bluuebunny/crossref_metadata_2025 huggingface dataset:
Multiplex Epigenome Editing ofMECP2to Rescue Rett Syndrome Neurons
Authors: Qian Junming , Guan Xiaonan , Xie Bing , Xu Chuanyun , Niu Jacqueline , Tang Xin , Li Charles H. , Colecraft Henry M. , Jaenisch Rudolf , Liu X. Shawn
Published: December 2022

Rett syndrome (RTT) is an X-linked neurodevelopmental disorder caused by loss-of-function heterozygous mutations of Methyl CpG-binding Protein 2 (MECP2) on the X chromosome in girls. Reactivation of the silent wild-typeMECP2allele from the inactive X chromosome (Xi) represents a promising therapeutic opportunity for female patients with RTT. Here, we applied a multiplex epigenome editing approach to reactivate MECP2 from Xi in RTT human embryonic stem cells (hESCs) and derived neurons. Demethylation of theMECP2promoter by dCas9-Tet1 with target sgRNA reactivated MECP2 from Xi in RTT hESCs without detectable off-target effects at the transcriptional level. Neurons derived from methylation-edited RTT hESCs maintained MECP2 reactivation and reversed the smaller soma size and electrophysiological abnormalities, two hallmarks of RTT. In RTT neurons, insulation of the methylation editedMECP2locus by dCpf1-CTCF with target CRISPR RNA enhanced MECP2 reactivation and rescued RTT-related neuronal defects, providing a proof-of-concept study for epigenome editing to treat RTT and potentially other dominant X-linked diseases.

One-Sentence Summary

Reactivation ofMECP2from the inactive X chromosome by multiplex epigenome editing rescues Rett syndrome neurons in vitro.
Improved Modeling of Droplet Motion in Open-Format Digital Microfluidic Devices
Authors: Singh Karanpartap , Hawkins Benjamin G.
Published: December 2022

Electrowetting is an electrokinetic effect whereby an applied electric field induces changes in the measured contact angle at a fluid-surface contact line. On hydrophobic, dielectric electrode surfaces, this effect generates droplet motion termed “electrowetting on dielectric” or EWOD. Applications of this phenomenon range from lab-on-a-chip to liquid lenses capable of altering their topology and focus within milliseconds. Electrowetting or EWOD theoretical models quantifying this effect fall into two paradigms: the Young-Lippman and the electromechanical theories. In this work, both paradigms were simulated to predict the velocity of a water droplet moving over an array of electrodes. Results were compared to experimental observations of measured velocities for two dielectric films: ETFE and household cling film. Theoretical model parameters, namely the length scale of the Maxwell force on the droplet, were also determined to align simulation and experiment. The results reveal the trend of droplet velocity in relation to applied voltage, and recapitulate the relationship between the two models.
Signaling Node at TSC2 S1365 Potently Regulates T-Cell Differentiation and Improves Adoptive Cellular Cancer Therapy
Authors: Patel Chirag H , Dong Yi , Dunkerly-Eyring Brittany L , Wen Jiayu , Ranek Mark J , Bartle Laura M , Henderson Daniel B , Sagert Jason , Kass David A , Powell Jonathan D
Published: December 2022

MTORC1 integrates signaling from the immune microenvironment to regulate T-cell activation, differentiation, and function. TSC2 in the tuberous sclerosis complex potently regulates mTORC1 activation. CD8+ T-cells lacking TSC2 have constitutively enhanced mTORC1 activity and generate potent effector T cells; however sustained mTORC1 activation prevents generation of long-lived memory CD8+ T-cells. Here we show manipulating TSC2 at Ser1365 potently regulates activated but not basal mTORC1 signaling in T cells. Unlike non-stimulated TSC2 knockout cells, CD8+ T-cells expressing mutant TSC2-S1365A (SA) have normal basal mTORC1 activity. PKC and T-cell Receptor (TCR) stimulation induces TSC2 S1365 phosphorylation and preventing this with the SA mutation markedly increases mTORC1 activation and T-cell effector function. Consequently, CD8+ SA T-cells display greater effector responses while retaining their capacity to become long-lived memory T-cells. CD8+ SA T-cells also display enhanced effector function under hypoxic and acidic conditions. In murine and human solid-tumor models, CD8+ SA T-cells used as adoptive cell therapy have greater anti-tumor immunity than WT CD8+ T-cells. These findings reveal an upstream mechanism to regulate mTORC1 activity in T-cells. The TSC2-SA mutation enhances both T-cell effector function and long-term persistence/memory formation, supporting a novel approach to engineer better CAR-T cells to treat cancer.
PfaSTer: A ML-powered serotype caller forStreptococcus pneumoniaegenomes
Authors: Lee Jonathan T. , Li Xingpeng , Hyde Craig , Liberator Paul A. , Hao Li
Published: December 2022

Streptococcus pneumoniae(pneumococcus) is a leading cause of morbidity and mortality worldwide. Although multi-valent pneumococcal vaccines have curbed the incidence of disease, their introduction has resulted in shifted serotype distributions that must be monitored. Whole genome sequence (WGS) data provides a powerful surveillance tool for tracking isolate serotypes, which can be determined from nucleotide sequence of the capsular polysaccharide biosynthetic operon (cps). Although software exists to predict serotypes from WGS data, their use is constrained by the requirement of high-coverage Next Generation Sequencing (NGS) reads. This can present a challenge in so far as accessibility and data sharing. Here we present PfaSTer, a method to identify 65 prevalent serotypes from individualS. pneumoniaegenome sequences rather than primary NGS data. PfaSTer combines dimensionality reduction from k-mer analysis with machine learning, allowing for rapid serotype prediction without the need for coverage-based assessments. We then demonstrate the robustness of this method, returning >97% concordance when compared to biochemical results and otherin-silicoserotypers. PfaSTer is open source and available at:https://github.com/pfizer-opensource/pfaster.
Sex-dependent interactions between prodromal intestinal inflammation and LRRK2 G2019S in mice promote symptoms of Parkinson’s disease
Authors: Fang Ping , Espey Hannah , Yu Lewis W. , Agirman Gulistan , Li Kai , Deng Yongning , Lee Jamie , Hrncir Haley , Arnold Arthur P. , Hsiao Elaine Y.
Published: December 2022

Gastrointestinal (GI) disruptions, such as inflammatory bowel disease (IBD), are common prodromal symptoms of Parkinson’s disease (PD), but how they may impact risk for PD remains poorly understood. Herein, we provide evidence that prodromal intestinal inflammation expedites and exacerbates PD symptoms in rodent carriers of the human PD risk allele LRRK2 G2019S in a sex-dependent manner. Chronic intestinal damage in genetically predisposed male, but not female, mice promotes α-synuclein aggregation in the substantia nigra, elevated α-synuclein loads in microglia, loss of dopaminergic neurons, and motor impairment. This male bias in gene-environment interaction is preserved in gonadectomized males, and similarly conferred by sex chromosomal complement in gonadal females expressing human LRRK2 G2019S, revealing that XY chromosomes, not testicular hormones, mediate the male bias in the gut-brain-driven risk for endophenotypes of PD. The early onset and heightened severity of neuropathological and behavioral outcomes in male LRRK2 G2019S mice is preceded by the accumulation of α-synuclein in the colon, increases in α-synuclein-positive macrophages in the colonic lamina propria, and elevations in α-synuclein loads within microglia in the substantia nigra. Taken together, these data reveal that prodromal intestinal inflammation promotes the pathogenesis of PD symptoms in male carriers of LRRK2 G2019S, through mechanisms that depend on genotypic sex and involve early accumulation of α-synuclein in myeloid cells within the gut and brain.
Trade-offs between baseline thermal tolerance and thermal tolerance plasticity are much less common than it appears
Authors: Gunderson Alex R.
Published: December 2022

Thermal tolerance plasticity is a core mechanism by which organisms can mitigate the effects of climate change. As a result, there is a need to understand how variation in tolerance plasticity arises. The Baseline Tolerance/Plasticity Trade-off Hypothesis (hereafter referred to as the Trade-off Hypothesis, TOH) has recently emerged as a potentially powerful explanation. The TOH posits that organisms with high baseline thermal tolerance have reduced thermal tolerance plasticity relative to those with low baseline tolerance. Many studies have found support for the TOH. However, this support must be regarded cautiously because the most common means of testing the TOH can yield spurious ‘trade-offs’ due to regression to the mean. I acquired data for 25 previously-published analyses that supported the TOH at the intraspecific level and reanalyzed them after applying a method that adjusts plasticity estimates for regression to the mean. Only six of the 25 analyses remained statistically significant after adjustment, and effect size and variance explained decreased in all cases. The few data sets in which support for the TOH was maintained after adjustment point to areas of future study, but are too few to make generalizations at this point. In sum, regression to the mean has led to a substantial overestimation of support for the TOH and must be accounted for in future tests of the hypothesis.
Effect of D128N mutation on OsSERK2 in Xa21 mediated immune complex: anin-silicostudy
Authors: Alvy Raghib Ishraq , Mubassir M H M
Published: December 2022

Receptor-like kinases (RLKs) are plant proteins that form signaling circuits to transduce information through the plant cell membrane to the nucleus and activate processes that direct growth, development, stress response, and disease resistance. Upon sensing various environmental stress stimuli, RLKs interact with specific targets and recruits several other proteins to initiate the defense mechanism. Among many RLK subfamilies, leucine-rich repeat RLKs (LRR-RLKs) are the largest. Xa21, a member of LRR-RLK, is a vital receptor protein in rice plants that binds with bacterial RaxX21-sY, whereas OsSERK2 is a somatic embryogenic receptor kinase (SERK) acts as a coreceptor. This study focuses on the effect of a substitution mutation of aspartate128 with asparagine128 (D128N) in OsSERK2 on the interdependent binding pattern of the mentioned Xa21, RaxX21-sY, and OsSERK2 D128N proteins. The results showed that the D128N mutation in OsSERK2 can significantly change the interaction pattern of the critical residues of the OsSERK2 and affects its receptor-ligand (Xa21-RaxX21-sY) interaction in the complex.
Mycobacterium tuberculosis-specific CD4 T cells expressing transcription factors associate with bacterial control in granulomas
Authors: Grant Nicole L. , Kelly Kristen , Maiello Pauline , Abbott Helena , O’Connor Shelby , Lin Philana Ling , Scanga Charles A. , Flynn JoAnne L.
Published: December 2022

Despite the extensive research on CD4 T cells within the context ofMycobacterium tuberculosis(Mtb) infection, few studies have focused on identifying and investigating the profile of Mtb-specific T cells within lung granulomas. To facilitate identification of Mtb-specific CD4 T cells, we identified immunodominant epitopes for two Mtb proteins, Rv1196 and Rv0125, using a Mauritian cynomolgus macaque model of Mtb infection, providing data for the synthesis of MHC Class II tetramers. Using tetramers, we identified Mtb-specific cells within different immune compartments post-infection. We found that granulomas were enriched sites for Mtb-specific cells and that tetramer+cells had increased frequencies of the activation marker CD69, and transcription factors T-bet and RORγT, compared to tetramer negative cells within the same sample. Our data revealed that while the frequency of Rv1196 tetramer+cells was positively correlated with granuloma bacterial burden, the frequency of RORγT or T-bet within tetramer+cells was inversely correlated with granuloma bacterial burden highlighting the importance of having activated, functional Mtb-specific cells for control of Mtb in lung granulomas.
Analysis of the ARTIC V4 and V4.1 SARS-CoV-2 primers and their impact on the detection of Omicron BA.1 and BA.2 lineage defining mutations
Authors: Ulhuq Fatima R. , Barge Madhuri , Falconer Kerry , Wild Jonathan , Fernandes Goncalo , Gallagher Abbie , McGinley Suzie , Sugadol Ahmad , Tariq Muhammad , Maloney Daniel , Kenicer Juliet , Dewar Rebecca , Templeton Kate , McHugh Martin
Published: December 2022

The ARTIC protocol uses a multiplexed PCR approach with two primer pools tiling the entire SARS-CoV-2 genome. Primer pool updates are necessary for accurate amplicon sequencing of evolving SARS-CoV-2 variants with novel mutations. The suitability of the ARTIC V4 and updated V4.1 primer scheme was assessed using whole genome sequencing of Omicron from clinical samples using Oxford Nanopore Technology. Analysis of Omicron BA.1 genomes revealed that 93.22% of clinical samples generated improved genome coverage at 50x read depth with V4.1 primers when compared to V4 primers. Additionally, the V4.1 primers improved coverage of BA.1 across amplicons 76 and 88, which resulted in the detection of the variant defining mutations G22898A, A26530G and C26577G. The Omicron BA.2 sub-variant (VUI-22JAN-01) replaced BA.1 as the dominant variant by March 2022, and analysis of 168 clinical samples showed reduced coverage across amplicons 15 and 75. Upon further interrogation of primer binding sites, a mutation at C4321T (present in 163/168, 97% of samples) was identified as a possible cause of complete dropout of amplicon 15. Furthermore, two mutations were identified within the primer binding regions for amplicon 75: A22786C (present in 90% of samples) and C22792T (present in 12.5% of samples). Together, these mutations may result in reduced coverage of amplicon 75 and further primer updates would allow the identification of the two BA.2 defining mutations present in amplicon 75; A22688G and T22679C. This work highlights the need for ongoing surveillance of primer matches as circulating variants evolve and change.
Genetic risk factor clustering within and across neurodegenerative diseases
Authors: Koretsky Mathew J. , Alvarado Chelsea , Makarious Mary B , Vitale Dan , Levine Kristin , Bandres-Ciga Sara , Dadu Anant , Scholz Sonja W. , Sargent Lana , Faghri Faraz , Iwaki Hirotaka , Blauwendraat Cornelis , Singleton Andrew , Nalls Mike , Leonard Hampton
Published: December 2022

Overlapping symptoms and copathologies are common in closely related neurodegenerative diseases (NDDs). Investigating genetic risk variants across these NDDs can give further insight into disease manifestations. In this study we have leveraged genome-wide single nucleotide polymorphisms (SNPs) and genome-wide association study (GWAS) summary statistics to cluster patients based on their genetic status across identified risk variants for five NDDs (Alzheimer’s disease [AD], Parkinson’s disease [PD], amyotrophic lateral sclerosis [ALS], Lewy body dementia [LBD], and frontotemporal dementia [FTD]). The multi-disease and disease-specific clustering results presented here provide evidence that NDDs have more overlapping genetic etiology than previously expected and how neurodegeneration should be viewed as a spectrum of symptomology. These clustering analyses also show potential subsets of patients with these diseases that are significantly depleted for any known common genetic risk factors suggesting environmental or other factors at work. Establishing that NDDs with overlapping pathologies share genetic risk loci, future research into how these variants might have different effects on downstream protein expression, pathology and NDD manifestation in general is important for refining and treating NDDs.
Stress and resilience during pregnancy: a comparative study between pregnant and non-pregnant women in Ethiopia
Authors: Abera Mubarek , Hanlon Charlotte , Fedlu Hikma , Fewtrell Mary , Tesfaye Markos , Wells Jonathan
Published: December 2022

Background

Stress occurring during pregnancy is associated with perturbances in maternal psychology and physiology, and results in adverse pregnancy and birth outcomes. However, little attention has been given to understand maternal stress and its potential negative consequences in many low- and middle-income countries. We aimed to investigate whether pregnancy is associated with greater stress and lower psychological resilience among women living in Jimma, Southwest Ethiopia.

Method

An institution-based comparative cross-sectional study design was implemented in Jimma University Medical Center from 15 September to 30 November 2021. Women attending antenatal care and family planning services were invited to participate in the study. Participants were interviewed using the Perceived Stress Scale (PSS-10), Brief Resilience Scale (BRS), distress questionnaire-5, and the Household Food Insecurity Access Scale (HFIAS). Linear regression analysis was used to test associations of pregnancy (exposure) with outcomes of stress and resilience scores, while adjusting for potential confounders. Stress and resilience were mutually adjusted for one another in the final model.

Results

A total of 166 pregnant and 154 non-pregnant women participated, with mean age of 27.0 SD 5.0 and 29.5 SD 5.3 years respectively. Pregnancy was associated with increased stress score by 4.1 points (β=4.1; 95% CI: 3.0, 5.2), and with reduced resilience by 3.3 points (β=3.3; 95% CI: -4.5, -2.2) in a fully adjusted model. In mutually-adjusted models, pregnancy was independently associated with greater stress (β=2.9, 95% CI 1.8, 3.9) and lower resilience (β=-1.3, 95% CI: -2.5, -0.2) compared to non-pregnant women.

Conclusion

In this low income setting, pregnancy is associated with greater vulnerability in the mental health of women, characterized by greater perceived stress and diminished resilience. Context-relevant interventions to improve resilience and reduce stress could help improve the health and wellbeing of mothers, with potential benefits for their offspring.
H3.1Cys96oxidation by mitochondrial ROS promotes chromatin remodeling, breast cancer progression to metastasis and multi-drug resistance
Authors: Palma Flavio R. , Ogata Fernando T. , Coelho Diego R. , Pulakanti Kirthi , Meyer Alison , Huang Yunping , Danes Jeanne M. , Schipma Matthew J. , Furdui Cristina M. , Spitz Douglas R. , Gantner Benjamin N. , Rao Sridhar , Backman Vadim , Bonini Marcelo G.
Published: December 2022

Transcription stability enforces cellular identity and is tightly controlled by restrictions imposed on both transcription factor function and target gene accessibility. Progression of cancer to metastasis and multi-drug resistance requires fluid transcriptional programs that can explore different genomic landscapes to enable clonal expansion of aggressive and treatment resistant phenotypes. Here, we show that increased levels of H2O2produced in mitochondria leads to H3.1 oxidation at Cys96, a distinctive redox sensitive amino acid residue restricted to this histone variant, in the nucleus. The oxidation of Cys96 promotes the eviction of H3.1 from chromatin and its exchange with H3.3, thereby opening silenced portions of the chromatin. Mutation of Cys96 by an oxidation-resistant serine residue or quenching nuclear H2O2reversed chemotherapy resistance and drove established metastatic disease into remission. Together, these results show that increased mitochondrial H2O2production, characteristic of metabolic dysfunction, promotes transcriptional plasticity by removing structural chromatin restrictions imposed by the redox sensitive histone variant H3.1. We suggest that this new regulatory nexus between cancer metabolism and chromatin remodeling controls chromatin states that enable cancer progression and drug resistance acquisition.
The plant nuclear lamina disassembles to regulate genome folding in stress conditions
Authors: Wang Nan , Wang Zhidan , Tzourtzou Sofia , Wang Xu , Bi Xiuli , Leimeister Julia , Xu Linhao , Sakamoto Takuya , Matsunaga Sachihiro , Schaller Andreas , Jiang Hua , Liu Chang
Published: December 2022

The nuclear lamina (NL) is a complex network of nuclear lamins and lamin-associated nuclear membrane proteins, which scaffold the nucleus to maintain structural integrity. InArabidopsisthaliana, Nuclear Matrix Constituent Proteins (NMCPs) are essential components of the NL and are required to maintain the structural integrity of the nucleus and specific perinuclear chromatin anchoring. At the nuclear periphery, suppressed chromatin overlapping with repetitive sequences and inactive protein coding genes are enriched. At a chromosomal level, plant chromatin organization in interphase nuclei displays flexibilities in response to various developmental cues and environmental stimuli. Based on these observations inArabidopsis, and given the role ofAtNMCPgenes (CRWN1andCRWN4) in organizing chromatin positioning at the nuclear periphery, one can expect considerable changes in chromatin-NL interactions when the global chromatin organization patterns are being altered in plants. Here, we report the highly flexible nature of plant nuclear lamina, which disassembles substantially under various stress conditions. Particularly, under heat stress, we reveal that chromatin domains, initially tethered to the nuclear envelope, remain largely associated with CRWN1 and become scattered in the inner nuclear space. Via investigating the three-dimensional chromatin contact network, we further reveal that CRWN1 proteins play a structural role in shaping the changes in genome folding under heat stress. Also, CRWN1 acts as a negative transcriptional co-regulator to modulate the shift of the plant transcriptome profile in response to heat stress.
Assessing the Nucleotide-Level Impact of Spaceflight Stress using RNA-Sequencing Data
Authors: Knight Montana S. , Doherty Colleen J. , Nielsen Dahlia M.
Published: December 2022

Understanding the effects of space radiation and microgravity on DNA integrity is critical to assess the impact of long-term spaceflight. However, studying spaceflight’s effect on terrestrial life is difficult. NASA created GeneLab, a public Omics database for spaceflight-related data, to help combat these limitations. While GeneLab has very few DNA-based data sets, transcriptome information is abundant. This study used RNA-Seq data from GeneLab to examine DNA sequence variants linked to spaceflight stress exposure. More mutations were observed in spaceflight samples than in the ground control samples. This increase in variants was not reduced in samples grown under artificial gravity in space, suggesting that microgravity did not significantly affect the amount of DNA damage in this experiment. There was also an increase in transversion mutations, consistent with known forms of radiation-induced damage. This work demonstrates that RNA-Seq data is a useful resource for evaluating DNA damage from spaceflight and provides a baseline for the types of mutations that could be detected.
Mercury contamination of an introduced generalist fish of intermediate trophic level
Authors: Gedig D. P. , Hauger M. , Armstrong D. A. , Jeffries K. M.
Published: December 2022

Mercury contamination is a global issue because mercury concentrations in aquatic systems are influenced by both natural and anthropogenic pathways, including the burning of fossil fuels and flooding during hydroelectric development. Mercury biomagnifies in aquatic ecosystems, leading to higher concentrations in piscivore fishes than those at lower trophic levels. Here, liver and muscle total mercury (THg) concentrations in black crappiePomoxis nigromaculatusfrom three lakes in southeastern Manitoba, Canada were related to age, morphology and physiological traits to better understand the dynamics of mercury accumulation in an introduced generalist fish species. Black crappie liver and muscle samples from Big Whiteshell Lake (relatively large lake, 17.5 km2; n=30), Caddy Lake (small lake surrounded by wetlands, 3.1 km2; n=42) and Lac du Bonnet (river widening influenced by hydroelectric dams, 84.0 km2; n=29) were analyzed for THg content. These THg concentrations were then compared to black crappie mercury concentrations in other Canadian water bodies to assess within species relative contamination levels, as well as to mercury concentrations in other freshwater fishes to examine biomagnification. Age and size had strong positive correlations (r>0.60) with muscle mercury concentrations. No evidence of acute point source contamination was found in the study area when compared to black crappie muscle mercury concentrations in other water bodies, and tissue THg concentration was not correlated with a reduction in gonadosomatic index (GSI) or hepatosomatic index (HSI). Analysis of liver THg in addition to muscle THg revealed the possible impacts of seasonal and ontogenetic differences in diet on exposure. Furthermore, THg analysis of liver and muscle tissue showed how generalist foraging techniques of black crappie may curb the progressively greater mercury exposure and resultant physiological consequences expected from ontogenetic diet shifts from invertebrates to fishes. Although there appeared to be temporally varied levels of mercury exposure (i.e., liver THg) by sex, there was no sex effect observed in long-term accumulation in the muscle. Flood risk is believed to be a key driver of differences in black crappie THg concentrations between lakes in the region. Black crappie bioaccumulated less mercury at age than primary piscivore species in the region. These results will help foster a better understanding of mercury biomagnification in boreal shield lakes within a region impacted by legacy mercury.
Deficiency in hyaluronan synthase 3 attenuates ruptures in a murine model of abdominal aortic aneurysms by reduced aortic monocyte infiltration
Authors: Suvorava Tatsiana , Brack Fedor , Kaczur Janet , Petzsch Patrick , Köhrer Karl , Quast Christine , Gerdes Nobert , Voigt Katharina , Krüger Martina , Fischer Jens W. , Brückner Alexander , Fleischmann Bernd K. , Wenzel Daniela , Zimmermann Laura-Maria A. , Sengle Gerhard , Flögel Ulrich , Grandoch Maria
Published: December 2022

Abdominal aortic aneurysms (AAA) are a common vascular disorder with a high mortality due to the prevalence of aortic ruptures. The underlying pathomechanisms are complex and involve immune cell infiltration and degradation of the vascular extracellular matrix (ECM). Hyaluronan (HA), synthesized at the plasma membrane by three HA synthase isoenzymes (HAS1-3), is not only a major constituent of the ECM but also known to directly affect the phenotype of vascular smooth muscle cells as well as immunological responses. Specifically, the HAS3 isoenzyme has been reported to play a major role in various inflammatory conditions. Therefore, the aim of the present study was to elucidate the role of HAS3-derived HA in the pathogenesis of abdominal aortic aneurysm. To this end, we used a murine model of Angiotensin II (AngII)-induced abdominal aortic aneurysms and dissections (AAAs/AADs) and could demonstrate that genetic depletion ofHas3improves survival inApoe/Has3double deficient (Apoe/Has3-DKO) mice via the reduced occurrence of aortic ruptures. Mechanistically, fewer elastica breaks were observed inApoe/Has3-DKO mice compared toApoe-KO littermates. This was associated with a decreased infiltration of myeloid immune cells into the vessel wall ofHas3-deficient mice while in parallel elevated numbers of circulating leukocytes were detected. RNA seq analysis from aortic tissue pointed towards a disturbed endothelial-myeloid cell communication as a cause for the diminished recruitment of immune cells to the aortic wall. While endothelial cells were unaffected, upregulation of adhesion receptors as well as the HA receptor CD44, known to mediate leukocyte adhesion to the endothelium, was blunted in monocytes fromApoe/Has3-DKO mice in response to AngII treatment. These findings underline the pivotal detrimental role of monocyte’s HAS3-dependent pericellular HA matrix for an exaggerated immune cell recruitment to inflammatory foci giving here rise for an increased incidence of ruptured aortic aneurysms.
Mice Humanized for Major Histocompatibility Complex and Angiotensin-Converting Enzyme 2 with High Permissiveness to SARS-CoV-2 Omicron Replication
Authors: Chevalier Fabien Le , Authié Pierre , Chardenoux Sébastien , Bourgine Maryline , Vesin Benjamin , Cussigh Delphine , Sassier Yohann , Fert Ingrid , Noirat Amandine , Nemirov Kirill , Anna François , Bérard Marion , Guinet Françoise , Hardy David , Charneau Pierre , Lemonnier François , Langa-Vives Francina , Majlessi Laleh
Published: December 2022

Human Angiotensin-Converting Enzyme 2 (hACE2) is the major receptor enabling host cell invasion by SARS-CoV-2 via interaction with Spike glycoprotein. The murine ACE2 ortholog does not interact efficiently with SARS-CoV-2 Spike and therefore the conventional laboratory mouse strains are not permissive to SARS-CoV-2 replication. Here, we generated newhACE2transgenic mice, which harbor thehACE2gene under the human keratin 18 promoter, in C57BL/6 “HHD-DR1” background. HHD-DR1 mice are fully devoid of murine Major Histocompatibility Complex (MHC) molecules of class-I and -II and express only MHC molecules from Human Leukocyte Antigen (HLA) HLA 02.01, DRA01.01, DRB1.01.01 alleles, widely expressed in human populations. We selected three transgenic strains, with varioushACE2mRNA expression levels and distinctive profiles of lung and/or brain permissiveness to SARS-CoV-2 replication. Compared to the previously available B6.K18-ACE22Prlmn/JAXmice, which have limited permissiveness to SARS-CoV-2 Omicron replication, these three new hACE2 transgenic strains display higher levels ofhACE2mRNA expression, associated with high permissiveness to the replication of SARS-CoV-2 Omicron sub-variants. As a first application, one of these MHC- and ACE2-humanized strains was successfully used to show the efficacy of a lentiviral vector-based COVID-19 vaccine candidate.
Multiomic Profiling of Human Clonal Hematopoiesis Reveals Genotype and Cell-Specific Inflammatory Pathway Activation
Authors: Heimlich J. Brett , Bhat Pawan , Parker Alyssa C. , Jenkins Matthew T. , Vlasschaert Caitlyn , Ulloa Jessica , Van Amburg Joseph C. , Potts Chad R. , Olson Sydney , Silver Alexander J. , Ahmad Ayesha , Sharber Brian , Brown Donovan , Hu Ningning , van Galen Peter , Savona Michael R. , Bick Alexander G. , Ferrell P. Brent
Published: December 2022

Clonal hematopoiesis (CH) is an age-associated phenomenon that increases risk for hematologic malignancy and cardiovascular disease. CH is thought to enhance disease risk through inflammation in the peripheral blood1. Here, we profile peripheral blood gene expression in 66,968 single cells from a cohort of 17 CH patients and 7 controls. Using a novel mitochondrial DNA barcoding approach, we were able to identify and separately compare mutantTET2andDNMT3Acells to non-mutant counterparts. We discovered the vast majority of mutated cells were in the myeloid compartment. Additionally, patients harboringDNMT3AandTET2CH mutations possessed a pro-inflammatory profile in CD14+ monocytes through previously unrecognized pathways such as galectin and macrophage Inhibitory Factor (MIF). We also found that T cells from CH patients, though mostly un-mutated, had decreased expression of GTPase of the immunity associated protein (GIMAP) genes, which are critical to T cell development, suggesting that CH may impair T cell function.

Key points

- CD14+ monocytes from clonal hematopoiesis patients stimulate inflammation through increased cytokine expression.

- T cells from clonal hematopoiesis are deficient in GIMAP expression, suggesting CH may impair T cell differentiation.
The Impact of Peri-implantitis on the Proteome Biology of Crevicular Fluid: A pilot study
Authors: Halstenbach Tim , Nelson Katja , Iglhaut Gerhard , Schilling Oliver , Fretwurst Tobias
Published: December 2022

Background

The proteome of the peri-implant crevicular fluid (PICF) has not been systematically investigated. The aim of the present study was to reveal the proteome biology of dental implants affected with peri-implantitis.

Methods

Patients with at least one diseased implant were included (probing depth ≥ 6 mm, ≥ 3 mm peri-implant radiological bone loss). Using sterile paper strips, samples were collected from healthy implants (I), healthy teeth (T) and peri-implantitis affected implants (P). Proteome analysis was performed using liquid chromatography – tandem mass spectrometry (LC-MS/MS) and data independent acquisition, allowing the identification and quantification of human and bacterial proteins as well as semi-specific peptides.

Results

38 samples from 13 patients were included in the study. 2332 different human proteins were identified across all samples. No differentially expressed proteins between T and I were found. Comparing P to I, 59 proteins were found upregulated and 31 downregulated in P with significance. Upregulated proteins included proinflammatory proteins such as immunoglobulins, dysferlin and S100P, as well as antimicrobial proteins, e.g. myeloperoxidase or azurocidin. Gene ontology analysis further revealed higher activity of immunological pathways. Proteolytic patterns indicated the activity of inflammatory proteins such as cathepsin G. 334 bacterial proteins were identified and quantified. Peri-implantitis showed elevated proteolytic activity.

Conclusion

I and T share similarities in their proteome, while diseased implants deviate strongly from healthy conditions. The PICF proteome of peri-implantitis affected sites exhibits an inflammatory fingerprint, dominated by neutrophile activity when compared to healthy implants.

Proteomic analysis of the peri-implant crevicular fluid revealed distinct proteome alterations in peri-implantitis when compared to healthy implants and teeth, while healthy teeth and implants share strong similarities.
Investigation on key aspects of mating biology in the mosquitoAedes koreicus
Authors: Ciocchetta Silvia , Frentiu Francesca D , Montarsi Fabrizio , Capelli Gioia , Devine Gregor J
Published: December 2022

Aedes koreicusis a mosquito (Diptera: Culicidae) from Northeast Asia with a rapidly expanding presence outside its original native range. Over the years the species has been discovered in several new countries, either spreading after first introduction or remaining localised to limited areas. Notably, recent studies have demonstrated the ability of the species to transmit zoonotic parasites and viruses both in the field and in laboratory settings. Combined with its invasive potential, the possible role ofAe. koreicusin pathogen transmission highlights the public health risks of its invasion. In this study, we used a recently established population from Italy to investigate aspects of biology that influence reproductive success inAe. koreicus: autogeny, mating behaviour, mating disruption by the sympatric invasive speciesAedes albopictus, and the presence of the endosymbiontWolbachia pipientis.

Our laboratory population did not exhibit autogenic behaviour and required a blood meal to complete its ovarian cycle. When we exposedAe. koreicusfemales to males ofAe. albopictus, we observed repeated attempts at insemination and an aggressive, disruptive mating behaviour initiated by males. Despite this, no sperm was identified inAe. koreicusspermathecae. Wolbachiawas not detected in thisAe. koreicuspopulation and therefore had no effect onAe. koreicusreproduction.
CD244 regulates both innate and adaptive immune axes in melanoma by inhibiting autophagy-mediated M1 macrophage maturation
Authors: Kim Jeongsoo , Kim Tae-Jin , Chae Sehyun , Park Sunghee , Ha Hyojeong , Park Yejin , Yoon Chul Joo , Kim Jiyoung , Kim Jungwon , Im Kyungtaek , Lee Hyemin , Lee Kyunghye , Kim Jeongmin , Kim Daham , Lee Eunju , Shin Min Hwa , Park Serk In , Rhee Inmoo , Lee Jeewon , Lee Keun Hwa , Hwang Daehee , Lee Kyung-Mi
Published: December 2022

Accumulating data have highlighted the role of monocytes/macrophages in immune escape by generating immunologically “cold” tumors that do not respond to immunotherapy. CD244 (SLAMF4, 2B4), a member of the signaling lymphocyte activation molecule family, is expressed on myeloid cells, but its precise role has not been elucidated. Using monocyte lineage-specific CD244-deficient (LysM-cre+/-CD244fl/fl;cKO) mice challenged with B16F10 melanoma, we report for the first time that CD244 negatively regulates tumor immunity by inhibiting the differentiation and functional maturation of CD11b+Ly6ChiF4/80lomonocytes into CD11b+Ly6CloF4/80himacrophages within the tumor microenvironment. CD244-deficient macrophages more effectively activated antigen-specific T cell responses compared to WT macrophages, thus delaying tumor growth in the B16F10 melanoma model. Moreover, combinatorial intervention of anti-PD-L1 antibodies with CD244-KO BMDM markedly improved tumor rejection compared to the anti-PD-L1 antibody alone or in combination with WT BMDM. Consistent with the murine data, transcriptome analysis of human melanoma tissue single-cell RNA-sequencing dataset (SCP398 from single-cell portal), revealed 221 differentially expressed genes of CD244-monocytes/macrophages were associated with phagocytosis, antigen presentation, and autophagy. Additionally, cell type deconvolution analysis within melanoma patients bulk RNA-seq datasets from TCGA database, revealed presence of CD244- monocytes/macrophages significantly increased patient survival in primary and metastatic tumors. Hence, we proposed that CD244 serve as a critical immune checkpoint receptor on macrophages, and CD244-deficient macrophages may represent a novel therapeutic modality to convert immunologically “cold” tumors to “hot” tumors, which can function synergistically with checkpoint blockade therapies.
Variational inference accelerates accurate DNA mixture deconvolution
Authors: Susik Mateusz , Sbalzarini Ivo F.
Published: December 2022

We investigate a class of DNA mixture deconvolution algorithms based on variational inference, and we show that this can significantly reduce computational runtimes with little or no effect on the accuracy and precision of the result. In particular, we consider Stein Variational Gradient Descent (SVGD) and Variational Inference (VI) with an evidence lower-bound objective. Both provide alternatives to the commonly used Markov-Chain Monte-Carlo methods for estimating the model posterior in Bayesian probabilistic genotyping. We demonstrate that both SVGD and VI significantly reduce computational costs over the current state of the art. Importantly, VI does so without sacrificing precision or accuracy, presenting an overall improvement over previously published methods.
Comprehensive regulatory networks for tomato organ development based on the genome and RNAome of microTom tomato
Authors: Xue Jia-Yu , Fan Hai-Yun , Zeng Zhen , Zhou Yu-Han , Hu Shuai-Ya , Li Sai-Xi , Cheng Ying-Juan , Meng Xiang-Ru , Chen Fei , Shao Zhu-Qing , Van de Peer Yves
Published: December 2022

MicroTom tomato has a short growth cycle and high transformation efficiency, and is a prospective model plant for studying organ development, metabolism, and plant-microbe interactions. Here, with a newly assembled reference genome for this tomato cultivar and abundant RNA-seq data derived from tissues of different organs/developmental stages/treatments, we constructed multiple gene co-expression networks, which will provide valuable clues for the identification of important genes involved in diverse regulatory pathways during plant growth, e.g., arbuscular mycorrhizal symbiosis and fruit development. Additionally, non-coding RNAs, including miRNAs, lncRNAs and circRNAs were also identified, together with their potential targets. Interacting networks between different types of non-coding RNAs (miRNA-lncRNA), and non-coding RNAs and genes (miRNA-mRNA and lncRNA-mRNA) were constructed as well. Our results and data will provide valuable information for the study of organ differentiation and development of this important fruit. Lastly, we established a database (http://eplant.njau.edu.cn/microTomBase/) with genomic and transcriptomic data, as well as details of gene co-expression and interacting networks on microTom, and this database should be of great value to those who wants to adopt microTom as a model plant for research.
Unprecedented yet gradual nature of first millennium CE intercontinental crop plant dispersal revealed in ancient Negev desert refuse
Authors: Fuks Daniel , Melamed Yoel , Langgut Dafna , Erickson-Gini Tali , Tepper Yotam , Bar-Oz Guy , Weiss Ehud
Published: December 2022

Global agro-biodiversity has resulted from processes of plant migration and agricultural adoption. Although critically affecting current diversity, crop diffusion from antiquity to the middle-ages is poorly researched, overshadowed by studies on that of prehistoric periods. A new archaeobotanical dataset from three Negev Highland desert sites demonstrates the first millennium CE’s significance for long-term agricultural change in southwest Asia. This enables evaluation of the “Islamic Green Revolution” (IGR) thesis compared to “Roman Agricultural Diffusion” (RAD), and both versus crop diffusion since the Neolithic. Among the finds, some of the earliestSolanum melongenaseeds in the Levant represent the proposed IGR. Several other identified economic plants, including two unprecedented in Levantine archaeobotany (Ziziphus jujuba, Lupinus albus), implicate RAD as the greater force for crop migrations. Altogether the evidence supports a gradualist model for Holocene-wide crop diffusion, within which the first millennium CE contributed more to global agro-diversity than any earlier period.
Drug repurposing of dopaminergic drugs to inhibit Ataxin-3 aggregation
Authors: Figueiredo Francisco , Sárkány Zsuzsa , Silva Alexandra , Martins Pedro M. , Ribeiro Sandra Macedo
Published: December 2022

The accumulation of mutant ataxin-3 (Atx3) in neuronal nuclear inclusions is a pathological hallmark of Machado-Joseph disease (MJD), also known as Spinocerebellar Ataxia Type 3. Decreasing the protein aggregation burden is a possible disease-modifying strategy to tackle MJD and other neurodegenerative disorders for which only symptomatic treatments are currently available. We performed a drug repurposing screening to identify inhibitors of Atx3 aggregation with known toxicological and pharmacokinetic profiles. Interestingly, dopamine hydrochloride and other catecholamines are among the most potent inhibitors of Atx3 aggregationin vitro. Our results indicate that low micromolar concentrations of dopamine markedly delay the formation of mature amyloid fibrils of mutant Atx3 through the inhibition of the earlier oligomerization steps. Although dopamine itself does not pass the blood-brain barrier, dopamine levels in the brain can be increased by low doses of dopamine precursors and dopamine agonists commonly used to treat Parkinsonian symptoms. These findings disclose a possible application of dopaminergic drugs to halt or reduce Atx3 accumulation in the brains of MJD patients.
Viability of HepG2 and MCF-7 Cells is not Correlated with Mitochondrial Bioenergetics
Authors: Doczi Judit , Karnok Noemi , Bui David , Azarov Victoria , Pallag Gergely , Nazarian Sara , Czumbel Bence , Seyfried Thomas N , Chinopoulos Christos
Published: December 2022

Alterations in metabolism is a hallmark of cancer. It is unclear, however, if oxidative phosphorylation (OXPHOS) is required for tumor cell survival. We investigated the effect of severe hypoxia, site-specific inhibition of respiratory chain (RC) components, and uncouplers on the survival of HepG2 and MCF-7 2D cultured cells. Comparable respiratory complex activities were observed in both cell lines, but HepG2 cells exhibited much higher oxygen consumption rates (OCR) and respiratory capacity than the MCF-7 cells. Significant non-mitochondrial OCR was found in MCF-7 cells that was insensitive to acute combined inhibition of complexes I and III. However, pre-treatment of either cell line with RC inhibitors for 24-72 hours abolished respective complex activities and OCRs completely, and this was associated with a time-dependent decrease in citrate synthase activity, suggesting mitophagy. HepG2 cells viability was mostly unaffected by any pharmacological treatment or severe hypoxia as temporally recorded from high-content automated microscopy. Conversely, MCF-7 cells viability exhibited strong sensitivity to CIV or CV inhibition, severe hypoxia, and uncoupling, but were only moderately affected by CI, CII and CIII inhibition. CII, CIII and CIV-inhibitor mediated MCF-7 cell death were partially abrogated by aspartate. The data show that OXPHOS activity and viability are uncorrelated in these cell lines indicating that a linkage of OXPHOS to cancer cell survival must be cell- and condition-defined.
Allosteric SHP2 Inhibition Increases Apoptotic Dependency on BCL2 and Synergizes with Venetoclax inFLT3-andKIT-Mutant AML
Authors: Popescu Bogdan , Stahlhut Carlos , Tarver Theodore C. , Wishner Sydney , Lee Bianca J. , Peretz Cheryl A. C. , Luck Cuyler , Phojanakong Paul , Serrano Juan Antonio Camara , Hongo Henry , Rivera Jose M. , Xirenayi Simayijiang , Chukinas John A. , Steri Veronica , Tasian Sarah K. , Stieglitz Elliot , Smith Catherine C.
Published: December 2022

Mutations in receptor tyrosine kinases (RTKs) FLT3 and KIT are frequent and associated with poor outcomes in acute myeloid leukemia (AML). Although FLT3 inhibitors (FLT3i) are clinically effective, remissions are short-lived due to secondary resistance characterized by acquired mutations constitutively activating the RAS/MAPK pathway. Hereby, we report pre-clinical efficacy of co-targeting SHP2, a critical node in MAPK signaling, and BCL2 in RTK-driven AML. The allosteric SHP2 inhibitor RMC-4550 suppressed proliferation of AML cell lines with FLT3 and KIT mutations, including cell lines with acquired resistance to FLT3i. We demonstrate that SHP2 inhibition unveils an Achilles’ heel of AML, increasing apoptotic dependency on BCL2 via MAPK-dependent mechanisms, including upregulation of BMF and downregulation of MCL1. Consequently, RMC-4550 and venetoclax are synergistically lethal inFLT3- orKIT-mutant AML cell lines, and in clinically relevant xenograft models. Our results provide new mechanistic rationale and preclinical evidence for co-targeting SHP2 and BCL2 in RTK-driven AML.

Significance

There is an unmet need for effective therapies targeting the MAPK pathway to overcome resistance in RTK-driven AML. We report that pharmacologic co-inhibition of SHP2 and BCL2 has synergistic anti-leukemia activity in preclinical models of AML with FLT3 and KIT mutations and holds potential clinical utility.