bluuebunny/crossref_metadata_2025 huggingface dataset:
Unveiling a unique macrophage population in exocrine glands sustained by ILC2-derived GM-CSF
Authors: Westermann Frederike , Tuzlak Selma , Kreiner Victor , Bejarano David , Bijnen Mitchell , Cecconi Virginia , van Hove Hannah , Wang Haiting , Litscher Gioana , Ignacio Aline , Lindemann Rachel , Oberbichler Laura , DeFeo Donatella , Liu Zhaoyuan , Kipar Anja , McCoy Kathy , Nixon Iain , Bain Calum C , Schneider Christoph , Tugues Sonia , Greter Melanie , Ginhoux Florent , Schlitzer Andreas , Emmerson Elaine , Becher Burkhard
Published: November 2024

Granulocyte-macrophage colony-stimulating factor (GM-CSF) has a non-redundant role in the emergence and maintenance of alveolar macrophages (AMs). However, its role in developmental and steady-state myelopoiesis outside the lung is largely unexplored.

Scanning through developing tissues using a Fate-map and reporter of GM-CSF mouse strain, we discovered that GM-CSF was produced by type 2 innate lymphoid cells (ILC2s) in the submandibular and sublingual salivary gland (SG) during postnatal development. GM-CSF producing ILC2s foster the development of a hitherto undescribed phagocyte subset, which we named adenophages. Detailed analysis focusing on phenotypic and transcriptional profiling revealed that adenophages display shared aspects of both, macrophages and dendritic cells (DCs). We found them to be homogenously distributed across the SG, but always in close proximity to GM-CSF producing ILC2s and myoepithelial cells. Importantly, adenophages were present throughout all analyzed exocrine glands such as lacrimal glands and mammary glands, and were also identified in human SG sections, indicating a conserved role in exocrine glands across species.
Identification of molecular and functional subtypes using chronic pancreatitis patient-derived organoid models
Authors: Osorio-Vasquez Victoria , Lumibao Jan C. , Peck Kristina L. , Lande Kathryn , Zhu Jonathan , Stamp McKenna , Okhovat Shira R. , Song Hyemin , Ogawa Satoshi , Hsu Jasper , Dai Yang , Rock Angelica , Bottomley Chelsea , Thomas Ethan , Fowler Alexandra , McGriff T’Onj , Larsen Siri , Abdulla Muhamad , Greer Phil , Gibson Jessica , Downes Michael , Evans Ronald , Zou Jingjing , Lowy Andrew M. , Whitcomb David C. , White Rebekah , Bellin Melena , Tiriac Herve , Engle Dannielle D.
Published: November 2024

Background and Aims

Chronic pancreatitis (CP) affects more than 200,000 Americans and 1 million individuals world wide, but treatment generally focuses on supportive care like pain management. 28-80% of CP cases are idiopathic and 10-15% are hereditary with mutations in PRSS1, SPINK1, CFTR, and other genes. Developing human models of pancreatitis to understand the drivers of the disease and targeting key players in this disease will provide novel therapeutic approaches for these patients who have limited options.

Methods

Utilizing patient samples from surgical resections or TPIAT procedures we have generated a first-of-its-kind human CP patient derived organoid (PDO) biobank. This biobank is representative of hereditary mutations found across patients, includes idiopathic cases, and histologically recapitulates features of this disease. Genetic concordance was determined between PDO and primary specimens using whole genome sequencing. RNAseq and cytokine analysis was conducted on PDO to determine inflammatory features of this model. Forskolin induced swelling assays were conducted to determine the function of CFTR in PDO models.

Results

There is a 98% concordance between PDO and primary tissue specimens showing the recapitulation of patient genotypes in our model. RNA-seq revealed that CP organoids are transcriptionally distinct from normal pancreas organoids and identified three distinct subtypes of CP that are driven by transcriptional features. Utilizing the PDO model, we identified a high prevalence of ductal CFTR dysfunction, which could be restored using a combination of CFTR correctors and potentiators.

Conclusions

There are three subtypes of CP that require further study to employ targeted therapeutics against these drivers. hCP PDO are a model that can be used to assess CFTR function and correction providing evidence for these drugs to be used in CP patients.
Structural basis of pseudoGTPase-mediated protein-protein interactions
Authors: Wang Bing , Yang Rui , Wan Chun , Tian Yuan , Wu Jingyi , Roy Sayantan , Li Suzhao , Shen Jingshi , Yin Qian
Published: November 2024

GTPases regulate various cellular processes through conformational changes triggered by GTP or GDP binding. Recently, pseudoGTPases, the catalytically inactive counterparts of GTPases, have been identified across species from bacteria to human, although their functions and mechanisms remain unexplored. In this study, we demonstrate that the N-terminal region of the assembly chaperone AAGAB is a type i pseudoGTPase using biochemistry and X-ray crystallography. Furthermore, we discovered that the AAGAB pseudoGTPase domain (psGD) interacts with the σ subunits of AP1 and AP2 adaptor complexes, heterotetrameric complexes involved in clathrin-mediated membrane trafficking. AAGAB psGD engages the σ subunits via a unique interface distinct from the conventional GTPase interacting regions. Further biochemical and cell-based assays confirmed the crucial role of the newly identified interface in binding and membrane trafficking. Collectively, our results establish AAGAB pseudoGTPase domain as a critical protein-protein interaction module. These findings offer new insight into the structural basis and molecular mechanisms of pseudoGTPases.

Highlights

AAGAB N-terminal region is a pseudoGTPase

AAGAB pseudoGTPase domain interacts with and stabilizes AP1 and AP2 σ subunits

The crystal structure of AAGAB psGD:AP1σ3 is the first reported psGD complex structure, revealing a unique interface independent of guanine nucleotide regulation

The psGD:AP1σ3 structure offers mechanistic insights into σ subunits stabilization and protection through adaptor complex assembly
Regulation of heterosis-associated gene expression complementation in maize hybrids
Authors: Pitz Marion , Baldauf Jutta , Piepho Hans-Peter , Yu Peng , Schoof Heiko , Mason Annaliese S. , Li Guoliang , Hochholdinger Frank
Published: November 2024

The dominance model of heterosis explains the superiority of F1-hybrids via the complementation of unfavorable by beneficial alleles in many genes. Consistent with this model, genes active in only one parent and the hybrid display single-parent expression (SPE) complementation. Here we demonstrated, that SPE can explain up to 29% of heterotic variance in maize (Zea maysL.). Moreover, expression quantitative trait loci (eQTL) revealed, that the genotype of the active parent determines the regulation mode of SPE patterns incisortrans, which might explain how phylogenetic distance translates to transcriptomic diversity and heterosis in hybrids. Furthermore, we showed that most eQTL are located in heterozygous regions of the genome and that atranseQTL controls the activity of a SPE gene which regulates lateral root density in hybrids. We anticipate that our study will stimulate further research elucidating the regulation and molecular mechanisms underlying heterosis.
Gene Therapy with the N-terminal Fragment of Nav1.5 for Cardiac Channelopathies: A Novel Transcomplementation Mechanism Potentiating the Cardiac Sodium Current
Authors: Gizon Marie , Ferrand Marine C. , Fontaine Vincent , Mougenot Nathalie , Laporte Pierre-Léo , Gaborit Nathalie , Extramiana Fabrice , Baró Isabelle , Guicheney Pascale , Charpentier Flavien , Doisne Nicolas , Neyroud Nathalie
Published: November 2024

BACKGROUND

Cardiac channelopathies, caused by mutations in ion-channel genes, can lead to sudden cardiac death (SCD)viaventricular arrhythmias. Brugada syndrome (BrS) is a rare inherited channelopathy characterized by a unique ECG pattern and a high incidence of ventricular fibrillation leading to SCD in the absence of structural heart defects. The main gene responsible for 20-25% of BrS cases isSCN5A, encoding the cardiac sodium channel α-subunit Nav1.5, which carries the sodium current (INa) responsible for the rapid depolarization phase of the action potential (AP). While current treatments do not target the genetic cause of channelopathies, this study explores the therapeutic potential of overexpressing the N-terminal region of Nav1.5 (Nter) to restore electrical activity by rescuingINa, in the context ofSCN5Adeficiency.

METHODS

We overexpressed the Nter peptide using viral vectors inScn5a+/-mice, in CRISPR/Cas9 edited-SCN5A+/-cardiomyocytes derived from induced-pluripotent stem cells (iPSC-CMs) and in BrS patient iPSC-CMs. We assessed molecular and functional effects of Nter overexpressionin vitroandin vivoby measuring Nav1.5 subcellular expression and electrophysiological activity and by recording ECGs and arrhythmias.

RESULTS

WhereasScn5a+/-mice showed an impairedINaassociated with a slowed-cardiac conduction characteristic of the BrS phenotype, cardiac-specific overexpression of Nter corrected AP parameters by restoringINadensity inScn5a+/-mouse cardiomyocytes. This increase inINadensity was caused by a translocation of Nav1.5 to the cell membrane in Nter-overexpressing mice. Most importantly, Nter overexpression normalized atrioventricular and ventricular conduction and protectedScn5a+/-mice from arrhythmias triggered by programmed electrical stimulation. Similarly, Nter overexpression inSCN5A+/-human iPSC-CMs led to a 2-fold increase in Nav1.5 cell-surface expression, resulting in normalization ofINaand AP parameters and abolition of early after depolarizations observed during spontaneous AP recordings. Similar results were obtained in iPSC-CMs derived from a BrS patient, confirming the potential of this therapy in human models.

CONCLUSIONS

This study identified a novel therapeutic peptide effective in restoring cardiac excitability in animal and cellular models of BrS, paving the way for future development of therapies for life-threatening arrhythmias in patients withSCN5Adeficiency.
FroM Superstring to Indexing: a space-efficient index for unconstrained k-mer sets using the Masked Burrows-Wheeler Transform (MBWT)
Authors: Sladký Ondřej , Veselý Pavel , Břinda Karel
Published: November 2024

The exponential growth of DNA sequencing data calls for efficient solutions for storing and querying large-scale 𝑘-mer sets. While recent indexing approaches use spectrum-preserving string sets (SPSS), full-text indexes, or hashing, they often impose structural constraints or demand extensive parameter tuning, limiting their usability across different datasets and data types. Here, we propose FMSI, a minimally parametrized, highly space-efficient membership index and compressed dictionary for arbitrary 𝑘-mer sets. FMSI combines approximated shortest superstrings with the Masked Burrows-Wheeler Transform (MBWT). Unlike traditional methods, FMSI operates without predefined assumptions on 𝑘-mer overlap patterns but exploits them when available. We demonstrate that FMSI offers superior memory efficiency over established indexes such as SSHash, SBWT, and CBL, with space savings up to 2-3x compared to the second-best competitor, depending on the dataset, 𝑘-mer size, sampling, and genomic complexity, while supporting fast membership and dictionary queries. Overall, this work establishes superstring-based indexing as a highly general, flexible, and scalable approach for genomic data, with direct applications in pangenomics, metagenomics, and large-scale genomic databases.
Crosstalk Between Drought-Induced ROS Regulation and Resistance to Xanthomonas oryzae Infection in Rice Plants
Authors: Ramu Dhruv , Reddy B. R. Brahmesh , Sheshshayee M. S. , Kumar M. K. Prasanna
Published: November 2024

Abstract

This study investigates the resilience of two genotypes ofOryza sativa(rice) with varying levels of tolerance to drought stress, focusing on their production of reactive oxygen species (ROS) and chlorophyll retention when exposed to Xanthomonas oryzae infection. A total of 36 high ATT (AC 39000) and low ATT (BPT5204) plants were subjected to three drought treatments: 100% field capacity (control), gradual drought (reduction to 50% field capacity over 10 days), and rapid drought (immediate reduction to 50%). ROS production was quantified using Evans Blue staining and thiobarbituric acid reactive substances (TBARS) assays, while chlorophyll content was measured using the Arnon method. Membrane damage was higher in the control and rapid stress groups (971 and 1053 ng respectively) compared to gradual drought stress (848.5 ng) on day 12. High-tolerance genotypes demonstrated superior ROS regulation under gradual drought conditions, with the Evans Blue content exceeding that of low-tolerance genotypes by 13 ng. Similarly, chlorophyll retention was significantly higher (p = 0.0005) in high tolerance genotypes (1.166 mg · g−1FW) compared to low tolerance genotypes (0.966 mg · g−1FW). The results indicate that gradual drought stress increases resilience to bacterial infection through enhanced ROS-scavenging mechanisms, which is accentuated in the High ATT genotype, allowing for the development of dual resistant rice varieties capable of withstanding both abiotic and biotic stresses.
BTS: scalable Bayesian Tissue Score for prioritizing GWAS variants and their functional contexts across omics data
Authors: Kuksa Pavel P. , Ionita Matei , Carter Luke , Cifello Jeffrey , Clark Kaylyn , Valladares Otto , Leung Yuk Yee , Wang Li-San
Published: November 2024

Motivation

Summary statistics from genome-wide association studies (GWAS) are widely used in fine-mapping and colocalization analyses to identify causal variants and their enrichment in functional contexts, such as affected cell types and genomic features. With the expansion of functional genomic (FG) datasets, which now include hundreds of thousands of tracks across various cell and tissue types, it is critical to establish scalable algorithms integrating thousands of diverse FG annotations with GWAS results.

Results

We propose BTS (Bayesian Tissue Score), a novel, highly efficient algorithm uniquely designed for 1) identifying affected cell types and functional elements (context-mapping) and 2) fine-mapping potentially causal variants in a context-specific manner using large collections of cell type-specific FG annotation tracks. BTS leverages GWAS summary statistics and annotation-specific Bayesian models to analyze genome-wide annotation tracks, including enhancers, open chromatin, and histone marks. We evaluated BTS on GWAS summary statistics for immune and cardiovascular traits, such as Inflammatory Bowel Disease (IBD), Rheumatoid Arthritis (RA), Systemic Lupus Erythematosus (SLE), and Coronary Artery Disease (CAD). Our results demonstrate that BTS is over100xmore efficient in estimating functional annotation effects and context-specific variant fine-mapping compared to existing methods. Importantly, this large-scale Bayesian approach prioritizes both known and novel annotations, cell types, genomic regions, and variants and provides valuable biological insights into the functional contexts of these diseases.

Availability and implementation

Docker image is available athttps://hub.docker.com/r/wanglab/btswith pre-installed BTS R package (https://bitbucket.org/wanglab-upenn/BTS-R) and BTS GWAS summary statistics analysis pipeline (https://bitbucket.org/wanglab-upenn/bts-pipeline).
Lifespan in rodents with MYT1L heterozygous mutation
Authors: Schreiber Allyson , Swift Raylynn G. , Wilson Leslie , Kroll Kristen L. , Dougherty Joseph D. , Maloney Susan E.
Published: November 2024

MYT1L syndrome is a newly recognized disorder characterized by intellectual disability, speech and motor delay, neuroendocrine disruptions, ADHD, and autism. In order to study this gene and its association with these phenotypes, our lab recently created aMyt1lheterozygous mutant mouse inspired by a clinically relevant mutation. This model recapitulates several of the physical and neurologic abnormalities seen in humans with MYT1L syndrome, such as weight gain, microcephaly, and behavioral disruptions. The majority of patients with this syndrome are young, and little is known about the impact of age on health and mortality in these patients. Using aMyt1lmutant mouse, we examined the impact ofMyt1lmutation on body weights, lifespan, and histopathology findings of mice at the end of life. This cohort of heterozygous mice demonstrated increased body weight across the lifespan, however there was no significant difference in lifespan, apparent cause of death, or end of life histopathological findings betweenMyt1lheterozygous and wildtype mice. These findings suggest whileMyt1lheterozygous mutation may influence overall brain development, it does not strongly impact other organ systems in the body over time.
PlacentalhIGF1nanoparticle gene therapy in guinea pigs ameliorates fetal growth restriction-associated changes in hepatic lipid and glucose metabolism-related signaling pathways in a fetal sex-specific manner
Authors: Davenport Baylea N , Williams Alyssa , Regnault Timothy RH , Jones Helen N , Wilson Rebecca L
Published: November 2024

Fetal development in an adverse in utero environment significantly increases the risk of developing metabolic diseases in later life, including dyslipidemia, non-alcoholic fatty liver diseases and diabetes. The aim of this study was to determine whether improving the in utero fetal growth environment with a placental nanoparticle gene therapy would ameliorate fetal growth restriction (FGR)-associated dysregulation of fetal hepatic lipid and glucose metabolism-related signaling pathways. Using the guinea pig maternal nutrient restriction (MNR) model of placental insufficiency and FGR, placenta efficiency was significantly improved following three administrations of a non-viral polymer-based nanoparticle gene therapy to the placenta from mid-pregnancy (gestational day 35) until gestational day 52. The nanoparticle gene therapy transiently increased expression ofhuman insulin-like growth factor 1(hIGF1) in placenta trophoblast. Fetal liver tissue was collected near-term at gestational day 60. Fetal sex specific differences in liver gene and protein expression of pro-fibrosis and glucose metabolism-related factors were demonstrated in sham-treated FGR fetuses but not observed in FGR fetuses who received placentalhIGF1nanoparticle treatment. Increased plasma bilirubin, and indirect measure of hepatic activity, was also increased with placentalhIGF1nanoparticle treatment. We speculate that the changes in liver gene and protein expression and increased liver activity that result in similar expression profiles to appropriately growing Control fetuses might confer protection against increased susceptibility to aberrant liver physiology in later-life. Overall, this work opens avenues for future research assessing the translational prospect of mitigating FGR-induced metabolic derangements.

NEW AND NOTEWORTHY

A placenta-specific non-viral polymer-based nanoparticle gene therapy that improves placenta nutrient transport and near-term fetal weight ameliorates growth restriction-associated changes to fetal liver activity, and cholesterol and glucose/nutrient homeostasis genes/proteins that might confer protection against increased susceptibility to aberrant liver physiology in later-life. This knowledge may have implications towards removing predispositions that increase the risk of metabolic diseases including diabetes, dyslipidemia and non-alcoholic fatty liver disease in later life.
HMGB1 mediates macrophage recruitment and regional intervertebral disc tissue functional and mechanical property changes following injury
Authors: Burt Kevin G. , Kim Min Kyu M. , Viola Dan C. , Genualdi Joseph R. , Marciano Gerard F. , Chahine Nadeen O.
Published: November 2024

Objective

Frequently evaluated in musculoskeletal disease, damage associated molecular patterns (DAMPs) respond to tissue damage and cellular stress by facilitating an inflammatory response via macrophage activation and broad inflammatory pathway activation. In the context of disc degeneration (DD), high mobility group box 1 (HMGB1), a potent intracellular DAMP, is seen to be increased within severely degenerated human IVDs and to directly mediate inflammatory responses within disc cellsin vitro. To further understand how HMGB1 mediated inflammation influences DD, this study evaluated the possible protective effect of an HMGB1 knockout on DD pathology following injury.

Methods

Using a needle puncture injury model in murine caudal IVDs we evaluated DD pathology within an IVD specificHmgb1knockout (KO) model. Structural and compositional changes in IVD cellularity, histopathology, disc height, and biomechanics were evaluated in addition to an assessment of disc inflammation via gene expression and macrophage presence throughout the course of degeneration.

Results

HMGB1 expression robustly increased shortly following needle puncture injury and elevated levels were sustained up to 28-days post injury both in injured IVDs and in the IVDs adjacent to the level of injury. IVD specificHmgb1KO mice had an increased disc height following injury both at the injured and adjacent to injury level compared to injured WT IVDs. Hmgb1 KO also protected against tissue mechanical property losses at both the injured (dynamic modulus) and adjacent to injury level (dynamic modulus, creep, and equilibrium modulus) compared to injured WT IVDs, however there was no significant effect on histopathologic scores post injury.Hmgb1KO resulted in alterations in macrophage (F4/80+) recruitment to the IVD post injuryin vivo.A lower macrophage migration was also observedin vitroin response to the secretome of an injuredHmgb1KO IVD compared to injured WT IVDs.Hmgb1KO had no effect on inflammatory gene expression changes following injury within adjacent to injury level or injury level IVDs.

Conclusion

Overall findings indicate that HMGB1 is upregulated regionally, at both the injured level and at the level adjacent to injury. Results suggest that HMGB1 plays a role in mediating structural, biomechanical, and inflammatory responses to IVD injury and serves as a potent chemoattractant, mediating macrophage recruitment to the IVD and overall migratory function.
A novelin-vitromodel of the bone marrow microenvironment in AML identifies CD44 and Focal Adhesion Kinase as therapeutic targets to reverse cell adhesion-mediated drug resistance
Authors: Ladikou Eleni Ε. , Sharp Kim , Simoes Fabio A. , Jones John , Burley Thomas , Stott Lauren , Vareli Aimilia , Kennedy Emma , Vause Sophie , Chevassut Timothy , Devi Amarpreet , Ashworth Iona , Ross David , Hartmann Tanja Nicole , Mitchell Simon , Pepper Chris , Best Giles , Pepper Andrea G.S.
Published: November 2024

Acute myeloid leukemia (AML) is an aggressive neoplasm. Although most patients respond to induction therapy, they commonly relapse due to recurrent disease in the bone marrow microenvironment (BMME). So, disruption of the BMME, releasing tumour cells into the peripheral circulation, has therapeutic potential. Using both primary donor AML cells and cell lines, we developed anin-vitroco-culture model of the AML BMME. We used this model to identify the most effective agent(s) to block AML cell adherence and reverse adhesion-mediated treatment resistanc E. We identified anti-CD44 treatment significantly increased the efficacy of cytarabine. However, some AML cells remained adhered, and transcriptional analysis identified focal adhesion kinase (FAK) signalling as a contributing factor; adhered cells showed elevated FAK phosphorylation that was reduced by the FAK inhibitor, defactinib. Importantly, we demonstrated that anti-CD44 and defactinib were highly synergistic at diminishing adhesion of the most primitive CD34highAML cells in primary autologous co-cultures. Taken together, we identified anti-CD44 and defactinib as a promising therapeutic combination to release AML cells from the chemoprotective AML BMME. As anti-CD44 is already available as a recombinant humanised monoclonal antibody, the combination of this agent with defactinib could be rapidly tested in AML clinical trials.
Unanchored ubiquitin chains promote the non-canonical inflammasome via UBXN1
Authors: Yang Duomeng , Cahoon Jason G. , Geng Tingting , Wang Chengliang , Harrison Andrew G. , Teran Evelyn , Wang Yanlin , Vella Anthony T. , Rathinam Vijay A. , Ruan Jianbin , Wang Penghua
Published: November 2024

Ubiquitination is a major posttranslational covalent modification that regulates numerous cellular processes including inflammasome signaling. Cells also contain unanchored ubiquitin chains (polyUb) that bind protein targets non-covalently, but their physiological functions in immunity have been appreciated only recently. Here, we report that ubiquitin regulatory x domain-containing protein 1 (UBXN1) activates the noncanonical inflammasome via unanchored Lysin (K) 48- or 63-linked polyUb. UBXN1 deficiency impairs the activation of caspase-4/11, secretion of inflammasome-dependent cytokines and pyroptosis in response to intracellular lipopolysaccharide (LPS). UBXN1-deficient mice are protected from LPS- and cecal-ligation-and-puncture-induced sepsis, evidenced by reduced mortality and systemic inflammation, compared to UBXN1-sufficient littermates. Mechanistically, UBXN1 together with unanchored K48/63-linked polyUb bind caspase-4/11, the intracellular sensors of LPS, and promote their assembly and activation. Depleting cellular unanchored polyUb with recombinant ubiquitin-specific proteinase 5 (USP5) reduces UBXN1 binding to caspase-4/11 and inflammasome signaling, while USP5 inhibitors enhance pyroptosis in an UBXN1-dependent manner. Thus, this study identifies a critical UBXN1-dependent posttranslational mechanism involved in noncanonical inflammasome activation and UBXN1 as a potential therapeutic target for sepsis and advances a fundamental understanding of unanchored polyUb biology.
N-Aldehyde-Modified Phosphatidylethanolamines generated by lipid peroxidation are robust substrates ofN-Acyl Phosphatidylethanolamine Phospholipase D
Authors: Fadaei Reza , Bernstein Annie C. , Jenkins Andrew N. , Pickens Allison G. , Zarrow Jonah E. , Alli-Oluwafuyi Abdul-Musawwir , Tallman Keri A. , Davies Sean S.
Published: November 2024

N-acyl phosphatidylethanolamine-hydrolyzing phospholipase D (NAPE-PLD) hydrolyzes phosphatidylethanolamines (PE) where the headgroup nitrogen has been enzymatically modified with acyl chains of four carbons or longer (N-acyl-PEs or NAPEs). The nitrogen headgroup of PE can also be non-enzymatically modified by reactive lipid aldehydes, thus formingN-aldehyde modified-PEs (NALPEs). Some NALPEs such asN-carboxyacyl-PEs are linked to PE via amide bonds similar to NAPEs, but others are linked by imine, pyrrole, or lactam moieties. Whether NAPE-PLD can hydrolyze NALPEs was unknown. We therefore characterized the major NALPE species formed during lipid peroxidation of arachidonic acid and linoleic acid and generated various NALPEs for characterization of their sensitivity to NAPE-PLD hydrolysis by reacting synthesized aldehydes with PE. We found that NAPE-PLD could act on NALPEs of various lengths and linkage types including those derived from PE modified by malondialdehyde (N-MDA-PE), butane dialdehyde (N-BDA-PE), 4-hydroxynonenal (N-HNE-PE), 4-oxo-nonenal (N-ONE-PE), 9-keto-12-oxo-dodecenoic acid (N-KODA-PE), and 15-E2-isolevuglandin (N-IsoLG-PE). To assess the relative preference of NAPE-PLD for various NALPEs versus its canonical NAPE substrates, we generated a substrate mixture containing roughly equimolar concentrations of the seven NALPEs as well as two NAPEs (N-palmitoyl-PE andN-linoleoyl-PE) and measured their rate of hydrolysis. Several NALPE species, including theN-HNE-PE pyrrole species, were hydrolyzed at a similar rate asN-linoleoyl-PE and many of the other NALPEs showed intermediate rates of hydrolysis. These results significantly expand the substrate repertoire of NAPE-PLD and suggest that it may play an important role in clearing products of lipid peroxidation in addition to its established role in the biosynthesis ofN-acyl-ethanolamines.
A forward-engineered muscle tissue driven soft robotic swimmer
Authors: Drennan William Cartwright , Aydin Onur , Emon Bashar , Li Zhengwei , JOY MD SADDAM HOSSAIN , Barishman Alexandra , Kim Yelim , Wei Margaret , Denham Danette , Carrillo Annika , Saif M. Taher A.
Published: November 2024

The integration of biological actuators with soft scaffolds has led to biohybrid robots including microscale flagellate-like swimmers which generate thrust by waving their flagella-like tails. However, they achieve swimming speeds of only 0.014 body lengths per minute, Reynolds number (Re) ~ 0.001, which is much slower than natural flagellates (O(100 - 1000) body lengths per minute). To investigate this, we applied theoretical and experimental methods, including fabrication of a swimmer that converts muscle contractions into large angular tail displacements, reaching swimming speeds of 86.8 μm/s (0.58 body lengths per minute), surpassing low-Re predictions. Swimming dynamics sharply transition from a low-Re (~ 0.001) to an intermediate-Re (~ 0.1) regime when the actuation angle exceeded 4°. We used the swimmer to study the ability of muscle to adapt to mechanical stiffness and the beneficial effects of neuromuscular coculture on muscle development. These insights into mechanical and chemical cues will help optimize future biobots.
A novel miniaturized filamentous phagemid as a gene delivery vehicle to target mammalian cells
Authors: Wong Shirley , Jimenez Salma , Pushparajah Deborah , Prakash Rohini , Slavcev Roderick
Published: November 2024

The filamentous phage M13 is a single-stranded DNA phage with several attractive characteristics for gene delivery, including a capsid amenable to the display of foreign peptides, and a simple well-characterized genome that is easy to genetically modify. Previously, we constructed a DNA minivector based on M13 (a miniphagemid), which minimized the inflammatory bacterial and phage DNA content in the vector. In general, DNA minivectors, devoid of their prokaryotic components have shown improved gene transfer and safety. We examined the miniphagemid’s capacity forin vitrotransgene delivery to target cells through phage display of epidermal growth factor to target its cognate receptor. The absence of the prokaryotic backbone and smaller vector size conferred by the miniphagemid was associated with improved transgene expression for purified single-stranded phagemid DNA and phagemid virion particles. We further engineered this system to enhance packaging of DNA minivectors by deletion of the packaging signal within the helper plasmid, used to produce miniphagemids, and observed improved phage-mediated gene expression in mammalian cells. Overall, here, we present a set of novel transgene delivery vectors that combine cell-targeting ligand display and vector minimization. This platform showcases the flexibility of M13 as a gene delivery tool with immense therapeutic potential.
AnE. coli-based platform for the production and assembly of anellovirus vectors
Authors: Prakash Rohini , Slavcev Roderick
Published: November 2024

Gene therapy offers immense potential for treating various diseases, including cancer, immunodeficiencies, and cardiovascular conditions. The efficacy of gene therapy (GT) largely depends on the vector used for gene delivery. Viral vectors, while effective, pose risks including insertional mutagenesis, immune responses, and high manufacturing costs. Non-viral vectors, although safer and easier to produce, often exhibit lower transfection efficiency and weaker transgene expression. This highlights the need for novel, more efficient vectors. Among emerging strategies, bacteriophages are gaining attention as promising GT delivery vehicles due to their adaptability and safety profile. Filamentous phages like M13 have demonstrated potential as targeted gene delivery vectors. This study proposes constructing a single-stranded DNA (ssDNA) phage-based vector incorporating a eukaryotic gene cassette. By leveraging Ff phage replication mechanisms inE. coli, the study explores encapsidating ssDNA within anellovirus capsids. These small, ssDNA viruses, known for their ability to transfect diverse tissues, offer a safer alternative to conventional viral vectors. Through successful expression and assembly of anellovirus capsid proteins, ssDNA viral particles were producedex vivo. This innovativeE. coli-based anellovirus-phagemid system provides a promising, cost-effective platform for developing next-generation viral vectors in gene therapy.
Deficiency of mitophagy mediator Parkin in aortic smooth muscle cells exacerbates abdominal aortic aneurysm
Authors: Wang Hui , Kazaleh Mattew , Gioscia-Ryan Rachel , Millar Jessica , Temprano-Sagrera Gerard , Wood Sherri , Van Den Bergh Fran , Blin Muriel G. , Wragg Kathleen M. , Luna Adrian , Hawkins Robert B. , Soleimanpour Scott A. , Sabater-Lleal Maria , Shu Chang , Beard Daniel A. , Ailawadi Gorav , Deng Jane C. , Goldstein Daniel R. , Salmon Morgan
Published: November 2024

Abdominal aortic aneurysms (AAAs) are a degenerative aortic disease and associated with hallmarks of aging, such as mitophagy. Despite this, the exact associations among mitophagy, aging, and AAA progression remain unknown. In our study, gene expression analysis of human AAA tissue revealed downregulation of mitophagy pathways, mitochondrial structure, and function-related proteins. Human proteomic analyses identified decreased levels of mitophagy mediators PINK1 and Parkin. Aged mice and, separately, a murine AAA model showed reduced mitophagy in aortic vascular smooth muscle cells (VSMCs) and PINK1 and Parkin expression. Parkin knockdown in VSMCs aggravated AAA dilation in murine models, with elevated mitochondrial ROS and impaired mitochondrial function. Importantly, inhibiting USP30, an antagonist of the PINK1/Parkin pathway, increased mitophagy in VSMCs, improved mitochondrial function, and reduced AAA incidence and growth. Our study elucidates a critical mechanism that proposes AAAs as an age-associated disease with altered mitophagy, introducing new potential therapeutic approaches.
Olfactory Training: Recommendation Frequency Amongst Rhinologists
Authors: Thomas Sherina R. , Nguyenkhoa Vincent L. , Mattos Jose L. , Munger Steven D.
Published: November 2024

Despite the prevalence and health impact of olfactory dysfunction (OD), therapeutic options remain limited. One potential therapy is olfactory training (OT), where patients repeatedly sniff a small set of odors over several weeks with the goal of improving olfactory function. Although double-blinded, placebo-controlled clinical trials supporting the efficacy of OT are lacking, anecdotal evidence suggests that the procedure is widely recommended to patients with anosmia or other olfactory disorders. To better understand the adoption of OT in clinical practice, we recruited a convenience sample of 95 rhinologists and other otolaryngologists to complete an online survey that assessed how often, and under what conditions, they recommend OT to their patients with OD. Our survey revealed that the majority of responding otolaryngologists (93.7%) routinely recommend OT. Further, they recommend OT more often for quantitative than for qualitative disorders, and most frequently for post-viral and idiopathic OD etiologies. These findings support the perception that OT is commonly recommended in otolaryngological practice for the treatment of OD.

Key Points

Most surveyed otolaryngologists routinely recommend olfactory training (OT).

OT is recommended more often for quantitative than qualitative olfactory dysfunction (OD).

OT is most often recommended for post-viral and idiopathic OD etiologies.
Utilizing artificial intelligence-driven virtual standardized pediatric patients to enhance the capabilities of primary healthcare doctors in China for managing common pediatric diseases: a study protocol for a randomized controlled trial
Authors: Mao Yanna , Luo Huanyuan , Cai Yiyuan , Huang Wanqing , Fang Fang , Lu Yue , Chen Xin , Zhao Qing , Wang Duolao , He Hua , Wang Xiaohui , Zhang Dexing , Li Guobao , Zhang Yichi , Xu Dong (Roman) , Zhao Yao
Published: November 2024

Background

China’s healthcare system for children faces significant challenges, particularly due to the limited pediatric service capacity of primary healthcare institutions. A shortage of effective and accessible training tools for primary care doctors further hinders progress in addressing this gap. Technological advancements, especially in artificial intelligence, offer a potential solution to improve pediatric care. Artificial intelligence-driven virtual standardized patients (VSPs), leveraging internet and virtual simulation technologies, simulate clinical cases with specific disease characteristics, providing an innovative, efficient, and flexible training method. VSPs are increasingly utilized in medical education, clinical reasoning, and licensure exams. This study focuses on using VSPs to improve the management of common pediatric conditions, which are major health concerns for children and impose significant psychological and financial burdens on families.

Methods

This study will involve a three-arm randomized controlled trial to evaluate the effectiveness of a virtual pediatric standardized patient platform in enhancing primary care doctors’ management of common pediatric diseases. At least 459 participants, including general practitioners, internal medicine practitioners, surgeons, and pediatricians from more than 10 provinces across China, will be randomly assigned to one of three groups: the virtual patient platform group, the case teaching manual group, or the case teaching video group. Five virtual patient cases covering pneumococcal pneumonia, rotavirus enteritis with hypovolemic shock, hand-foot-and-mouth disease, acute appendicitis, and respiratory failure will be developed, along with corresponding case teaching materials. After a two-week learning period, participants’ disease management abilities will be assessed using clinical vignettes. The primary outcome is adherence to best clinical practice guidelines, categorized into full adherence, partial adherence, and nonadherence.

Discussion

This study aims to leverage artificial intelligence for capacity enhancement, targeting the shortcomings of primary care pediatrics and using VSP to help enhance primary care pediatrics capacity. It is a randomized controlled trial involving over 300 primary healthcare institutions across more than 10 provinces in China, ensuring broad and representative participation from both developed and underdeveloped regions.

Trial registration

Chictr.org.cn,ChiCTR2400085808. Registered on 19 June 2024.
Monkeypox virus pangenomics reveals determinants of clade Ib
Authors: Sganzerla Martinez Gustavo , Kumar Anuj , Kiganda-Lusamaki Eddy , Dutt Mansi , Wawina Bokalanga Tony , Toloue Ali , Francisca Muyembe Mawete , Makangara-Cigolo Jean Claude , Kelvin Patricia , Adrienne Amuri Aziza , Richardson Christopher D , Lokilo Emmanuel , Luakanda Gradi , Ayouba Ahidjo , Rimoin Anne W. , Mukadi-Bamuleka Daniel , Delaporte Eric , Pilarowski Genay , Kindrachuk Jason , Liesenborghs Laurens , Hensley Lisa E. , Subissi Lorenzo , Peeters Martine , Hoff Nicole A. , Tshiani-Mbaya Olivier , Tessema Sofonias , Muyembe Tamfum Jean-Jaques , Ahuka-Mundeke Steve , Kelvin Alyson A , Archibald John M , Mbala-Kingebeni Placide , Flores-Giron Luis , Kelvin David J
Published: November 2024

Mpox, formerly monkeypox, is a viral zoonotic disease caused by the monkeypox virus (MPXV). MPXV, which is taxonomically divided into clades I and II, was declared a Public Health Emergency of International Concern for the second time in August 2024 due to rapid geographic expansion of clade I viruses including the newly identified clade Ib [1]. With a unique set of genomic mutations and sustained human-to-human transmission, clade Ib has rapidly spread throughout the eastern Democratic Republic of the Congo as well as neighboring non-endemic regions outside the African continent [2–6]. Currently, there is a lack of comparative genomic data with which to address potential zoonotic transmissibility and pathobiology of clade Ib. Here we show MPXV clades I and II share a core genome composed of 68 protein-coding genes which are common in the genomes of other poxviruses such as camelpox, cowpox, and vaccinia. The first documented and all subsequently examined isolates of clade Ib lack the gene pairOPG032andOPG033, which encode the complement control protein (a vaccinia ortholog associated with virulence), and a Kelch-like protein, respectively. The genomic rearrangement of MPXV suggests a functional evolution that might play an important role in the pathobiology of the novel clade Ib virus. Our results lay the groundwork to exploit the genomic of elements of MPXV as potential targets for therapeutics development/repurposing, vaccine design, and molecular diagnostic expansion, as well as to uncover the viral diversity, and zoonosis of MPXV.
SCD-Tron: Leveraging Large Clinical Language Model for Early Detection of Cognitive Decline from Electronic Health Records
Authors: Guan Hao , Novoa-Laurentiev John , Zhou Li
Published: November 2024

Background

Early detection of cognitive decline during the preclinical stage of Alzheimer’s disease is crucial for timely intervention and treatment. Clinical notes, often found in unstructured electronic health records (EHRs), contain valuable information that can aid in the early identification of cognitive decline. In this study, we utilize advanced large clinical language models, fine-tuned on clinical notes, to improve the early detection of cognitive decline.

Methods

We collected clinical notes from 2,166 patients spanning the 4 years preceding their initial mild cognitive impairment (MCI) diagnosis from the Enterprise Data Warehouse (EDW) of Mass General Brigham (MGB). To train the model, we developed SCD-Tron, a large clinical language model on 4,949 note sections labeled by experts. For evaluation, the trained model was applied to 1,996 independent note sections to assess its performance on real-world unstructured clinical data. Additionally, we used explainable AI techniques, specifically SHAP values, to interpret the models predictions and provide insight into the most influential features. Error analysis was also facilitated to further analyze the model’s prediction.

Results

SCD-Tron significantly outperforms baseline models, achieving notable improvements in precision, recall, and AUC metrics for detecting Subjective Cognitive Decline (SCD). Tested on many real-world clinical notes, SCD-Tron demonstrated high sensitivity with only one false negative, crucial for clinical applications prioritizing early and accurate SCD detection. SHAP-based interpretability analysis highlighted key textual features contributing to model predictions, supporting transparency and clinician understanding.

Conclusion

SCD-Tron offers a novel approach to early cognitive decline detection by applying large clinical language models to unstructured EHR data. Pretrained on real-world clinical notes, it accurately identifies early cognitive decline and integrates SHAP for interpretability, enhancing transparency in predictions.
The Relationship Between Biological Aging with Interdisciplinary Health Indicators: A Scoping Review
Authors: Reeves Jennifer T. H. , Knock Emma , Gilson Zoë M. , Derry Leah , McGhee Miki C. , Taylor-Hood Katherine , Ziesel Alison , Jabbari Hosna , Newton Lorelei , Miller Jo Ann , Zhang Jie , Rhodes Ryan , Mallidou Anastasia , Paterson Theone S. E.
Published: November 2024

Objectives

This review aims to provide a comprehensive examination of biomarkers and interdisciplinary variables related to aging.

Methods

This scoping review included studies which involved adult participants, and which reported on the relationship between any biomarker or biological age with chronological age.

Results

After screening, 447 articles met the selection criteria. Results were categorized into 10 distinct categories through an iterative process.

Conclusions

This review contributes information regarding the interdisciplinary influences on the rate of aging. Telomere length was the most commonly examined biomarker, and Horvath’s 353-CpG Pan-Tissue clock was the most common clock, with both demonstrating a strong and consistent relationship with chronological age. The interdisciplinary variables demonstrated relationships with biological aging with varying strengths and consistencies.
Executive Functioning and Processing Speed as Predictors of Global Cognitive Decline in Alzheimer Disease
Authors: Haran John P. , Barrett A M , Lai YuShuan , Odjidja Samuel N. , Dutta Protiva , McGrath Patrick M , Samari Imane , Romeiro Lethycia , Lopes Abigail , Bucci Vanni , McCormick Beth A.
Published: November 2024

INTRODUCTION

There is a lack of cognitive tools to predict disease progression in mild cognitive impairment (MCI) and Alzheimer’s disease (AD).

METHODS

We assessed patients with MCI, AD, and cognitively healthy controls (cHC) using NIH toolbox assessments for attention/concentration and executive functioning and overall cognitive decline by the Alzheimer’s Disease Assessment Scale-Cognitive (ADAS-Cog).

RESULTS

Among 183 participants over a median follow-up of 540 days, both between- and within-subjects variance in NIH toolbox and ADAS-Cog assessments increased from cHC to MCI to AD patients. Among patients with AD, pattern comparison processing speed (PCPS) and dimensional change card sort tests (DCCS) declined at 3 and 6 months prior to global cognitive decline (p=0.008 & 0.0012). A 5-point decrease in either PCPS or DCCS increased risk of global cognitive decline (HR 1.32 (1.08-1.60) and 1.62 (1.16-2.26)).

DISCUSSION

Testing for cognitive domains of attention/concentration and executive functioning may predict subsequent global cognitive, and functional decline.
Immune history shapes human antibody responses to H5N1 influenza viruses
Authors: Garretson Tyler A. , Liu Jiaojiao , Li Shuk Hang , Scher Gabrielle , Santos Jefferson J.S. , Hogan Glenn , Vieira Marcos Costa , Furey Colleen , Atkinson Reilly K. , Ye Naiqing , Ort Jordan , Kim Kangchon , Hernandez Kevin A. , Eilola Theresa , Schultz David C. , Cherry Sara , Cobey Sarah , Hensley Scott E.
Published: November 2024

Avian H5N1 influenza viruses are circulating widely in cattle and other mammals and pose a risk for a human pandemic. Previous studies suggest that older humans are more resistant to H5N1 infections due to childhood imprinting with other group 1 viruses (H1N1 and H2N2); however, the immunological basis for this is incompletely understood. Here we show that antibody titers to historical and recent H5N1 strains are highest in older individuals and correlate more strongly with year of birth than with age, consistent with immune imprinting. After vaccination with an A/Vietnam/1203/2004 H5N1 vaccine, both younger and older humans produced H5-reactive antibodies to the vaccine strain and to a clade 2.3.4.4b isolate currently circulating in cattle, with higher seroconversion rates in young children who had lower levels of antibodies before vaccination. These studies suggest that younger individuals might benefit more from vaccination than older individuals in the event of an H5N1 pandemic.