bluuebunny/crossref_metadata_2025 huggingface dataset:
A CAG repeat threshold for therapeutics targeting somatic instability in Huntington’s disease
Authors: Aldous Sarah G. , Smith Edward J. , Landles Christian , Osborne Georgina F. , Cañibano-Pico Maria , Nita Iulia M. , Phillips Jemima , Zhang Yongwei , Jin Bo , Hirst Marissa B. , Benn Caroline L. , Bond Brian C. , Edelmann Winfried , Greene Jonathan R. , Bates Gillian P.
Published: December 2023

The Huntington’s disease mutation is a CAG repeat expansion in the huntingtin gene that results in an expanded polyglutamine tract in the huntingtin protein. The CAG repeat is unstable, and expansions of hundreds of CAGs have been detected in Huntington’s diseasepost-mortembrains. The age of disease onset can be predicted partially from the length of the CAG repeat as measured in blood. Onset age is also determined by genetic modifiers, which in six cases involve variation in DNA mismatch repair pathways genes. Knocking-out specific mismatch repair genes in mouse models of Huntington’s disease prevents somatic CAG repeat expansion. Taken together, these results have led to the hypothesis that somatic CAG repeat expansion in Huntington’s disease brains is required for pathogenesis. Therefore, the pathogenic repeat threshold in brain is longer than (CAG)40, as measured in blood, and is currently unknown.

The mismatch repair geneMSH3has become a major focus for therapeutic development, as unlike other mismatch repair genes, nullizygosity forMSH3does not cause malignancies associated with mismatch repair deficiency. Potential treatments targetingMSH3currently under development include gene therapy, biologics and small molecules, which will be assessed for efficacy in mouse models of Huntington’s disease. The zQ175 knock-in model carries a mutation of approximately (CAG)185and develops early molecular and pathological phenotypes that have been extensively characterised. Therefore, we crossed the mutant huntingtin allele onto heterozygous and homozygousMsh3knock-out backgrounds to determine the maximum benefit of targetingMsh3in this model. Ablation ofMsh3prevented somatic expansion throughout the brain and periphery, and reduction ofMsh3by 50% decreased the rate of expansion. This had no effect on the deposition of huntingtin aggregation in the nuclei of striatal neurons, nor on the dysregulated striatal transcriptional profile. This contrasts with ablatingMsh3in knock-in models with shorter CAG repeat expansions. Therefore, further expansion of a (CAG)185repeat in striatal neurons does not accelerate the onset of molecular and neuropathological phenotypes. It is striking that highly expanded CAG repeats of a similar size in humans cause disease onset before 2 years of age, indicating that somatic CAG repeat expansion in the brain is not required for pathogenesis. Given that the trajectory for somatic CAG expansion in the brains of Huntington’s disease mutation carriers is unknown, our study underlines the importance of administering treatments targeting somatic instability as early as possible.
Prognostic pan-cancer and single-cancer models: A large-scale analysis using a real-world clinico-genomic database
Authors: McGough Sarah F. , Lyalina Svetlana , Incerti Devin , Huang Yunru , Tyanova Stefka , Mace Kieran , Harbron Chris , Copping Ryan , Narasimhan Balasubramanian , Tibshirani Robert
Published: December 2023

Prognostic models in oncology have a profound impact on personalized cancer care and patient profiling, but tend to be heterogeneously developed and implemented in narrow patient cohorts. Here, we develop and benchmark multiple machine learning models to predict survival in pan-cancer and 16 single-cancer settings using a de-identified clinico-genomic database of 28,079 US patients with cancer. We identify key predictors of cancer prognosis, including 15 shared across seven or more cancer types, revealing strong consistency in cancer prognostic factors. We demonstrate that pan-cancer models generally outperform or match single-cancer models in predicting survival and risk stratifying patients, especially in smaller cancer cohorts, suggesting a unique transfer learning advantage of pan-cancer models. This work demonstrates the potential of pan-cancer approaches in enhancing the accuracy and applicability of prognostic models in oncology, paving the way for more personalized and effective cancer care strategies.
Interferon signaling in the nasal epithelium distinguishes among lethal and common cold respiratory viruses and is critical for viral clearance
Authors: Otter Clayton J. , Renner David M. , Fausto Alejandra , Tan Li Hui , Cohen Noam A. , Weiss Susan R.
Published: December 2023

All respiratory viruses establish primary infections in the nasal epithelium, where efficient innate immune induction may prevent dissemination to the lower airway and thus minimize pathogenesis. Human coronaviruses (HCoVs) cause a range of pathologies, but the host and viral determinants of disease during common cold versus lethal HCoV infections are poorly understood. We model the initial site of infection using primary nasal epithelial cells cultured at air-liquid interface (ALI). HCoV-229E, HCoV-NL63 and human rhinovirus-16 are common cold-associated viruses that exhibit unique features in this model: early induction of antiviral interferon (IFN) signaling, IFN-mediated viral clearance, and preferential replication at nasal airway temperature (33°C) which confers muted host IFN responses. In contrast, lethal SARS-CoV-2 and MERS-CoV encode antagonist proteins that prevent IFN-mediated clearance in nasal cultures. Our study identifies features shared among common cold-associated viruses, highlighting nasal innate immune responses as predictive of infection outcomes and nasally-directed IFNs as potential therapeutics.
Neuropathological assessment of the olfactory bulb and tract in individuals with COVID-19
Authors: Lengacher Nathalie A. , Tomlinson Julianna J. , Jochum Ann-Kristin , Franz Jonas , Ali Omar Hasan , Flatz Lukas , Jochum Wolfram , Penninger Josef ,   aSCENT-PD Investigators, Stadelmann-Nessler Christine , Woulfe John M. , Schlossmacher Michael G.
Published: December 2023

The majority of patients with Parkinson disease (PD) experience a loss in their sense of smell and accumulate insoluble α-synuclein aggregates in their olfactory bulbs (OB). Subjects affected by a SARS-CoV-2-linked illness (COVID-19) frequently experience hyposmia. We previously hypothesized that α-synuclein and tau misprocessing could occur following host responses to microbial triggers. Using semiquantitative measurements of immunohistochemical signals, we examined OB and olfactory tract specimens collected serially at autopsies between 2020 and 2023. Deceased subjects comprised 50 adults, which included COVID19+ patients (n=22), individuals with Lewy body disease (e.g., PD and dementia with Lewy bodies (DLB; n=6)), Alzheimer disease (AD; n=3), other non-synucleinopathy-linked degenerative diseases (e.g., progressive supranuclear palsy (PSP; n=2) and multisystem atrophy (MSA; n=1)). Further, we included neurologically healthy controls (HCO; n=9) and those with an inflammation-rich brain disorder as neurological controls (NCO; n=7). When probing for inflammatory changes focusing on anterior olfactory nuclei (AON) using anti-CD68 immunostaining, scores were consistently elevated in NCO and AD cases. In contrast, inflammation on average was not significantly altered in COVID19+ patients relative to controls, although anti-CD68 reactivity in their OB and tracts declined with progression in age. Mild-to-moderate increases in phospho-αSyn and phospho-tau signals were detected in the AON of tauopathy-and synucleinopathy-afflicted brains, respectively, consistent with mixed pathology, as described by others. Lastly, when both sides were available for comparison in our case series, we saw no asymmetry in the degree of pathology of the left versus right OB and tracts. We concluded from our autopsy series that after a fatal course of COVID-19, microscopic changes -when present-in the rostral, intracranial portion of the olfactory circuitry generally reflected neurodegenerative processes seen elsewhere in the brain. In general, inflammation correlated best with the degree of Alzheimer’s-linked tauopathy and declined with progression of age in COVID19+ patients.
Assessing yellow fever outbreak potential and implications for vaccine strategy
Authors: Fraser Keith , Hamlet Arran , Jean Kévin , Ramos Daniel Garkauskas , Romano Alessandro , Horton Jennifer , Cibrelus Laurence , Ferguson Neil , Gaythorpe Katy A.M.
Published: December 2023

Background

Yellow fever (YF), a vector-borne viral hemorrhagic fever, is endemic in tropical regions of Africa and South America, with large vaccination programmes being used for control. However, significant outbreaks have occurred in recent years. Data on infection rates and seroprevalence is often sparse, requiring robust mathematical models to estimate the burden of yellow fever. In particular, modelling is required to estimate the risk of outbreaks and inform policy decisions regarding the targeting of vaccination.

Methods

We present a dynamic, stochastic model of YF transmission which uses environ-mental covariates to estimate the force of infection due to spillover from the sylvatic (non-human primate) reservoir and the basic reproduction number for human-to-human transmission. We examine the potential for targets identified by the World Health Organization EYE Strategy (50%, 60% or 80% vaccination coverage in 1-60 year olds) to achieve different threshold values for the effective reproduction number. Threshold values are chosen to reflect the potential for seasonal and/or climatic variation in YF transmission even in a scenario where vaccination lowers the median reproduction number below 1.

Results

Based on parameter estimates derived from epidemiological data, it is found that the 2022 EYE Strategy target coverage is sufficient to reduce the static averaged annual effective reproduction numberRbelow 1 across most or all regions in Africa depending on the effectiveness of reported vaccinations, but insufficient to reduce it below 0.5 and thereby eliminate outbreaks in areas with high seasonal range. Coverage levels aligned with the 2026 targets are found to significantly decrease the proportion of regions whereRis greater than 0.5.
The molecular landscape of premature aging diseases defined by multilayer network exploration
Authors: Beust Cécile , Valdeolivas Alberto , Baptista Anthony , Brière Galadriel , Lévy Nicolas , Ozisik Ozan , Baudot Anaïs
Published: December 2023

Premature Aging (PA) diseases are rare genetic disorders that mimic some aspects of physiological aging at an early age. Various causative genes of PA diseases have been identified in recent years, providing insights into some dysfunctional cellular processes. However, the identification of PA genes also revealed significant genetic heterogeneity and highlighted the gaps in our understanding of PA-associated molecular mechanisms. Furthermore, many patients remain undiagnosed. Overall, the current lack of knowledge about PA diseases hinders the development of effective diagnosis and therapies and poses significant challenges to improving patient care.

Here, we present a network-based approach to systematically unravel the cellular functions disrupted in PA diseases. Leveraging a network community identification algorithm, we delved into a vast multilayer network of biological interactions to extract the communities of 67 PA diseases from their 132 associated genes. We found that these communities can be grouped into six distinct clusters, each reflecting specific cellular functions: DNA repair, cell cycle, transcription regulation, inflammation, cell communication, and vesicle-mediated transport. We propose that these clusters collectively represent the landscape of the molecular mechanisms that are perturbed in PA diseases, providing a framework for better understanding their pathogenesis. Intriguingly, most clusters also exhibited a significant enrichment in genes associated with physiological aging, suggesting a potential overlap between the molecular underpinnings of PA diseases and natural aging.
Neratinib Synergizes with Trastuzumab Antibody Drug Conjugate or with Vinorelbine to Treat HER2 Mutated Breast Cancer Patient Derived Xenografts and Organoids
Authors: Li Shunqiang , Primeau Tina M. , Highkin Maureen K. , Pratt Stephanie L. , Tipton Ashley R. , Vemalapally Nagalaxmi , Monsey John , Tao Yu , Luo Jingqin , Hagemann Ian S. , Lin Chieh-Yu , Eli Lisa D. , Ma Cynthia X. , Bose Ron
Published: December 2023

HER2 (ERBB2) is a major therapeutic drug target in breast cancer and The Cancer Genome Atlas (TCGA) Breast Cancer project and other studies have identified HER2 activating mutations in breast cancers without HER2 gene amplification. HER2 activating mutations occur in 2-5% of metastatic breast cancer patients (MBC), and clinical trials have shown that the irreversible pan-HER tyrosine kinase inhibitor, neratinib, produces a 31-40% clinical benefit rate for HER2 mutated MBC patients. We developed breast cancer patient-derived xenografts (PDX) from ER+, HER2 mutated MBC patients and used them to test neratinib-based drug combinations. Using organoid culture of these PDX breast cancer cells, we performed rapid, high-throughputex vivoscreening assays to test novel drug combinations. These organoid culture experiments identified drug synergy with the neratinib plus ado-trastuzumab emtansine (T-DM1) and neratinib plus vinorelbine combinations and we validated these results within vivoPDX experiments.

Statement of Significance

PDX’s are a ready source of human cancer organoids, and with thousands of PDX’s already available worldwide, PDX derived organoids (PDxO’s) can dramatically accelerate cancer drug testing. This strategy of PDxO drug testing is particularly useful for rare cancer subtypes or mutations to identify the most promising treatment strategies for clinical trials testing.
Conformational states of the microtubule nucleator, the γ-tubulin ring complex
Authors: Romer Brianna , Travis Sophie M. , Mahon Brian P. , McManus Collin T. , Jeffrey Philip D. , Coudray Nicolas , Raghu Rishwanth , Rale Michael J. , Zhong Ellen D. , Bhabha Gira , Petry Sabine
Published: December 2023

Microtubules (MTs) perform essential functions in the cell, and it is critical that they are made at the correct cellular location and cell cycle stage. This nucleation process is catalyzed by the γ-tubulin ring complex (γ-TuRC), a cone-shaped protein complex composed of over 30 subunits. Despite recent insight into the structure of vertebrate γ-TuRC, which shows that its diameter is wider than that of a MT, and that it exhibits little of the symmetry expected for an ideal MT template, the question of how γ-TuRC achieves MT nucleation remains open. Here, we utilized single particle cryo-EM to identify two conformations of γ-TuRC. The helix composed of 14 γ-tubulins at the top of the γ-TuRC cone undergoes substantial deformation, which is predominantly driven by bending of the hinge between the GRIP1 and GRIP2 domains of the γ-tubulin complex proteins. However, surprisingly, this deformation does not remove the inherent asymmetry of γ-TuRC. To further investigate the role of γ-TuRC conformational change, we used cryo electron-tomography (cryo-ET) to obtain a 3D reconstruction of γ-TuRC bound to a nucleated MT, providing insight into the post-nucleation state. Rigid-body fitting of our cryo-EM structures into this reconstruction suggests that the MT lattice is nucleated by spokes 2 through 14 of the γ-tubulin helix, which entails spokes 13 and 14 becoming more structured than what is observed in apo γ-TuRC. Together, our results allow us to propose a model for conformational changes in γ-TuRC and how these may facilitate MT formation in a cell.
Regulation of lactose and galactose growth: Insights from a unique metabolic gene cluster inCandida intermedia
Authors: Peri Kameshwara V. R. , Yuan Le , Oliveira Fábio Faria , Persson Karl , Alalam Hanna D , Olsson Lisbeth , Larsbrink Johan , Kerkhoven Eduard J , Geijer Cecilia
Published: December 2023

Lactose assimilation is a relatively rare trait in yeasts, andKluyveromycesyeast species have long served as model organisms for studying lactose metabolism. Meanwhile, the metabolic strategies of most other lactose-assimilating yeasts remain unknown. In this work, we have elucidated the genetic determinants of the superior lactose-growing yeastCandida intermedia. Through genomic and transcriptomic analyses and deletion mutant phenotyping, we identified three interdependent gene clusters responsible for the metabolism of lactose and its hydrolysis product galactose: the conservedLACcluster (LAC12, LAC4) for lactose uptake and hydrolysis, the conservedGALcluster (GAL1, GAL7, GAL10) for galactose catabolism, and a unique “GALLAC”cluster. This novelGALLACcluster, which has evolved through gene duplication and divergence, proved indispensable forC. intermedia’sgrowth on lactose and galactose. The cluster contains the transcriptional activator geneLAC9, second copies ofGAL1andGAL10and theXYL1gene encoding an aldose reductase involved in carbon overflow metabolism. Notably, the regulatory network inC. intermedia, governed by Lac9 and Gal1 from theGALLACcluster, differs significantly from the (ga)lactose regulons inSaccharomyces cerevisiae,Kluyveromyces lactisandCandida albicans. Moreover, although lactose and galactose metabolism are closely linked inC. intermedia, our results also point to important regulatory differences. This study paves the way to a better understanding of lactose and galactose metabolism inC. intermediaand provides new evolutionary insights into yeast metabolic pathways and regulatory networks. In extension, the results will facilitate future development and use ofC. intermediaas a cell-factory for conversion of lactose-rich whey into value-added products.
Excitable Rho dynamics drive cell contractions by sequentially inducing ERM protein-mediated actin-membrane attachment and actomyosin contractility
Authors: Marshall-Burghardt Seph , Migueles-Ramírez Rodrigo A. , Lin Qiyao , El Baba Nada , Saada Rayan , Umar Mustakim , Hayer Arnold
Published: December 2023

Migration of endothelial and many other cells requires spatiotemporal regulation of protrusive and contractile cytoskeletal rearrangements that drive local cell shape changes. Unexpectedly, the small GTPase Rho, a crucial regulator of cell movement, has been reported to be active in both local cell protrusions and retractions, raising the question of how Rho activity can coordinate cell migration. Here we show that Rho activity is absent in local protrusions and active during retractions. During retractions, Rho rapidly activated ezrin-radixin-moesin proteins (ERMs) to increase actin-membrane attachment, and, with a delay, non-muscle myosin II (NMII). Rho activity was excitable, with NMII acting as a slow negative feedback regulator. Strikingly, inhibition of SLK/LOK kinases, through which Rho activates ERMs, caused elongated cell morphologies, impaired Rhoinduced cell contractions, and reverted Rho-induced blebbing. Together, our study demonstrates that Rho activity drives retractions by sequentially enhancing ERM-mediated actin-membrane attachment for force transmission and NMII-dependent contractility.
The potential role of liquid-liquid phase separation in the cellular fate of the compartments for unconventional protein secretion
Authors: Mendes Luis Felipe S. , Gimenes Carolina O. , Silva Marília D. O. da , Rout Saroj K. , Riek Roland , Costa-Filho Antonio J.
Published: December 2023

Eukaryotic cells have developed sophisticated mechanisms for biomolecule transport, particularly under stress conditions. This study focuses on the unconventional protein secretion (UPS) pathways activated during starvation stress, facilitating the export of soluble leaderless proteins. Specifically, we examine the role of the GRASP family, which is crucial in these processes but has largely unexplored mechanisms, especially regarding the biogenesis and cargo recruitment for the vesicular-like compartment for UPS. Our results reveal that under the circumstances mimicking starvation conditions in yeast, liquid-liquid phase separation (LLPS) is instrumental in the self-association of Grh1, the yeast homologue of GRASP. This association is likely a precursor to the biogenesis of the so-called Compartment for Unconventional Protein Secretion. We demonstrate that Grh1’s self-association involves complex interactions and is regulated by electrostatic, hydrophobic, and hydrogen-bonding forces. Importantly, our study shows that phase-separated states of Grh1 can recruit UPS cargo under starvation-like situations, a significant finding given the minimal interaction between these proteins under normal conditions. Additionally, we address how droplet ageing might affect the ability of cells to return to normal post-stress states. Our findings can potentially enhance our understanding of intracellular protein dynamics and their adaptive responses to stress in eukaryotic cells.
CDCA7 is a hemimethylated DNA adaptor for the nucleosome remodeler HELLS
Authors: Wassing Isabel E. , Nishiyama Atsuya , Hiruta Moeri , Jia Qingyuan , Shikimachi Reia , Kikuchi Amika , Sugimura Keita , Hong Xin , Chiba Yoshie , Peng Junhui , Jenness Christopher , Nakanishi Makoto , Zhao Li , Arita Kyohei , Funabiki Hironori
Published: December 2023

Mutations of the SNF2 family ATPase HELLS and its activator CDCA7 cause immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome, characterized by hypomethylation at heterochromatin. The unique zinc-finger domain, zf-4CXXC_R1, of CDCA7 is widely conserved across eukaryotes but is absent from species that lack HELLS and DNA methyltransferases, implying its specialized relation with methylated DNA. Here we demonstrate that zf-4CXXC_R1 acts as a hemimethylated DNA sensor. The zf-4CXXC_R1 domain of CDCA7 selectively binds to DNA with a hemimethylated CpG, but not unmethylated or fully methylated CpG, and ICF disease mutations eliminated this binding. CDCA7 and HELLS interact via their N-terminal alpha helices, through which HELLS is recruited to hemimethylated DNA. While placement of a hemimethylated CpG within the nucleosome core particle can hinder its recognition by CDCA7, cryo-EM structure analysis of the CDCA7-nucleosome complex suggests that zf-4CXXC_R1 recognizes a hemimethylated CpG in the major groove at linker DNA. Our study provides insights into how the CDCA7-HELLS nucleosome remodeling complex uniquely assists maintenance DNA methylation.
Network-based anomaly detection algorithm reveals proteins with major roles in human tissues
Authors: Kagan Dima , Jubran Juman , Yeger-Lotem Esti , Fire Michael
Published: December 2023

Background

Anomaly detection in graphs is critical in various domains, notably in medicine and biology, where anomalies often encapsulate pivotal information. Here, we focused on network analysis of molecular interactions between proteins, which is commonly used to study and infer the impact of proteins on health and disease. In such a network, an anomalous protein might indicate its impact on the organism’s health.

Results

We propose Weighted Graph Anomalous Node Detection (WGAND), a novel machine learning-based method for detecting anomalies in weighted graphs. WGAND is based on the observation that edge patterns of anomalous nodes tend to deviate significantly from expected patterns. We quantified these deviations to generate features, and utilized the resulting features to model the anomaly of nodes, resulting in node anomaly scores. We created four variants of the WGAND methods and compared them to two previously-published (baseline) methods. We evaluated WGAND on data of protein interactions in 17 human tissues, where anomalous nodes corresponded to proteins with major roles in tissue contexts. In 13 of the tissues, WGAND obtained higher AUC and P@K than baseline methods. We demonstrate that WGAND effectively identified proteins that participate in tissue-specific processes and diseases.

Conclusion

We present WGAND, a new approach to anomaly detection in weighted graphs. Our results underscore its capability to highlight critical proteins within protein-protein interaction networks. WGAND holds the promise to enhance our understanding of intricate biological processes and might pave the way for novel therapeutic strategies targeting tissue-specific diseases. Its versatility ensures its applicability across diverse weighted graphs, making it a robust tool for detecting anomalous nodes.
The dual role of Spn-E in supporting heterotypic ping-pong piRNA amplification in silkworms
Authors: Izumi Natsuko , Shoji Keisuke , Negishi Lumi , Tomari Yukihide
Published: December 2023

The PIWI-interacting RNA (piRNA) pathway plays a crucial role in silencing transposons in the germline. piRNA-guided target cleavage by PIWI proteins triggers biogenesis of new piRNAs from the cleaved RNA fragments. This process, known as the ping-pong cycle, is mediated by the two PIWI proteins, Siwi and BmAgo3, in silkworms. However, the detailed molecular mechanism of the ping-pong cycle remains largely unclear. Here, we show that Spindle-E (Spn-E), a putative ATP-dependent RNA helicase, is essential for BmAgo3-dependent production of Siwi-bound piRNAs in the ping-pong cycle and that this function of Spn-E requires its ATPase activity. Moreover, Spn-E acts to suppress homotypic Siwi-Siwi ping-pong, but this function of Spn-E is independent of its ATPase activity. These results highlight the dual role of Spn-E in facilitating proper heterotypic ping-pong in silkworms.
A FUNCTIONAL PERSPECTIVE ON THE CONDITIONAL COVARIANCE COMPARISON PROBLEM IN DEMENTIA ANALYSIS
Authors: Guan Calvin , Gangopadhyay Ashis
Published: December 2023

Although there are many methods to compare the covariance structures of two populations available in the literature, few are suitable for clinical application due to the inability to account for covariate(s) that affect the dependence structure of the variables being investigated. A common method is to adjust the effect of the covariates via a linear model and work with the resulting residuals. However, removing the effects of the covariates could potentially eliminate valuable information from the analysis. We propose a functional nonparametric covariance matrix estimator to account for any given value in the covariate(s), which allows a comparison of the functional covariance structures of the multivariate data. This comparison is facilitated via a test statistic involving the first eigenvalue of the combined form of covariance matrices of the two groups. Three different approaches, namely, the parametric Tracy-Widom, the semi-parametric Forkman’s test, and the nonparametric Permutation method, are used to compute the approximate p-values of the test statistic. We have conducted extensive simulation studies to determine the type I error and power of the proposed hypothesis testing methods and developed practical recommendations for implementing this novel approach. Finally, we apply our methods to the Alzheimer’s Disease Neuroimaging Initiative (ADNI) study to compare cerebrospinal fluid (CSF) biomarkers between dementia and non-dementia cohorts, which offers a fascinating insight into the differences between covariance structures of biomarkers amyloidβ(1-42) (Aβ42), total tau (tau), and phosphorylated tau (ptau) for given values of age, sex, and years of education.
Carotenoid composition and sequestration in cassava (Manihot esculentumCrantz) roots
Authors: Drapal Margit , Ovalle Rivera Tatiana M. , Becerra Lopez-Lavalle Luis Augusto , Fraser Paul D.
Published: December 2023

Cassava (Manihot esculentum Crantz) is a staple food source for many developing countries. Its edible roots are high in starch but lack micronutrients such as β-carotene. In the present study, analysis of pedigree breeding populations has led to the identification of cassava accessions with enhanced β-carotene contents up to 40 μg/g DW. This represents 0.2% of the Recommended Daily Allowance (RDA) for vitamin A. The β-branch of the carotenoid pathway predominates in cassava roots, with dominant levels of β-carotene followed by other minor epoxides of β-ring derived carotenoids. Metabolomic analysis revealed that steady state levels of intermediary metabolism were not altered by the formation of carotenoids, similar to starch and carbohydrate levels. Apocarotenoids appeared to be independent of their carotenoid precursors. Lipidomic analysis provided evidence of a significant positive correlation between carotenoid and lipid content, in particular plastid specific galactolipids. Proteomic analysis of isolated amyloplasts revealed an abundance of carbohydrate/starch biosynthetic associated proteins (e.g. glucose-1-phosphate adenylyltransferase). No carotenoid related proteins were detected even in the highest carotenoid containing lines. Carotenoids were associated with fractions typically annotated as plastoglobuli and plastid membranes (particularly the envelope). Proteomic analysis confirmed these structures apart from plastoglobuli, thus potentially amyloplast structures may not contain classical plastoglobuli structures.

Highlight

Cassava genotypes with enhanced provitamin A content (β-carotene) reveals interconnectivity between the carotenoid pathway, starch and lipid biosynthesis.
Reversal of pathologic changes in fibroblasts from Niemann-Pick type C disease patients by inhibition of bromodomain and extraterminal proteins
Authors: Parente Martina , Barthelemy Amélie , Tonini Claudia , Sacchi Alessandra , Leone Stefano , Segatto Marco , Pfrieger Frank W. , Pallottini Valentina
Published: December 2023

Niemann-Pick type C disease (NPCD) is a lysosomal disorder whith patients presenting highly variable onset, neurovisceral symptoms and life spans due to defective lipid homeostasis. At present, therapeutic options are limited to palliative and disease-modifying drugs, and there is a continued need for new approaches. Here, we explored bromodomain and extraterminal (BET) proteins as new drug target for NPCD using patient-derived fibroblasts. Treatment of cells with JQ1, a prototype BET inhibitor, enhanced the level of NPC1 protein and increased its presence in lysosomes, diminished lysosomal expansion and cholesterol accumulation and induced extracellular release of lysosomal components in a time- and dose-dependent manner. The reversal of pathologic changes in an established cell model suggest inhibition of BET protein as new therapeutic approach for NPCD.
Intraspecific density changes the impact of interspecific competitors on parasite infection traits in multiple infections
Authors: Godinho Diogo P. , Rodrigues Leonor R. , Lefèvre Sophie , Magalhães Sara , Duncan Alison B.
Published: December 2023

Co-infections are frequent, with consequences for parasite life-history traits expressed at within- and between-host levels. However, little is known about whether the effect of interspecific competitors on traits are correlated or independent or if they change with intraspecific competition. To address this, we investigated the occurrence of genetic correlations among within- and betweenhost traits at different intra-specific densities of inbred lines of the spider mite,Tetranychus urticaewith its competitorT. evansi. First, we foundT. evansipresence on a shared host leaf produced a negative (non-genetic) correlation between virulence (leaf damage) and number of daughters (transmitting stages) at intermediate intraspecific densities; this same relationship was not significant without competitors. Second, we show interspecific competitors increases transmission to adjacent leaf discs, measured as movement of adultT. urticaefemales, but only at low and intermediate intraspecific densities. Finally we tested whether within-host traits (virulence and transmitting stages) were correlated with between-host traits (movement to adjacent patches), with or without competitors, at different conspecific densities. We found traits were mostly independent; interspecific competitors may increase transmission across hosts without affecting virulence (or vice versa). These independent effects on within- and between-host traits indicate competition may impact epidemiology and parasite trait evolution.
Dynamical structure-function correlations provide robust and generalizable signatures of consciousness in humans
Authors: Castro Pablo , Luppi Andrea , Tagliazucchi Enzo , S-Perl Yonatan , Naci Lorina , Owen Adrian M. , Sitt Jacobo D. , Destexhe Alain , Cofré Rodrigo
Published: December 2023

Resting-state functional magnetic resonance imaging evolves through a repertoire of functional connectivity patterns which might reflect ongoing cognition, as well as the contents of conscious awareness. We investigated whether the dynamic exploration of these states can provide robust and generalizable markers for the state of consciousness in human participants, across loss of consciousness induced by general anaesthesia or slow wave sleep. By clustering transient states of functional connectivity, we demonstrated that brain activity during unconsciousness is dominated by a recurrent pattern primarily mediated by structural connectivity and with a reduced capacity to transition to other patterns. Our results provide evidence supporting the pronounced differences between conscious and unconscious brain states in terms of whole-brain dynamics; in particular, the maintenance of rich brain dynamics measured by entropy is a critical aspect of conscious awareness. Collectively, our results may have significant implications for our understanding of consciousness and the neural basis of human awareness, as well as for the discovery of robust signatures of consciousness that are generalizable among different brain conditions.
Emergence of a senescent and inflammatory pulmonary CD4+T cell population prior to lung allograft failure
Authors: Moshkelgosha Sajad , Levy Liran , Safavi Shahideh , Karunagaran Sumiha , Wilson Gavin , Renaud-Picard Benjamin , Madu Goodness , Ramchandani Rashi , Oliver Jillian , Watanabe Tatsuaki , Bei Ke Fan , Joe Betty , Li Qixuan , Huszti Ella , Cheung May , Hedley David , Yeung Jonathan , Keshavjee Shaf , Martinu Tereza , Juvet Stephen
Published: December 2023

Lung transplantation is a life-saving therapy for end-stage pulmonary disease, but its long-term outlook is poor due to a high incidence of chronic lung allograft dysfunction (CLAD). CLAD results from alloimmune-mediated progressive fibrosis and culminates in death or the need for re-transplantation after a median of 6 years. Existing immunosuppression fails to prevent CLAD, suggesting the existence of alloimmune pathways resistant to these drugs. Here, we used mass cytometry to identify cell populations enriched in the bronchoalveolar lavage (BAL) of patients with subsequent allograft dysfunction. We show that CD4+CD57+PD1+T cells emerge in stable lung transplant recipients in the first year post-transplant, conferring heightened risks for CLAD and death or re-transplantation. CD4+CD57+PD1+T cells display features of senescence and secrete inflammatory cytokines. Cellular indexing by transcriptomes and epitopes (CITE-Seq) on BAL CD4+T cells revealed the existence of 2 oligoclonal CD57+subsets with putative cytotoxic and follicular helper functions. Finally, we observed that CD4+CD57+PD1+T cells are associated with lung allograft fibrosis in a mouse model and in human explanted CLAD lungs, where they localize near airway epithelium and B cells. Together, our findings reveal the existence of an inflammatory T cell population that predicts future lung allograft dysfunction and may represent a rational therapeutic target in lung transplant recipients.
Concurrent action observation but not motor imagery modulates interhemispheric inhibition during physical execution
Authors: Vallido Kyle A. , Scott Matthew W. , Peters Carrie M. , Spriggs Kelly , Hodges Nicola J. , Kraeutner Sarah N.
Published: December 2023

Motor control relies on an inhibitory connection between the motor cortices of the brain, known as interhemispheric inhibition (IHI). This phenomenon is well established during the execution of unilateral motor tasks. It is unknown if the neurophysiological effects associated with IHI during physical execution (PE) also occur during action observation (AO) and motor imagery (MI) and/or if the addition of these covert processes to PE moderates IHI; speaking to differences in neurophysiology and functional equivalence. Participants (N=23) performed unilateral concentric wrist contractions (50% maximum voluntary contraction) under three conditions: PE alone, concurrent PE+AO, and concurrent PE+MI. To index IHI, we induced an ipsilateral silent period (iSP) and assessed iSP duration during each condition via neuro-navigated single-pulse transcranial magnetic stimulation (TMS) over the ipsilateral motor cortex. Relative to PE alone, iSP decreased during PE+AO, yet only when this condition preceded PE+MI. iSP duration was not modulated during PE+MI. Together, these data suggest that PE+AO promotes bilateral recruitment and ‘interhemispheric cooperation’ rather than inhibition. AO and MI differentially impact interhemispheric coordination, serving to suppress inhibition only when AO is primed by MI.
Modulation of prion protein expression through cryptic splice site manipulation
Authors: Gentile Juliana E. , Corridon Taylor L. , Mortberg Meredith A. , D’Souza Elston Neil , Whiffin Nicola , Minikel Eric Vallabh , Vallabh Sonia M.
Published: December 2023

Lowering expression of prion protein (PrP) is a well-validated therapeutic strategy in prion disease, but additional modalities are urgently needed. In other diseases, small molecules have proven capable of modulating pre-mRNA splicing, sometimes by forcing inclusion of cryptic exons that reduce gene expression. Here, we characterize a cryptic exon located in humanPRNP’s sole intron and evaluate its potential to reduce PrP expression through incorporation into the 5’ untranslated region (5’UTR). This exon is homologous to exon 2 in non-primate species, but contains a start codon that would yield an upstream open reading frame (uORF) with a stop codon prior to a splice site if included inPRNPmRNA, potentially downregulating PrP expression through translational repression or nonsense-mediated decay. We establish a minigene transfection system and test a panel of splice site alterations, identifying mutants that reduce PrP expression by as much as 78%. Our findings nominate a new therapeutic target for lowering PrP.
Reinforcement Learning for Control of Human Locomotion in Simulation
Authors: Dashkovets Andrii , Laschowski Brokoslaw
Published: December 2023

Control of robotic leg prostheses and exoskeletons is an open challenge. Computer modeling and simulation can be used to study the dynamics and control of human walking and extract principles that can be programmed into robotic legs to behave similar to biological legs. In this study, we present the development of an efficient two-layer Q-learning algorithm, with k-d trees, that operates over continuous action spaces and a reward model that estimates the degree of muscle activation similarity between the agent and human state-to-action pairs and state-to-action sequences. We used a human musculoskeletal model acting in a high-dimensional, physics-based simulation environment to train and evaluate our algorithm to simulate biomimetic walking. We used imitation learning and artificial bio-mechanics data to accelerate training via expert demonstrations and used experimental human data to compare and validate our predictive simulations, achieving 79% accuracy. Also, when compared to the previous state-of-the-art that used deep deterministic policy gradient, our algorithm was significantly more efficient with lower computational and memory storage requirements (i.e., requiring 7 times less RAM and 87 times less CPU compute), which can benefit real-time embedded computing. Overall, our new two-layer Q-learning algorithm using sequential data for continuous imitation of human locomotion serves as a first step towards the development of bioinspired controllers for robotic prosthetic legs and exoskeletons. Future work will focus on improving the prediction accuracy compared to experimental data and expanding our simulations to other locomotor activities.
ElectroPhysiomeGAN: Generation of Biophysical Neuron Model Parameters from Recorded Electrophysiological Responses
Authors: Kim Jimin , Peng Minxian , Chen Shuqi , Liu Qiang , Shlizerman Eli
Published: December 2023

Recent advances in connectomics, biophysics, and neuronal electrophysiology warrant modeling of neurons with further details in both network interaction and cellular dynamics. Such models may be referred to as ElectroPhysiome, as they incorporate the connectome and individual neuron electrophysiology to simulate neuronal activities. The nervous system ofC. elegansis considered a viable framework for such ElectroPhysiome studies due to advances in connectomics of its somatic nervous system and electrophysiological recordings of neuron responses. In order to achieve a simulated ElectroPhysiome, the set of parameters involved in modeling individual neurons need to be estimated from electrophysiological recordings. Here, we address this challenge by developing a deep generative estimation method called ElectroPhysiomeGAN (EP-GAN), which once trained, can instantly generate parameters associated with the Hodgkin-Huxley neuron model (HH-model) for multiple neurons with graded potential response. The method combines Generative Adversarial Network (GAN) architecture with Recurrent Neural Network (RNN) Encoder and can generate an extensive number of parameters (>170) given the neuron’s membrane potential responses and steady-state current profiles. We validate our method by estimating HH-model parameters for 200 synthetic neurons with graded membrane potential followed by 9 experimentally recorded neurons (where 6 of them newly recorded) in the nervous system ofC. elegans. Comparison of EP-GAN with existing estimation methods shows EP-GAN advantage in the accuracy of estimated parameters and in the inference speed. The advantage is especially significant when a large number of parameters is being inferred. In addition the architecture of EP-GAN permits inference of parameters even when partial membrane potential and steady-state currents profile are given as inputs. EP-GAN is designed to leverage the generative capability of GAN to align with the dynamical structure of HH-model, and thus able to achieve such performance.
CRISPRi screens identify the lncRNA,LOUP,as a multifunctional locus regulating macrophage differentiation epigenetically and inflammatory signaling through a short, encoded peptide
Authors: Halasz Haley , Malekos Eric , Covarrubias Sergio , Yitiz Samira , Montano Christy , Sudek Lisa , Katzman Sol , John Liu S , Holbeck Max A. , Weissman Jonathan S , Carpenter Susan
Published: December 2023

Long non-coding RNAs (lncRNAs) account for the largest portion of RNA from the transcriptome, yet most of their functions remain unknown. Here we performed two independent high-throughput CRISPRi screens to understand the role of lncRNAs in monocyte function and differentiation. The first was a reporter-based screen to identify lncRNAs that regulate TLR4-NFkB signaling in human monocytes and the second screen identified lncRNAs involved in monocyte to macrophage differentiation. We successfully identified numerous novel non-coding and protein-coding genes that can positively or negatively regulate inflammation and differentiation. To understand the functional roles of lncRNAs in both processes, we chose to further study the lncRNALOUP(lncRNA originating from upstream regulatory element ofSPI1[also known as PU.1]), as it emerged as a top hit in both screens. Not only doesLOUPregulate its neighboring gene, the myeloid fate determining factorSPI1, thereby affecting monocyte to macrophage differentiation, but knockdown ofLOUPleads to a broad upregulation of NFkB-targeted genes at baseline and upon TLR4-NFkB activation.LOUPalso harbors three small open reading frames (sORFs) capable of being translated and are responsible forLOUP’s ability to negatively regulate TLR4/NFkB signaling. This work emphasizes the value of high-throughput screening to rapidly identify functional lncRNAs in the innate immune system.
A bipolar taxonomy of adult human brain sulcal morphology related to timing of fetal sulcation and trans-sulcal gene expression gradients
Authors: Snyder William E. , Vértes Petra E. , Kyriakopoulou Vanessa , Wagstyl Konrad , Williams Logan Z. J. , Moraczewski Dustin , Thomas Adam G. , Karolis Vyacheslav R. , Seidlitz Jakob , Rivière Denis , Robinson Emma C. , Mangin Jean-Francois , Raznahan Armin , Bullmore Edward T.
Published: December 2023

We developed a computational pipeline (now provided as a resource) for measuring morphological similarity between cortical surface sulci to construct a sulcal phenotype network (SPN) from each magnetic resonance imaging (MRI) scan in an adult cohort (N=34,725; 45-82 years). Networks estimated from pairwise similarities of 40 sulci on 5 morphological metrics comprised two clusters of sulci, represented also by the bipolar distribution of sulci on a linear-to-complex dimension. Linear sulci were more heritable and typically located in unimodal cortex; complex sulci were less heritable and typically located in heteromodal cortex. Aligning these results with an independent fetal brain MRI cohort (N=228; 21-36 gestational weeks), we found that linear sulci formed earlier, and the earliest and latest-forming sulci had the least between-adult variation. Using high-resolution maps of cortical gene expression, we found that linear sulcation is mechanistically underpinned by trans-sulcal gene expression gradients enriched for developmental processes.
The Garden of Forking Paths: Reinterpreting Haseman-Elston Regression for a Genotype-by-Environment Model
Authors: Chen Guo-Bo
Published: December 2023

Haseman-Elston regression (HE-reg) has been known as a classic tool for detecting an additive genetic variance component. However, in this study we find that HE-reg can capture GxE under certain conditions, so we derive and reinterpret the analytical solution of HE-reg. In the presence of GxE, it leads to a natural discrepancy of linkage and association results, the latter of which is not able to capture GxE if the environment is unknown. Considering linkage and association as symmetric designs, we investigate how the symmetry can and cannot hold in the absence and presence of GxE, and consequently we propose a pair of statistical tests, Symmetry Test I and Symmetry Test II, both of which can be tested using summary statistics. Test statistics, and their statistical power issues are also investigated for Symmetry Tests I and II. Increasing the number of sib pairs is important to improve statistical power for detecting GxE.
Sensitization of Human and Rat Nociceptors by Low Dose Morphine is TLR4-dependent
Authors: Khomula Eugen V. , Levine Jon D.
Published: December 2023

While opioids remain amongst the most effective treatments for moderate-to-severe pain, their substantial side effect profile remains a major limitation to broader clinical use. One such side effect is opioid-induced hyperalgesia (OIH), which includes a transition from opioid-induced analgesia to pain enhancement. Evidence in rodents supports the suggestion that OIH may be produced by the action of opioids at Toll-like Receptor 4 (TLR4) either on immune cells that, in turn, produce pronociceptive mediators to act on nociceptors, or by a direct action at nociceptor TLR4. And, sub-analgesic doses of several opioids have been shown to induce hyperalgesia in rodents by their action as TLR4 agonists. In the presentin vitropatch-clamp electrophysiology experiments, we demonstrate that low dose morphine directly sensitizes human as well as rodent dorsal root ganglion (DRG) neurons, an effect of this opioid analgesic that is antagonized by LPS-RS Ultrapure, a selective TLR4 antagonist. We found that morphine (100 nM) reduced rheobase in human (by 36%) and rat (by 26%) putative C-type nociceptors, an effect of morphine that was markedly attenuated by preincubation with LPS-RS Ultrapure. Our findings support the suggestion that in humans, as well as in rodents, OIH is mediated by the direct action of opioids at TLR4 on nociceptors.