bluuebunny/crossref_metadata_2025 huggingface dataset:
Application of an EEG-based deep learning model to discriminate children with epileptic spasms from normal controls
Authors: Lu Mingjian , Zhang Yipeng , Diada Atsuro , Oana Shingo , Rajaraman Rajsekar R. , Nariai Hiroki , Roychowdhury Vwani , Hussain Shaun A.
Published: July 2023

Objective

Given that epileptic spasms are often subtle, and that identification of hypsarrhythmia is limited by inadequate inter-rater reliability, there is a significant need for novel tools to aid the clinical identification of Infantile Epileptic Spasms Syndrome (IESS). Deep learning is an emerging technology which may enable efficient classification of disease states and may facilitate discovery of novel biomarkers. In this study, we set out to evaluate whether children with epileptic spasms can be distinguished from normal controls with use of an EEG-based deep learning model.

Methods

A deep learning model was trained and validated (5-fold cross validation) using 400 EEG samples (2 awake and 2 sleep samples from 50 children with epileptic spasms and 50 normal controls). Salient frequency bands and specific morphologic EEG features were identified with occlusion sensitivity analysis and targeted input perturbation, respectively.

Results

The model accurately distinguishes children with epileptic spasms from normal controls, solely on the basis of relatively short EEG samples. Using sleep data, accuracy = 0.95, recall = 0.96, precision (sensitivity) = 0.94, specificity = 0.94, and F1 score = 0.95. With awake data, accuracy = 0.91, recall = 0.84, precision = 0.98, specificity = 0.98, and F1 score = 0.90. The salient frequency bands for classification are 9.7 – 22.0 Hz and 1.0 – 6.8 Hz in sleep and awake EEG, respectively. With visual analysis of extracted salient features, we suspect that the model is identifying cases on the basis of paroxysmal fast activity in sleep and spike-wave activity in wakefulness.

Conclusion

This deep learning model represents a first step in the development of efficient algorithms that may aid in identification of epileptic spasms and IESS. More importantly, this approach may facilitate novel EEG-based biomarkers of epileptic spasms.
Multifactorial analysis of terminator performance on heterologous gene expression in Physcomitrella
Authors: Niederau Paul Alexander , Eglé Pauline , Willig Sandro , Parsons Juliana , Hoernstein Sebastian N.W. , Decker Eva L. , Reski Ralf
Published: July 2023

The production of recombinant proteins for health applications accounts for a large share of the biopharmaceutical market. While many drugs are produced in microbial and mammalian systems, plants gain more attention as expression hosts to produce eukaryotic proteins. In particular the GMP-compliant moss Physcomitrella (Physcomitrium patens) has outstanding features such as excellent genetic amenability, reproducible bioreactor cultivation, and humanized protein glycosylation patterns. In this study, we selected and characterized novel terminators for their effects on heterologous gene expression. The Physcomitrella genome contains 53,346 unique 3’UTRs (untranslated regions) of which 7,964 transcripts contain at least one intron. Over 91% of 3’UTRs exhibit more than one polyadenylation site, indicating the prevalence of alternative polyadenylation in Physcomitrella. Out of all 3’UTRs, 14 terminator candidates were selected and characterized via transient Dual Luciferase assays, yielding a collection of endogenous terminators performing equally high as established heterologous terminators CaMV35S, AtHSP90, and NOS. High performing candidates were selected for testing as double terminators which impact reporter levels, dependent on terminator identity and positioning. Testing of 3’UTRs among the different promoters NOS, CaMV35S, and PpActin5 showed an increase of more than 1,000-fold between promoters PpActin5 and NOS, whereas terminators increased reporter levels by less than 10-fold, demonstrating the stronger effect promoters play as compared to terminators. The number of polyadenylation sites as well as polyadenylation signals were found to be major determinants of terminator performance. Our results improve the biotechnology platform Physcomitrella and further our understanding of how terminators influence gene expression in plants in general.

Key message

Characterization of Physcomitrella 3’UTRs across different promoters yields endogenous single and double terminators for usage in molecular pharming and indicates promoters and terminators to synergistically control gene expression.
Carbon source and surface type influence the early-stage biofilm formation by rhizosphere bacteriumPseudomonas donghuensisP482
Authors: Rajewska Magdalena , Maciąg Tomasz , Jafra Sylwia
Published: July 2023

The competence of bacteria to colonize different environmental niches is often determined by their ability to form biofilms. This depends on both cellular and extracellular factors, such as individual characteristics of a strain, type of colonized surface (abiotic or biotic) or availability and source of nutrients.Pseudomonas donghuensisP482 efficiently colonizes rhizosphere of various plant hosts, but a connection between plant tissue colonization and biofilm formation has not been verified for P482 up to date. Here we demonstrate that the ability of P482 to form biofilm on abiotic surfaces and the structural characteristics of the biofilm are connected to the type of carbon source available to the bacteria, with glycerol promoting formation of developed biofilm at early stages. Also, the type of substratum, polystyrene or glass, significantly influences the ability of P482 to attach to the surface, possibly due to hydrophobic effects. Moreover, mutants in genes associated with motility or chemotaxis, synthesis of polysaccharides, and encoding proteases or regulatory factors, affected in biofilm formation on glass were fully capable of colonizing root tissue of both tomato and maize hosts. This indicates that the ability to form biofilm on distinct abiotic surfaces does not simply correlate with the efficient colonization of rhizosphere and formation of biofilm on plant tissue by P482.
S-nitrosylation-mediated unfolded protein response maintains hematopoietic progenitors
Authors: Cho Bumsik , Shin Mingyu , Chang Eunji , Son Seogho , Shim Jiwon
Published: July 2023

TheDrosophilalymph gland houses blood progenitors that give rise to myeloid-like blood cells. Initially, blood progenitors proliferate, but later become quiescent to maintain multipotency before differentiation. Despite the identification of various factors involved in multipotency maintenance, the cellular mechanism regulating blood progenitor quiescence remains elusive. Here, we reveal the expression of nitric oxide synthase in blood progenitors, generating nitric oxide for post-translational S-nitrosylation of protein cysteine residues. S-nitrosylation activates the Ire1-Xbp1-mediated unfolded protein response, leading to G2 cell cycle arrest. Specifically, we identify the epidermal growth factor receptor as a target of S-nitrosylation, resulting in its retention within the endoplasmic reticulum and blockade of its receptor function. Collectively, our findings highlight developmentally programmed S-nitrosylation as a critical mechanism that induces protein quality control in blood progenitors, maintaining their undifferentiated state by inhibiting cell cycle progression and rendering them unresponsive to paracrine factors.
Environmental enrichment promotes adaptive responding during tests of behavioral regulation in male heterogeneous stock rats
Authors: Ishiwari Keita , King Christopher P. , Martin Connor D. , Tripi Jordan A. , George Anthony M. , Lamparelli Alexander C. , Chitre Apurva , Polesskaya Oksana , Richards Jerry B. , Solberg Woods Leah C. , Gancarz Amy , Palmer Abraham A. , Dietz David M. , Mitchell Suzanne H. , Meyer Paul J.
Published: July 2023

Organisms must regulate their behavior flexibly in the face of environmental challenges. Failure can lead to a host of maladaptive behavioral traits associated with a range of neuropsychiatric disorders, including attention deficit hyperactivity disorder, autism, and substance use disorders. This maladaptive dysregulation of behavior is influenced by genetic and environmental factors. For example, environmental enrichment produces beneficial neurobehavioral effects in animal models of such disorders. The present study determined the effects of environmental enrichment on a range of measures related to behavioral regulation using a large cohort of male, outbred heterogeneous stock (HS) rats as subjects to mimic the genetic variability found in the human population. Subjects were reared from late adolescence onwards either in pairs in standard housing with minimal enrichment (n=200) or in groups of 16 in a highly enriched environment consisting of a large multi-level cage filled with toys, running wheels, and shelters (n=64). Rats were subjected to a battery of tests, including: (i) locomotor response to novelty, (iI) light reinforcement, (iii) social reinforcement, (iv) reaction time, (v) a patch-depletion foraging test, (vi) Pavlovian conditioned approach, (vii) conditioned reinforcement, and (viii) cocaine conditioned cue preference. Results indicated that rats housed in the enriched environment were able to filter out irrelevant stimuli more effectively and thereby regulate their behavior more efficiently than standard-housing rats. The dramatic impact of environmental enrichment suggests that behavioral studies using standard housing conditions may not generalize to more complex environments that may be more ethologically relevant.
Identifying distinct neural features between the initial and corrective phases of precise reaching using AutoLFADS
Authors: Lee Wei-Hsien , Karpowicz Brianna M , Pandarinath Chethan , Rouse Adam G.
Published: July 2023

Many initial movements require subsequent corrective movements, but how motor cortex transitions to make corrections and how similar the encoding is to initial movements is unclear. In our study, we explored how the brain’s motor cortex signals both initial and corrective movements during a precision reaching task. We recorded a large population of neurons from two male rhesus macaques across multiple sessions to examine the neural firing rates during not only initial movements but also subsequent corrective movements. AutoLFADS, an auto-encoder-based deep-learning model, was applied to provide a clearer picture of neurons’ activity on individual corrective movements across sessions. Decoding of reach velocity generalized poorly from initial to corrective submovements. Unlike initial movements, it was challenging to predict the velocity of corrective movements using traditional linear methods in a single, global neural space. We identified several locations in the neural space where corrective submovements originated after the initial reaches, signifying firing rates different than the baseline before initial movements. To improve corrective movement decoding, we demonstrate that a state-dependent decoder incorporating the population firing rates at the initiation of correction improved performance, highlighting the diverse neural features of corrective movements. In summary, we show neural differences between initial and corrective submovements and how the neural activity encodes specific combinations of velocity and position. These findings are inconsistent with assumptions that neural correlations with kinematic features are global and independent, emphasizing that traditional methods often fall short in describing these diverse neural processes for online corrective movements.

Significance Statement

We analyzed submovement neural population dynamics during precision reaching. Using an auto- encoder-based deep-learning model, AutoLFADS, we examined neural activity on a single-trial basis. Our study shows distinct neural dynamics between initial and corrective submovements. We demonstrate the existence of unique neural features within each submovement class that encode complex combinations of position and reach direction. Our study also highlights the benefit of state-specific decoding strategies, which consider the neural firing rates at the onset of any given submovement, when decoding complex motor tasks such as corrective submovements.
IgG sialylation occurs via the FcRn-mediated recycling pathway in endothelial cells
Authors: Glendenning Leandre M. , Reynero Kalob M. , Kukan Emily N. , Long Megan D. , Cobb Brian A.
Published: July 2023

IgG is a key mediator of immune responses throughout the human body, and the structure of the conserved glycan on the Fc region has been identified as a key inflammatory switch regulating its downstream effects. In particular, the absence of terminal sialic acid has been shown to increase the affinity of IgG for activating Fc receptors, cascading the inflammatory response in a variety of diseases and conditions. Previously, we have shown that IgG sialylation is mediated by B cell-extrinsic processes. Here, we show that the FcRn-mediated recycling pathway within endothelial cells is a critical modulator of IgG sialylation. Building a deeper understanding of how IgG sialylation is regulated will drive the development of novel therapeutics which dynamically tune IgG functionalityin vivo.

One-Sentence Summary

Endothelial cells remodel IgG glycans within the FcRn-mediated recycling pathway.
Readiness of nociceptor cell bodies to generate spontaneous activity results from background activity of diverse ion channels and high input resistance
Authors: Tian Jinbin , Bavencoffe Alexis G. , Zhu Michael X. , Walters Edgar T.
Published: July 2023

Nociceptor cell bodies generate “spontaneous” discharge that can promote ongoing pain in persistent pain conditions. Little is known about the underlying mechanisms. Recordings from nociceptor cell bodies (somata) dissociated from rodent and human dorsal root ganglia (DRGs) have shown that prior pain in vivo is associated with low-frequency discharge controlled by irregular depolarizing spontaneous fluctuations of membrane potential (DSFs), likely produced by transient inward currents across the somal input resistance. Here we show that DSFs are associated with high somal input resistance over a wide range of membrane potentials, including depolarized levels where DSFs approach action potential (AP) threshold. Input resistance and both the amplitude and frequency of DSFs were increased in neurons exhibiting spontaneous activity. Ion substitution experiments indicated that the depolarizing phase of DSFs is generated by spontaneous opening of channels permeable to Na+and/or Ca2+, and that Ca2+-permeable channels are especially important for larger DSFs. Partial reduction of the amplitude and/or frequency of DSFs by perfusion of pharmacological inhibitors indicated small but significant contributions from Nav1.7, Nav1.8, TRPV1, TRPA1, TRPM4, and N-type Ca2+channels. Less specific blockers suggested a contribution from NALCN channels, and global knockout suggested a role for Nav1.9. The combination of high somal input resistance plus background activity of diverse ion channels permeable to Na+and/or Ca2+produces DSFs that are poised to reach AP threshold if resting membrane potential (RMP) depolarizes, AP threshold decreases, and/or DSFs become enhanced -- all of which have been reported under painful neuropathic and inflammatory conditions.
A Rationally Designed Antimicrobial Peptide from Structural and Functional Insight ofClostridium difficileTranslation Initiation Factor 1
Authors: Alanis Elvira , Aguilar Faith , Banaei Niaz , Dean Frank B. , Alanis Miguel , Bullard James M. , Zhang Yonghong
Published: July 2023

A significant increase of hospital-acquired bacterial infections during the COVID-19 pandemic has become an urgent medical problem.Clostridioides difficileis an urgent antibiotic-resistant bacterial pathogen and a leading causative agent of nosocomial infections. The increasing recurrence ofC. difficileinfection and antibiotic resistance inC. difficilehas led to an unmet need for discovery of new compounds distinctly different from present antimicrobials, while antimicrobial peptides as promising alternatives to conventional antibiotics have attracted growing interest recently. Protein synthesis is an essential metabolic process in all bacteria and a validated antibiotic target. Initiation factor 1 fromC. difficile(Cd-IF1) is the smallest of the three initiation factors that acts to establish the 30S initiation complex to initiate translation during protein biosynthesis. Here we report the solution NMR structure of Cd-IF1 which adopts a typical β-barrel fold and consists of a five-stranded β-sheet and one short α-helix arranged in the sequential order β1-β2-β3-α1-β4-β5. The interaction of Cd-IF1 with the 30S ribosomal subunit was studied by NMR titration for the construction of a structural model of Cd-IF1 binding with the 30S subunit. The short α-helix in IF1 was found to be critical for IF1 ribosomal binding. A peptide derived from this α-helix was tested and displayed a high ability to inhibit the growth ofC. difficileand other bacterial strains. These results provide a clue for rational design of new antimicrobials.
The CB1 Negative Allosteric Modulator PSNCBAM-1 Reduces Ethanol Self-Administration via a Nonspecific Hypophagic Effect
Authors: Buechler Harley M. , Sumi Mousumi , Madhuranthakam Indu Mithra , Donegan Christa , DiGiorgio Frank , Acosta Alisha A , Uribe Sarah , Rahman Mohammad A , Sorbello Alison , Fischer Bradford D. , Keck Thomas M.
Published: July 2023

Alcohol use disorder (AUD) affects more than 15 million people in the United States. Current pharmacotherapeutic treatments for AUD are only modestly effective, necessitating the identification of new targets for medications development. The cannabinoid receptor type 1 (CB1) has been a target of interest for the development of medications for substance use disorders and other compulsive disorders. However, CB1 antagonists/inverse agonists (e.g., rimonabant) have severe side effects that limit their clinical utility, including anxiety, depression, and suicide. Recent development of CB1 negative allosteric modulators (NAMs), including PSNCBAM-1, may provide an alternative mechanism of attenuating CB1 signaling with reduced side effects. PSNCBAM-1 has not yet been evaluated for effects in models of AUD. In this study, we investigated the effects of the CB1 NAM, PSNCBAM-1, in rodent models of AUD using adult male mice. PSNCBAM-1 dose-dependently attenuated oral ethanol self-administration (8% w/v ethanol in water), significantly reducing ethanol rewards at a dose of 30 mg/kg, but not at 10 or 18 mg/kg. PSNCBAM-1 also dose-dependently attenuated palatable food self-administration (diluted vanilla Ensure), significantly reducing food rewards at 18 and 30 mg/kg PSNCBAM-1. PSNCBAM-1 did not affect conditioned place preference for 2 g/kg ethanol. These results suggest PSNCBAM-1 reduces ethanol-taking behavior via a nonspecific hypophagic effect and does not reduce the rewarding effects of ethanol.
Loss of NR2E3 disrupts rod photoreceptor cell maturation causing a fate switch late in human retinal development
Authors: Mullin Nathaniel K. , Bohrer Laura R. , Voigt Andrew P. , Lozano Lola P. , Wright Allison , Mullins Robert F. , Stone Edwin M. , Tucker Budd A.
Published: July 2023

While dysfunction and death of light-detecting photoreceptor cells underlie most inherited retinal dystrophies, knowledge of the species-specific details of human rod and cone photoreceptor cell development remains limited. Here, we generate retinal organoids using induced pluripotent stem cells (iPSC) derived from a patient with genetic photoreceptor disease due to mutations inNR2E3, an isogenic control, and an unrelated control. Organoids were sampled using single-cell RNA sequencing across the developmental window encompassing photoreceptor specification, emergence, and maturation, up to 260 days ofin vitrodifferentiation. Using single-cell transcriptomics data, we reconstruct the rod photoreceptor developmental lineage and identify a branchpoint in development unique to the disease state that gives rise to a divergent rod photoreceptor cell population. We show that the rod-specific transcription factor NR2E3 is required for the proper expression of genes involved in phototransduction, including expression of the light-sensitive protein rhodopsin, which is absent in divergent rods. NR2E3-null rods additionally misexpress several cone-specific phototransduction genes at both the transcript and protein level. Using joint multimodal single-cell sequencing on late-stage retinal organoids, we further identify specific putative regulatory sites where rod-specific factors act to steer rod and cone photoreceptor cell development. Importantly, these findings are strikingly different than those observed in rodent models of disease. Together, these data provide a roadmap of human photoreceptor development and leverage patient iPSCs to define the specific roles of rod transcription factors in photoreceptor cell emergence and maturation.
Identification of State Markers in Anorexia Nervosa: Replication and Extension of Inflammation Associated Biomarkers Using Multiplex Profiling in Anorexia Nervosa and Atypical Anorexia Nervosa
Authors: Breithaupt Lauren , Holsen Laura M. , Ji Chunni , Hu Jie , Petterway Felicia , Rosa-Caldwell Megan , Nilsson Ida A.K. , Thomas Jennifer J. , Williams Kyle A. , Boutin Regine , Slattery Meghan , Bulik Cynthia M. , Arnold Steven E. , Lawson Elizabeth A. , Misra Madhusmita , Eddy Kamryn T.
Published: July 2023

Proteomics provides an opportunity for detection and monitoring of anorexia nervosa (AN) and its related variant, atypical-AN (atyp-AN). However, research to date has been limited by the small number of proteins explored, exclusive focus on adults with AN, and lack of replication across studies. This study performed Olink Proseek Multiplex profiling of 92 proteins involved in inflammation among females with AN and atyp-AN (N = 64), all<90% of expected body weight, and age-matched healthy controls (HC; N=44). After correction for multiple testing, nine proteins differed significantly in the AN/atyp-AN group relative to HC group (lowerlevels: CXCL1, HGF, IL-18R1, TNFSF14, TRANCE;higherlevels: CCL23, Flt3L, LIF-R, MMP-1). The expression levels of three proteins (lowerIL-18R1, TRANCE;higherLIF-R) were uniquely disrupted in females with AN. No unique expression levels emerged for atyp-AN. Across the whole sample, twenty-one proteins correlated positively with BMI (ADA, AXIN1, CD5, CD244, CD40, CD6, CXCL1, FGF-21, HGF, IL-10RB, IL-12B, IL18, IL-18R1, IL6, LAP TGF-beta-1, SIRT2, STAMBP, TNFRSF9, TNFSF14, TRAIL, TRANCE) and six (CCL11, CCL23, FGF-19, IL8, LIF-R, OPG) were negatively correlated with BMI. Overall, our results replicate the prior study demonstrating a dysregulated inflammatory status in AN, and extend these results to atyp-AN (AN/atyp-AN all<90% of expected body weight). Of the 27 proteins correlated with BMI, 18 were replicated from a prior study using similar methods, highlighting the promise of inflammatory protein expression levels as biomarkers of disease monitoring. Additional studies of individuals across the entire weight spectrum are needed to understand the role of inflammation in atyp-AN.
Germline Mutations Associated with Triple Negative Breast Cancer in US Hispanic and Guatemalan Women using Hospital and Community-Based Recruitment Strategies
Authors: Paredes Jesica Godinez , Rodriguez Isabel , Ren Megan , Orozco Anali , Ortiz Jeremy , Albanez Anaseidy , Jones Catherine , Nahleh Zeina , Barreda Lilian , Garland Lisa , Gonzalez Edmundo Torres , Wu Dongjing , Luo Wen , Liu Jia , Argueta Victor , Orozco Roberto , Gharzouzi Eduardo , Dean Michael
Published: July 2023

Purpose

Identify optimum strategies to recruit Latin American and Hispanic women into genetic studies of breast cancer. We evaluated hospital and community-based recruitment strategies.

Methods

We used targeted gene sequencing to identify mutations in DNA from unselected Hispanic breast cancer cases from community and hospital-based recruitment in the US and Guatemala.

Results

We recruited 287 Hispanic US women, 38 (13%) from community-based and 249 (87%) from hospital-based strategies. In addition, we ascertained 801 Guatemalan women using hospital-based recruitment. In our experience, a hospital-based approach was more efficient than community-based recruitment. In this study, we sequenced 103 US and 137 Guatemalan women and found 11 and 10 pathogenic variants, respectively. The most frequently mutated genes wereBRCA1, BRCA2, CHEK2, andATM. In addition, an analysis of 287 US Hispanic patients with pathology reports showed a significantly higher percentage of triple-negative disease in patients with pathogenic mutations (41% vs. 15%). Finally, an analysis of mammography usage in 801 Guatemalan patients found reduced screening in women with a lower socioeconomic status (P<0.001).

Conclusions

Guatemalan and US Hispanic women have rates of hereditary breast cancer mutations similar to other populations and are more likely to have early age at diagnosis, a family history, and a more aggressive disease. Patient recruitment was higher using hospital-based versus community enrollment. This data supports genetic testing in breast cancer patients to reduce breast cancer mortality in Hispanic women.
Identification Cure Hub Genes of Chromophobe Cell Renal Carcinoma : A study based on Weighted Gene Co-expression Network Analysis (WGCNA) and the Cure Defective Models
Authors: Ahmadian Maryam , Molavi Zahra , Baghestani Ahmad Reza , Maboudi Ali Akbar
Published: July 2023

Renal cell carcinoma (RCC) is a prevalent and aggressive tumor of the urinary system with limited treatment success and poor patient outcomes. However, some patients exhibit long-term symptom relief and are considered ’cured’ after successful treatment. This study explores the genetic and pathway mechanisms underlying RCC cure for the first time, utilizing a survival model called the 3-parameter defective Gompertz cure model.

The study methodology involved two main steps: Firstly, employing Weighted Gene Co-expression Network Analysis (WGCNA) for gene network analysis, which identified six key modules associated with different aspects of cancer progression and survival. Hub genes, pivotal in cellular interactions, were pinpointed through network analysis. Secondly, the 3-parameter defective Gompertz model was utilized to identify therapeutic genes linked to successful treatment outcomes (CSRGs) in RCC. These genes were then compared with genes associated with patient survival (SRGs) using a cox model.

The study found ten hub genes commonly identified by both the defective 3-parameter Gompertz and Cox models, with six genes (NCAPG, TTK, DLGAP5, TOP2A, BUB1B, and BUB1) showing strong predictive values. Moreover, six hub genes (TTK, KIF20A, DLGAP5, BUB1, AURKB, and CDC45) were highlighted by the defective Gompertz model as significantly impacting cure when expressed at high levels. Targeting these hub genes may hold promise for improving RCC treatment outcomes and prognosis prediction.

Overall, this study provides valuable insights into the molecular mechanisms of RCC and underscores the potential of the defective 3-parameter Gompertz model in guiding targeted therapeutic approaches.
Polymerized type I collagen down-regulates STAT-1 phosphorylation through engagement to LAIR-1 in M1-macrophages avoiding long COVID
Authors: Olivares-Martínez Elizabeth , Hernández-Ramírez Diego Francisco , Núñez-Álvarez Carlos Alberto , Chapa-Ibarguengoitia Mónica , Méndez-Flores Silvia , Ranero Ángel Priego- , Azamar-Llamas Daniel , Olvera-Prado Héctor , Rivas-Redonda Kenia Ilian , Ochoa-Hein Eric , López-Mosqueda Luis Gerardo , Rojas-Castañeda Estefano , Urbina-Terán Said , Septién-Stute Luis , Hernández-Gilsoul Thierry , Aguilar-León Diana , Torres-Villalobos Gonzalo , Furuzawa-Carballeda Janette
Published: July 2023

Background

The polymerized type I collagen (PTIC) is a γ-irradiated mixture of pepsinized porcine type I collagen and polyvinylpyrrolidone (PVP). It has immunomodulatory properties. However, the receptor and signaling pathway through which it exerts its therapeutic effects has not yet been identified.

Aim

To evaluate LAIR-1 as a potential receptor for PTIC and the signaling pathway evoked by ligand-receptor binding.

Methods

LAIR-1 binding assay was performed by incubating various concentrations of recombinant human LAIR-1 with native type I collagen or PTIC. Macrophages M1- derived from THP-1 cells were cultured with 2-10% PTIC for 24 h. Cell lysates from THP- 1, monocytes-like cells (MLCs), M1, M1+IFN-γ, M1+LPS, and 2 or 10% PTIC treated M1 were analyzed by western blot for the transcription factors NF-κB (p65), p38, STAT-1, and pSTAT-1. Cytokines, Th1 cells, and M1/M2 macrophages were analyzed by luminometry and flow cytometry from blood samples of symptomatic COVID-19 outpatients on treatment with intramuscular administration of PTIC.

Results

PTIC binds LAIR-1 with a similar affinity to native collagen. This binding decreases STAT-1 signaling IFN-γ-induced and IL-1β expression in M1 macrophages by down-regulating STAT-1 phosphorylation. Moreover, intramuscular PTIC treatment of symptomatic COVID-19 outpatients decreased at statistically significant levels the percentage of M1 macrophages and cytokines (IP-10, MIF, eotaxin, IL-8, IL-1RA, and M- CSF) associated with STAT-1 transcription factor and increased M2 macrophages and Th1 cells. The downregulation of inflammatory mediators was related to better oxygen saturation and decreased dyspnea, chest pain, cough, and chronic fatigue syndrome in the acute phase of infection and the long term.

Conclusion

PTIC is an agonist of LAIR-1 and down-regulates STAT-1 phosphorylation. PTIC could be relevant for treating STAT-1-mediated inflammatory diseases, including COVID-19 and long COVID
CHAPERONg: A tool for automated GROMACS-based molecular dynamics simulations and trajectory analyses
Authors: Yekeen Abeeb Abiodun , Durojaye Olanrewaju Ayodeji , Idris Mukhtar Oluwaseun , Muritala Hamdalat Folake , Arise Rotimi Olusanya
Published: July 2023

Molecular dynamics (MD) simulation is a powerful computational tool used in biomolecular studies to investigate the dynamics, energetics, and interactions of a wide range of biological systems at the atomic level. GROMACS is a widely used free and open-source biomolecular MD simulation software recognized for its efficiency, accuracy, and extensive range of simulation options. However, the complexity of setting up, running, and analyzing MD simulations for diverse systems often poses a significant challenge, requiring considerable time, effort, and expertise. Here, we introduce CHAPERONg, a tool that automates the GROMACS MD simulation pipelines for protein and protein-ligand systems. CHAPERONgalso integrates seamlessly with GROMACS modules and third-party tools to provide comprehensive analyses of MD simulation trajectories, offering up to 20 post-simulation processing and trajectory analyses. It also streamlines and automates established pipelines for conducting and analyzing biased MD simulations via the steered MD-umbrella sampling workflow. Thus, CHAPERONgmakes MD simulations more accessible to beginner GROMACS users whilst empowering experts to focus on data interpretation and other less programmable aspects of MD simulation workflows.
A Spatiotemporal Proteomic Map of Human Adipogenesis
Authors: Klingelhuber Felix , Frendo-Cumbo Scott , Omar-Hmeadi Muhmmad , Taylor Austin J. , Kakimoto Pamela , Couchet Morgane , Ribicic Sara , Wabitsch Martin , Messias Ana C. , Iuso Arcangela , Müller Timo D. , Rydén Mikael , Mejhert Niklas , Krahmer Natalie
Published: July 2023

White adipocytes function as the major energy reservoir in humans by storing substantial amounts of triglycerides and their dysfunction is associated with metabolic disorders. However, the mechanisms underlying cellular specialization during adipogenesis remain unknown. Here, using a high-sensitivity-high throughput workflow, we generated a spatiotemporal proteomic atlas of human adipogenesis encompassing information for ~8.000 proteins. Our systematic approach gives insights into cellular remodeling and the spatial reorganization of metabolic pathways to optimize cells for lipid accumulation and highlights the coordinated regulation of protein localization and abundance during adipogenesis. More specifically, we identified a compartment-specific regulation of protein levels and localization changes of metabolic enzymes to reprogram branched chain amino acid and one-carbon metabolism to provide building blocks and reduction equivalents for lipid synthesis. Additionally, we identified C19orf12 as a differentiation induced and adipocyte-specific lipid droplet (LD) protein, which interacts with the translocase of the outer membrane (TOM) complex of LD associated mitochondria and regulates adipocyte lipid storage. Overall, our study provides a comprehensive resource for understanding human adipogenesis and for future discoveries in the field.

KEY POINTS

Human adipogenesis induces distinct temporal changes in protein abundance

20% of all detected proteins change organellar localization during adipogenesis

BCAA and one-carbon metabolism enzyme levels and localizations are coordinately regulated to promote adipogenesis

C19orf12 is an adipocyte specific LD protein and regulator of lipid storage
Grapevine bacterial communities across the Central Valley of California
Authors: Swift Joel F. , Migicovsky Zoë , Trello Grace E. , Miller Allison J.
Published: July 2023

Plant organs (compartments) host distinct microbiota which shift in response to variation in both development and climate. Grapevines are woody perennial crops that are clonally propagated and cultivated across vast geographic areas, and as such, their microbial communities may also reflect site-specific influences. These site-specific influences, and the microbial differences across site compose ‘terroir’, the environmental influence on wine produced in a given region. Commercial grapevines are typically composed of a genetically distinct root (rootstock) grafted to a shoot system (scion) which adds an additional layer of complexity. In order to understand spatial and temporal patterns of bacterial diversity in grafted grapevines, we used 16S rRNA metabarcoding to quantify soil and compartment microbiota (berries, leaves, and roots) for grafted grapevines in commercial vineyards across three counties in the Central Valley of California over two successive growing seasons. Community composition revealed compartment-specific dynamics. Roots assembled site-specific bacterial communities that reflect rootstock genotype and environment influences, whereas bacterial communities of leaves and berries displayed associations with time. These results provide further evidence of a microbial terroir within the grapevine root systems but also reveal that the microbiota of above-ground compartments are only weakly associated with the local microbiome in the Central Valley of California.
A familial missense variant in the Alzheimer’s Disease geneSORL1impairs its maturation and endosomal sorting
Authors: Fazeli Elnaz , Child Daniel D. , Bucks Stephanie A. , Stovarsky Miki , Edwards Gabrielle , Rose Shannon E. , Yu Chang-En , Latimer Caitlin , Kitago Yu , Bird Thomas , Jayadev Suman , Andersen Olav M. , Young Jessica E.
Published: July 2023

TheSORL1gene has recently emerged as a strong Alzheimer’s Disease (AD) risk gene. Over 500 different variants have been identified in the gene and the contribution of individual variants to AD development and progression is still largely unknown. Here, we describe a family consisting of 2 parents and 5 offspring. Both parents were affected with dementia and one had confirmed AD pathology with an age of onset >75 years. All offspring were affected with AD with ages at onset ranging from 53yrs-74yrs. DNA was available from the parent with confirmed AD and 5 offspring. We identified a coding variant, p.(Arg953Cys), inSORL1in 5 of 6 individuals affected by AD. Notably, variant carriers had severe AD pathology, and theSORL1variant segregated with TDP-43 pathology (LATE-NC). We further characterized this variant and show that this Arginine substitution occurs at a critical position in the YWTD-domain of theSORL1translation product, SORL1. Functional studies further show that the p.R953C variant leads to retention of the SORL1 protein in the endoplasmic reticulum which leads to decreased maturation and shedding of the receptor and prevents its normal endosomal trafficking. Together, our analysis suggests that p.R953C is a pathogenic variant ofSORL1and sheds light on mechanisms of how missenseSORL1variants may lead to AD.
Blood prognostic biomarker signatures for hemorrhagic cerebral cavernous malformations (CCMs)
Authors: Croft Jacob , Grajeda Brian , Abou-Fadel Johnathan S , Ellis Cameron C , Igor Estevao , Almeida Igor C. , Zhang Jun
Published: July 2023

Background

Cerebral cavernous malformations (CCMs) is a neurological disorder that causes enlarged intracranial capillaries in the brain, leading to an increased risk of hemorrhagic strokes, which is a leading cause of death and disability worldwide.

Objectives

The current treatment options for CCMs are limited, highlighting the need for prognostic biomarkers to predict the risk of hemorrhagic events to better inform treatment decisions and identify future pharmacological targets.

Eligibility Criteria

The study is centered on a comparative proteomic analysis between hemorrhagic CCMs (HCs) and healthy controls, while excluding patients with non-hemorrhagic CCMs (NHCs) from the analysis due to the experimental design.

Sources of Evidence

Recent research has identified several serum biomarkers and blood circulating biomarkers in a selected cohort of homogeneous CCM patients and animal models.

Method

Proteomic profiles from both human and mouse CCM models were examined, and pathway enrichment analyses were performed using three approaches (GO, KEGG, and DOSE). To account for multiple comparisons, t-tests were employed to evaluate differences. A p-value below 0.05 was deemed statistically significant.

Results

The authors have developed the first panel of candidate biomarker signatures, featuring both etiological and prognostic markers in two distinct pathways. This panel of biomarker signatures demonstrates a robust correlation with the likelihood of hemorrhagic CCMs.

Conclusions

This groundbreaking biomarker panel paves the way for further investigation of potential blood biomarkers to determine the risk of hemorrhagic CCMs.
Strain-release alkylation of Asp12 enables mutant selective GTP-state targeting of K-Ras(G12D)
Authors: Zheng Qinheng , Zhang Ziyang , Guiley Keelan G. , Shokat Kevan M.
Published: July 2023

K-Ras is the most commonly mutated oncogene in human cancer, yet direct small-molecule targeting of K-Ras mutants has been mostly unsuccessful until recently. The discovery of an allosteric pocket under Switch-II with covalent cysteine-crosslinking molecules has allowed for the development of targeted therapies that selectively engage the highly reactive acquired cysteine in the K-Ras(G12C) mutation without affecting the wild-type protein. Sotorasib and adagrasib, two advanced Switch-II Pocket inhibitors, have received FDA approval to treat K-Ras(G12C)-driven non-small cell lung cancer. However, the most frequent K-Ras mutation G12D particularly prevalent in pancreatic ductal adenocarcinoma has remained untargetable with covalent drugs due to the poor nucleophilicity of the somatic aspartate residue. Here we present a set of malolactone-based electrophiles which exploit ring strain to crosslink K-Ras(G12D) at the mutant aspartate to form stable covalent complexes. Structural insights from x-ray crystallography and exploitation of the stereoelectronic requirements for attack of the electrophile allowed development of a substituted malolactone which resisted attack by aqueous buffer but rapidly crosslink with the aspartate-12 of K-Ras in both GDP- and GTP-state. The signaling-competent GTP-state targeting allowed effective suppression of downstream signaling and proliferation of cancer cells harboring K-Ras(G12D) mutation, and tumor growth of cell line-derive xenograft in mice. Our results demonstrate the rational design of covalent inhibitors to target a non-catalytic carboxylic acid side chain in K-Ras(G12D) which has resisted traditional drug discovery efforts.
Patterns of Rising HIV Positivity in Northern Madagascar: Evidence of an Urgent Public Health Concern
Authors: Robinson Kyle E. , Long Jackson K. , Fardine Mamantsara , Stephano Adriantiana M. , Grewal Eric P.
Published: July 2023

Despite over two decades of progress against HIV/AIDS in adjacent sub-Saharan Africa, HIV rates and deaths due to AIDS are exponentially rising in Madagascar. Furthermore, a growing body of evidence suggests that, due to a scarcity of general-population screening data, even the startling increase demonstrated by official models vastly underestimates the true population prevalence of HIV. Thus, we aimed to implement a real-world HIV screening and treatment protocol to serve a general population stemming from across Northern Madagascar. In collaboration with the Malagasy Ministry of Health, we provided point-of-care HIV screening and confirmatory testing for over 1,000 participants from 73 towns, villages, and cities recording an overall HIV prevalence of2.94%. Notably, we observed a13.1%HIV prevalence rate among urban populations and showed that proximity to a major route of travel was significantly associated with HIV risk. We also observed a link between HIV risk and various occupations, including those associated with increased mobility (such as mining). Importantly, all HIV-positive individuals were initiated on antiretroviral therapy in concordance with local health authorities. To our knowledge, this study marks the largest primary test data-based HIV study to date among Madagascar’s general population, showing a greatly higher HIV prevalence (3.0%) than previously reported modeling based figures (0.3%). Our rates aligned with the pattern of higher prevalence demonstrated in smaller general-population screening studies occuring more commonly prior to political strife in the mid-2000s. These findings demonstrate evidence of a growing HIV epidemic in Northern Madagascar and underscore the need for future investment into more comprehensive HIV screening and control initiatives in Madagascar.
Oculomotor analysis to assess brain health: preliminary findings from a longitudinal study of multiple sclerosis using novel tablet-based eye-tracking software
Authors: de Villers-Sidani Étienne , Voss Patrice , Bastien Natacha , Cisneros-Franco J. Miguel , Hussein Shamiza , Mayo Nancy E. , Koch Nils A. , Blanchette François , Guitton Daniel , Giacomini Paul S.
Published: July 2023

A growing body of evidence supports the link between eye movement anomalies and brain health. Indeed, the oculomotor system is composed of a diverse network of cortical and subcortical structures and circuits that are susceptible to a variety of degenerative processes. Here we show preliminary findings from the baseline measurements of an ongoing longitudinal cohort study in MS participants, designed to determine if disease and cognitive status can be estimated and tracked with high accuracy based on eye movement parameters alone. Using a novel gaze-tracking technology that can reliably and accurately track eye movements with good precision without the need for infrared cameras, using only an iPad Pro embedded camera, we show that several eye movement parameters significantly correlated with clinical outcome measures of interest. Eye movement parameters were extracted from fixation, pro-saccade anti-saccade, and smooth pursuit visual tasks, whereas the clinical outcome measures were the scores of several disease assessment tools and standard cognitive tests such as the Expanded Disability Status Scale (EDSS), Brief International Cognitive Assessment for MS (BICAMS), the Multiple Sclerosis Functional Composite (MSFC) and the Symbol Digit Modalities Test (SDMT). Furthermore, multiple regression analyses show that a small set of oculomotor parameters can explain up to 74% of the variance of the clinical outcome measures. Taken together, these findings not only replicate previously known associations between eye movement parameters and clinical scores, this time using a novel mobile-based technology, but also the notion that interrogating the oculomotor system with a novel eye-tracking technology can inform us of disease severity and evolution, as well as the cognitive status of MS participants.
Dysregulation of N-terminal acetylation causes cardiac arrhythmia and cardiomyopathy
Authors: Yoshinaga Daisuke , Feng Rui , Prondzynski Maksymilian , Shani Kevin , Tharani Yashasvi , Milosh Joseph , Walker David , Carreon Chrystalle Katte , Boss Bridget , Upton Sheila , Parker Kevin Kit , Pu William T. , Bezzerides Vassilios J.
Published: July 2023

BACKGROUND

N-terminal-acetyltransferases catalyze N-terminal acetylation (Nt-acetylation), an evolutionarily conserved co-translational modification. Nt-acetylation regulates diverse signaling pathways, yet little is known about its effects in the heart. To gain insights, we studied NAA10-related syndrome, in which mutations in NAA10, which catalyzes Nt-acetylation, causes severe QT prolongation, hypotonia, and neurodevelopmental delay.

METHODS

We identified a missense variant in NAA10 (c.10C>A; p.R4S) that segregated with severe QT prolongation, arrhythmia, cardiomyopathy, and sudden death in a large kindred. We developed patient-derived and genome-edited human induced pluripotent stem cell (iPSC) models and deeply phenotyped iPSC-derived cardiomyocytes (iPSC-CMs) to dissect the mechanisms underlying NAA10-mediated cardiomyocyte dysfunction.

RESULTS

The NAA10-R4S mutation reduced enzymatic activity, decreased expression levels of NAA10/NAA15 proteins, and destabilized the NatA complex. In iPSC-CM models of NAA10 dysfunction, dysregulation of the late sodium and slow rectifying potassium currents caused severe repolarization abnormalities, consistent with clinical QT prolongation and increased risk for arrhythmogenesis. Engineered heart tissues generated from mutant NAA10 cell lines had significantly decreased contractile force and sarcomeric disorganization, consistent with the cardiomyopathic phenotype in the identified family members. Diastolic calcium levels were increased with corresponding alterations in calcium handling pathways. We identified small molecule and genetic therapies that reversed the effects of NAA10 dysregulation of iPSC-CMs.

CONCLUSIONS

Our study defines novel roles of Nt-acetylation in cardiac ion channel regulation and delineates mechanisms underlying QT prolongation, arrhythmia, and cardiomyopathy caused by NAA10 dysfunction.