bluuebunny/crossref_metadata_2025 huggingface dataset:
Influential factors of saliva microbiota composition
Authors: Wells Philippa M. , Sprockett Daniel D. , Bowyer Ruth C E , Kurushima Yuko , Relman David A. , Williams Frances M.K. , Steves Claire J.
Published: December 2021

Background

The oral microbiota is emerging as an influential factor of host physiology and disease state. Factors influencing oral microbiota composition have not been well characterised. In particular, there is a lack of population-based studies. We undertook a large hypothesis-free study of the saliva microbiota, considering potential influential factors of host health (frailty; diet; periodontal disease), demographics (age; sex; BMI) and sample processing (storage time), in a sample (n=679) of the TwinsUK cohort of adult twins.

Results

Alpha and beta diversity of the saliva microbiota was associated most strongly with frailty (alpha diversity: Q = 0.003, Observed; Q=0.002, Shannon; Q=0.003, Simpson; Beta diversity: Q = 0.002, Bray Curtis dissimilarity) and age (alpha diversity: Q=0.006, Shannon; Q=0.003, Simpson; beta diversity: Q=0.002, Bray Curtis dissimilarity; Q= 0.032, Weighted UniFrac) in multivariate models including age, frailty, sex, BMI, frailty and diet, and adjustment for multiple testing. Those with a more advanced age were more likely to be dissimilar in the saliva microbiota composition than younger participants (P = 5.125e-06, ANOVA). In subsample analyses, including consideration of periodontal disease (total n=138, periodontal disease n=66), the association with frailty remained for alpha diversity (Q=0.002, Observed ASVs; Q= 0.04 Shannon Index), but not beta diversity, whilst age was not demonstrated to associate with alpha or beta diversity in this subsample, potentially due to insufficient statistical power. Length of time that samples were stored prior to sequencing was associated with beta diversity (Q = 0.002, Bray Curtis dissimilarity). Six bacterial taxa were associated with age after adjustment for frailty and diet.

Conclusions

Frailty and age emerged as the most influential factors of saliva microbiota composition. Whilst frailty and age are correlates, the associations were independent of each other, suggesting that both biological and chronological ageing are key drivers of saliva microbiota composition.
Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants : Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability
Authors: Verkhivker Gennady
Published: December 2021

The experimental and computational studies of the SARS-CoV-2 spike protein variants revealed an important role of the D614G mutation that is shared across variants of concern(VOCs), linking the effect of this mutation with the enhanced virus infectivity and transmissibility. The recent structural and biophysical studies characterized the closed and open states of the B.1.1.7 (B.1.1.7) and B.1.351 (Beta) spike variants allowing for a more detailed atomistic characterization of the conformational landscapes and functional changes. In this study, we employed coarse-grained simulations of the SARS-CoV-2 spike variant trimers together with the ensemble-based mutational frustration analysis to characterize the dynamics signatures of the conformational landscapes. By combining the local frustration analysis of the conformational ensembles with collective dynamics and residue-based mutational scanning of protein stability, we determine protein stability hotspots and identify potential energetic drivers favoring the receptor-accessible open spike states for the B.1.1.7 and B.1.351 spike variants. Through mutational scanning of protein stability changes we quantify mutational adaptability of the S-G614, S-B.1.1.7 and S-B.1.351 variants in different functional forms. Using this analysis, we found a significant conformational and mutational plasticity of the open states for all studied variants. The results of this study suggest that modulation of the energetic frustration at the inter-protomer interfaces can serve as a mechanism for allosteric couplings between mutational sites, the inter-protomer hinges of functional motions and motions of the receptor-binding domain required for binding of the host cell receptor. The proposed mechanism of mutation-induced energetic frustration may result in the greater adaptability and the emergence of multiple conformational substates in the open form. This study also suggested functional relationships between mutation-induced modulation of protein dynamics, local frustration and allosteric regulation of the SARS-CoV-2 spike protein.
Growth-limiting drought stress induces time-of-day dependent transcriptome and physiological responses in hybrid poplar
Authors: Robertson Sean M. , Sakariyahu Solihu Kayode , Bolaji Ayooluwa J. , Belmonte Mark F. , Wilkins Olivia
Published: December 2021

Drought stress negatively impacts the health of long-lived trees. Understanding the genetic mechanisms that underpin response to drought stress is requisite for selecting or enhancing climate change resilience. We aimed to determine how hybrid poplars respond to prolonged and uniform exposure to drought; how responses to moderate and more severe growth-limiting drought stresses differed; and, how drought responses change throughout the day. We established hybrid poplar trees (Populus x ‘Okanese’) from unrooted stem cutting with abundant soil moisture for six weeks. We then withheld water to establish well-watered, moderate, and severe growth-limiting drought conditions. These conditions were maintained for three weeks during which growth was monitored. We then measured photosynthetic rates and transcriptomes of leaves that had developed during the drought treatments at two times of day. The moderate and severe drought treatments elicited distinct changes in growth and development, photosynthetic rates, and global transcriptome profiles. Notably, the time of day of sampling produced the strongest signal in the transcriptome data. The moderate drought treatment elicited global transcriptome changes that were intermediate to the severe and well-watered treatments in the early evening, but did not elicit a strong drought response in the morning, emphasizing the complex nature of drought regulation in long-lived trees.

Highlight

Poplar drought transcriptome is defined by the time of day of sampling and by the extent of water deficit.
Regulation of KHNYN antiviral activity by the extended di-KH domain and nucleo-cytoplasmic trafficking
Authors: Lista María José , Galão Rui Pedro , Ficarelli Mattia , Kmiec Dorota , Wilson Harry , Winstone Helena , Morris Elizabeth R , Mischo Hannah E , Wanford Joseph , Youle Rebecca , Odendall Charlotte , Taylor Ian A , Neil Stuart J D , Swanson Chad M
Published: December 2021

The zinc finger antiviral protein (ZAP) restricts a broad range of viruses by binding CpG dinucleotides in viral RNA to target it for degradation and inhibit its translation. KHNYN was recently identified as an antiviral protein required for ZAP to inhibit retroviral replication, though little is known about its functional determinants. KHNYN contains an N-terminal extended di-KH-like domain, a PIN endoribonuclease domain and a C-terminal CUBAN domain that binds NEDD8 and ubiquitin. We show that deletion of the extended di-KH domain reduces its antiviral activity. However, despite its similarity to RNA binding KH domains, the extended di-KH domain in KHNYN does not appear to bind RNA. Mutation of residues in the CUBAN domain that bind NEDD8 increase KHNYN abundance but do not alter its antiviral activity, suggesting that this interaction regulates KHNYN homeostatic turnover. In contrast, a CRM1-dependent nuclear export signal (NES) at the C-terminus of the CUBAN domain is required for antiviral activity. Deletion of this signal retains KHNYN in the nucleus and inhibits its interaction with ZAP. Interestingly, this NES appeared in the KHNYN lineage at a similar time as when ZAP evolved in tetrapods, indicating that these proteins may have co-evolved to restrict viral replication.

AUTHOR SUMMARY

Antiviral proteins restrict viral replication in many different ways, including inhibiting viral gene expression. ZAP is an antiviral RNA binding protein that must interact with other cellular proteins to inhibit viral protein synthesis. KHNYN is a ZAP cofactor that is required for it to inhibit retroviral replication. Because little is known about how KHNYN functions in this role, we have analyzed how two of its domains regulate its antiviral activity. We first show that the extended di-KH domain in KHNYN is required for its antiviral activity. While it is related to di-KH domains in RNA binding proteins, it appears to have lost its ability to bind RNA and KHNYN likely acts in the restriction pathway after ZAP binds a target viral RNA. Second, we show that the KHNYN CUBAN domain regulates both its protein abundance and trafficking within the cell. The CUBAN domain contains a nuclear export signal and, when this signal is mutated, KHNYN is sequestered in the nucleus, has substantially reduced antiviral activity and does not interact with ZAP. Overall, we show that the extended di-KH and CUBAN domains in KHNYN are required for it to act as a cofactor for ZAP to restrict viral replication.
TROPONIN IS INDEPENDENTLY ASSOCIATED WITH DEATH IN PATIENTS WITH COVID: A RETROSPECTIVE STUDY
Authors: Shyam-Sundar Vijay , Stein Dan , Spazzapan Martina , Sullivan Andrew , Qin Cathy , Voon Victor
Published: December 2021

Objective

We performed a single-centre retrospective observational study investigating the association between troponin positivity in patients hospitalised with COVID-19 and increased mortality in the short term.

Methods

All adults admitted with swab-proven RT-PCR COVID-19 to Homerton University Hospital (HUH) from 04.02.20 to 30.04.20 were eligible for inclusion.

We retrospectively analysed demographic and biochemical data collected from the physical and electronic patient records according to the primary outcome of death at 28 days during hospital admission.

Troponin positivity was defined above the upper limit of normal according to our local laboratory assay (>15.5ng/l for females, >34 ng/l for males). Univariate and multivariate logistical regression analyses were performed to evaluate the link between troponin positivity and death.

Results

Mean length of stay for all 402 hospitalised COVID-19 patients at HUH was 9.1 days (SD 12.0). Mean age was 65.3 years for men compared to 63.8 years for women. A chi-squared test showed that survival of COVID-19 patients was significantly higher in those with a negative troponin (p = 3.23 ×10−10) compared to those with a positive troponin. In the multivariate logistical regression, lung disease, age, troponin positivity and CPAP were all significantly associated with death, with an AUC of 0.8872, sensitivity of 0.9004 and specificity of 0.6292 for the model. Within this model, troponin positivity was independently associated with short term mortality (OR 3.23, 95% CI 1.53-7.16, p=0.00278).

Conclusions

We demonstrated an independent association between troponin positivity and increased short-term mortality in COVID-19 in a London district general hospital.

Key Questions

What is already known about this subject?

An elevated Troponin is associated with increased mortality. Troponin is known to be elevated in some patients who test positive for COVID-19 infection.

What does this study add?

This study shows an association between an elevated troponin in hospitalised COVID-19 patients and increased short-term mortality.

How might this impact on clinical practice?

Troponin is a readily available, easy to measure biomarker which can be used to predict the severity of COVID-19 illness and could aid prognostication in hospital.
Dynamics of immune recall following SARS-CoV-2 vaccination or breakthrough infection
Authors: Koutsakos Marios , Lee Wen Shi , Reynaldi Arnold , Tan Hyon-Xhi , Gare Grace , Kinsella Paul , Liew Kwee Chin , Williamson Deborah A. , Kent Helen E. , Stadler Eva , Cromer Deborah , Khoury David S. , Wheatley Adam K. , Juno Jennifer A. , Davenport Miles P. , Kent Stephen J.
Published: December 2021

Vaccination against SARS-CoV-2 results in protection from acquisition of infection as well as improved clinical outcomes even if infection occurs, likely reflecting a combination of residual vaccine-elicited immunity and the recall of immunological memory. Here, we define the early kinetics of spike-specific humoral and T cell immunity after vaccination of seropositive individuals, and after breakthrough infection in vaccinated individuals. Intensive and early longitudinal sampling reveals the timing and magnitude of recall, with the phenotypic activation of B cells preceding an increase in neutralizing antibody titres. In breakthrough infections, the delayed kinetics of humoral immune recall provides a mechanism for the lack of early control of viral replication but likely underpins accelerated viral clearance and the protective effects of vaccination against severe COVID-19.
Exploration of attitudes regarding uptake of COVID-19 vaccines among vaccine hesitant adults in the UK: A qualitative analysis
Authors: Denford Sarah , Mowbray Fiona , Towler Lauren , Wehling Helena , Lasseter Gemma , Amlôt Richard , Oliver Isabel , Yardley Lucy , Hickman Mathew
Published: December 2021

Background

The aim of this work was to explore barriers and facilitators to uptake of COVID-19 vaccines and to explore views and reactions to efforts to improve vaccine uptake among those who were vaccine hesitant.

Methods

Semi-structured interviews were conducted with people between the age of 18-29 years who had not had a COVID-19 vaccine, and those between 30-49 years who had not received a second dose of a COVID-19 vaccine (more than 12 weeks after receiving a first).

Results

A total of 70 participants took part in the study, 35 participants had received one dose of the vaccine, and 35 had not received any vaccine.

Participants described a possible willingness to be vaccinated to keep themselves and those around them safe, and to avoid restrictions and return to normal. Barriers to uptake included: 1) perceived lack of need for COVID-19 vaccinations, 2) concerns about the efficacy of vaccinations, 3) concerns about safety, and 4) access issues. Uptake appeared to be influenced by the age and health status of the individual, trust in government and knowledge and understanding of science. Introduction of vaccine passes may provide a motive for having a vaccine but may also be viewed as coercive.

Conclusion

Participants were hesitant, rather than opposed, and had questions about their need for, and the safety and efficacy of the vaccine. Young people did not consider themselves to be at risk of becoming ill from COVID-19, did not think the vaccination was effective in preventing infection and transmission, and did not think sufficient research had been conducted with regard to the possible long-term side-effects. These concerns were exacerbated by a lack of trust in the government, and misunderstanding of science. In order to promote uptake, public health campaigns should focus on the provision of information from trusted sources that carefully explains the benefits of vaccination and addresses safety concerns more effectively. To overcome inertia in people with low levels of motivation to be vaccinated, appointments must be easily accessible.
Conserved angio-immune subtypes of the cancer microenvironment predict response to immune checkpoint blockade therapy
Authors: Subramanian Madhav , Kabir Ashraf Ul , Barisas Derek A.G. , Krchma Karen , Choi Kyunghee
Published: December 2021

Tumor microenvironment (TME) shapes the tumor progression and therapy outcome. Particularly, tumor angiogenesis and immunity impact the effect of immune checkpoint blockade (ICB) therapy. Here, we analyzed the transcriptome from 11,069 patients from The Cancer Genome Atlas (TCGA) to assess 91 functional gene sets corresponding to endothelial and T-cell activity. Intriguingly, TME across 30 non-hematological tumors can be classified into three distinct conserved angio-immune subtypes: high angiogenesis with low immune activity, low angiogenesis with high immune activity, and the one in-between. Remarkably, patients displaying TME with poor angiogenic activity with corresponding high immune activity show the most significant responses to ICB therapy in many cancer types. Notably, re-evaluation of the Javelin Renal 101, renal cell carcinoma clinical trial, provided compelling evidence that the baseline angiogenic state is critical in determining responses to checkpoint blockade. This study offers a clear rationale for incorporating baseline angiogenic state for ICB treatment decision-making.
Blood-brain Barrier Crossing using Magnetic Stimulated Nanoparticles
Authors: Chen Jingfan , Yuan Muzhaozi , Madison Caitlin A , Eitan Shoshana , Wang Ya
Published: December 2021

Due to the low permeability and high selectivity of the blood-brain barrier (BBB), existing brain therapeutic technologies are limited by the inefficient BBB crossing of conventional drugs. Magnetic nanoparticles (MNPs) have shown great potential as nano-carriers for efficient BBB crossing under the external static magnetic field (SMF). To quantify the impact of SMF on MNPs’ in vivo dynamics towards BBB crossing, we developed a physiologically based pharmacokinetic (PBPK) model for intraperitoneal (IP) injected superparamagnetic iron oxide nanoparticles coated by gold and conjugated with poly(ethylene glycol) (PEG) (SPIO-Au-PEG NPs) in mice. Unlike most reported PBPK models that ignore brain permeability, we first obtained the brain permeabilities with and without SMF by determining the concentration of SPIO-Au-PEG NPs in the cerebral blood and brain tissue. This concentration in the brain was simulated by the advection-diffusion equations and was numerically solved in COMSOL Multiphysics. The results from the PBPK model after incorporating the brain permeability showed a good agreement (regression coefficient R2 = 0.825) with the in vivo results, verifying the capability of using the proposed PBPK model to predict the in vivo biodistribution of SPIO-Au-PEG NPs under the exposure to SMF. Furthermore, the in vivo results revealed that the brain bioavailability under the exposure to SMF (4.01%) is slightly better than the control group (3.68%). In addition, the modification of SPIO-Au-PEG NPs with insulin (SPIO-Au-PEG-insulin) showed an improvement of the brain bioavailability by 24.47 % in comparison to the non-insulin group. With the SMF stimulation, the brain bioavailability of SPIO-Au-PEG-insulin was further improved by 3.91 % compared to the group without SMF.
Disruption of synaptic transmission in the Bed Nucleus of the Stria Terminalis reduces seizure-induced death in DBA/1 mice and alters brainstem E/I balance
Authors: Xia Maya , Owen Benjamin , Chiang Jeremy , Levitt Alyssa , Yan Wen Wei , Nobis William P.
Published: December 2021

Sudden unexpected death in epilepsy (SUDEP) is the leading cause of death in refractory epilepsy patients. Accumulating evidence from recent human studies and animal models suggests that seizure-related respiratory arrest may be important for initiating cardiorespiratory arrest and death. Prior evidence suggests that apnea onset can coincide with seizure spread to the amygdala and that stimulation of the amygdala can reliably induce apneas in epilepsy patients, potentially implicating amygdalar regions in seizure-related respiratory arrest and subsequent postictal hypoventilation and cardiorespiratory death. This study aimed to determine if an extended amygdalar structure, the dorsal bed nucleus of the stria terminalis (dBNST), is involved in seizure-induced respiratory arrest (S-IRA) and death using DBA/1 mice, a mouse strain which has audiogenic seizures and a high incidence of postictal respiratory arrest and death. The presence of S-IRA significantly increased c-Fos expression in the dBNST of DBA/1 mice. Furthermore, disruption of synaptic output from the dBNST via viral-induced tetanus neurotoxin significantly improved survival following S-IRA in DBA/1 mice without affecting baseline breathing or hypercapnic and hypoxic ventilatory response. This disruption in the dBNST resulted in changes to the balance of excitatory/inhibitory synaptic events in the downstream brainstem regions of the lateral parabrachial nucleus (PBN) and the periaqueductal gray (PAG). These findings suggest that the dBNST is a potential subcortical forebrain site necessary for the mediation of seizure-induced respiratory arrest, potentially through its outputs to brainstem respiratory regions.

SUMMARY STATEMENT

This study used a viral expression technique to disrupt synaptic output in the bed nucleus of the stria terminalis (BNST) of DBA/1 audiogenic seizure mice. Inactivating the BNST significantly improved survival following seizures and altered brainstem excitation/inhibition balance.
Protein homeostasis is maintained by proteasomes containing PSMB9 induced by EEF1A2 upon mitochondrial stress
Authors: Kim Minji , Samluk Lukasz , Stępkowski Tomasz Maciej , Suppanz Ida , Serwa Remigiusz Adam , Kodroń Agata , Warscheid Bettina , Chacinska Agnieszka
Published: December 2021

Perturbed proteostasis and mitochondrial dysfunction are often associated with age-related diseases such as Alzheimer’s and Parkinson’s diseases. However, the link between them remains incompletely understood. Mitochondrial dysfunction causes proteostasis imbalance, and cells respond to restore proteostasis by increasing proteasome activity and molecular chaperons in yeast and C. elegans. Here, we demonstrate the presence of similar responses in humans. Mitochondrial dysfunction upregulates a small heat shock protein HSPB1 and an immunoproteasome subunit PSMB9 leading to an increase in proteasome activity. HSPB1 and PSMB9 are required to prevent protein aggregation upon mitochondrial dysfunction. Moreover, PSMB9 expression is dependent on a translation elongation factor EEF1A2, and PSMB9-containing proteasomes are located near mitochondria, enabling fast local degradation of aberrant proteins. Our findings put a step forward in understanding the stress response triggered by mitochondrial dysfunction, and may be useful for therapeutic strategies to prevent or delay the onset of age-related diseases and attenuate their progression.
Regulation of the PKD2 Channel Function by TACAN
Authors: Liu Xiong , Zhang Rui , Fatehi Mohammad , Wang Yifang , Long Wentong , Tian Rui , Deng Xiaoling , Weng Ziyi , Xu Qinyi , Light Peter E , Tang Jingfeng , Chen Xing-Zhen
Published: December 2021

Autosomal dominant polycystic kidney disease (ADPKD) is caused by mutations in membrane receptor PKD1 or cation channel PKD2. TACAN (also named TMEM120A), recently reported as an ion channel in neuron cells for mechano and pain sensing, is also distributed in diverse non-neuronal tissues such as kidney, heart and intestine, suggesting its involvement in other functions. In this study, we found that TACAN is in complex with PKD2 in native renal cell lines. Using the two-electrode voltage clamp in Xenopus oocytes we found that TACAN inhibited the channel activity of PKD2 gain-of-function mutant F604P. The first and last transmembrane domains of TACAN were found to interact with the PKD2 C-and N-terminal portions, respectively. We showed that the TACAN N-terminus acted as a blocking peptide and that TACAN inhibits the PKD2 function through the PKD2/TACAN binding. By patch clamping in mammalian cells, we found that TACAN inhibits both the single channel conductance and open probability of PKD2 and mutant F604P. PKD2 co-expressed with TACAN, but not PKD2 alone, exhibited pressure sensitivity. Furthermore, we also found that TACAN aggravates PKD2-dependent tail curvature and pronephric cysts in larval zebrafish, in support of the in vitro inhibitory effects of TACAN. In summary, this study revealed that TACAN acts as a PKD2 inhibitor and mediates mechano sensitivity of the PKD2/TACAN channel complex.
XAB2 Dynamics during DNA Damage-Dependent Transcription Inhibition
Authors: Donnio Lise-Marie , Cerutti Elena , Magnani Charlène , Neuillet Damien , Mari Pierre-Olivier , Giglia-Mari Giuseppina
Published: December 2021

Xeroderma Pigmentosum group A (XPA)-binding protein 2 (XAB2) is a multi-functional protein that plays a critical role in distinct cellular processes including transcription, splicing, DNA repair and mRNA export. In this study, we detailed XAB2 involvement during Nucleotide Excision Repair (NER), a repair pathway that guarantees genome integrity against UV light-induced DNA damage and that specifically removes transcription-blocking damage in a dedicated process known as Transcription-Coupled repair (TC-NER). Here, we demonstrated that XAB2 is involved specifically and exclusively in TC-NER reaction and solely for RNA Polymerase 2 transcribed genes. Surprisingly, contrary to all the other NER proteins studied so far, XAB2 does not accumulate on the local UV-C damage but on the contrary is remobilized after damage induction. This fast change in mobility is restored when DNA repair reactions are completed. By scrutinizing from which cellular complex/partner/structure XAB2 is released, we have identified that XAB2 is detached after DNA damage induction from the DNA:RNA hybrids, commonly known as R-loops, and from the CSA and XPG protein and this release is thought to contribute to the DNA damage recognition step during TC-NER. Importantly, we have disclosed a role for XAB2 in retaining RNAP2 on its substrate.
Hypersensitivity to uncertainty is key feature of subjective cognitive impairment
Authors: Attaallah Bahaaeddin , Petitet Pierre , Slavkova Elista , Turner Vicky , Saleh Youssuf , Manohar Sanjay G. , Husain Masud
Published: December 2021

With an increasingly ageing global population, more people are presenting with concerns about their cognitive function, but not all have an underlying neurodegenerative diagnosis. Subjective cognitive impairment (SCI) is a common condition describing self-reported deficits in cognition without objective evidence of cognitive impairment. Many individuals with SCI suffer from depression and anxiety, which have been hypothesised to account for their cognitive complaints. Despite this association between SCI and affective features, the cognitive and brain mechanisms underlying SCI are poorly understood. Here, we show that people with SCI are hypersensitive to uncertainty and that this might be a key mechanism accounting for their affective burden. Twenty-seven individuals with SCI performed an information sampling task, where they could actively gather information prior to decisions. Across different conditions, SCI participants sampled faster and obtained more information than matched controls to resolve uncertainty. Remarkably, despite their ‘urgent’ sampling behaviour, SCI participants were able to maintain their efficiency. Hypersensitivity to uncertainty indexed by this sampling behaviour correlated with the severity of affective burden including depression and anxiety. Analysis of MRI resting functional connectivity revealed that both uncertainty hypersensitivity and affective burden were associated with stronger insular-hippocampal connectivity. These results suggest that altered uncertainty processing is a key mechanism underlying the psycho-cognitive manifestations in SCI and implicate a specific brain network target for future treatment.
Neurons burdened by DNA double strand breaks incite microglia activation through antiviral-like signaling in neurodegeneration
Authors: Welch Gwyneth , Boix Carles , Schmauch Eloi , Davila-Velderrain Jose , Victor Matheus B. , Dileep Vishnu , Bozzelli Lorenzo , Su Qiao , Cheng Jemmie , Lee Audrey , Leary Noelle , Pfenning Andreas , Kellis Manolis , Tsai Li-Huei
Published: December 2021

DNA double strand breaks (DSBs) are linked to aging, neurodegeneration, and senescence1,2. However, the role played by neurons burdened with DSBs in disease-associated neuroinflammation is not well understood. Here, we isolate neurons harboring DSBs from the CK-p25 mouse model of neurodegeneration through fluorescence-activated nuclei sorting (FANS), and characterize their transcriptomes using single-nucleus, bulk, and spatial sequencing techniques. We find that neurons harboring DSBs enter a late-stage DNA damage response marked by the activation of senescent and antiviral-like immune pathways. We identify the NFkB transcription factor as a master regulator of immune gene expression in DSB-bearing neurons, and find that the expression of cytokines like Cxcl10 and Ccl2 develop in DSB-bearing neurons before glial cell types. Alzheimer’s Disease pathology is significantly associated with immune activation in excitatory neurons, and direct purification of DSB-bearing neurons from Alzheimer’s Disease brain tissue further validates immune gene upregulation. Spatial transcriptomics reveal that regions of brain tissue dense with DSB-bearing neurons also harbor signatures of inflammatory microglia, which is ameliorated by NFkB knock down in neurons. Inhibition of NFkB or depletion of Ccl2 and Cxcl10 in DSB-bearing neurons also reduces microglial activation in organotypic brain slice culture. In conclusion, we find that in the context of age-associated neurodegenerative disease, DSBs activate immune pathways in neurons, which in turn adopt a senescence associated secretory phenotype to elicit microglia activation. These findings highlight a novel role for neurons in the mechanism of age-associated neuroinflammation.

It is unclear how age-associated DNA double strand break (DSB) accumulation in neurons influences the progression of cellular senescence and neurodegenerative disease. Here, we leverage mouse models of neurodegeneration, single-nucleus, bulk, and spatial transcriptomics from Alzheimer’s disease patients, mouse models, and primary neuron cultures to dissect the immune signaling pathways initiated by DSB-bearing neurons that trigger neuroinflammation.
Pattern and component responses of primate MT neurons recorded with multi-contact electrodes, stimulated with 1D and 2D noise patterns
Authors: Quaia Christian , Kang Incheol , Cumming Bruce G
Published: December 2021

Direction selective neurons in primary visual cortex (area V1) are affected by the aperture problem, i.e., they are only sensitive to motion orthogonal to their preferred orientation. A solution to this problem first emerges in the middle temporal (MT) area, where a subset of neurons (called pattern cells) combine motion information across multiple orientations and directions, becoming sensitive to pattern motion direction. These cells are expected to play a prominent role in subsequent neural processing, but they are intermixed with cells that behave like V1 cells (component cells), and others that do not clearly fall in either group. The picture is further complicated by the finding that cells that behave like pattern cells with one type of pattern, might behave like component cells for another.

We recorded from macaque MT neurons using multi-contact electrodes while presenting both type I and unikinetic plaids, in which the components were 1D noise patterns. We found that the indices that have been used in the past to classify neurons as pattern or component cells work poorly when the properties of the stimulus are not optimized for the cell being recorded, as is always the case with multi-contact arrays. We thus propose alternative measures, which considerably ameliorate the problem, and allow us to gain insights in the signals carried by individual MT neurons.

We conclude that arranging cells along a component-to-pattern continuum is an oversimplification, and that the signals carried by individual cells only make sense when embodied in larger populations.
Age-related susceptibility to grey matter demyelination and neurodegeneration is associated with meningeal neutrophil accumulation in an animal model of Multiple Sclerosis
Authors: Zuo Michelle , Fettig Naomi , Bernier Louis-Philippe , Pössnecker Elisabeth , Spring Shoshana , Pu Annie , Ma Xianjie I. , Lee Dennis S. W. , Ward Lesley , Sharma Anshu , Kuhle Jens , Sled John G. , Pröbstel Anne-Katrin , MacVicar Brian , Osborne Lisa , Gommerman Jennifer L. , Ramaglia Valeria
Published: December 2021

People living with multiple sclerosis (MS) experience episodic central nervous system (CNS) white matter lesions instigated by autoreactive T cells. With age, MS patients show evidence of grey matter demyelination and experience devastating non-remitting symptomology. What drives progression is unclear and has been hampered by the lack of suitable animal models. Here we show that passive experimental autoimmune encephalomyelitis (EAE) induced by an adoptive transfer of young Th17 cells induces a non-remitting clinical phenotype that is associated with persistent leptomeningeal inflammation and cortical pathology in old, but not young SJL/J mice. While the quantity and quality of T cells did not differ in the brains of old vs young EAE mice, an increase in neutrophils and a decrease in B cells was observed in the brains of old mice. Neutrophils were also found in the leptomeninges of a subset of progressive MS patient brains that showed evidence of leptomeningeal inflammation and subpial cortical demyelination. Taken together, our data show that while Th17 cells initiate CNS inflammation, subsequent clinical symptoms and grey matter pathology are dictated by age and associated with other immune cells such as neutrophils.
Sensory axons induce epithelial lipid microdomain remodeling and determine the distribution of junctions in the epidermis
Authors: Rosa Jeffrey B. , Nassman Khaled Y. , Sagasti Alvaro
Published: December 2021

Epithelial cell properties are determined by the polarized distribution of membrane lipids, the cytoskeleton, and adhesive junctions. Epithelia are often profusely innervated, but little work has addressed how contact with neurites affects the polarized organization of epithelial components. In previous work, we found that basal keratinocytes in the larval zebrafish epidermis wrap around axons to enclose them in ensheathment channels sealed by autotypic cell junctions. In this study, we used live imaging to characterize how sensory axons remodel cell membranes, the actin cytoskeleton, and adhesive junctions in basal keratinocytes. At the apical surface of basal keratinocytes, axons promoted the formation of lipid microdomains quantitatively enriched in reporters for PI(4,5)P2 and liquid-ordered (Lo) membranes. Lipid microdomains supported the formation of cadherin-enriched F-actin protrusions, which wrapped around axons, likely initiating the formation of ensheathment channels. Lo reporters, but not reporters of liquid-disordered (Ld) membranes, became progressively enriched at axon-associated membrane domains as autotypic junctions matured at ensheathment channels. In the absence of axons, cadherin-enriched lipid microdomains still formed on basal cell membranes, but were not organized into the contiguous domains normally associated with axons. Instead, these isolated domains formed ectopic heterotypic junctions with overlying periderm cells, a distinct epithelial cell type in the epidermis. Thus, axons inhibit the formation of epithelial heterotypic junctions by recruiting cadherin-rich lipid microdomains to form autotypic junctions at ensheathment channels. These findings demonstrate that sensory nerve endings dramatically remodel polarized epithelial components and regulate the adhesive properties of the epidermis.
Profiling the Landscape of Drug Resistance Mutations in Neosubstrates to Molecular Glue Degraders
Authors: Gosavi Pallavi M. , Ngan Kevin C. , Yeo Megan , Su Cindy , Li Jiaming , Lue Nicholas Z. , Hoenig Samuel M. , Liau Brian B.
Published: December 2021

Targeted protein degradation (TPD) holds immense promise for drug discovery but mechanisms of acquired resistance to degraders remain to be fully identified. Here we used CRISPR-suppressor scanning to identify mechanistic classes of drug resistance mutations to molecular glue degraders in GSPT1 and RBM39, neosubstrates targeted by E3 ligase substrate receptors cereblon and DCAF15, respectively. While many mutations directly alter the ternary complex heterodimerization surface, distal resistance sites were also identified. Several distal mutations in RBM39 led to modest decreases in degradation yet can enable cell survival, underscoring how small differences in degradation can lead to resistance. Integrative analysis of resistance sites across GSPT1 and RBM39 revealed varying levels of sequence conservation and mutational constraint that control the emergence of different resistance mechanisms, highlighting that many regions co-opted by TPD are inessential. Altogether, our study identifies common resistance mechanisms for molecular glue degraders and outlines a general approach to survey neosubstrate requirements necessary for effective degradation.
Pharmacological blockade of muscle afferents and perception of effort: a systematic review with meta-analysis
Authors: Bergevin Maxime , Steele James , Payen de la Garanderie Marie , Feral-Basin Camille , Marcora Samuele M. , Rainville Pierre , Caron Jeffrey G. , Pageaux Benjamin
Published: December 2021

Background

The perception of effort (PE) provides information on task difficulty and influences physical exercise regulation and human behavior. This perception differs from other-exercise related perceptions such as pain. There is no consensus on the role of group III-IV muscle afferents as a signal processed by the brain to generate PE.

Objective

The aim of this meta-analysis was to investigate the effect of pharmacologically blocking muscle afferents on the PE.

Methods

Six databases were searched to identify studies measuring the ratings of perceived effort (RPE) during physical exercise, with and without pharmacological blockade of muscle afferents. Articles were coded based on the operational measurement used to distinguish studies in which PE was assessed specifically (effort dissociated) or as a composite experience including other exercise-related perceptions (effort not dissociated). Articles that did not provide enough information for coding were assigned to theuncleargroup.

Results

Theeffort dissociatedgroup (n=6) demonstrated a slight RPE increase with reduced muscle afferents feedback (standard mean change raw (SMCR), 0.39; 95%CI, 0.13 to 0.64). The groupeffort not dissociated(n=2) did not reveal conclusive results (SMCR, −0.29; 95%CI, −2.39 to 1.8). The groupunclear(n=8) revealed a slight RPE decrease with reduced muscle afferents feedback (SMCR, −0.27; 95%CI, −0.50 to −0.04).

Conclusions

The heterogeneity in results between groups reveals that the inclusion of perceptions other than effort in its rating influences the RPE scores reported by the participants. The absence of decreased RPE in theeffort dissociatedgroup suggests that muscle afferents feedback is not a sensory signal of PE.

Key points

To date, there is no consensus on the neurophysiological signal processed by the brain to generate the perception of effort.

Following a systematic search in six databases, this meta-analysis suggests that reducing afferent feedback from the working muscles via epidural anesthesia does not reduce perception of effort.

This systematic review suggests that afferent feedback from the working muscles is not the neurophysiological signal processed by the brain to generate the perception of effort.
MAFFIN: Metabolomics Sample Normalization Using Maximal Density Fold Change with High-Quality Metabolic Features and Corrected Signal Intensities
Authors: Yu Huaxu , Huan Tao
Published: December 2021

Sample normalization is a critical step in metabolomics to remove differences in total sample amount or concentration of metabolites between biological samples. Here, we present MAFFIN, an accurate and robust post-acquisition sample normalization workflow that works universally for metabolomics data collected by mass spectrometry (MS)-based platforms. The most important design of MAFFIN is the calculation of normalization factor using maximal density fold change (MDFC) value computed by a kernel density-based approach. MDFC is more accurate than traditional median FC-based normalization, especially when the numbers of up- and down-regulated metabolic features are different. In addition, we showcase two essential steps that are overlooked by conventional normalization methods, and incorporated them into MAFFIN. First, instead of using all detected metabolic features, MAFFIN automatically extracts and uses only the high-quality features to calculate FCs and determine the normalization factor. In particular, multiple orthogonal criteria are proposed to pick up the high-quality features. Second, to guarantee the accuracy of the FCs, the MS signal intensities of the high-quality features are corrected using serial quality control (QC) samples. Using simulated data and urine metabolomics datasets, we demonstrated the critical need of high-quality feature selection, MS signal correction, and MDFC. We also show the superior performance of MAFFIN over other commonly used post-acquisition sample normalization methods. Finally, a biological application on a human saliva metabolomics study shows that MAFFIN provides robust sample normalization, leading to better data separation in principal component analysis (PCA) and the identification of more significantly altered metabolic features.

TOC
Homogeneity of antibody-drug conjugates critically impacts the therapeutic efficacy in brain tumors
Authors: Anami Yasuaki , Otani Yoshihiro , Xiong Wei , Ha Summer Y. Y. , Yamaguchi Aiko , Zhang Ningyan , An Zhiqiang , Kaur Balveen , Tsuchikama Kyoji
Published: December 2021

Glioblastoma multiforme (GBM) is characterized by aggressive growth and the poorest prognosis of all brain tumor types. Most therapies rarely provide clinically meaningful improvements in outcomes of patients with GBM. Antibody-drug conjugates (ADCs) are emerging chemotherapeutics with stunning success in cancer management. Although promising, clinical studies of three ADCs for treating GBM, including Depatux-M, have been discontinued because of safety concerns and limited therapeutic benefits. Here, we report that ADC homogeneity is a critical parameter to maximize the therapeutic potential in GBM therapy. We demonstrate that homogeneous conjugates generated using our linker show enhanced drug delivery to intracranial brain tumors. Notably, compared to heterogeneous ADCs, including a Depatux-M analog, our ADCs provide greatly improved antitumor effects and survival benefits in orthotopic brain tumor models, including a patient-derived xenograft model of GBM. Our findings warrant the future development of homogeneous ADCs as promising molecular entities toward cures for intractable brain tumors.
A novel high-throughput assay using mixed genomic DNA for fast screening germline pathogenic variants in breast cancer susceptibility genes
Authors: Wan Qiting , Hu Li , Yao Lu , Chen Jiuan , Sun Jie , Zhang Juan , Xu Ye , Xie Yuntao
Published: December 2021

The demand for genetic testing for breast cancer susceptibility genes is increasing for both breast cancer patients and healthy individuals. Here we established a novel high-throughput assay to detect germline pathogenic variants in breast cancer susceptibility genes. In general, up 10 to 50 individual genomic DNA samples were mixed together to create a mixed DNA sample and the mixed DNA sample was subjected to a next-generation multigene panel. Germline pathogenic variants in breast cancer susceptibility genes could be found in the mixed DNA sample; next, site-specific Sanger sequencing was performed to identify individuals who carried he pathogenic variant in the mixed samples. We found that the recall and precision rates were 89.9% and 92.9% when twenty individual genomic samples were mixed. Therefore, our new assay can increase an approximately 20-fold of efficacy to identify the pathogenic variants in breast cancer susceptibility genes in individuals when compared with current assay.
Experimental Evolution Reveals Redox State Modulates Mycobacterial Pathogenicity
Authors: Jiang Zheng , Zhuang Zengfang , Mi Kaixia
Published: December 2021

Understanding how Mycobacterium tuberculosis has evolved into a professional pathogen is helpful in studying its pathogenesis and for designing vaccines. We investigated how the evolutionary adaptation of M. smegmatis mc251 to an important clinical stressor H2O2 allows bacteria undergo coordinated genetic mutations, resulting in increased pathogenicity. Whole-genome sequencing identified a mutation site in the fur gene, which caused increased expression of katG. Using a Wayne dormancy model, mc251 showed a growth advantage over its parental strain mc2155 in recovering from dormancy under anaerobic conditions. Meanwhile, the high level of KatG in mc251 was accompanied by a low level of ATP, which meant that mc251 is at a low respiratory level. Additionally, the redox-related protein Rv1996 showed different phenotypes in different specific redox states in M. smegmatis mc2155, mc251, M. bovis BCG and M. tuberculosis mc27000. In conclusion, our study shows that the same gene presents different phenotypes under different physiological conditions. This may partly explain why M. smegmatis and M. tuberculosis have similar virulence factors and signaling transduction systems such as two-component systems and sigma factors, but due to the different redox states in the corresponding bacteria, M. smegmatis is a nonpathogen, while M. tuberculosis is a pathogen. As mc251 overcomes its shortcomings of rapid removal, it can be potentially developed as a vaccine vector.
ROKET: Associating Somatic Mutation with Clinical Outcomes through Kernel Regression and Optimal Transport
Authors: Little Paul , Hsu Li , Sun Wei
Published: December 2021

Somatic mutations in cancer patients are inherently sparse and potentially high dimensional. Cancer patients may share the same set of deregulated biological processes perturbed by different sets of somatically mutated genes. Therefore, when assessing the associations between somatic mutations and clinical outcomes, gene-by-gene analyses is often under-powered because it does not capture the complex disease mechanisms shared across cancer patients. Rather than testing genes one by one, an intuitive approach is to aggregate somatic mutation data of multiple genes to assess the joint association. The challenge is how to aggregate such information. Building on the optimal transport method, we propose a principled approach to estimate the similarity of somatic mutation profiles of multiple genes between tumor samples, while accounting for gene-gene similarity defined by gene annotations or empirical mutational patterns. Using such similarities, we can assess the associations between somatic mutations and clinical outcomes by kernel regression. We have applied our method to analyze somatic mutation data of 17 cancer types and identified at least three cancer types harboring associations between somatic mutations and overall survival, progression-free interval or cytolytic activity.