bluuebunny/crossref_metadata_2025 huggingface dataset:
Strong Neutralizing Antibody Responses to SARS-CoV-2 Variants Following a Single Vaccine Dose in Subjects With Previous SARS-CoV-2 Infection
Authors: Ekström Nina , Haveri Anu , Solastie Anna , Virta Camilla , Österlund Pamela , Nohynek Hanna , Nieminen Tuomo , Ivaska Lauri , Tähtinen Paula A , Lempainen Johanna , Jalkanen Pinja , Julkunen Ilkka , Palmu Arto A , Melin Merit
Published: November 2022

Background

Previous severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection primes the immune system; thus individuals who have recovered from infection have enhanced immune responses to subsequent vaccination (hybrid immunity). However, it remains unclear how well hybrid immunity induced by severe or mild infection can cross-neutralize emerging variants. We aimed to compare the strength and breadth of antibody responses in vaccinated recovered and uninfected subjects.

Methods

We measured spike-specific immunoglobulin (Ig)G and neutralizing antibodies (NAbs) from vaccinated subjects including 320 with hybrid immunity and 20 without previous infection. From 29 subjects with a previous severe or mild infection, we also measured NAb responses against Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617.2), and Omicron (B.1.1.529/BA.1) variants following vaccination.

Results

A single vaccine dose induced 2-fold higher anti-spike IgG concentrations and up to 4-fold higher neutralizing potency of antibodies in subjects with a previous infection compared with vaccinated subjects without a previous infection. Hybrid immunity was more enhanced after a severe than a mild infection, with sequentially decreasing NAb titers against Alpha, Beta, Delta, and Omicron variants. We found similar IgG concentrations in subjects with a previous infection after 1 or 2 vaccine doses.

Conclusions

Hybrid immunity induced strong IgG responses, particularly after severe infection. However, the NAb titers were low against heterologous variants, especially against Omicron.
Determinants of Antiretroviral Treatment Success and Adherence in People With Human Immunodeficiency Virus Treated for Tuberculosis
Authors: De Castro Nathalie , Chazallon Corine , N'takpe Jean-Baptiste , Timana Isabel , Escada Rodrigo , Wagner Sandra , Messou Eugène , Eholie Serge , Bhatt Nilesh , Khosa Celso , Laureillard Didier , Do Chau Giang , Veloso Valdilea G , Delaugerre Constance , Anglaret Xavier , Molina Jean-Michel , Grinsztejn Beatriz , Marcy Olivier ,   for the ANRS 12300 Reflate TB2 Study Group
Published: November 2022

Background

In people with human immunodeficiency virus [HIV] presenting with advanced disease, rates of virologic success may be lower than expected. The Reflate TB2 trial did not show non-inferiority of raltegravir versus efavirenz in people with HIV (PWH) treated for tuberculosis. We aimed to identify factors associated with virologic success and higher adherence in the trial.

Methods

In this analysis, we included participants enrolled in the Reflate TB2 trial with adherence data available. The primary outcome was virologic success (HIV-1 ribonucleic acid [RNA] <50 copies/mL) at week 48, and the secondary outcome was adherence as assessed by the pill count adherence ratio. We used logistic regression to study determinants of virologic success and optimal adherence in 2 separate analyses.

Results

Four hundred forty-four participants were included in the present analysis. Over the 48-week follow-up period, 290 of 444 (65%) participants had a pill count adherence ratio ≥95%. At week 48, 288 of 444 (65%) participants were in virologic success. In the multivariate analysis, female sex (adjusted odds ratio [aOR], 1.77; 95% confidence interval [CI], 1.16–2.72; P = .0084), lower baseline HIV-1 RNA levels (<100 000; aOR, 2.29; 95% CI, 1.33–3.96; P = .0087), and pill count adherence ratio ≥95% (aOR, 2.38; 95% CI, 1.56–3.62; P < .0001) were independently associated with virologic success. Antiretroviral pill burden was the only factor associated with pill count adherence ratio ≥95% (OR, 0.81; 95% CI, .71–.92; P = .0018).

Conclusions

In PWH with tuberculosis receiving raltegravir or efavirenz-based regimens, female sex, optimal adherence, and baseline HIV-1 RNA <100 000 copies/mL were associated with virologic success, and the number of antiretroviral tablets taken daily was a strong predictor of adherence.
Pro-Inflammatory Alterations of Circulating Monocytes in Latent Tuberculosis Infection
Authors: Feria Manuel G , Chang Cecilia , Ticona Eduardo , Moussa Anissa , Zhang Bin , Ballena Isabel , Azañero Ruben , Ticona Cesar , De Cecco Carlo N , Fichtenbaum Carl J , O’Donnell Robert E , La Rosa Alberto , Sanchez Jorge , Andorf Sandra , Atehortua Laura , Katz Jonathan D , Chougnet Claire A , Deepe George S , Huaman Moises A
Published: November 2022

Background

Latent tuberculosis infection (LTBI) has been associated with increased cardiovascular risk. We investigated the activation and pro-inflammatory profile of monocytes in individuals with LTBI and their association with coronary artery disease (CAD).

Methods

Individuals 40–70 years old in Lima, Peru, underwent QuantiFERON-TB testing to define LTBI, completed a coronary computed tomography angiography to evaluate CAD, and provided blood for monocyte profiling using flow cytometry. Cells were stimulated with lipopolysaccharide to assess interleukin-6 (IL-6) and tumor necrosis factor (TNF)–α responses.

Results

The clinical characteristics of the LTBI (n = 28) and non-LTBI (n = 41) groups were similar. All monocyte subsets from LTBI individuals exhibited higher mean fluorescence intensity (MFI) of CX3CR1 and CD36 compared with non-LTBI individuals. LTBI individuals had an increased proportion of nonclassical monocytes expressing IL-6 (44.9 vs 26.9; P = .014), TNF-α (62.3 vs 35.1; P = .014), and TNF-α+IL-6+ (43.2 vs 36.6; P = .042). Among LTBI individuals, CAD was associated with lower CX3CR1 MFI on classical monocytes and lower CD36 MFI across all monocyte subsets. In multivariable analyses, lower CD36 MFI on total monocytes (b = −0.17; P = .002) and all subsets remained independently associated with CAD in LTBI.

Conclusions

Individuals with LTBI have distinct monocyte alterations suggestive of an exacerbated inflammatory response and tissue migration. Whether these alterations contribute to cardiovascular disease pathogenesis warrants further investigation.
Knowing behavior matters doesn’t hurt: the effect of individual climate behavior messaging on green policy support
Authors: Rakhimov Abdurakhim , Thulin Erik
Published: November 2022

Individual behavior change offers a large potential to curb greenhouse gas emissions. However, messaging promoting individual behavior change has been criticized as a strategy for addressing climate change due to its potential to diminish climate policy support. In a pre-registered study with a representative sample of American adults (n = 1069), we found that messages recommending the adoption of high-impact individual climate behaviors, such as flying less, eating less meat and reducing food waste, and highlighting their large impact do not affect support for a carbon tax. In an exploratory analysis, we found that this messaging results in a higher intention to adopt several climate behaviors. We recommend that interventions that advocate for individual climate action be best understood as complements, rather than undermining substitutes, to broad carbon regulatory policy.
Confirmation bias and vaccine-related beliefs in the time of COVID-19
Authors: Malthouse Eugene
Published: November 2022

Background

In recent history mass vaccination has proved essential to dealing with pandemics. However, the effectiveness of a vaccine depends on the number of people willing to take it. One approach to encouraging uptake is to publish information about safety and effectiveness. But confirmation bias research in other domains suggests that people may evaluate this information through the lens of their existing beliefs.

Methods

This study used a simple 2 × 2 design to investigate whether people’s (n = 3899) existing beliefs influenced their ability to correctly evaluate data from a fictional trial presented in a frequency table. Treatment groups saw different trial outcomes (intervention effective versus ineffective and trial related versus unrelated to vaccines).

Results

Results provided robust evidence for confirmation bias in the domain of vaccines: people made systematic errors (P < 0.01) when evaluating evidence that was inconsistent with their prior beliefs. This pattern emerged among people with both pro-vaccination and anti-vaccination attitudes. Errors were attributed to confirmation bias because no such differences were detected when participants evaluated data unrelated to vaccines.

Conclusions

People are prone to misinterpreting evidence about vaccines in ways that reflect their underlying beliefs. Confirmation bias is an important consideration for vaccine communication.
Increased Enhancer-Promoter Interactions during Developmental Enhancer Activation in Mammals
Authors: Chen Zhuoxin , Snetkova Valentina , Bower Grace , Jacinto Sandra , Clock Benjamin , Dizehchi Atrin , Barozzi Iros , Mannion Brandon J. , Alcaina-Caro Ana , Lopez-Rios Javier , Dickel Diane E. , Visel Axel , Pennacchio Len A. , Kvon Evgeny Z.
Published: November 2022

Remote enhancers are thought to interact with their target promoters via physical proximity, yet the importance of this proximity for enhancer function remains unclear. Here, we investigate the 3D conformation of enhancers during mammalian development by generating high-resolution tissue-resolved contact maps for nearly a thousand enhancers with characterized in vivo activities in ten murine embryonic tissues. 61% of developmental enhancers bypass their neighboring genes, which are often marked by promoter CpG methylation. The majority of enhancers display tissue-specific 3D conformations, and both enhancer-promoter and enhancer-enhancer interactions are moderately but consistently increased upon enhancer activation in vivo. Less than 14% of enhancer-promoter interactions form stably across tissues; however, these invariant interactions form in the absence of the enhancer and are likely mediated by adjacent CTCF binding. Our results highlight the general significance of enhancer-promoter physical proximity for developmental gene activation in mammals.
NLP-based tools for localization of the Epileptogenic Zone in patients with drug-resistant focal epilepsy
Authors: Mora Sara , Turrisi Rosanna , Chiarella Lorenzo , Tassi Laura , Mai Roberto , Nobili Lino , Barla Annalisa , Arnulfo Gabriele
Published: November 2022

Background

Drug-resistant focal epilepsy, defined by failure of two antiepileptic drugs, affects about 30% of patients with epilepsy. Epilepsy surgery may represent an alternative options for this population. However, defining the epileptogenic zone to be surgically removed requires highly specialised medical expertise as well as advanced technologies. The aim of this work is building a cost-effective support system based on text, in particular based on the semiological descriptions of the seizures (temporal vs extratemporal lobe; right vs left hemisphere), in order to predict the localization of seizure origin.

Methods

Among a population of 121 surgically treated and seizure-free drug-resistant patients suffering with focal epilepsy, recruited at the Niguarda Hospital in Milan, we extracted a total number of 509 descriptions of seizures. After a data pre-processing phase, we used natural language processing tools to build numerical representations of the seizures descriptions, both using embedding and countbased methods. We then used machine learning models performing a binary classification into right/left and temporal/extra-temporal.

Results

All predictive models show a better performance when using the representations relying on embedding models respect to count-based ones. Between all the combinations of representations and classifiers, the best performance obtained in terms of F1-score is 84.7%±0.6.

Discussion

This preliminary work reached encouraging results considering both localization tasks. The main advantage is that no specific knowledge about epilepsy is used to build the models, rendering our pipeline applicable also in other scenarios. The major limitation lies in the fact that the text is highly specific to the writer.
Accurate Computational Design of 3D Protein Crystals
Authors: Li Zhe , Wang Shunzhi , Nattermann Una , Bera Asim K. , Borst Andrew J. , Bick Matthew J. , Yang Erin C. , Sheffler William , Lee Byeongdu , Seifert Soenke , Nguyen Hannah , Kang Alex , Dalal Radhika , Lubner Joshua M. , Hsia Yang , Haddox Hugh , Courbet Alexis , Dowling Quinton , Miranda Marcos , Favor Andrew , Etemadi Ali , Edman Natasha I. , Yang Wei , Sankaran Banumathi , Negahdari Babak , Baker David
Published: November 2022

Protein crystallization plays a central role in structural biology1, with broad impact2in pharmaceutical formulation3, drug delivery4, biosensing5, and biocatalysis6,7. Despite this importance, the process of protein crystallization remains poorly understood and highly empirical8–10, with largely unpredictable crystal contacts, lattice packing arrangements, and space group preferences, and the programming of protein crystallization through precisely engineered sidechain-sidechain interactions across multiple protein-protein interfaces is an outstanding challenge. Here we develop a general computational approach to designing three-dimensional (3D) protein crystals with pre-specified lattice architectures at atomic accuracy that hierarchically constrains the overall degree of freedoms (DOFs) of the system. We use the approach to design three pairs of oligomers that can be individually purified, and upon mixing, spontaneously self-assemble into large 3D crystals (>100 μm). Small-angle X-ray scattering and X-ray crystallography show these crystals are nearly identical to the computational design models, with the design targetF4132 andI432 space groups and closely corresponding overall architectures and protein-protein interfaces. The crystal unit cell dimensions can be systematically redesigned while retaining space group symmetry and overall architecture, and the crystals are both extremely porous and highly stable, enabling the robust scaffolding of inorganic nanoparticle arrays. Our approach thus enables the computational design of protein crystals with high accuracy, and since both structure and assembly are encoded in the primary sequence, provides a powerful new platform for biological material engineering.
Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state
Authors: Barrett Thomas F. , Patel Bhuvic , Khan Saad M. , Yim Aldrin K.Y. , Pugazenthi Sangami , Mahlokozera Tatenda , Mullins Riley D.Z. , Zipfel Gregory J. , Herzog Jacques A. , Chicoine Michael R. , Wick Cameron C. , Durakovic Nedim , Osbun Joshua W. , Shew Matthew , Sweeney Alex D. , Patel Akash J. , Buchman Craig A. , Petti Allegra A. , Puram Sidharth V. , Kim Albert H.
Published: November 2022

Vestibular schwannomas (VS) are benign tumors that lead to significant neurologic and otologic morbidity. How VS heterogeneity and the tumor microenvironment (TME) contribute to the pathogenesis of these tumors remains poorly understood. We performed scRNA-seq on 15 VS samples, with paired scATAC-seq in six samples. We identified diverse Schwann cell (SC), stromal, and immune populations in the VS TME and found that repair-like and MHC-II antigen presenting subtype SCs are associated with increased myeloid cell infiltrate, implicating a nerve injury-like process. Deconvolution analysis of RNA-expression data from 175 tumors revealed Injury-like tumors are associated with larger tumor size, and scATAC-seq identified transcription factors associated with nerve repair among SCs from Injury-like tumors. Ligand-receptor analysis and functionalin vitroexperiments suggested that SCs recruit monocytes. Our study indicates that Injury-like SCs may cause tumor growth via myeloid cell recruitment and identifies molecular pathways that may be targeted to prevent tumor progression.
Dandelionutilizes single cell adaptive immune receptor repertoire to explore lymphocyte developmental origins
Authors: Suo Chenqu , Polanski Krzysztof , Dann Emma , Lindeboom Rik G.H. , Vilarrasa-Blasi Roser , Vento-Tormo Roser , Haniffa Muzlifah , Meyer Kerstin B. , Dratva Lisa M. , Tuong Zewen Kelvin , Clatworthy Menna R. , Teichmann Sarah A.
Published: November 2022

Assessment of single-cell gene expression (scRNA-seq) and adaptive immune receptor sequencing (scVDJ-seq) has been invaluable in studying lymphocyte biology. Here, we introduceDandelion, a computational pipeline for scVDJ-seq analysis. It enables the application of standard V(D)J analysis workflows to single-cell datasets, delivering improved V(D)J contig annotation and the identification of non-productive and partially spliced contigs. We devised a novel strategy to create an adaptive immune receptor feature space that can be used for both differential V(D)J usage analysis and pseudotime trajectory inference. The application ofDandelionimproved the alignment of human thymic development trajectories of double positive T cells to mature single-positive CD4/CD8 T cells, with important new predictions of factors regulating lineage commitment.Dandelionanalysis of other cell compartments provided novel insights into the origins of human B1 cells and ILC/NK cell development, illustrating the power of our approach.Dandelionis an open access resource (https://www.github.com/zktuong/dandelion)that will enable future discoveries.
Structural, functional and evolutionary analysis of wheat WRKY45 protein: A combined bioinformatics and MD simulation approach
Authors: Ranjan Prashant , Yadav Ashok , Behera Ananta Keshari , Singh Dhiraj Kumar , Singh Premkant , Singh Ganga Prasad
Published: November 2022

Bread wheat (Triticum aestivum L.) is the world’s second-most important cereal crop, as well as India’s. It is an allohexaploid composed of three homeologous sub-genomes (AA, BB, and DD), which is a constraint in determining the complete genome sequence. Several transcription factors have been implicated in both abiotic and biotic stress. WRKY transcription factors are among the best characterised in the context of pathogen defence mechanisms. Different members of the WRKY transcription factors have been shown to confer resistance to stress. But very little is known about the wheat WRKY transcription factors. In silico analysis of the TaWRKY45 protein was performed in the present study using several bioinformatics tools like motif scan, CD search, Netphos, NGlycos, GRAVY, and the SWISS MODEL. The study revealed that TaWRKY45 belongs to the group III family and contains hydrophilic proteins with 19 potential phosphorylation sites. TaWRKY45 protein was found to be orthologous to rice OsWRKY45 by phylogenetic analysis. The catalytic domain was analysed by motif scan which showed that TaWRKY45 has one WRKY domain and a C2-HC zinc finger motif. TaWRKY45’s structure was determined to be more stable, more constrained, more compact, and have greater potential to interact with other molecules than OsWRKY45, according to MD simulation analysis. Thus, in silico analysis of transcription factors helps study protein function, interaction, and regulatory pathways.
A therapeutic hepatitis B mRNA vaccine with strong immunogenicity and persistent virological suppression
Authors: Zhao Huajun , Shao Xianyu , Yu Yating , Huang Lulu , Amor Narh Philip , Guo Kun , Weng Changzhen , Zhao Weijun , Yang Ailu , Hu Jiesen , Yang Hongbao , Liu Zhenguang , Han Qiuju , Shi Leilei , Sun Shiyu , Zhang Jian , Yang Yong , Lin Ang
Published: November 2022

BRIEF ABSTRACT

Here we report on the development and comprehensive evaluations of an mRNA vaccine for chronic hepatitis B (CHB) treatment. In two different HBV carrier mouse models generated by viral vector-mediated HBV transfection (pAAV-HBV1.2 and rAAV8-HBV1.3), this vaccine demonstrates sufficient and persistent virological suppression, and robust immunogenicity in terms of induction of strong innate immune activation, high-level virus-specific antibodies, memory B cells and T cells. mRNA platform therefore holds prospects for therapeutic vaccine development to combat CHB.
Transcriptomic profiling of reward and sensory brain areas in perinatal fentanyl exposed juvenile mice
Authors: Olusakin Jimmy , Kumar Gautam , Basu Mahashweta , Calarco Cali A. , Fox Megan E. , Alipio Jason B. , Haga Catherine , Turner Makeda D. , Keller Asaf , Ament Seth A. , Lobo Mary Kay
Published: November 2022

Use of the synthetic opioid fentanyl increased ∼300% in the last decade, including among women of reproductive ages. Adverse neonatal outcomes and long-term behavioral disruptions are associated with perinatal opioid exposure. Our previous work demonstrated that perinatal fentanyl exposed mice displayed enhanced negative affect and somatosensory circuit and behavioral disruptions during adolescence. However, little is known about molecular adaptations across brain regions that underlie these outcomes. We performed RNA-sequencing across three reward and two sensory brain areas to study transcriptional programs in perinatal fentanyl exposed juvenile mice. Pregnant dams received 10μg/ml fentanyl in the drinking water from embryonic day 0 (E0) through gestational periods until weaning at postnatal day 21 (P21). RNA was extracted from nucleus accumbens (NAc), prelimbic cortex (PrL), ventral tegmental area (VTA), somatosensory cortex (S1) and ventrobasal thalamus (VBT) from perinatal fentanyl exposed mice of both sexes at P35. RNA-sequencing was performed, followed by analysis of differentially expressed genes (DEGs) and gene co-expression networks. Transcriptome analysis revealed DEGs and gene modules significantly associated with exposure to perinatal fentanyl in a sex-wise manner. The VTA had the most DEGs, while robust gene enrichment occurred in NAc. Genes enriched in mitochondrial respiration were pronounced in NAc and VTA of perinatal fentanyl exposed males, extracellular matrix (ECM) and neuronal migration enrichment were pronounced in NAc and VTA of perinatal fentanyl exposed males, while genes associated with vesicular cycling and synaptic signaling were markedly altered in NAc of perinatal fentanyl exposed female mice. In sensory areas from perinatal fentanyl exposed females, we found alterations in mitochondrial respiration, synaptic and ciliary organization processes. Our findings demonstrate distinct transcriptomes across reward and sensory brain regions, with some showing discordance between sexes. These transcriptome adaptations may underlie structural, functional, and behavioral changes observed in perinatal fentanyl exposed mice.
Interferon-γ Elicits Pathological Hallmarks of ALS in Human Motor Neurons
Authors: Chun Changho , Lee Jung Hyun , Smith Alec S.T. , Mack David L. , Bothwell Mark , Nghiem Paul
Published: November 2022

Neuroinflammation is an established factor contributing to amyotrophic lateral sclerosis (ALS) pathology, implicating the possible detrimental effects of inflammatory cytokines on motor neurons. The RNA/DNA-binding protein TDP-43 has emerged as a pivotal actor in ALS, because TDP-43 mutations cause familial ALS and loss of nuclear TDP-43, associated with its redistribution into cytoplasmic aggregates (TDP-43 proteinopathy) in motor neurons occurs in 97% of ALS cases. However, mechanisms linking neuroinflammation to TDP-43 mislocalization have not been described. Programmed death-ligand 1 (PD-L1) is an immune-modulatory protein, highly expressed on cell surfaces following acute inflammatory stress. To determine which inflammatory cytokines might impact motor neuron function, seven cytokines known to be elevated in ALS patients’ cerebrospinal fluid were tested for their effects on PD-L1 expression in human iPSC-derived motor neurons. Among the tested cytokines, only interferon-γ (IFN-γ) was found to strongly promote PD-L1 expression. Thus, we hypothesized that excessive exposure to IFN-γ may contribute to motor neuron degeneration in ALS. We observed that neuronal populations exposed to IFN-γ exhibited severe TDP-43 cytoplasmic aggregation and excitotoxic behavior correlated with impaired neural firing activity, hallmarks of ALS pathology, in both normal and ALS mutant (TARDB1K+/-) neurons. Single-cell RNA sequencing revealed possible mechanisms for these effects. Motor neurons exposed to IFN-γ exhibited an extensive shift of their gene expression profile toward a neurodegenerative phenotype. Notably, IFN-γ treatment induced aberrant expression levels for 70 genes that are listed in the recent literature as being dysregulated in various ALS subtypes. Additionally, we found that genes related to neuronal electrophysiology, protein aggregation, and TDP-43 misregulation were abnormally expressed in IFN-γ treated cells. Moreover, IFN-γ induced a significant reduction in the expression of genes that encode indispensable proteins for neuromuscular synapse development and maintenance, implying that the continuous cytokine exposure could directly impair signal transmission between motor axons and muscle membranes. Our findings suggest that IFN-γ could be a potent upstream pathogenic driver of ALS and provide potential candidates for future therapeutic targets to treat sporadic forms of ALS, which account for roughly 90% of reported cases.
Vascular fungi alter the apoplastic purinergic signaling in plants by deregulating the homeostasis of extracellular ATP and its metabolite adenosine
Authors: Kesten Christopher , Leitner Valentin , Dora Susanne , Sims James W. , Dindas Julian , Zipfel Cyril , De Moraes Consuelo M. , Sánchez-Rodríguez Clara
Published: November 2022

Purinergic signaling activated by extracellular nucleotides and their derivative nucleosides trigger sophisticated signaling networks. The outcome of these pathways determine the capacity of the organism to survive under challenging conditions. Both extracellular ATP (eATP) and Adenosine (eAdo) act as secondary messengers in mammals, essential for immunosuppressive responses. Despite the clear role of eATP as a plant damage-associated molecular pattern, the function of its nucleoside, eAdo, and of the eAdo/eATP balance in plant stress response remain to be fully elucidated. This is particularly relevant in the context of plant/microbe interaction, where the intruder manipulates the extracellular matrix. Here, we identify Ado as a main elicitor secreted by the vascular fungusFusarium oxysporum. We show that eAdo modulates the plant’s susceptibility to fungal colonization by altering eATP-mediated physiological immune responses, such as apoplastic pH and calcium homeostasis. Our work indicates that plant pathogens actively imbalance the eAdo/eATP levels as a virulence mechanism.

One Sentence Summary

The apoplastic Adenosine/ATP balance is a messenger for plant defense and can be manipulated by the fungal pathogenF. oxysporum.
Runx factors launch T-cell and innate lymphoid programs via direct and gene network-based mechanisms
Authors: Shin Boyoung , Zhou Wen , Wang Jue , Gao Fan , Rothenberg Ellen V.
Published: November 2022

Runx factors are essential for lineage specification of various hematopoietic cells, including T lymphocytes. However, they regulate context-specific genes and occupy distinct genomic regions in different cell types. Here, we show that dynamic Runx binding shifts in early T-cell development are mostly not restricted by local chromatin state but regulated by Runx dosage and functional partners. Runx co-factors compete to recruit a limited pool of Runx factors in early T-progenitors, and a modest increase in Runx protein availability at pre-commitment stages causes premature Runx occupancy at post-commitment binding sites. This results in striking T-lineage developmental acceleration by selectively activating T-identity and innate lymphoid cell programs. These are collectively regulated by Runx together with other, Runx-induced transcription factors that co-occupy Runx target genes and propagate gene network changes.
CryoEM Reveals Oligomeric Isomers of a Multienzyme Complex and Assembly Mechanics
Authors: Lee Jane K.J. , Liu Yun-Tao , Hu Jason J. , Aphasizheva Inna , Aphasizhev Ruslan , Zhou Z. Hong
Published: November 2022

Propionyl-CoA carboxylase (PCC) is a multienzyme complex consisting of up to six α-subunits and six ß-subunits. Belonging to a metabolic pathway converging on the citric acid cycle, it is present in most forms of life and irregularities in its assembly lead to serious illness in humans, known as propionic acidemia. Here, we report the cryogenic electron microscopy (cryoEM) structures and assembly of different oligomeric isomers of endogenous PCC from the parasitic protozoanLeishmania tarentolae(LtPCC). These structures and their statistical distribution reveal the mechanics of PCC assembly and disassembly at equilibrium. We show that, in solution, endogenous LtPCC ß-subunits form stable homohexamers, to which different numbers of α-subunits attach. Sorting LtPCC particles into seven classes (i.e., oligomeric formulas α0β6, α1β6, α2β6, α3β6, α4β6, α5β6, α6β6) enables formulation of a model for PCC assembly. Our results suggest how multimerization regulates PCC enzymatic activity and showcase the utility of cryoEM in revealing the statistical mechanics of reaction pathways.
Distinct states of nucleolar stress induced by anti-cancer drugs
Authors: Potapova Tamara A. , Unruh Jay R. , Conkright-Fincham Juliana , Banks Charles A. S. , Florens Laurence , Schneider David A. , Gerton Jennifer L.
Published: November 2022

Ribosome biogenesis is a vital and energy-consuming cellular function occurring primarily in the nucleolus. Cancer cells have an especially high demand for ribosomes to sustain continuous proliferation. This study evaluated the impact of existing anticancer drugs on the nucleolus by screening a library of anticancer compounds for drugs that induce nucleolar stress. For a readout, a novel parameter termed “nucleolar normality score” was developed that measures the ratio of the fibrillar center and granular component proteins in the nucleolus and nucleoplasm. Multiple classes of drugs were found to induce nucleolar stress, including DNA intercalators, inhibitors of mTOR/PI3K, heat shock proteins, proteasome, and cyclin-dependent kinases (CDKs). Each class of drugs induced morphologically and molecularly distinct states of nucleolar stress accompanied by changes in nucleolar biophysical properties. In-depth characterization focused on the nucleolar stress induced by inhibition of transcriptional CDKs, particularly CDK9, the main CDK that regulates RNA Pol II. Multiple CDK substrates were identified in the nucleolus, including RNA Pol I – recruiting protein Treacle, which was phosphorylated by CDK9in vitro. These results revealed a concerted regulation of RNA Pol I and Pol II by transcriptional CDKs. Our findings exposed many classes of chemotherapy compounds that are capable of inducing nucleolar stress, and we recommend considering this in anticancer drug development.

Types of nucleolar stresses identified in this study

(1) DNA intercalators and RNA Pol inhibitors induced canonical nucleolar stress manifested by partial dispersion of granular component (GC) and segregation of rDNA and fibrillar center (FC) components UBF, Treacle, and POLR1A within nucleolar stress caps. (2) Inhibition of mTOR and PI3K growth pathways induced a metabolic suppression of function accompanied by the decrease in nucleolar normality score, size, and rRNA production, without dramatic re-organization of nucleolar anatomy. (3) Inhibitors targeting HSP90 and proteasome induced proteotoxicity, resulting in the disruption of protein homeostasis and the accumulation of misfolded and/or undegraded proteins. These effects were accompanied by a decrease in nucleolar normality score, rRNA output, and in some cases formation of protein aggregates (aggresomes) inside the nucleolus. (4) Inhibition of transcriptional CDK activity led to the disruption of interactions between rDNA, RNA Pol I, and GC proteins. This resulted in almost complete nucleolar dissolution, leaving behind an extended bare rDNA scaffold with only a few associated FC proteins remaining. UBF and PolI-recruiting protein Treacle remained associated with the rDNA, while POLR1A and GC dispersed in the nucleoplasm. rRNA production ceased and the nucleolar normality score was greatly reduced.
Mapping single-cell responses to population-level dynamics during antibiotic treatment
Authors: Kim Kyeri , Wang Teng , Ma Helena R. , Şimşek Emrah , Li Boyan , Andreani Virgile , You Lingchong
Published: November 2022

Treatment of sensitive bacteria with beta-lactam antibiotics often leads to two salient population-level features: a transient increase in total population biomass before a subsequent decline, and a linear correlation between growth and killing rates. However, it remains unclear how these population-level responses emerge from collective single-cell responses. During beta-lactam treatment, it is well recognized that individual cells often exhibit varying degrees of filamentation before lysis. We show that the probability of cell lysis increases with the extent of filamentation and that this dependence is characterized by unique parameters that are specific to bacterial strain, antibiotic dose, and growth condition. Modeling demonstrates how the single-cell lysis probabilities can give rise to population-level biomass dynamics, which were experimentally validated. This mapping provides insights into how the population biomass time-kill curve emerges from single cells and allows the representation of both single-and population-level responses with universal parameters.
Germline variation contributes to false negatives in CRISPR-based experiments with varying burden across ancestries
Authors: Misek Sean A. , Fultineer Aaron , Kalfon Jeremie , Noorbakhsh Javad , Boyle Isabella , Dempster Joshua , Petronio Lia , Huang Katherine , Saadat Alham , Green Thomas , Brown Adam , Doench John G. , Root David , McFarland James , Beroukhim Rameen , Boehm Jesse S.
Published: November 2022

Reducing disparities is critical to promote equity of access to precision treatments for all patients with cancer. While socioenvironmental factors are a major driver behind such disparities, biological differences also are likely to contribute. The prioritization of cancer drug targets is foundational for drug discovery, yet whether ancestry-related signals in target discovery pipelines exist has not been systematically explored due to the absence of data at the appropriate scale. Here, we analyzed data from 611 genome-scale CRISPR/Cas9 viability experiments in human cell line models as part of the Cancer Dependency Map to identify ancestry-associated genetic dependencies. Surprisingly, we found that most putative associations between ancestry and dependency arose from artifacts related to germline variants that are present at different frequencies across ancestry groups. In 2-5% of genes profiled in each cellular model, germline variants in sgRNA targeting sequences likely reduced cutting by the CRISPR/Cas9 nuclease. Unfortunately, this bias disproportionately affected cell models derived from individuals of recent African descent because their genomes tended to diverge more from the consensus genome typically used for CRISPR/Cas9 guide design. To help the scientific community begin to resolve this source of bias, we report three complementary methods for ancestry-agnostic CRISPR experiments. This report adds to a growing body of literature describing ways in which ancestry bias impacts cancer research in underappreciated ways.
Biofilm characterization in the maize pathogen,Fusarium verticillioides
Authors: Peremore Chizné , Wingfield Brenda , Santana Quentin , Steenkamp Emma T , Motaung Thabiso E
Published: November 2022

Nearly all microbes, including fungal pathogens, form biofilms, which are structured communities of microbial aggregates enclosed in self-produced extracellular polymeric substances (EPS) and attached to a surface. Studying plant-associated fungal biofilms can enhance understanding of fungal biology and knowledge of the links between fungal diseases and plants. However, only a few plant-associated fungi are reported to form biofilms. This study aimed to examine the ability of a mycotoxigenic fungus of maize,Fusarium verticillioides, to form biofilms under laboratory conditions. During our investigation,F. verticillioidesstationary phase cultures incubated in liquid media developed a biofilm-like pellicle with a hyphal assemblage that appears in the form of a cloudy and thin slime material. Under the microscope, the biofilms exhibited a highly heterogeneous architecture made of dense, entangled, and compact hyphae, which were accompanied by a quantifiable EPS and extracellular DNA (eDNA). The biofilm was also found to respond to different abiotic conditions including pH and temperature, suggesting their relevance in a field setting. We further demonstrate the biofilm structural maintenance role of eDNA through treatment with DNase, which was only marginally effective during late biofilm stages, suggesting that it forms complex interactions with the EPS during biofilm maturation. Based on these results, we propose thatF. verticillioidesforms a ‘true’ biofilm that may act as a potential virulence factor.
Subcellular niche segregation of co-obligate symbionts in whiteflies
Authors: Fujiwara Akiko , Meng Xian-Ying , Kamagata Yoichi , Tsuchida Tsutomu
Published: November 2022

Many insects contain endosymbiotic bacteria within their bodies. In multiple endosymbiotic systems comprising two or more symbionts, each of the symbionts is generally localized in a different host cell or tissue.Bemisia tabaci(Sweet potato whitefly)possesses a unique endosymbiotic system where co-obligate symbionts are localized in the same bacteriocytes. Using fluorescencein situhybridization, we found that endosymbionts inB. tabaciMEAM1 occupy distinct subcellular habitats, or niches, within a single bacteriocyte.Hamiltonellawas located adjacent to the nucleus of the bacteriocyte, whilePortierawas present in the cytoplasm surroundingHamiltonella. Immunohistochemical analysis revealed that the endoplasmic reticulum separates the two symbionts. Habitat segregation was maintained for longer durations in female bacteriocytes. The same segregation was observed in three genetically distinctB. tabacigroups (MEAM1, MED Q1, and Asia II 6) andTrialeurodes vaporariorum, which shared a common ancestor withBemisiaover 80 million years ago, even though the coexisting symbionts and the size of bacteriocytes were different. These results suggest that the habitat segregation system existed in the common ancestor and was conserved in both lineages, despite different bacterial partners coexisting withPortiera. Our findings provide insights into the evolution and maintenance of complex endosymbiotic systems and highlight the importance of organelles for the construction of separate niches for endosymbionts.

Importance

Co-obligate endosymbionts inB. tabaciare exceptionally localized within the same bacteriocyte (a specialized cell for endosymbiosis), but the underlying mechanism for their coexistence remains largely unknown. This study provides evidence for niche segregation at the subcellular level between the two symbionts. We showed that the endoplasmic reticulum is a physical barrier separating the two species. Despite differences in co-obligate partners, this subcellular niche segregation was conserved across various whitefly species. The physical proximity of symbionts may enable the efficient biosynthesis of essential nutrients via shared metabolic pathways. The expression “Good fences make good neighbors” appears to be true for insect endosymbiotic systems.
Comprehension of Antimicrobial Peptides Modulation of the Type VI Secretion System inVibrio cholerae
Authors: Mathieu-Denoncourt Annabelle , Duperthuy Marylise
Published: November 2022

The Type VI secretion System (T6SS) is a versatile weapon used by bacteria for virulence, resistance to grazing and competition with other bacteria. We previously demonstrated that the role of the T6SS in interbacterial competition and in resistance to grazing is enhanced inVibrio choleraein the presence of subinhibitory concentrations of polymyxin B (PmB). In this study, we performed a global quantitative proteomic analysis by liquid chromatography coupled to mass spectrometry and a transcriptomic analysis by quantitative PCR of the T6SS known regulators inV. choleraegrown with and without PmB. The proteome ofV. choleraeis greatly modified in the presence of PmB at subinhibitory concentrations with more than 39 % of the identified cellular proteins displaying a difference in their abundance, including T6SS-related proteins (Hcp, VasC, TsaB and ClpV). We identified a regulator whose abundance and expression are increased in the presence of PmB,vxrB, the response regulator of the two-component system VxrAB. In avxrABdeficient mutant, the expression ofhcpmeasured by quantitative PCR, although globally reduced, was not modified in the presence of PmB, confirming its role inhcpupregulation with PmB. The upregulation of the T6SS in the presence of PmB appears to be, at least in part, due to the two-component system VxrAB.

Importance

The type VI secretion system is important for bacterial competition, virulence and resistance to grazing by predators. In this study, we investigated the regulation leading to the type VI secretion system activation in the presence of polymyxin B (PmB), an antimicrobial used in veterinary and human health to treat infection caused by multi-resistant Gram-negative bacteria, inV. cholerae. In addition to making an overall portrait of the modifications to the proteome, we identified the VxrAB two-component system as the main regulator responsible for this activation. Our results provide evidence that subinhibitory concentrations of antimicrobials are responsible for important modifications of the proteome of pathogenic bacteria, inducing the production of proteins involved in virulence, host colonisation, resistance and environmental survival.
Characterization of HcaA, a novel autotransporter protein inHelicobacter cinaedi, and its role in host cell adhesion
Authors: Aoki Sae , Mori Shigetarou , Matsui Hidenori , Shibayama Keigo , Kenri Tsuyoshi , Rimbara Emiko
Published: November 2022

Helicobacter cinaediinfects the human gut and causes invasive infections such as bacteremia and cellulitis through bacterial translocation. However, the mechanism by whichH. cinaediattaches to host cells and establishes infection remains unclear. This study aimed to investigate the relationship between a novel putative autotransporter protein,H. cinaediautotransporter protein A (HcaA), and its role in pathogenicity. The cytotoxicity ofH. cinaediinfection in colon epithelial cell lines (Caco-2 and HT-29) was assessed using a lactate dehydrogenase assay, and it was found that cytotoxicity significantly decreased upon HcaA knockout. Adhesion assays further revealed that the HcaA-knockout strain showed significantly reduced attachment to the human epithelial colorectal adenocarcinoma cell line (Caco-2) compared to that of the wild-type strain. Moreover, the recombinant HcaA protein demonstrated strong adhesion properties to the human monocytic cell line (U937). The adhesive activity was diminished when the RGD motif in HcaA was replaced with RAD, indicating that the RGD motif in HcaA is crucial for host cell adhesion. To determine the role of HcaA inH. cinaediinfectionin vivo, C57BL/6 mice were orally infected with wild-type and HcaA-knockoutH. cinaedistrains. Bacterial colonization was assessed 7, 14, and 28 days post-infection. At 7 days post-infection, colonization was significantly lower in mice infected with the HcaA-knockout strain compared to those infected with the wild-type strain. In conclusion, our findings suggest that HcaA, a novel putative autotransporter protein inH. cinaedi, plays a significant role as an adhesin in establishing colonization.

IMPORTANCE

Helicobacterspecies are classified as gastric or enterohepatic according to their habitat. Among enterohepaticHelicobacterspecies, which inhabit the intestine, colon and liver,H. cinaedihas been most frequently isolated from humans.H. cinaedioften causes bacteremia and cellulitis in immunocompromised hosts. Here, we focused on theH. cinaediautotransporter protein A (HcaA), a novel virulence factor inH. cinaedi. We discovered that HcaA contributes to cell adhesion via its RGD motif. Furthermore, in animal experiments, bacterial colonization was reduced in mice infected with HcaA-knockout strains, supporting the hypothesis that HcaA contributes toH. cinaediadhesion to host cells. Our study provides a novel mechanism for the establishment ofH. cinaediinfections and provides new insights into the role of autotransporter proteins in the establishment ofHelicobacterinfection.
Taxonomic and carbon metabolic diversification of Bathyarchaeia during its co-evolution history with the early Earth surface environment
Authors: Hou Jialin , Wang Yinzhao , Zhu Pengfei , Yang Na , Liang Lewen , Yu Tiantian , Niu Mingyang , Konhauser Kurt , Wang Fengping
Published: November 2022

Bathyarchaeia, as one of the most abundant microorganisms on Earth, play vital roles in the global carbon cycle. However, our understanding of their origin, evolution and ecological functions remains poorly constrained. Based on the phylogeny of the present largest dataset of Bathyarchaeia metagenome assembled genome (MAG), we reclassified Bathyarchaeia into eight order-level units and corresponded to the former subgroup system. Highly diversified and versatile carbon metabolisms were discovered among different orders, particularly atypical C1 metabolic pathways, indicating that Bathyarchaeia represent overlooked important methylotrophs. Molecular dating results indicate that Bathyarchaeia diverged at ∼3.3 Ga, followed by three major diversifications at ∼3.0 Ga, ∼2.5 Ga and ∼1.8-1.7 Ga, likely driven by continental emergence, growth and intensive submarine volcanism, respectively. The lignin-degrading Bathyarchaeia clade emerged at ∼300 Ma and perhaps contributed to the sharply decreased carbon sequestration rate during the Late Carboniferous period. The evolutionary pathway of Bathyarchaeia potentially have been shaped by geological forces, which in turn impacted the Earth’s surface environment.

Teaser

The origin and divergence of Bathyarchaeia linked to the early Earth tectonics and surface environment changes
Targeted degradation of PRC1 components, BMI1 and RING1B, via a novel protein complex degrader strategy
Authors: Park Kwang-Su , Qin Lihuai , Kabir Md , Luo Kaixiu , Dale Brandon , Zhong Yue , Kim Arum , Wang Gang Greg , Kaniskan H. Ümit , Jin Jian
Published: November 2022

Polycomb repressive complex 1 (PRC1) is an essential epigenetic regulator that mainly controls histone H2A Lys119 mono-ubiquitination (H2AK119ub). BMI1 and RING1B are PRC1 core components and play critical roles in the development of various cancers. However, therapeutic agents targeting PRC1 are very limited, and small-molecule inhibitors of PRC1 displayed limited effectiveness in killing cancer cells. In this study, MS147, the first degrader of PRC1 core components, BMI1 and RING1B, was discovered via a novel protein complex degradation strategy that utilizes the target protein’s interacting partner protein (EED) to degrade BMI1 and RING1B. MS147, which comprises an EED small-molecule binder linked to a ligand of the E3 ligase VHL, degrades BMI1 and RING1B in an EED-, VHL-, ubiquitination- and time-dependent manner. MS147 is selective and preferentially degrades BMI1 and RING1B over PRC2 core components: EED, EZH2 and SUZ12. Consequently, MS147 effectively reduces H2AK119ub, but not H3K27me3, which is catalyzed by PRC2. Furthermore, MS147, but not the parent EED binder or known PRC2 degraders, effectively inhibits the proliferation of cancer cell lines that are insensitive to EZH2 knockout or PRC2 degraders. Overall, this study provides a novel degrader targeting BMI1 and RING1B, which is a useful chemical tool to further investigate the roles of PRC1 in cancer, and a novel protein complex degradation strategy, which could potentially expand the degradable human proteome.