bluuebunny/crossref_metadata_2025 huggingface dataset:
The Utility of Long-Read Sequencing in Diagnosing Genetic Autosomal Recessive Parkinson’s Disease: a genetic screening study
Authors: Daida Kensuke , Yoshino Hiroyo , Malik Laksh , Baker Breeana , Ishiguro Mayu , Genner Rylee , Paquette Kimberly , Li Yuanzhe , Nishioka Kenya , Masuzugawa Satoshi , Hirano Makito , Takahashi Kenta , Kolmogolv Mikhail , Billingsley Kimberley J , Funayama Manabu , Blauwendraat Cornelis , Hattori Nobutaka
Published: June 2024

Background

Mutations within the genesPRKNandPINK1are the leading cause of early onset autosomal recessive Parkinson’s disease (PD). However, the genetic cause of most early-onset PD (EOPD) cases still remains unresolved. Long-read sequencing has successfully identified many pathogenic structural variants that cause disease, but this technology has not been widely applied to PD. We recently identified the genetic cause of EOPD in a pair of monozygotic twins by uncovering a complex structural variant that spans over 7 Mb, utilizing Oxford Nanopore Technologies (ONT) long-read sequencing. In this study, we aimed to expand on this and assess whether a second variant could be detected with ONT long-read sequencing in other unresolved EOPD cases reported to carry one heterozygous variant inPRKNorPINK1.

Methods

ONT long-read sequencing was performed on patients with one reportedPRKN/PINK1pathogenic variant. EOPD patients with an age at onset younger than 50 were included in this study. As a positive control, we also included EOPD patients who had already been identified to carry two knownPRKNpathogenic variants. Initial genetic testing was performed using either short-read targeted panel sequencing for single nucleotide variants and multiplex ligation-dependent probe amplification (MLPA) for copy number variants.

Results

48 patients were included in this study (PRKN“one-variant” n = 24,PINK1“one-variant” n = 12,PRKN“two-variants” n = 12). Using ONT long-read sequencing, we detected a second pathogenic variant in sixPRKN“one-variant” patients (26%, 6/23) but none in thePINK1“one-variant” patients (0%, 0/12). Long-read sequencing identified one case with a complex inversion, two instances of structural variant overlap, and three cases of duplication. In addition, in the positive controlPRKN“two-variants” group, we were able to identify both pathogenic variants inPRKNin all the patients (100%, 12/12).

Conclusions

This data highlights that ONT long-read sequencing is a powerful tool to identify a pathogenic structural variant at thePRKNlocus that is often missed by conventional methods. Therefore, for cases where conventional methods fail to detect a second variant for EOPD, long-read sequencing should be considered as an alternative and complementary approach.
Enhancing genotype-phenotype association with optimized machine learning and biological enrichment methods
Authors: Jangale Vaishnavi , Sharma Jyoti , Shekhawat Rajveer Singh , Yadav Pankaj
Published: June 2024

Genome-wide association studies (GWAS) are surging again owing to newer high-quality T2T-CHM13 and human pangenome references. Conventional GWAS methods have several limitations, including high false negatives. Non-conventional machine learning-based methods are warranted for analyzing newly sequenced, albeit complex, genomic regions.

We present a robust machine learning-based framework for feature selection and association analysis, incorporating functional enrichment analysis to avoid false negatives. We benchmarked four popular single nucleotide polymorphism (SNP) feature selection methods: least absolute shrinkage and selection operator, ridge regression, elastic-net, and mutual information. Furthermore, we evaluated four association methods: linear regression, random forest, support vector regression (SVR), and XGBoost. We assessed proposed framework on diverse datasets, including subsets of publicly available PennCATH datasets as well as imputed, rare-variants, and simulated datasets. Low-density lipoprotein (LDL) cholesterol level was used as a phenotype for illustration. Our analysis revealed elastic-net combined with SVR consistently outperformed other methods across various datasets. Functional annotation of top 100 SNPs from PennCATH-real dataset revealed their expression in LDL cholesterol-related tissues. Our analysis validated three previously known genes (APOB, TRAPPC9, and EEPD1) implicated in cholesterol-regulated pathways. Also, rare-variant dataset analysis confirmed 37 known genes associated with LDL cholesterol. We identified several important genes, including APOB (familial-hypercholesterolemia), PTK2B (Alzheimer’s disease), and PTPN12 (myocardial ischemia/reperfusion injuries) as potential drug targets for cholesterol-related diseases.

Our comprehensive analyses highlight elastic-net combined with SVR for association analysis could overcome limitations of conventional GWAS approaches. Our framework effectively detects common and rare variants associated with complex traits, enhancing the understanding of complex diseases.
Anti-Neuraminidase Antibodies Reduce the Susceptibility to and Infectivity of Influenza A/H3N2 Virus
Authors: Hoy Gregory , Cortier Thomas , Maier Hannah E. , Kuan Guillermina , Lopez Roger , Sanchez Nery , Ojeda Sergio , Plazaola Miguel , Stadlbauer Daniel , Shotwell Abigail , Balmaseda Angel , Krammer Florian , Cauchemez Simon , Gordon Aubree
Published: June 2024

Immune responses against neuraminidase (NA) are of great interest for developing more robust influenza vaccines, but the role of anti-NA antibodies on influenza infectivity has not been established. We conducted household transmission studies in Managua, Nicaragua to examine the impact of anti-NA antibodies on influenza A/H3N2 susceptibility and infectivity. Analyzing these data with mathematical models capturing household transmission dynamics and their drivers, we estimated that having higher preexisting antibody levels against the hemagglutinin (HA) head, HA stalk, and NA was associated with reduced susceptibility to infection (relative susceptibility 0.67, 95% Credible Interval [CrI] 0.50-0.92 for HA head; 0.59, 95% CrI 0.42-0.82 for HA stalk; and 0.56, 95% CrI 0.40-0.77 for NA). Only anti-NA antibodies were associated with reduced infectivity (relative infectivity 0.36, 95% CrI 0.23-0.55). These benefits from anti-NA immunity were observed even among individuals with preexisting anti-HA immunity. These results suggest that influenza vaccines designed to elicit NA immunity in addition to hemagglutinin immunity may not only contribute to protection against infection but reduce infectivity of vaccinated individuals upon infection.
Assessing knowledge, attitudes, and behaviours toward salt and sugar consumption in the Central Division of Fiji
Authors: Waqa Gade , Bell Colin , Santos Joseph Alvin , Rogers Kris , Silatolu Anasaini Moala , Reeve Erica , Palu Aliyah , Deo Alvina , Webster Jacqui , McKenzie Briar
Published: June 2024

Background

Excessive salt and sugar intake influence the global burden of non-communicable diseases. This study aimed to describe the knowledge, attitudes and behaviours (KAB) of Fijian adults relating to salt and sugar consumption to inform policy interventions in Fiji.

Methods

A randomised stratified sample of 700 adults in the Central Division of Fiji were selected. Questions on salt-related KAB were adapted from the World Health Organization Noncommunicable Disease Risk Factor survey, and questions on sugar were developed following a similar structure. Locally trained research assistants collected data. For analyses, population and sample weights were applied, and difference between predefined subgroups (sex, age, ethnicity and area of residence) were compared using weighted chi-square tests.

Results

534 adults participated (response rate,76%). Over 80% of participants (82% (95% CI 78.5 to 84.9%)) identified that consuming too much salt or salty sauce can lead to hypertension. More than 90% recognized that consuming too much sugar can lead to diabetes (92.3% (89.7 to 94.3%)). Approximately 80% of participants thought it was somewhat or very important to lower salt and sugar intake in their diet (79.8% (95%CI, 76.1 to 83.0) and 84.2% (80.8 to 87.1%), respectively). However, self-reported behaviours did not align, with almost 40% adding salt or salty sauces as standard practice when cooking (37.3% (32.7 to 42.2%)) and 65% (60.6 to 68.5%) reporting that they add sugar to drinks daily. Younger compared to older individuals (18 to 44 years vs 45 years and older) and men compared to women, had lower levels of KAB.

Conclusion

Despite having knowledge of the health impacts of consuming excess salt and sugar and positive attitudes towards reducing consumption, many people reported behaviours likely to contribute to high salt and sugar intake. These findings highlight the need for interventions that incentivise healthier choices, through behaviour change communications and the creation of supportive food environments.
Impact of data labeling protocol on the quality of LGE-MRI atrial segmentation
Authors: Berezhnoy A.K. , Kalinin A.S. , Parshin D.A. , Selivanov A.G. , Demin A.G. , Zubov A.G. , Shaidullina R.S. , Aitova A.A. , Slotvitsky M. M. , Kalemberg A.A. , Kirillova V.S. , Syrovnev V.A. , Tsvelaya V.A.
Published: June 2024

Atrial fibrillation affects up to 2% of the adult population in developed countries, and ablation as the main method of treatment leads to a high probability of recurrence. For such procedures, the approach of creating an in silico model of the patient’s atrium to be used for navigation during the catheter ablation procedure itself is extremely promising. In this case, the MRI data on which the model is based must be loaded into the system and segmented with high accuracy. This paper describes a new universal protocol for the segmentation of LGE MRI images. This protocol has been used to train state-of-the-art neural networks for automatic MRI segmentation. It is shown that the new data labeling protocol significantly improves the training quality of the network. Using this approach, it is possible to improve the quality of the reproduction of the patient’s atrial parameters and the performance of all related services. The presented protocol is also accompanied by a labeled image dataset. In the future, the data from such labels can be used for predictive modeling and the creation of digital twins of patients’ atria.
A single center retrospective study to examine the effect of concomitant metformin treatment on cisplatin induced nephrotoxicity in adult HNSCC patients between 2015-2021
Authors: Ellayan Dawud
Published: June 2024

Purpose

Examine the effect of AMPK activation in addition to OCT2 competitive blockage through metformin concomitant treatment on the incidence rate of nephrotoxicity in adult head and neck cancer patients treated with cisplatin-based chemoradiation.

Methods

A single center retrospective three to one controlled study in HNSCC patients treated at a single academic health center between January 1st 2015 to December 31st 2021. Patients treated with cisplatin based chemoradiation regimen at a dose of either 40 mg/m2 weekly, or 100 mg/m2 every 3 weeks for a total of 7 weeks were identified and were divided into two cohorts; Cohort A with patients who received concomitant metformin therapy, where concomitant is defined as taken prior to the time of cisplatin start and continued during treatment. And cohort B with a control group of patients who did not receive metformin during cisplatin treatment.

Results

18 patients were enrolled retrospectively in cohort A and 54 in cohort B. Our data shows a lower incidence of nephrotoxicity than reported in historical controls. However, no statistically significant differences were identified in direct comparison between the two cohorts.

Conclusion

Our data reaffirms the higher risk of nephrotoxicity for patients on Q3weeks regimen compared to weekly regimen, however, we were unable to show a statistically significant effect in direct comparison between the cohorts due to sample size limitation.
The sexual and gender-diverse face more health challenges during COVID-19: A large-scale social media analysis with natural language processing
Authors: Zhang Zhiyun , Hua Yining , Zhou Peilin , Lin Shixu , Li Minghui , Zhang Yujie , Zhou Li , Liao Yanhui , Yang Jie
Published: June 2024

Background:The COVID-19 pandemic has caused a disproportionate impact on the sex and gender diversity (SGD) community. Compared with non-SGD populations, their social relations and health status are more vulnerable, whereas public health data regarding SGD is scarce.Methods:To analyze the concerns and health status of SGD individuals, this cohort study leveraged 471,371,477 tweets from 251,455 SGD and 22,644,411 non-SGD users, spanning from February 1, 2020, to April 30, 2022. The outcome measures comprised the distribution and dynamics of COVID-related topics, attitudes towards vaccines and the prevalence of symptoms.Results:Topic analysis revealed that SGD users engaged more frequently in discussions related to “friends and family” (20.5% vs 13.1%, P<0.001) and “wear masks” (10.1% vs 8.3%, P<0.001) compared to non-SGD users. Additionally, SGD users exhibited a significantly higher proportion of positive sentiment in tweets about vaccines, including Moderna, Pfizer, AstraZeneca, and Johnson & Johnson. Among 102,464 users who self-reported COVID-19 diagnoses, SGD users disclosed significantly higher frequencies of mentioning 61 out of 69 COVID-related symptoms to non-SGD users, encompassing both physical and mental health challenges.Conclusion:The results provide insights to an understanding of the unique needs and experiences of the SGD community during the pandemic, emphasizing the value of social media data in epidemiological and public health research.
Hybrid adaptive immunity to SARS-CoV-2 protects against breakthrough infection after COVID-19 vaccination in ALSPAC participants
Authors: Baum Holly E. , Santopaolo Marianna , Francis Ore , Milowdowski Emily , Entwistle Katrina , Oliver Elizabeth , Hitchings Benjamin , Diamond Divya , Thomas Amy C. , Mitchell Ruth E. , Kibble Milla , Gupta Kapil , Di Bartolo Natalie , Klenerman Paul , Brown Anthony , Morales-Aza Begonia , Oliver Jennifer , Berger Imre , Toye Ash M. , Finn Adam , Goenka Anu , Davidson Andrew D. , Ring Susan , Molloy Lynn , Lewcock Melanie , Northstone Kate , Roth Firona , Timpson Nicholas J. , Wooldridge Linda , Halliday Alice , Rivino Laura
Published: June 2024

Immunological memory to vaccination and viral infection involves coordinated action of B and T-cells, thus integrated analysis of these two components is critical for understanding their contributions to protection against breakthrough infections (BI). We investigated cellular and humoral immune responses to SARS-CoV-2 infection and/or COVID-19 vaccination in participants from the Avon Longitudinal Study of Parents and Children (ALSPAC). The magnitude of antibody and T-cell responses following the second vaccine dose was associated with protection against BI in participants with a history of SARS-CoV-2 infection (cases), but not in infection-naïve controls. Youden’s index thresholds for protection against BI were calculated for all immune measures. Anti-Spike IgG (>666.4 BAU/mL) and anti-Nucleocapsid pan Ig (>0.1332 BAU/mL) thresholds combined were 100% specific and 83.3% sensitive for cases without BI over 8-months follow-up. Collectively these results point to the superior protective effect of hybrid immunity and have implications for the design of next-generation COVID-19 vaccines.
Racial Disparities and Trends in Anticoagulant Use among Ambulatory Care Patients with Atrial Fibrillation and Atrial Flutter in the United States from 2007-2019
Authors: Kan Vincent , Lapane Kate , McManus David , Baek Jonggyu , Darling Chad , Alcusky Matthew
Published: June 2024

Introduction

Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia, significantly increasing the risk of stroke. The introduction of direct oral anticoagulants (DOACs) since 2010 has transformed anticoagulation therapy, offering an alternative to warfarin with improved safety profiles. Despite the increased adoption of DOACs, disparities in their use among different racial and ethnic groups in the United States remain understudied.

Methods

This study utilized a repeated cross-sectional design, analyzing data from the National Ambulatory Medical Care Survey (NAMCS) from 2007 to 2019. The study population included adults diagnosed with AF or atrial flutter (AFL). We analyzed the temporal trends of DOAC and warfarin use from 2007 to 2019. We examined the prevalence of DOAC versus warfarin use and assessed associations between race/ethnicity, patient characteristics, and DOAC utilization from 2011 to 2019. Multivariable modified Poisson regression models were used to calculate adjusted prevalence ratios (aPR) for the associations.

Results

From 2011 to 2019, NAMCS recorded 3,224 visits involving AF or AFL, representing a weighted estimate of 103.6 million visits. DOAC use increased significantly, with apixaban becoming the predominant anticoagulant by 2016. Non-Hispanic Black patients were less likely to use DOACs compared to non-Hispanic White patients over time (aPR 0.75; 95% CI, 0.63-0.90). Patients with Medicaid insurance were also less likely to use DOACs (aPR 0.14; 95% CI: 0.04-0.46).

Conclusion

Despite the shift from warfarin to DOACs for AF and AFL treatment, significant racial and socioeconomic disparities persist. Non-Hispanic Black patients and those with Medicaid insurance are less likely to use DOACs. These findings highlight the need for targeted strategies to ensure equitable access to advanced anticoagulant therapies.
The expression patterns of different cell types and their interactions in the tumor microenvironment are predictive of breast cancer patient response to neoadjuvant chemotherapy
Authors: Dhruba Saugato Rahman , Sahni Sahil , Wang Binbin , Wu Di , Rajagopal Padma Sheila , Schmidt Yael , Shulman Eldad D. , Sinha Sanju , Sammut Stephen-John , Caldas Carlos , Wang Kun , Ruppin Eytan
Published: June 2024

The tumor microenvironment (TME) is a complex ecosystem of diverse cell types whose interactions govern tumor growth and clinical outcome. While the TME’s impact on immunotherapy has been extensively studied, its role in chemotherapy response remains less explored. To address this, we developed DECODEM (DEcouplingCell-type-specificOutcomes usingDEconvolution andMachine learning), a generic computational framework leveraging cellular deconvolution ofbulk transcriptomicsto associate the gene expression of individual cell types in the TME with clinical response. Employing DECODEM to analyze the gene expression of breast cancer (BC) patients treated with neoadjuvant chemotherapy, we find that the gene expression of specific immune cells (myeloid,plasmablasts,B-cells) and stromal cells (endothelial,normal epithelial,CAFs) are highly predictive of chemotherapy response, going beyond that of the malignant cells. These findings are further tested and validated in a single-cell cohort of triple negative breast cancer. To investigate the possible role of immune cell-cell interactions (CCIs) in mediating chemotherapy response, we extended DECODEM to DECODEMi to identify such CCIs, validated in single-cell data. Our findings highlight the importance of active pre-treatment immune infiltration for chemotherapy success. The tools developed here are made publicly available and are applicable for studying the role of the TME in mediating response from readily available bulk tumor expression in a wide range of cancer treatments and indications.
Top-Down Modulation of Visual Action Perception: Distinct Task Effects in the Action Observation Network
Authors: Eroğlu Aslı , Urgen Burcu A.
Published: June 2024

Perceiving others’ actions is essential for survival and social interaction. Cognitive neuroscience research has identified a network of brain regions crucial to visual action perception, known as the Action Observation Network (AON), comprising the posterior superior temporal cortex (pSTS), posterior parietal cortex, and premotor cortex. Recent research highlights the importance of integrating top-down processes, such as attention, to gain a deeper understanding of action perception. This study investigates how attention modulates the AON during human action perception. We conducted a two-session fMRI experiment with 27 participants. They viewed eight videos of pushing actions, varying in actor (female vs. male), effector (hand vs. foot), and target (human vs. object). In the first session, participants focused on specific features of the videos (actor, effector, or target). In the second, they passively viewed the videos. From the passive viewing session data, we defined regions of interest (ROIs) in the pSTS, parietal, and premotor cortices for each hemisphere. We then performed model-based representational similarity analysis (RSA) and decoding analysis. RSA results showed that only the task model, among all tested models, exhibited a significant correlation with neural representational similarity matrices (RDMs) across all ROIs, indicating a specific alignment between AON nodes and the ongoing task. Decoding analysis further showed that different task types uniquely affected each AON node, indicating feature- and region-specific interactions. These findings underscore that top-down attentional processes significantly alter neural representations within the AON, highlighting the dynamic interplay between attention and action perception in the brain.
A type IVB secretion system contributes to the pathogenicity ofYersinia pseudotuberculosisstrains responsible for the Far East scarlet-like fever
Authors: Lemarignier Marion , Savin Cyril , Torres Inés Ruedas , Derbise Anne , Coluzzi Charles , Burlaud-Gaillard Julien , Madej Julien , Beau Rémi , Roingeard Philippe , Lechat Pierre , Rocha Eduardo , Gomez-Laguna Jaime , Pizarro-Cerdá Javier
Published: June 2024

Yersinia pseudotuberculosisis a food-borne pathogen responsible for a self-limiting gastrointestinal disease in humans known as mesenteric lymphadenitis. A phylogenetically distinctY. pseudotuberculosiscluster from lineages 1 and 8 is associated to a specific syndrome called the Far East scarlet-like fever (FESLF), characterized by skin rash, hyperemic tongue and desquamation. Genome sequencing of FESLF strains previously revealed the presence in the plasmid pVM82 ofdot/icmgenes, homologous to those known to encode a T4BSS in the intracellular pathogensLegionella pneumophilaandCoxiella burnetii.In the present article, we characterized the genomic features and functionality of theY. pseudotuberculosisT4BSS (yT4BSS). We found higherdot/icmgene identity betweenY. pseudotuberculosisandPseudomonas putidagenes than with those ofL. pneumophilaorC. burnetii. We validated the presence of all essentialdot/icmgenes required for the structure of a T4BSS. We then evaluated the conditions required foryT4BSS gene expressionin vitroand identified an influence of temperature, with higher expression at 37°C, which mimicks the mammalian host temperature. TheyT4BSS is also expressedin celluloduring theY. pseudotuberculosisintracellular life cycle andin vivoduring mouse infection. Although T4BSS functions are well characterized in the intracellular life cycle ofL. pneumophilaandC. burnetii, theyT4BSS appears to not be required for the intracellular survival nor for the establishment of a replication niche within cells ofY. pseudotuberculosis. Interestingly, theyT4BSS is implicated inY. pseudotuberculosisFESLF strain pathogenicity when orally inoculated to mice but not during intravenous inoculation. Despite a role in virulence during oral infection, theyT4BSS does not influence organ colonization. However, theyT4BSS appears to be implicated in induction of important necrosis lesions in mesenteric lymph nodes and cæca of mice. Cytokine profil analyses revealed an induction of production of innate immunity related cytokines and chemokines depending on theyT4BSSin cellulousing a mouse bone marrow-derived macrophages infection model. Thus, theyT4BSS modulates cytokine responses of the host innate immune system during oral infection. In conclusion, theyT4BSS is a newly characterized virulence factor implicated in pathogenicity ofY. pseudotuberculosisstrains from lineage 8 responsible for FESLF.
Interpretable machine learning reveals a diverse arsenal of anti-defenses in bacterial viruses
Authors: Lopatina Anna , Ferenc Mariusz , Bartlau Nina , Wolfram Michael , Steensen Kerrin , Muscia Sebastiano , Hussain Fatima , Schnurer Madeleine , Afjehi-Sadat Leila , Pollak Shaul , Polz Martin F.
Published: June 2024

Antagonistic interactions with viruses are an important driver of the ecology and evolution of bacteria, and associating genetic signatures to these interactions is of fundamental importance to predict viral infection success. Recent studies have highlighted that bacteria possess a large, rapidly changing arsenal of defense genes and that viruses can neutralize at least some of these genes with matching anti-defenses. However, a broadly applicable approach for discovering the genetic underpinnings of such interactions is missing since typically used methods such as comparative genomics are limited by the rampant horizontal gene transfer and poor annotation of viral and bacterial genes. Here we show that genes that allow the viruses to overcome bacterial defenses can be systematically identified using an interpretable machine-learning approach even when using diverse bacteria-virus infection data. To verify the predictions, we experimentally characterized eight previously unknown anti-defense proteins in viruses specific for Vibrio bacteria and showed that they counteract a wide range of bacterial immune systems, including AbiH, AbiU, Septu, DRT, CBASS, and Retron. The power of our computational approach is highlighted by the identification of anti-defense proteins that inhibit non-homologous defense systems, which we verify for Retron and AbiH. We suggest that the computational prediction based on experimental interactions offers a promising avenue to unravel the genetic mechanisms of co-evolution between bacteria and their viruses.
DeMBA: a developmental atlas for navigating the mouse brain in space and time
Authors: Carey Harry , Kleven Heidi , Øvsthus Martin , Yates Sharon C. , Csucs Gergely , Puchades Maja A. , McMullan Simon , Bjaalie Jan G. , Leergaard Trygve B. , Bjerke Ingvild E.
Published: June 2024

Studies of the adult mouse brain have benefited from three-dimensional (3D) atlases providing standardised frameworks for data analysis and integration. However, few 3D atlases exist for the developing mouse brain, and none cover more than a few ages. This fails to represent the dynamic nature of development and is insufficient for researchers whose data fall between the ages of existent atlases. Existing atlases also neglect the spatial correspondence between ages, making comparison across ages difficult. We present the Developmental Mouse Brain Atlas (DeMBA), a 4D atlas encompassing every postnatal day from 4 to 56. DeMBA is incorporated in software for spatial registration and analysis, enabling brain-wide quantification of features of interest. Furthermore, we provide a software package, the CCF translator, allowing coordinates or image volumes to be transformed between ages for comparison. These resources provide age-specific spatial frameworks incorporated in accessible analytic pipelines for developmental mouse brain data.
Early Developmental Origins of Cortical Disorders Modeled in Human Neural Stem Cells
Authors: Mato-Blanco Xoel , Kim Suel-Kee , Jourdon Alexandre , Ma Shaojie , Tebbenkamp Andrew T.N. , Liu Fuchen , Duque Alvaro , Vaccarino Flora M. , Sestan Nenad , Colantuoni Carlo , Rakic Pasko , Santpere Gabriel , Micali Nicola
Published: June 2024

The implications of the early phases of human telencephalic development, involving neural stem cells (NSCs), in the etiology of cortical disorders remain elusive. Here, we explored the expression dynamics of cortical and neuropsychiatric disorder-associated genes in datasets generated from human NSCs across telencephalic fate transitions in vitro and in vivo. We identified risk genes expressed in brain organizers and sequential gene regulatory networks across corticogenesis revealing disease-specific critical phases, when NSCs are more vulnerable to gene dysfunctions, and converging signaling across multiple diseases. Moreover, we simulated the impact of risk transcription factor (TF) depletions on different neural cell types spanning the developing human neocortex and observed a spatiotemporal-dependent effect for each perturbation. Finally, single-cell transcriptomics of newly generated autism-affected patient-derived NSCs in vitro revealed recurrent alterations of TFs orchestrating brain patterning and NSC lineage commitment. This work opens new perspectives to explore human brain dysfunctions at the early phases of development.

One-sentence summary

The temporal analysis of gene regulatory networks in human neural stem cells reveals multiple early critical phases associated with cortical disorders and neuropsychiatric traits.
Development of capsaicin derivatives as prohibitin ligands to modulate the Aurora kinase A/PHB2 interaction in cancer cells
Authors: Djehal Amel , Caron Claire , Giordano Deborah , Pizza Valentina , Farin Kimberley , Facchiano Angelo , Désaubry Laurent , Bertolin Giulia
Published: June 2024

Aurora kinase A/AURKA is a serine/threonine kinase overexpressed in a variety of solid and hematological malignancies. In the last decades, clinical trials aiming to counteract the overexpression of AURKA turned out to be largely unsuccessful. Meanwhile, recent discoveries pointed at new functions of AURKA at the subcellular level, including at mitochondria. At this location, AURKA induces organelle clearance by mitophagy by acting in complex with the mitophagy mediator LC3, and its inner mitochondrial membrane receptor PHB2. The natural polyphenol xanthohumol was shown to act as a PHB2 ligand, altering the interaction between AURKA and PHB2 and restoring mitochondrial functions in cancer cells. However, its chemical nature prevents its broader use as an anti-cancer agent.

Using Förster’s Resonance Energy Transfer/Fluorescence Lifetime Imaging Microscopy (FRET/FLIM) in live breast cancer cells, we here explore the effects of alternative PHB ligands in altering the proximity between AURKA and PHB2. Among the already-available compounds, we found that the pungent natural product capsaicin partially alters the AURKA/PHB2 protein-protein proximity. We then synthesized 16 novel capsaicin analogues to enhance the effects of capsaicin. We found that replacing the long hydrophobic acyl moiety by a butyryl one increases the AURKA/PHB2 interaction. Among the capsaicin derivatives carrying this modification, we uncover that compound 12 and 13 enhance the AURKA/PHB2 proximity. Molecular docking approaches corroborate FRET/FLIM data, and we visualize compound 12 and 13 in complex with AURKA, PHB2 and LC3. We show that compound 12 and 13 stabilize the AURKA/PHB2 interaction, and that they can bind to the inhibitory pocket of PHB2 and to the AURKA active site.

Together, our data indicate that compound 12 and 13 are promising PHB ligands acting on the AURKA/PHB2 interaction. Through their molecular action on either AURKA or PHB2, they may provide the basis for the development of new anticancer drugs targeting the mitochondrial functions of AURKA.

Highlights

The cancer-related kinase Aurora A/AURKA interacts with the mitochondrial protein PHB2 to induce mitophagy in cancer cells.

Among the available PHB ligands, capsaicin mildly lowers the AURKA/PHB2 interaction.

Screening of 16 newly-synthesized capsaicin derivatives show differential effects on the AURKA/PHB2 interaction.

Compound 12 and 13 stabilize the AURKA/PHB2 interaction.

Compound 12 and 13 bind to the AURKA active site and to the PHB2 inhibitory pocket.
Specific presynaptic functions require distinct Drosophila Cav2 splice isoforms
Authors: Bell Christopher , Kilo Lukas , Gottschalk Daniel , Arian Jashar , Deneke Lea , Kern Hanna , Rickert Christof , Kobler Oliver , Strauß Julia , Heine Martin , Duch Carsten , Ryglewski Stefanie
Published: June 2024

The multiplicity of neural circuits that accommodate the sheer infinite number of computations conducted by brains requires diverse synapse and neuron types. At many vertebrate synapses release probability and other aspects of presynaptic function are tuned by different combinations of Cav2.1, Cav2.2, and Cav2.3 channels. By contrast, most invertebrate genomes contain only oneCav2gene. The one Drosophila Cav2 homolog, cacophony (cac), localizes to presynaptic active zones (AZs) to induce synaptic vesicle release. We hypothesize that Drosophila cac functional diversity is enhanced by two specific exon pairs that are mutually exclusively spliced and not conserved in vertebrates, one in the voltage sensor and one in the intracellular loop containing the binding site(s) for Caβand G-protein βγ subunits. We test our hypothesis by combining opto– and electrophysiological with neuroanatomical approaches at a fast glutamatergic model synapse, the Drosophila larval neuromuscular junction. We find that alternative splicing in the voltage sensor affects channel activation voltage and is imperative for normal synapse function. Only the isoform with the higher activation voltage localizes to the presynaptic AZ and mediates evoked release. Removal of these cac splice isoforms renders fast glutamatergic synapses non-functional. By contrast, alternative splicing at the other alternative exon that encodes the intracellular loop between the first and the second homologous repeats does not affect cac presynaptic AZ localization, but it tunes multiple aspects of presynaptic function. While expression of one exon yields normal transmission, expression of the other exon reduces channel number in the AZ and thus release probability. This also abolishes presynaptic homeostatic plasticity. Moreover, reduced channel number upon selective exon excision increases paired pulse ratios and the variability of synaptic depression during low frequency stimulation trains (1 and 10 Hz), and thus affects short term plasticity. Effects on short term plasticity can be rescued by increasing the external calcium concentration to match release probability to control. In sum, in Drosophila alternative splicing provides a mechanism to regulate different aspects of presynaptic functions with only oneCav2gene.
Sequencing whole genomes of the West Javanese population in Indonesia reveals novel variants and improves imputation accuracy
Authors: Ardiansyah Edwin , Riza Anca-Lelia , Dian Sofiati , Ganiem Ahmad Rizal , Alisjahbana Bachti , Setiabudiawan Todia P , Laarhoven Arjan van , Crevel Reinout van , Kumar Vinod
Published: June 2024

Existing genotype imputation reference panels are mainly derived from European populations, limiting their accuracy in non-European populations. To improve imputation accuracy for Indonesians, the world’s fourth most populous country, we combined Whole Genome Sequencing (WGS) data from 227 West Javanese individuals with East Asian data from the 1000 Genomes Project. This created three reference panels: EAS 1KGP3 (EASp), Indonesian (INDp), and a combined panel (EASp+INDp). We also used ten West-Javanese samples with WGS and SNP-typing data for benchmarking. We identified 1.8 million novel single nucleotide variants (SNVs) in the West Javanese population, which, while similar to the East Asians, are distinct from the Central Indonesian Flores population. Adding INDp to the EASp reference panel improved imputation accuracy (R2) from 0.85 to 0.90, and concordance from 87.88% to 91.13%. These findings underscore the importance of including Indonesian genetic data in reference panels, advocating for broader WGS of diverse Indonesian populations to enhance genomic studies.
Temporal Structure of Music Improves the Cortical Encoding of Speech
Authors: Fernández-Merino Laura , Lizarazu Mikel , Molinaro Nicola , Kalashnikova Marina
Published: June 2024

Long and short-term musical training has been proposed to improve efficiency of cortical tracking of speech, the mechanism through which brain oscillations synchronize to the acoustic temporal structure of external stimuli. Here, we study how different rhythm structures of the musical signal can guide the temporal dynamics of auditory oscillations phase-aligned to the speech envelope. For this purpose, we investigated the effects of prior exposure to rhythmically structured musical sequences on cortical tracking of speech in Basque-Spanish bilingual adults. We conducted two EEG experiments where participants were presented with sentences in Basque and Spanish preceded by musical sequences that differed in their beat structure. The beat structure of the musical sequences was created to 1) reflect and match the syllabic structure of the sentences, 2) reflect a regular rhythm but not match the syllabic structure of the sentences, and 3) follow an irregular rhythm. First, we showed that the regularity found in the rhythmic structure of music acts as a temporal guide for brain oscillations. Second, our findings suggest that not only the regularity in music is crucial but so is adjusting this regularity to optimally reflect the rhythmic characteristics of the language. Third, despite finding some differences across frequencies for each language, we still found a strong effect of rhythm regularity on cortical tracking of speech. We showed that rhythm, inherent in musical signals, guides the adaptation of brain oscillations, by adapting the temporal dynamics of the oscillatory activity to the rhythmic scaffolding of the musical signal.
AIVE: accurate predictions of SARS-CoV-2 infectivity from comprehensive analysis
Authors: Park Jongkeun , Choi Won Jong , Seong Do Young , Jeong Seung Pil , Lee Ju Young , Park Hyo Jeong , Chung Dae Sun , Yi Ki Jong , Kim Uijin , Yoon Ga-Yeon , Kim Hyeran , Kim Taehoon , Go Sooyeon , Min Eun Jeong , Cho Hyun-Soo , Cho Nam-Hyuk , Hong Dongwan
Published: June 2024

An unprecedented amount of SARS-CoV-2 data has been accumulated compared with previous infectious diseases, enabling insights into its evolutionary process and more thorough analyses. This study investigates SARS-CoV-2 features as it evolved to evaluate its infectivity. We examined viral sequences and identified the polarity of amino acids in the Receptor Binding Motif (RBM) region. We detected an increased frequency of amino acid substitutions to lysine (K) and arginine (R) in Variants of Concern (VOCs). As the virus evolved to Omicron, commonly occurring mutations became fixed components of the new viral sequence. Furthermore, at specific positions of VOCs, only one type of amino acid substitution and a notable absence of mutations at D467 was detected. We found that the binding affinity of SARS-CoV-2 lineages to the ACE2 receptor was impacted by amino acid substitutions. Based on our discoveries, we developed APESS, an evaluation model evaluating infectivity from biochemical and mutational properties. In silico evaluation using real-world sequences and in vitro viral entry assays validated the accuracy of APESS and our discoveries. Using Machine Learning, we predicted mutations that had the potential to become more prominent. We created AIVE, a web-based system, accessible athttps://ai-ve.orgto provide infectivity measurements of mutations entered by users. Ultimately, we established a clear link between specific viral properties and increased infectivity, enhancing our understanding of SARS-CoV-2 and enabling more accurate predictions of the virus.
Multi-protein assemblies orchestrate co-translational enzymatic processing on the human ribosome
Authors: Klein Marius , Wild Klemens , Sinning Irmgard
Published: June 2024

Most nascent chains undergo rapid co-translational enzymatic processing as soon as their N-terminus becomes accessible at the ribosomal polypeptide tunnel exit (PTE). In eukaryotes, N-terminal methionine excision (NME) by Methionine Aminopeptidases (MAP1 and MAP2), and N-terminal acetylation (NTA) by N-Acetyl-Transferase A (NatA), is the most common set of subsequent modifications carried out on the ribosome. How these two enzymatic processes are coordinated in quick succession in the context of a rapidly translating ribosome has remained elusive.

Here, we report that human NatA occupies a non-intrusive ‘distal’ binding site on the ribosome which does not interfere with most other ribosome associated factors (RAFs). In this position, NatA can partake in a coordinated and dynamic assembly with MAP1 through a complex scaffolding function of the abundant Nascent Polypeptide Associated Complex (NAC). Alternatively, MAP2 can co-occupy the PTE with NatA in preparation for successive NME and NTA. In contrast to MAP1, MAP2 completely covers the PTE and is thus incompatible with NAC and MAP1 recruitment. Both assemblies can compile on the human ribosome independent of nascent chain substrates. Together, our structures provide the structural framework for the rapid coordinated orchestration of NME and NTA in protein biogenesis.
Structural studies of KCTD1 and its disease-causing mutant P20S provide insights into the protein function and misfunction
Authors: Balasco Nicole , Ruggiero Alessia , Smaldone Giovanni , Pecoraro Giovanni , Coppola Luigi , Pirone Luciano , Pedone Emilia M. , Esposito Luciana , Berisio Rita , Vitagliano Luigi
Published: June 2024

Members of the KCTD protein family play key roles in fundamental physio-pathological processes. A plethora of literature studies have demonstrated their involvement in cancer, neurodevelopmental disorders, and genetic diseases. Despite two decades of intense investigations, the definition of structure-(mis)function relationships for these proteins is still rather limited. Here, we derived atomic-level structural data on KCTD1, by determining the crystal structure of its P20S mutant, which causes the scalp-ear-nipple syndrome, and performing molecular dynamics simulations. In addition to the expected folded domains (BTB and CTD) the crystal structure unravels that also the N-terminal region that precedes the BTB domain (preBTB) adopts a folded polyproline II (PPII) state. The global structure of the KCTD1 pentamer is characterized by an intricate architecture in which the different subunits mutually exchange domains to generate a closed domain swapping motif. In this framework, the BTB domain of each chain makes peculiar contact with the preBTB and the CTD regions of an adjacent chain. Indeed, the BTB-preBTB interaction is made of a PPII-PPII recognition motif whereas the BTB-CTD contacts are mediated by an unusual (+/-) helix discontinuous association. The inspection of the protein structure, along with the data that emerged from the MD data, provides a clear explanation of the pathogenicity of the SENS mutation P20S and unravels the role of the BTB-preBTB interaction in the insurgence of the disease. Finally, the presence of potassium bound to the central cavity of the CTD pentameric assembly provides insights into the role of the protein in metal homeostasis.
Lineage tracing ofShh+floor plate cells and dynamics of dorsal-ventral gene expression in the regenerating axolotl spinal cord
Authors: Arbanas Laura I. , Costa Emanuel Cura , Chara Osvaldo , Otsuki Leo , Tanaka Elly M.
Published: June 2024

Both development and regeneration depend on signalling centres, which are sources of locally secreted tissue-patterning molecules. As many signalling centres are decommissioned before the end of embryogenesis, a fundamental question is how signalling centres can be re-induced later in life to promote regeneration after injury. Here, we use the axolotl salamander model (Ambystoma mexicanum) to address how the floor plate is assembled for spinal cord regeneration. The floor plate is an archetypal vertebrate signalling centre that secretesShhligand and patterns neural progenitor cells during embryogenesis. Unlike mammals, axolotls continue to express floor plate genes (includingShh) and downstream dorsal-ventral patterning genes in their spinal cord throughout life, including at steady state. The parsimonious hypothesis thatShh+ cells give rise to functional floor plate cells for regeneration had not been tested. Using HCRin situhybridisation and mathematical modelling, we first quantitated the behaviours of dorsal-ventral spinal cord domains, identifying significant increases in gene expression level and floor plate size during regeneration. Next, we established a transgenic axolotl to specifically label and fate mapShh+ cellsin vivo. We found that labelledShh+cells gave rise to regeneration floor plate, and not to other neural progenitor domains, after tail amputation. Thus, despite changes in domain size and downstream patterning gene expression,Shh+ cells retain their floor plate identity during regeneration, acting as a stable cellular source for this regeneration signalling centre in the axolotl spinal cord.
Interactions with multiple inner kinetochore proteins determine mitotic localization of FACT
Authors: Schweighofer Julia , Mulay Bhagyashree , Hoffmann Ingrid , Vogt Doro , Pesenti Marion E. , Musacchio Andrea
Published: June 2024

The FAcilitates Chromatin Transcription (FACT) complex is a dimeric histone chaperone that operates on chromatin during transcription and replication. FACT also interacts with a specialized centromeric nucleosome containing the histone H3 variant CENP-A and with CENP-TW, two subunits of CCAN, a 16-protein complex associated with CENP-A. The significance of these interactions remains elusive. Here, we show that FACT has multiple additional binding sites on CCAN. The interaction with CCAN is strongly stimulated by casein kinase II (CK2) phosphorylation of FACT. Mitotic localization of FACT to kinetochores is strictly dependent on specific CCAN subcomplexes. Unexpectedly, we also find that DNA readily displaces FACT from CCAN, suggesting that FACT becomes recruited through a pool of CCAN that is not stably integrated into chromatin. Collectively, our results point to a potential role of FACT in chaperoning CCAN during transcription or in the stabilization of CCAN at the centromere during the cell cycle.

Teaser

DNA-sensitive, direct interactions with multiple inner kinetochore subunits deliver FACT to the kinetochore.