the network in signal transduction. We further explore the model’s potential in predicting targets of signaling elements not yet connected to the CO2network. Our combination of network science,in silicomodel simulation, and experimental assays demonstrates an effective interdisciplinary approach to understanding system-level biology.
De novogenome assemblies from two Indigenous Americans from Arizona identify new polymorphisms in non-reference sequences
Authors: Köroğlu Çiğdem , Chen Peng , Traurig Michael , Altok Serdar , Bogardus Clifton , Baier Leslie J
Published: October 2023

There is a collective push to diversify human genetic studies by including underrepresented populations. However, analyzing DNA sequence reads involves the initial step of aligning the reads to the GRCh38/hg38 reference genome which is inadequate for non-European ancestries. To help address this issue, we created a modified hg38 reference map usingde novosequence assemblies from Indigenous Americans living in Arizona (IAZ). Using HiFi SMRT long-read sequencing technology, we generatedde novogenome assemblies for one female and one male IAZ individual. Each assembly included ∼17 Mb of DNA sequence not present (non-reference sequence; NRS) in hg38, which consists mostly of repeat elements. Forty NRSs totaling 240 kb were uniquely anchored to the hg38 primary assembly generating a modified hg38-NRS reference genome. DNA sequence alignment and variant calling were then conducted with WGS sequencing data from 387 IAZ cohorts using both the hg38 and modified hg38-NRS reference maps. Variant calling with the hg38-NRS map identified ∼50,000 single nucleotide variants present in at least 5% of the WGS samples which were not detected with the hg38 reference map. We also directly assessed the NRSs positioned within genes. Seventeen NRSs anchored to regions including an identical 187 bp NRS found in both de novo assemblies. The NRS is located inHCN279 bp downstream of exon 3 and contains several putative transcriptional regulatory elements. Genotyping of theHCN2-NRS revealed that the insertion is enriched in IAZ (MAF = 0.45) compared to Caucasians (MAF = 0.15) and African Americans (MAF = 0.03). This study shows that inclusion of population-specific NRSs can dramatically change the variant profile in an under-represented ethnic groups and thereby lead to the discovery of previously missed common variations.

AUTHOR SUMMARY

GRCh38/hg38 reference genome has been the standard reference for large-scale human genetics studies. However, it does not adequately represent sequences of non-European ancestry. In this study, using long-read sequencing technology, we constructedde novosequence assemblies from two Indigenous Americans from Arizona. We then compared thede novoassemblies to the hg38 reference genome to identify non-reference sequences (NRSs). We integrated these NRSs into our whole-genome sequencing (WGS) variant calling pipeline to improve read alignment and variant detection. We also directly assessed the NRSs positioned within genes. Inclusion of population-specific NRSs dramatically changed the variant profile of our study group with under-represented ethnicity, revealing common variation not detected by our previous population-level WGS and genotyping studies.
Quantitative dynamics of intracellular NMN by genetically encoded biosensor
Authors: Chen Liuqing , Wang Pei , Huang Guan , Cheng Wenxiang , Liu Kaijing , Yu Qiuliyang
Published: October 2023

Nicotinamide mononucleotide (NMN) is a major precursor for NAD+metabolism with promising effects in treating NAD+- and aging-related pathologies. However, measuring live cell NMN dynamics was not possible, leaving key questions in intracellular NMN uptake and regulation unanswered. Here we developed a genetically encoded bioluminescent sensor to quantify subcellular NMN in live cells by fusing engineered NMN-responsive binding domain to bioluminescent and fluorescent proteins from BRET pairs. The sensor dissected the multimechanistic uptake of extracellular NMN and precursors in live cells. We then captured the notably low mitochondrial NMN content and the thereafter vulnerable NMN/NAD+ratio and SARM1 activation in mitochondria, establishing NMN/NAD+ratio as an important parameter in evaluating NAD+boosting strategies. Moreover, we characterized the signature of major NAD+regulating enzymes on NMN and NMN/NAD+ratios, in which Slc25a45 was identified to be a potential mitochondrial NMN transporter for its unique fingerprint on mitochondrial NMN/NAD+ratio.
Improving forest ecosystem functions by optimizing tree species spatial arrangement
Authors: Beugnon Rémy , Albert Georg , Hähn Georg , Haider Sylvia , Hättenschwiler Stephan , Davrinche Andréa , Rosenbaum Benjamin , Gauzens Benoit , Eisenhauer Nico
Published: October 2023

Reforestation and afforestation programs are promoted as strategies to mitigate rising atmospheric CO2concentrations and enhance ecosystem services. Planting diverse forests is supposed to foster such benefits, but optimal tree planting techniques, especially regarding species spatial arrangement, are underexplored.

Here, using field measurements from the subtropical BEF-China experiment, we simulated leaf litterfall and decomposition, as a function of various spatial arrangements of tree species, from clusters of species to random distributions.

We show that increasing tree species spatial heterogeneity in forests composed of nine tree species led to more evenly distributed litterfall, increased litter decomposition and associated nitrogen cycling by 45%. These effects were amplified with increasing plot species richness, while species functional trait identity and diversity modulated these relationships.

The spatial arrangement of tree species is a critical component determining biodiversity-ecosystem functioning relationships, and considering such spatial aspects is crucial for operationalizing biodiversity-ecosystem functioning theory in realistic re-/afforestation projects.
Sex and species associated differences in Complement-mediated immunity in Humans and Rhesus macaques
Authors: Kelkar Natasha S. , Goldberg Benjamin S. , Dufloo Jérémy , Bruel Timothée , Schwartz Olivier , Hessell Ann J. , Ackerman Margaret E.
Published: October 2023

The complement system can be viewed as a ‘moderator’ of innate immunity, ‘instructor’ of humoral immunity, and ‘regulator’ of adaptive immunity. While sex and aging are known to affect humoral and cellular immune systems, their impact on the complement pathway in humans and rhesus macaques, a commonly used non-human primate model system, have not been well-studied. To address this knowledge gap, we analyzed serum samples from 90 humans and 75 rhesus macaques for the abundance and activity of the complement system components. While sequences of cascade proteins were highly conserved, dramatically different levels were observed between species. Whereas the low levels detected in rhesus samples raised questions about the suitability of the test, differences in levels of complement proteins were observed in male and female humans. Levels of total and antibody-dependent deposition of C1q and C3b on a glycosylated antigen differed between human and rhesus, suggesting differential recognition of glycans. Functional differences in complement-mediated lysis of antibody-sensitized cells were observed in multiple assays and showed that human females frequently exhibited higher lytic activity than human males or rhesus macaques, which typically did not exhibit such sexual dimorphism. Other differences between species and sexes were observed in more narrow contexts—for only certain antibodies, antigens, or assays. Collectively, these results expand our knowledge of sexual dimorphism in the complement system in humans, identifying differences that appear to be absent from rhesus macaques.
Multi-Factor Coral Disease Risk Forecasting for Early Warning and Management
Authors: Caldwell Jamie M , Liu Gang , Geiger Erick , Heron Scott F , Eakin C Mark , De La Cour Jacqueline , Greene Austin , Raymundo Laurie , Dryden Jen , Schlaff Audrey , Stella Jessica S , Kindinger Tye L , Couch Courtney S , Fenner Douglas , Hoot Whitney , Manzello Derek , Donahue Megan J
Published: October 2023

Ecological forecasts are becoming increasingly valuable tools for conservation and management. However, there are few examples of near real-time forecasting systems that account for the wide range of ecological complexities. We developed a new coral disease ecological forecasting system that explores a suite of ecological relationships and their uncertainty and investigates how forecast skill changes with shorter lead times. The Multi-Factor Coral Disease Risk product introduced here uses a combination of ecological and marine environmental conditions to predict risk of white syndromes and growth anomalies across reefs in the central and western Pacific and along the east coast of Australia and is available through the U.S. National Oceanic and Atmospheric Administration Coral Reef Watch program. This product produces weekly forecasts for a moving window of six months at ∼5 km resolution based on quantile regression forests. The forecasts show superior skill at predicting disease risk on withheld survey data from 2012-2020 compared with predecessor forecast systems, with the biggest improvements shown for predicting disease risk at mid-to high-disease levels. Most of the prediction uncertainty arises from model uncertainty and therefore prediction accuracy and precision do not improve substantially with shorter lead times. This result arises because many predictor variables cannot be accurately forecasted, which is a common challenge across ecosystems. Weekly forecasts and scenarios can be explored through an online decision support tool and data explorer, co-developed with end-user groups to improve use and understanding of ecological forecasts. The models provide near real-time disease risk assessments and allow users to refine predictions and assess intervention scenarios. This work advances the field of ecological forecasting with real world complexities, and in doing so, better supports near term decision making for coral reef ecosystem managers and stakeholders. Secondarily, we identify clear needs and provide recommendations to further enhance our ability to forecast coral disease risk.
A Germline Point Mutation in the MYC-FBW7 Phosphodegron Initiates Hematopoietic Malignancies
Authors: Freie Brian , Carroll Patrick A. , Varnum-Finney Barbara J. , Ramani Vijay , Bernstein Irwin , Eisenman Robert N.
Published: October 2023

Oncogenic activation of MYC in cancers predominantly involves increased transcription rather than coding region mutations. However, MYC-dependent lymphomas frequently contain point mutations in the MYC phospho-degron, including at threonine-58 (T58), where phosphorylation permits binding by the FBW7 ubiquitin ligase triggering MYC degradation. To understand how T58 phosphorylation functions in normal cell physiology, we introduced an alanine mutation at T58 (T58A) into the endogenousc-Myclocus in the mouse germline. While MYC-T58A mice develop normally, lymphomas and myeloid leukemias emerge in ∼60% of adult homozygous T58A mice. We find that primitive hematopoietic progenitor cells from MYC-T58A mice exhibit aberrant self-renewal normally associated with hematopoietic stem cells (HSCs) and upregulate a subset of Myc target genes important in maintaining stem/progenitor cell balance. Genomic occupancy by MYC-T58A was increased at all promoters, compared to WT MYC, while genes differentially expressed in a T58A-dependent manner were significantly more proximal to MYC-bound enhancers. MYC-T58A lymphocyte progenitors exhibited metabolic alterations and decreased activation of inflammatory and apoptotic pathways. Our data demonstrate that a single point mutation in Myc is sufficient to produce a profound gain of function in multipotential hematopoietic progenitors associated with self-renewal and initiation of lymphomas and leukemias.
Intrinsic properties of spinal motoneurons degrade ankle torque control in humans
Authors: Beauchamp James. A. , Pearcey Gregory E. P. , Khurram Obaid U. , Negro Francesco , Dewald Julius P.A. , Heckman CJ.
Published: October 2023

Motoneurons are the final common pathway for all motor commands and possess intrinsic electrical properties that must be tuned to control muscle across the full range of motor behaviors. Neuromodulatory input from the brainstem is likely essential for adapting motoneuron properties to match this diversity of motor tasks. A primary mechanism of this adaptation, control of dendritic persistent inward currents (PICs) in motoneurons by brainstem monoaminergic systems, generates both amplification and prolongation of synaptic inputs. While essential, there is an inherent tension between this amplification and prolongation. Although amplification by PICs allows for quick recruitment and acceleration of motoneuron discharge during discrete motor tasks, PICs must be deactivated to de-recruit motoneurons upon movement cessation. In contrast, during stabilizing or postural tasks, PIC-induced prolongation of synaptic inputs is likely critical for sustained motoneuron discharge. Here, we designed two motor tasks that show PIC amplification and prolongation may conflict and generate errors that degrade the precision of motor output in humans. This included a paradigm comprised of a discrete motor task superimposed atop a stabilizing task and a paradigm with muscle length-induced changes to the balance of excitatory and inhibitory inputs available for controlling PICs. We show that prolongation from PICs introduces deficits in ankle torque control and that these deficits are further degraded at shorter muscle lengths when PIC prolongation is greatest. These results highlight the necessity for inhibitory control of PICs and showcase issues that are introduced when inhibitory control is perturbed or constrained. Our findings suggest that, like sensory systems, errors are inherent in motor systems. These errors are not due to problems in the perception of movement-related sensory input but are embedded in the final stage of motor output.
A geometrical model of cell fate specification in the mouse blastocyst
Authors: Raju Archishman , Siggia Eric D.
Published: October 2023

The lineage decision that generates the epiblast and primitive endoderm from the inner cell mass (ICM) is a paradigm for cell fate specification. Recent mathematics has formalized Waddington’s landscape metaphor and proven that lineage decisions in detailed gene network models must conform to a small list of low dimensional stereotypic changes called bifurcations. The most plausible bifurcation for the ICM is the so-called heteroclinic flip that we define and elaborate here. Our reanalysis of recent data suggests that there is sufficient cell movement in the ICM so the FGF signal, which drives the lineage decision, can be treated as spatially uniform. We thus extend the bifurcation model for a single cell to the entire ICM by means of a self-consistently defined time-dependent FGF signal. This model is consistent with available data and we propose additional dynamic experiments to test it further. This demonstrates that simplified, quantitative, and intuitively transparent descriptions are possible when attention is shifted from specific genes to lineages. The flip bifurcation is a very plausible model for any situation where the embryo needs control over the relative proportions of two fates by a morphogen feedback.
Acoustomechanically activatable liposomes for ultrasonic drug uncaging
Authors: Purohit Mahaveer P. , Roy Kanchan Sinha , Xiang Yun , Yu Brenda J. , Azadian Matine M. , Muwanga Gabriella , Hart Alex R. , Taoube Ali K. , Lopez Diego Gomez , Airan Raag D.
Published: October 2023

Ultrasound-activatable drug-loaded nanocarriers enable noninvasive and spatiotemporally-precise on-demand drug delivery throughout the body. However, most systems for ultrasonic drug uncaging utilize cavitation or heating as the drug release mechanism and often incorporate relatively exotic excipients into the formulation that together limit the drug-loading potential, stability, and clinical translatability and applicability of these systems. Here we describe an alternate strategy for the design of such systems in which the acoustic impedance and osmolarity of the internal liquid phase of a drug-loaded particle is tuned to maximize ultrasound-induced drug release. No gas phase, cavitation, or medium heating is necessary for the drug release mechanism. Instead, a non-cavitation-based mechanical response to ultrasound mediates the drug release. Importantly, this strategy can be implemented with relatively common pharmaceutical excipients, as we demonstrate here by implementing this mechanism with the inclusion of a few percent sucrose into the internal buffer of a liposome. Further, the ultrasound protocols sufficient for in vivo drug uncaging with this system are achievable with current clinical therapeutic ultrasound systems and with intensities that are within FDA and society guidelines for safe transcranial ultrasound application. Finally, this current implementation of this mechanism should be versatile and effective for the loading and uncaging of any therapeutic that may be loaded into a liposome, as we demonstrate for four different drugs in vitro, and two in vivo. These acoustomechanically activatable liposomes formulated with common pharmaceutical excipients promise a system with high clinical translational potential for ultrasonic drug uncaging of myriad drugs of clinical interest.

One Sentence Summary

Incorporating a few percent sucrose into a liposome transforms it into an immediately translatable vehicle for noninvasive, on-demand ultrasound-targeted drug delivery.
Decoding Genetics, Ancestry, and Geospatial Context for Precision Health
Authors: Koyama Satoshi , Wang Ying , Paruchuri Kaavya , Uddin Md Mesbah , Cho So Mi J. , Urbut Sarah M. , Haidermota Sara , Hornsby Whitney E. , Green Robert C. , Daly Mark J. , Neale Benjamin M. , Ellinor Patrick T. , Smoller Jordan W. , Lebo Matthew S. , Karlson Elizabeth W. , Martin Alicia R. , Natarajan Pradeep
Published: October 2023

Mass General Brigham, an integrated healthcare system based in the Greater Boston area of Massachusetts, annually serves 1.5 million patients. We established the Mass General Brigham Biobank (MGBB), encompassing 142,238 participants, to unravel the intricate relationships among genomic profiles, environmental context, and disease manifestations within clinical practice. In this study, we highlight the impact of ancestral diversity in the MGBB by employing population genetics, geospatial assessment, and association analyses of rare and common genetic variants. The population structures captured by the genetics mirror the sequential immigration to the Greater Boston area throughout American history, highlighting communities tied to shared genetic and environmental factors. Our investigation underscores the potency of unbiased, large-scale analyses in a healthcare-affiliated biobank, elucidating the dynamic interplay across genetics, immigration, structural geospatial factors, and health outcomes in one of the earliest American sites of European colonization.
COVID-19 vaccination-induced antibody responses and waning by age and comorbidity status in a large population-based prospective cohort study
Authors: Hoeve CE , Huiberts AJ , de Gier B , Andeweg SP , den Hartog G , de Melker HE , Hahne SJM , van de Wijgert JHHM , van den Hof S , Knol MJ
Published: October 2023

Background

Information on the magnitude and duration of antibody levels after COVID-19 vaccination in different groups may be useful for prioritizing of additional vaccinations.

Methods

Serum samples were collected every six months in a prospective cohort study among adults in the Netherlands. Geometric mean concentrations (GMCs) of antibodies against the receptor binding domain of the SARS-CoV-2 spike protein were calculated after the primary series, first, and second booster vaccinations. Effects of age (18-59 vs 60-85 years) and medical risk conditions on GMC 2-6 weeks and 21-25 weeks after each vaccination, and on waning during 3-25 weeks after each vaccination, were estimated by linear regression.

Results

We included 20,816, 16,820 and 5,879 samples collected after primary, first and second booster vaccination, respectively. GMCs at 2-6 and 21-25 weeks after primary series were lower in participants with older age or medical risk conditions. After the first booster, older age was associated with lower GMC at 2-6 weeks, higher GMC at 21-25 weeks, and slower waning. GMCs or waning after the first and second boosters (only 60-85) were not associated with medical risk conditions.

Conclusions

Since antibody differences by age and medical risk groups have become small with increasing number of doses, other factors such as disease severity rather than antibody levels are useful for prioritization of additional vaccinations.
Frequency of Variants in Mendelian Alzheimer’s Disease Genes within the Alzheimer’s Disease Sequencing Project (ADSP)
Authors: Wang Dongyu , Scalici Alexandra , Wang Yanbing , Lin Honghuang , Pitsillides Achilleas , Heard-Costa Nancy , Cruchaga Carlos , Ziegemeier Ellen , Bis Joshua C. , Fornage Myriam , Boerwinkle Eric , De Jager Philip L , Wijsman Ellen , Dupuis Josée , Renton Alan E. , Seshadri Sudha , Goate Alison M. ,   Alzheimer’s Disease Neuroimaging Initiative (ADNI),   The Alzheimer’s Disease Sequencing Project, DeStefano Anita L. , Peloso Gina M.
Published: October 2023

Background

Prior studies using the ADSP data examined variants within presenilin-2 (PSEN2), presenilin-1 (PSEN1), and amyloid precursor protein (APP) genes. However, previously-reported clinically-relevant variants and other predicted damaging missense (DM) variants have not been characterized in a newer release of the Alzheimer’s Disease Sequencing Project (ADSP).

Objective

To characterize previously-reported clinically-relevant variants and DM variants inPSEN2, PSEN1, APPwithin the participants from the ADSP.

Methods

We identified rare variants (MAF <1%) previously-reported inPSEN2,PSEN1,andAPPin the available ADSP sample of 14,641 individuals with whole genome sequencing and 16,849 individuals with whole exome sequencing available for research-use (Ntotal= 31,490). We additionally curated variants in these three genes from ClinVar, OMIM, and Alzforum and report carriers of variants in clinical databases as well as predicted DM variants in these genes.

Results

We detected 31 previously-reported clinically-relevant variants with alternate alleles observed within the ADSP: 4 variants inPSEN2, 25 inPSEN1, and 2 inAPP. The overall variant carrier rate for the 31 clinically-relevant variants in the ADSP was 0.3%. We observed that 79.5% of the variant carriers were cases compared to 3.9% were controls. In those with AD, the mean age of onset of AD among carriers of these clinically-relevant variants was 19.6 ± 1.4 years earlier compared with noncarriers (p-value=7.8×10-57).

Conclusion

A small proportion of individuals in the ADSP are carriers of a previously-reported clinically-relevant variant allele for AD and these participants have significantly earlier age of AD onset compared to noncarriers.
Adverse Childhood Events, Mood and Anxiety Disorders, and Substance Dependence: Gene X Environment Effects and Moderated Mediation
Authors: Kranzler Henry R. , Davis Christal N. , Feinn Richard , Jinwala Zeal , Khan Yousef , Oikonomou Ariadni , Silva-Lopez Damaris , Burton Isabel , Dixon Morgan , Milone Jackson , Ramirez Sarah , Shifman Naomi , Levey Daniel , Gelernter Joel , Hartwell Emily E. , Kember Rachel L.
Published: October 2023

Background:Adverse childhood events (ACEs) contribute to the development of mood and anxiety disorders and substance dependence. However, the extent to which these effects are direct or indirect and whether genetic risk moderates them is unclear.Methods:We examined associations among ACEs, mood/anxiety disorders, and substance dependence in 12,668 individuals (44.9% female, 42.5% African American/Black, 42.1% European American/White). We generated latent variables for each phenotype and modeled direct and indirect effects of ACEs on substance dependence, mediated by mood/anxiety disorders (forward or “self-medication” model) and of ACEs on mood/anxiety disorders, mediated by substance dependence (reverse or “substance-induced” model). In a sub-sample, we also generated polygenic scores for substance dependence and mood/anxiety disorder factors, which we tested as moderators in the mediation models.Results:Although there were significant indirect effects in both directions, mediation by mood/anxiety disorders (forward model) was greater than by substance dependence (reverse model). Greater genetic risk for substance dependence was associated with a weaker direct effect of ACEs on substance dependence in both the African- and European-ancestry groups (i.e., gene-environment interaction) and a weaker indirect effect in European-ancestry individuals (i.e., moderated mediation).Conclusion:We found greater evidence that substance dependence results from self-medication of mood/anxiety disorders than that mood/anxiety disorders are substance induced. Among individuals at higher genetic risk for substance dependence who are more likely to develop a dependence diagnosis, ACEs exert less of an effect in promoting that outcome. Following exposure to ACEs, multiple pathways lead to mood/anxiety disorders and substance dependence. Specification of these pathways could inform individually targeted prevention and treatment approaches.
Multiple Treatment Interruptions and Protecting HIV-Specific CD4 T-Cells Enables Durable CTL Response and Viral Control
Authors: Jain Anshika , Canepa Gaspar E. , Liou Mei-Ling , Fledderman Emily L. , Chapoval Andrei I. , Xiao Lingzhi , Mukherjee Ipsita , Galvin Jeffrey A. , Kumar Princy N. , Bordon José , Conant Marcus A. , Boyle Jefferey S.
Published: October 2023

BACKGROUND

The cell and gene therapy product AGT103-T was evaluated (NCT04561258) for safety, immunogenicity, and persistence for up to 180 days post infusion. We sought to investigate the impact following analytical treatment interruptions (ATIs).

METHODS

Six patients suspended their antiretroviral therapy (ART) until their viral load reached 100,000 copies/mL in two successive visits, or their CD4 count fell below 300 cells/μL. We measured the magnitude of viral rebound, the persistence of AGT103-T transduced CD4+ T-cells and the impact on HIV-specific immune responses.

RESULTS

During the ATI, all patients experienced logarithmic viral rebound followed by a 2-5-fold increase in total CD8 counts, that coincided with a rise in HIV-specific CD8 T-cells. This was attributed to the increase in antigen availability and memory recall. Thus, to determine if the immune response generated during this “auto-vaccination” event can contribute to viral suppression upon subsequent exposures, a second ATI was initiated. During the second ATI, the Gag-specific CD8 T cells were either maintained or rose and the peak viremia was substantially decreased with viral set-points ranging from 7,000-25,000 copies/mL. Upon ART resumption, faster viral control was demonstrated without any serious adverse events (SAEs) or drug resistance.

CONCLUSION

AGT103-T gene therapy and multiple ATIs were not associated with SAEs and allowed subjects to establish a low viral set-point with relatively stable CD4 T cell counts. Additionally, multiple ATIs are beneficial for the study design when induction of CD8 T cells is required to establish viral control.

REGISTRATION

ClinicalTrials.govNCT05540964

FUNDING

American Gene Technologies International Inc.
Prospective validation of a predictive non-invasive SNP-based biomarker signature in resectable pancreatic cancer: a study protocol
Authors: Seeger Nico , Gutknecht Stefan , Zschokke Irin , Fleischmann Isabella , Roth Nadja , Metzger Juerg , Weber Markus , Breitenstein Stefan , Grochola Lukasz Filip
Published: October 2023

Background

A growing body of work suggests that inherited genetic variants can be utilized as non-invasive biomarkers to predict cancer-specific patient outcomes and guide therapy after resection of pancreatic ductal adenocarcinoma (PDAC). Specifically, two recent retrospective analyses led to the identification and retrospective validation of three single nucleotide polymorphisms (SNPs) in the CD44 and CHI3L2 genes (SNPrs187115, SNPrs353630, SNPrs684559) genes that can serve as predictive biomarkers to help select patients who are likely to benefit from pancreatic resection. Those SNPs have been shown to associate with an over 2-fold increased risk for tumour-related death in three independent PDAC study cohorts from Europe and the U.S (Hazard ratio (HR) up-to 0.38; p-value up-to 1x10−8).

Methods

In order to translate these retrospective findings into clinical practice, we aim to utilise a cohort of PDAC patients who undergo pancreatic resection in three hospitals in Switzerland to prospectively validate the association of the identified SNPs in the CD44 and CHI3L2 genes with PDAC survival after resection in a controlled clinical setting. All patients with a histopathological diagnosis of PDAC who undergo pancreatic resection and fulfil the inclusion criteria will be included consecutively. The SNP genotypes will be determined using standard genotyping techniques from patient blood samples. For each genotyped locus, log-rank and Cox multivariate regression tests will be performed, accounting for the relevant covariates AJCC-stage and resection-status. Clinical follow-up data will be collected for at least 3 years. Sample size calculation resulted in a number of 150 patients (80% power to detect allelic differences in survival; effect size>2.0 between genotypes; two-sided α-level of 0.05; drop-out rate of 10%; potential additional error margin of 10%).

Discussion

This is the first prospective study of the CD44 and CHI3L2 gene SNP-based biomarker signature in PDAC. A prospective validation of these biomarkers would enable its utilization as a non-invasive, predictive signature of survival after pancreatic resection that is readily available at the time of PDAC diagnosis. The results of this study may lead to improved patient outcomes in resectable PDAC.

Trial registration

Not listed in a registry, because no results of a health care intervention are reported.
Associations of Skeletal Muscle Mass, Muscle Fat Infiltration, Mitochondrial Energetics, and Cardiorespiratory Fitness with Liver Fat Among Older Adults
Authors: Igudesman Daria , Mucinski Justine , Harrison Stephanie , Cawthon Peggy M. , Linge Jennifer , Goodpaster Bret H. , Cummings Steven R. , Hepple Russell T. , Jurczak Michael J. , Kritchevsky Stephen B. , Marcinek David , Coen Paul M. , Corbin Karen D.
Published: October 2023

Background

Muscle mass loss may be associated with liver fat accumulation, yet scientific consensus is lacking and evidence in older adults is scant. It is unclear which muscle characteristics might contribute to this association in older adults.

Methods

We associated comprehensive muscle-related phenotypes including muscle mass normalized to body weight (D3-creatine dilution), muscle fat infiltration (MRI), carbohydrate-supported muscle mitochondrial maximal oxidative phosphorylation (respirometry), and cardiorespiratory fitness (VO2peak) with liver fat among older adults. Linear regression models adjusted for age, gender, technician (respirometry only), daily minutes of moderate to vigorous physical activity, and prediabetes/diabetes status tested main effects and interactions of each independent variable with waist circumference (high: women—≥88 cm, men—≥102 cm) and gender.

Results

Among older adults aged 75 (IQR 73, 79 years; 59.8% women), muscle mass and liver fat were not associated overall but were positively associated among participants with a high waist circumference (β: 25.2; 95%CI 11.7, 40.4;p=.0002; N=362). Muscle fat infiltration and liver fat were positively associated (β: 15.2; 95%CI 6.8, 24.3;p=.0003; N=378). Carbohydrate-supported maximum oxidative phosphorylation and VO2peak (adjusted β: −12.9; 95%CI −20.3, −4.8;p=0.003; N=361) were inversely associated with liver fat; adjustment attenuated the estimate for maximum oxidative phosphorylation although the point estimate remained negative (β: −4.0; 95%CI −11.6, 4.2;p=0.32; N=321).

Conclusions

Skeletal muscle-related characteristics are metabolically relevant factors linked to liver fat in older adults. Future research should confirm our results to determine whether trials targeting mechanisms common to liver and muscle fat accumulation are warranted.