bluuebunny/crossref_metadata_2025 huggingface dataset:
Bridging the gap – estimation of 2022/2023 SARS-CoV-2 healthcare burden in Germany based on multidimensional data from a rapid epidemic panel
Authors: Harries M , Jaeger V.K , Rodiah I , Hassenstein M.J. , Ortmann J , Dreier M , von Holt I , Brinkmann M , Dulovic A , Gornyk D , Hovardovska O , Kuczewski C , Kurosinki MA , Schlotz M , Schneiderhan-Marra N , Strengert M , Krause G , Sester M , Klein F , Petersmann A , Karch A , Lange B
Published: December 2022

Throughout the SARS-CoV-2 pandemic, Germany lacked an adaptive population panel for epidemic diseases and a modelling platform to rapidly incorporate panel estimates.

We evaluated how a cross-sectional analysis of 9922 participants of the MuSPAD study in June/July 2022 combined with a newly developed modelling platform could bridge the gap and analyzed antibody levels, neutralizing serum activity and interferon-gamma release response of serum samples. We categorized the population into four groups with differing protection against severe course of disease (validated by neutralizing serum activity), and found that 30% were in the group with highest protection, and 85% in either the highest categories or second highest group regarding protection level.

Estimated hospitalizations due to SARS-CoV-2 were predicted to be between 30 to 300% of the peak in 02/2021 dependent on assumed variant characteristics. We showed the feasibility of a rapid epidemic panel able to evaluate complex endpoints for SARS-CoV-2 and inform scenario modelling.
Phages are important unrecognized players in the ecology of the oral pathogenPorphyromonas gingivalis
Authors: Matrishin Cole B. , Haase Elaine M. , Dewhirst Floyd E. , Mark Welch Jessica L. , Miranda-Sanchez Fabiola , MacFarland Donald C. , Kauffman Kathryn M.
Published: December 2022

Background

Porphyromonas gingivalis(hereafter “Pg”) is an oral pathogen that can act as a keystone driver of inflammation and periodontal disease. AlthoughPgis most readily recovered from individuals with actively progressing periodontal disease, healthy individuals and those with stable non-progressing disease are also colonized byPg. Insights into the factors shaping the striking strain-level variation inPg, and its variable associations with disease, are needed to achieve a more mechanistic understanding of periodontal disease and its progression. A key force shaping strain level diversity in all microbial communities is infection of bacteria by their viral (phage) predators and symbionts. Surprisingly, althoughPghas been the subject of study for over 40 years, essentially nothing is known of its phages, and the prevailing paradigm is that phages are not important in the ecology ofPg.

Results

Here we systematically addressed the question of whetherPgare infected by phages - and we found that they are. We found that prophages are common inPg, they are genomically diverse, and they encode genes that have the potential to alterPgphysiology and interactions. We found that phages represent unrecognized targets of the prevalent CRISPR-Cas defense systems inPg, and thatPgstrains encode numerous additional mechanistically diverse candidate anti-phage defense systems. We also found that phages and candidate anti-phage defense system elements together are major contributors to strain level diversity and the species pangenome of this oral pathogen. Finally, we demonstrate that prophages harbored by a modelPgstrain are active in culture, producing extracellular viral particles in broth cultures.

Discussion

This work definitively establishes that phages are a major unrecognized force shaping the ecology and intraspecies strain-level diversity of the well-studied oral pathogenPg. The foundational phage sequence datasets and model systems that we establish here add to the rich context of all that is already known aboutPg, and point to numerous avenues of future inquiry that promise to shed new light on fundamental features of phage impacts on human health and disease broadly.
Copy number variants alter local and global mutational tolerance
Authors: Avecilla Grace , Spealman Pieter , Matthews Julia , Caudal Elodie , Schacherer Joseph , Gresham David
Published: December 2022

Copy number variants (CNVs), duplications and deletions of genomic content, contribute to evolutionary adaptation, but can also confer deleterious effects, and cause disease. Whereas the effects of amplifying individual genes or whole chromosomes (i.e., aneuploidy) have been studied extensively, much less is known about the genetic and functional effects of CNVs of differing sizes and structures. Here, we investigatedSaccharomyces cerevisiae(yeast) strains that have CNVs of variable structures but with multiple copies of the geneGAP1. Although beneficial in glutamine-limited chemostats, CNVs result in decreased fitness compared with the euploid ancestor in rich media. We used transposon mutagenesis to investigate mutational tolerance and genetic interactions with CNVs. We find that CNVs confer novel mutational tolerance in amplified essential genes and novel genetic interactions. We validated a novel genetic interaction withBMH1. CNV strains have increased mutational tolerance in genes related to translation, and reduced mutational tolerance in genes related to mitochondrial function. We performed RNAseq and found that transcriptional dosage compensation does not affect the majority of genes amplified by CNVs. Furthermore, we do not find that CNV strains exhibit previously described transcriptional signatures of aneuploidy. Instead, CNV strains exhibit downregulation of genes involved in cellular respiration, nucleoside biosynthetic processes, and small molecule metabolism, and upregulation of genes involved in transposition, nucleic acid metabolic processes, and siderophore transport. Our study reveals the extent to which local and global mutational tolerance is modified by CNVs with implications for genome evolution and CNV associated diseases, such as cancer.
Sleep increases firing rate modulation during interictal epileptic activities in mesial temporal structures
Authors: Whitmarsh Stephen , Nguyen-Michel Vi-Huong , Lehongre Katia , Mathon Bertrand , Adam Claude , Lambrecq Virginie , Frazzini Valerio , Navarro Vincent
Published: December 2022

Epileptic seizures and interictal epileptiform discharges (IEDs) are strongly influenced by sleep and circadian rhythms. However, human data on the effect of sleep on neuronal behavior during interictal activity have been lacking. We analyzed EEG data from epileptic patients implanted with macro and micro electrodes targeting mesial temporal structures. Sleep staging was performed on concomitantly recorded polysomnography and video-EEG. Automated IED detection identified thousands of IEDs per patient. Both the rate and amplitude of IEDs were increased with deeper stages of NREM sleep. Single unit activity (SUA) and multi-unit activity (MUA) increased their firing during the IED spike, and strongly decreased during the subsequent slow wave. These time-locked firing rate modulations were shown to increase during deeper stages of NREM sleep. Finally, during resting behaviour, neuronal firing rate, bursting rate and firing regularity were all shown to progressively decrease with deeper stages of NREM sleep.
Specificity, synergy, and mechanisms of splice-modifying drugs
Authors: Ishigami Yuma , Wong Mandy S. , Martí-Gómez Carlos , Ayaz Andalus , Kooshkbaghi Mahdi , Hanson Sonya , McCandlish David M. , Krainer Adrian R. , Kinney Justin B.
Published: December 2022

Drugs that target pre-mRNA splicing hold great therapeutic potential, but the quantitative understanding of how these drugs work is limited. Here we introduce mechanistically interpretable quantitative models for the sequence-specific and concentration-dependent behavior of splice-modifying drugs. Using massively parallel splicing assays, RNA-seq experiments, and precision dose-response curves, we obtain quantitative models for two small-molecule drugs, risdiplam and branaplam, developed for treating spinal muscular atrophy. The results quantitatively characterize the specificities of risdiplam and branaplam for 5’ splice site sequences, suggest that branaplam recognizes 5’ splice sites via two distinct interaction modes, and disprove the prevailing two-site hypothesis for risdiplam activity atSMN2exon 7. The results also show that anomalous single-drug cooperativity, as well as multi-drug synergy, are widespread among small-molecule drugs and antisense-oligonucleotide drugs that promote exon inclusion. Our quantitative models thus clarify the mechanisms of existing treatments and provide a basis for the rational development of new therapies.
Interplay between acetylation and ubiquitination of imitation switch chromatin remodeler Isw1 confers multidrug resistance inCryptococcus neoformans
Authors: Meng Yang , Li Zhuoran , Jiang Tianhang , Sun Tianshu , Li Yanjian , Gao Xindi , Li Hailong , Suo Chenhao , Li Chao , Yang Sheng , Lan Tian , Liao Guojian , Liu Tong-Bao , Wang Ping , Ding Chen
Published: December 2022

Cryptococcus neoformansposes a threat to human health, but anticryptococcal therapy is hampered by the emergence of drug resistance, whose underlying mechanisms remain poorly understood. Herein, we discovered that Isw1, an imitation switch chromatin remodeling ATPase, functions as a master modulator of genes responsible for multidrug resistance inC. neoformans. Cells with the disruptedISW1gene exhibited profound resistance to multiple antifungal drugs. Mass spectrometry analysis revealed that Isw1 is both acetylated and ubiquitinated, suggesting that an interplay between these two modification events exists to govern Isw1 function. Mutagenesis studies of acetylation and ubiquitination sites revealed that the acetylation status of Isw1K97coordinates with its ubiquitination processes at Isw1K113and Isw1K441through modulating the interaction between Isw1 and Cdc4, an E3 ligase. Additionally, clinical isolates ofC. neoformansoverexpressing the degradation-resistantISW1K97Qallele showed impaired drug-resistant phenotypes. Collectively, our studies revealed a sophisticated acetylation-Isw1-ubiquitination regulation axis that controls multidrug resistance inC. neoformans.
Annotating metabolite mass spectra with domain-inspired chemical formula transformers
Authors: Goldman Samuel , Wohlwend Jeremy , Stražar Martin , Haroush Guy , Xavier Ramnik J. , Coley Connor W.
Published: December 2022

Metabolomic studies have succeeded in identifying small molecule metabolites that mediate cell signaling, competition, and disease pathology in part due to large-scale community efforts to measure mass spectra for thousands of metabolite standards. Nevertheless, the vast majority of spectra observed in clinical samples cannot be unambiguously matched to known structures, suggesting powerful opportunities for further discoveries in the dark metabolome. Deep learning approaches to small molecule structure elucidation have surprisingly failed to rival classical statistical methods, which we hypothesize is due to the lack of in-domain knowledge incorporated into current neural network architectures. We introduce a new neural network driven workflow for untargeted metabolomics, Metabolite Inference with Spectrum Transformers (MIST), to annotate mass spectrometry peaks with chemical structures generalizing beyond known standards. Unlike other neural approaches, MIST incorporates domain insights into its architecture by forcing the network to more directly link peaks to physical atom representations, neutral losses, and chemical substructures. MIST outperforms both standard neural architectures and the state-of-the-art kernel method on fingerprint prediction from spectra for over 70% of metabolite standards and retrieves over 66% of metabolites with equal or improved accuracy, with 29% strictly better. We further demonstrate the utility of MIST in a prospective setting to identify new differentially abundant metabolite structures from an inflammatory bowel disease patient cohort and subsequently annotate dipeptides and alkaloid compounds without spectral standards.
Alternative Complement Pathway Regulates Thermogenic Fat Function via Adipsin and Adipocyte-derived C3aR1 in a Sex-dependent Fashion
Authors: Ma Lunkun , Gilani Ankit , Rubio-Navarro Alfonso , Cortada-Almar Eric , Li Ang , Reilly Shannon M. , Tang Liling , Lo James C.
Published: December 2022

Thermogenesis in beige/brown adipose tissues can be leveraged to combat metabolic disorders such as type 2 diabetes and obesity. The complement system plays pleiotropic roles in metabolic homeostasis and organismal energy balance with canonical effects on immune cells and non-canonical effects on non-immune cells. The adipsin/C3a/C3aR1 pathway stimulates insulin secretion and sustains pancreatic beta cell mass. However, its role in adipose thermogenesis has not been defined. Here, we show thatAdipsinknockout mice exhibit increased energy expenditure and white adipose tissue (WAT) browning. C3a, a downstream product of adipsin, is generated from complement component 3 and decreasesUcp1expression in subcutaneous adipocytes. In addition, adipocyte-specificC3aR1knockout male mice show enhanced WAT thermogenesis and increased respiration. In stark contrast, adipocyte-specificC3aR1knockout female mice display decreased brown fat thermogenesis and are cold intolerant. Female mice express lower levels ofAdipsinin thermogenic adipocytes and adipose tissues than males.C3aR1is also lower in female subcutaneous adipose tissue than males. Collectively, these results reveal sexual dimorphism in the adipsin/C3a/C3aR1 axis in regulating adipose thermogenesis. Our findings establish a newly discovered role of the alternative complement pathway in adipose thermogenesis and highlight sex-specific considerations in potential therapeutic targets for metabolic diseases.
The bHLH-PAS transcriptional complex Sim:Tgo plays active roles in late oogenesis to promote follicle maturation and ovulation
Authors: Oramas Rebecca , Knapp Elizabeth , Zeng Baosheng , Sun Jianjun
Published: December 2022

Across species, ovulation is a process induced by a myriad of signaling cascades that ultimately results in activation of proteolytic enzymes and degradation of the follicle wall to release encapsulated oocytes. Follicles need to first mature and gain ovulatory competency before ovulation. However, the signaling pathways regulating follicle maturation are incompletely understood inDrosophilaand other species. Our previous work showed that bHLH-PAS transcription factor Single-minded (Sim) likely plays important roles for follicle maturation downstream of the NR5A-family nuclear receptor Ftz-f1 inDrosophila. Here, we explore the mechanism of Sim-regulated follicle maturation. We demonstrate that Tango (Tgo), another bHLH-PAS protein acts as a cofactor of Sim to promote follicle cell differentiation from stages 10 to 12. In addition, we discovered that re-upregulation of Sim in stage-14 follicle cells is also essential to promote ovulatory competency by upregulating octopamine receptor in mushroom body (OAMB), matrix metalloproteinase 2 (Mmp2), and NADPH oxidase (NOX), either independent of or in conjunction with the zinc-finger protein Hindsight (Hnt). All of these factors are critical for successful ovulation. Together, our work indicates that the transcriptional complex Sim:Tgo plays multiple roles in late-stage follicle cells to promote follicle maturation and ovulation.
Dynamic decomposition of transcriptome responses during plant effector-triggered immunity revealed conserved responses in two distinct cell populations
Authors: Liu Xiaotong , Igarashi Daisuke , Hillmer Rachel A. , Stoddard Thomas , Lu You , Tsuda Kenichi , Myers Chad L. , Katagiri Fumiaki
Published: December 2022

Rapid plant immune responses in the appropriate cells are needed for effective defense against pathogens. Although transcriptome analysis is often used to describe overall immune responses, collecting transcriptome data with sufficient resolution in both space and time is challenging.

We reanalyzed public Arabidopsis time-course transcriptome data obtained after a low-dose inoculation of aPseudomonas syringaestrain expressing the effector AvrRpt2, which induces Effector-Triggered Immunity (ETI) in Arabidopsis. Double-peak time-course patterns were prevalent among thousands of upregulated genes. We implemented a multi-compartment modeling approach to decompose the double-peak pattern into two single-peak patterns for each gene.

The decomposed peaks revealed an “echoing” pattern: the peak times of the first and second peaks correlated well across most upregulated genes. We demonstrated that two peaks likely represent responses of two distinct cell populations, which respond either cell-autonomously or indirectly to AvrRpt2. Thus, the peak decomposition extracted spatial information from the time-course data.

The echoing pattern also indicated a conserved transcriptome response between two cell populations despite different elicitor types. WRKY transcription factors appeared to underlie the conserved transcriptome response. Activation of a WRKY network via different entry-point WRKYs could explain the conserved transcriptome response elicited by different elicitor types.
Biomechanical modeling of Border Collies (Canis familiaris) for insights of tail and limb use during the aerial phase of jumping
Authors: Rottier Tom , Schulz Andrew K. , Söhnel Katja , Mccarthy Kathryn , Fischer Martin S. , Jusufi Ardian
Published: December 2022

Dogs and other members of Canidae utilize their tails for different purposes, including agile movements, such as running and jumping. In this study, we utilized motion capture biomechanical data of a border collie executing an agile rotational jump maneuver. This data created a 17-segment biomechanical model of the border collie’s (Canis familiaris)limb movement during agile jumps. This model was verified by comparing it to the biomechanical movement and fitting the dog’s agile task with an RMSE less than 2.5%. Using this joint model, we held specific segments constant to view their inertial impact on the dog during the aerial phase of jumping. Results suggest that the tail, hind limbs, and fore limb provides little to no inertial advantage during these rotational jump maneuvers. The tail of dogs likely does have a minimal impact on inertia, the opposite of animals like the gecko. This work could alleviate unknown biomechanical use of the tails to understand the behavioral biomechanics of lesser-known species in their ability to use their tail for rapid and taxing behaviors, including sprinting or climbing.
Oat species and interspecific amphiploids show predominance of diploid nuclei in the syncytial endosperm
Authors: Tomaszewska Paulina , Kosina Romuald
Published: January 2023

Apart from apomictic types, thePolygonum-type eight-nuclear embryo sac is considered to be dominant in grasses. A triploid endosperm is formed as a result of double fertilisation. This study showed, for the first time, the dominance of diploid nuclei in the syncytial stage of the central cell of embryo sac in oat species and amphiploids. The dominance of diploid nuclei, which were the basis for the formation of polyploid nuclei, was weaker in amphiploids due to aneuploid events. The genomicin situhybridisation method applied in the study did not distinguish the maternal and paternal haploid nuclei of embryo sac. However, this method demonstrated the lack of a set of genomes of one haploid nucleus. It can be assumed that the formation of diploid oat endosperm occurred after the fusion of one polar nucleus and the nucleus of a sperm cell, while the second polar nucleus formed 1nnuclei. The levels of syncytial ploidy were not influenced by both aneuploid events and correlated with pollen developmental anomalies. The differences in the analysed cytogenetic events distinguished amphiploids and their parental species in the ordination space.
AntiRef: reference clusters of human antibody sequences
Authors: Briney Bryan
Published: December 2022

Motivation

Biases in the human antibody repertoire result in publicly available antibody sequence datasets containing many duplicate or highly similar sequences. These redundant sequences are a barrier to rapid similarity searches and reduce the efficiency with which these datasets can be used to train statistical or machine learning models of human antibodies. Identity-based clustering provides a solution; however, the extremely large size of available antibody repertoire datasets makes such clustering operations computationally intensive and potentially out of reach for many scientists and researchers who would benefit from such data.

Results

AntiRef (Antibody Reference Clusters), which is modeled after UniRef, provides clustered datasets of filtered human antibody sequences. Due to the modular nature of recombined antibody genes, the clustering thresholds used by UniRef to cluster general protein sequences (100, 90, and 50 percent identity) are suboptimal for antibody clustering. Starting from a dataset of ∼451 million full-length, productive human antibody sequences from the Observed Antibody Space (OAS) repository, AntiRef provides antibody sequence datasets clustered at a range of identity thresholds better suited to antibody sequences. AntiRef90, which uses the least stringent clustering threshold, is roughly one-third the size of the input dataset and less than half the size of the non-redundant AntiRef100.

Availability

AntiRef is freely available via Zenodo (zenodo.org/record/7474336) under the CC-BY 4.0 license, which matches the licensing of OAS datasets. All code used to download and filter sequences, generate AntiRef clusters, and create the figures used in this publication is freely available under the MIT license via GitHub (github.com/briney/antiref). We anticipate AntiRef updates will be released bi-annually, with the option for supplementary out-of-band updates when large or particularly interesting datasets are made available. The AntiRef versioning scheme (current version: v2022.12.14) refers to the date on which sequences were retrieved from OAS.

Contact

briney@scripps.edu
Traumatic brain injury induced microglial and Caspase3 activation in the retina
Authors: Kovács-Öller Tamás , Zempléni Renáta , Balogh Boglárka , Szarka Gergely , Fazekas Bálint , Tengölics Ádám J , Amrein Krisztina , Czeiter Endre , Hernádi István , Büki András , Völgyi Béla
Published: December 2022

Traumatic brain injury (TBI) is among the main causes of sudden death after head trauma. These injuries can result in severe degeneration and neuronal cell death in the CNS, including the retina which is a crucial part of the brain responsible for perceiving and transmitting visual information. The long-term effects of mild-repetitive TBI (rmTBI) are far less studied thus far, even though damages induced by repetitive injuries occurring in the brain are more common, especially amongst athletes. rmTBI can also have a detrimental effect on the retina and the pathophysiology of these injuries are likely to differ from the severe TBI (sTBI) retinal injury.

Here we showed how rmTBI and sTBI can dissimilarly affect the retina. Our results indicate an increase in the number of activated microglial cells and Caspase3-positive cells in the retina in both traumatic models, suggesting a rise in the level of inflammation and cell death after TBI. The pattern of microglial activation appears evenly distributed and widespread but differs amongst the various retinal layers. sTBI induced microgial activation in both the superficial and deep retinal layers. In contrast to sTBI, no significant change occurred following the repetitive mild injury in the superficial layer, only the deep layer (spanning from the inner nuclear layer to the outer plexiform layer) shows microglial activation. This difference suggests that alternate response mechanisms play a role in the case of the different TBI incidents. The Caspase3 activation pattern showed a uniform increase in both the superficial and deep layers of the retina. This suggests a different action in the course of the disease in sTBI and rmTBI models and points to the need for new diagnostic procedures. Our present results suggest that the retina might serve as such a model of head injuries since the retinal tissue reacts to both forms of TBI and is the most accessible part of the human brain.
Hematopoietic-specific heterozygous loss ofDnmt3aexacerbates colitis-associated colon cancer
Authors: Feng Yang , Newsome Rachel C , Robinson Troy , Bowman Robert L , Zuniga Ashley N , Hall Kendra N , Bernsten Cassandra M , Shabashvili Daniil E , Krajcik Kathryn I , Gunaratne Chamara , Zaroogian Zachary J , Venugopal Kartika , Casellas Roman Heidi L , Levine Ross L , Chatila Walid K , Yaeger Rona , Riva Alberto , Kopinke Daniel , Jobin Christian , Avram Dorina , Guryanova Olga A
Published: December 2022

Clonal hematopoiesis (CH) is defined as clonal expansion of mutant hematopoietic stem cells absent diagnosis of a hematologic malignancy. Presence of CH in solid tumor patients, including colon cancer, correlates with shorter survival. We hypothesized that bone marrow-derived cells with heterozygous loss-of-function mutations ofDNMT3A, the most common genetic alteration in CH, contribute to the pathogenesis of colon cancer.

In a mouse model that combines colitis-associated colon cancer with experimental CH driven byDnmt3a+/Δ, we found higher tumor penetrance and increased tumor burden compared to controls. Histopathological analysis revealed accentuated colonic epithelium injury, dysplasia and adenocarcinoma formation. Transcriptome profiling of colon tumors identified enrichment of gene signatures associated with carcinogenesis, including angiogenesis. Treatment with the angiogenesis inhibitor axitinib eliminated the colon tumor-promoting effect of experimental CH driven byDnmt3ahaploinsufficiency. This study provides conceptually novel insights into non-tumor-cell-autonomous effect of hematopoietic alterations on colon carcinogenesis and identifies potential therapeutic strategies.

A pre-clinical mouse model demonstrates that genetic alterations in the blood system characteristic of clonal hematopoiesis (CH) contribute to an aggressive solid tumor phenotype. It further identifies cancer angiogenesis as a potential therapeutic target to mitigate adverse CH effects.
Garments that measure EEG: Evaluation of an EEG sensor layer fully implemented with smart textiles
Authors: López-Larraz Eduardo , Escolano Carlos , Robledo Almudena , Morlas Leyre , Alda Alexandra , Minguez Javier
Published: January 2023

This paper presents the first garment capable of measuring EEG activity with accuracy comparable to state-of-the art dry EEG systems. The main innovation is an EEG sensor layer (i.e., the electrodes, the signal transmission, and the cap support) fully implemented as a garment, using threads, fabrics and smart textiles, without relying on any metal or plastic materials. The garment is interfaced via a connector to a mobile EEG amplifier to complete the measurement system. The new EEG system (Garment-EEG) has been characterized with respect to a state-of-the-art Ag/AgCl dry-EEG system (Dry-EEG) over the forehead area of healthy participants in terms of: (1) skin-electrode impedance; (2) electrophysiological measurements (spontaneous and evoked EEG activity); (3) artifacts; and (4) user ergonomics and comfort. The results show that the Garment-EEG system provides comparable recordings to Dry-EEG, but it is more prone to getting affected by artifacts in adverse recording conditions due to poorer contact impedances. Ergonomics and comfort favor the textile-based sensor layer with respect to its metal-based counterpart. User acceptance is the main obstacle for EEG systems to democratize neurotechnology and non-invasive brain-computer interfaces. EEG sensor layers encapsulated in wearables have the potential to enable neurotechnology that is naturally accepted by people in their daily lives. Furthermore, by supporting the EEG implementation in the textile industry it is manufactured with lower cost and much less pollution compared to the metal and plastic industries.
The bacterial genetic determinants ofEscherichia colicapacity to cause bloodstream infections in humans
Authors: Burgaya Judit , Marin Julie , Royer Guilhem , Condamine Bénédicte , Gachet Benoit , Clermont Olivier , Jaureguy Françoise , Burdet Charles , Lefort Agnès , de Lastours Victoire , Denamur Erick , Galardini Marco , Blanquart François ,   the Colibafi/Septicoli and Coliville groups
Published: January 2023

Escherichia coliis both a highly prevalent commensal and a major opportunistic pathogen causing bloodstream infections (BSI). A systematic analysis characterizing the genomic determinants of extra-intestinal pathogenic vs. commensal isolates in human populations, which could inform mechanisms of pathogenesis, diagnostics, prevention and treatment is still lacking. We used a collection of 1282 BSI and commensalE. coliisolates collected in France over a 17-year period (2000-2017) and we compared their pangenomes, genetic backgrounds (phylogroups, STs, O groups), presence of virulence-associated genes (VAGs) and antimicrobial resistance genes, finding significant differences in all comparisons between commensal and BSI isolates. A machine learning linear model trained on all the genetic variants derived from the pangenome and controlling for population structure reveals similar differences in VAGs, discovers new variants associated with pathogenicity (capacity to cause BSI), and accurately classifies BSI vs. commensal strains. Pathogenicity is a highly heritable trait, with up to 69% of the variance explained by bacterial genetic variants. Lastly, complementing our commensal collection with an older collection from 1980, we predict that pathogenicity increased steadily from 23% in 1980 to 46% in 2010. Together our findings imply thatE. coliexhibit substantial genetic variation contributing to the transition between commensalism and pathogenicity and that this species evolved towards higher pathogenicity.
Implementation of a flavin biosynthesis operon improves extracellular electron transfer in bioengineered Escherichia coli
Authors: Mouhib Mohammed , Reggente Melania , Boghossian Ardemis A.
Published: January 2023

Bioelectrochemical systems (BES) are promising for energy, sensing, environmental, and synthesis applications.Escherichia coliwere previously bioengineered for application in BES by introduction of extracellular electron transfer (EET) pathways. Inspired by the metal-reducing (Mtr) pathway ofShewanella oneidensisMR-1, several of its cytochromes were heterologously expressed inE. coli, leading to increased EET rates and successful application in BES. Besides direct electron transfer, S. oneidensisMR-1 is known to secrete flavins that act as redox mediators and are crucial for high EET rates.

Here we co-express the Mtr pathway and a flavin biosynthesis pathway inE. coli, to enhance EET in engineered strains. The secretion of both flavin mononucleotide and riboflavin was increased up to 3-fold in engineered strains. Chronoamperometry revealed an up to ~3.4-fold increase in current over the wild type when co-expressing cytochromes and flavin biosynthesis genes, and a ~2.3-fold increase when expressing flavin biosynthesis genes on their own. Thus, the introduction of flavin biosynthesis genes yields in a distinct, yet complementary EET mechanism, and holds promise for application in BES.
Development of digital Hi-C assay
Authors: Mori Akihiro , Schweikert Gabriele
Published: January 2023

Abstracts

Enhancers are genomic elements and contain all necessary cis-regulatory contexts. Such enhancers are convened to the appropriate promoter of target genes for gene regulations even though the enhancers and the promoters are apart a few mega-base pairs away from each other. In addition to physical distance, nucleotide mutations in enhancers influence a partial group of the target genes. Those make it more complicated to reveal the paired relationship between enhancer and promoter of target genes. Recently, advanced computational approaches are employed to predict such interactions. One approach requires a large number of different high-throughput datasets to predict such interactions; however, in practical aspects, all datasets for tissues and conditions of interest are not available. Whereas the alternative approach requires only genome sequences for particular predictions, their predictions are insufficient for practical applications. We address those issues by developing the digital Hi-C assay with a transformer-algorithm basis. This assay allows us to create models from simple/small/limited sequence-based datasets only. We apply the trained models to be able to identify long-distance interactions of genomic loci and three-dimensional (3D) genomic architectures in any other tissue/cell datasets; additionally, we demonstrated the predictions of genomic contexts by analysing the prediction patterns around the target locus in the three following genomic-context problems: enhancer-promoter interactions (i.e., promoter-capture Hi-C), the CTCF-enriched regions, and TAD-boundary regions. Because our approach adopted a sequence-based approach, we can predict the long-distance interactions of genomic loci by using the genomic sequences of the user’s interest (e.g., input sequences from high-throughput assay datasets such as ATAC-seq and ChIP-seq assays). Consequently, we provide an opportunity to predict interactions of genomic loci from a minimum dataset.
ERBB4-mediated signaling is a mediator of resistance to BTK and PI3K inhibitors in B cell lymphoid neoplasms
Authors: Arribas Alberto J. , Napoli Sara , Cascione Luciano , Barnabei Laura , Sartori Giulio , Cannas Eleonora , Gaudio Eugenio , Tarantelli Chiara , Mensah Afua A. , Spriano Filippo , Zucchetto Antonella , Rossi Francesca M. , Rinaldi Andrea , de Moura Manuel Castro , Jovic Sandra , Pittau Roberta Bordone , Stathis Anastasios , Stussi Georg , Gattei Valter , Brown Jennifer R. , Esteller Manel , Zucca Emanuele , Rossi Davide , Bertoni Francesco
Published: January 2023

BTK and PI3K inhibitors are among the drugs approved for the treatment of patients with lymphoid neoplasms. Although active, their ability to lead as single agents to long-lasting complete remission is rather limited especially in the lymphoma setting. This indicates that tumor cells often develop resistance to the drugs. Here, we show that the overexpression of ERBB4 and its ligands represents a modality for B cell neoplastic cells to bypass the anti-tumor activity of BTK and PI3K inhibitors and that targeted pharmacological interventions can restore sensitivity to the small molecules.

We started from a marginal zone lymphoma (MZL) cell line, Karpas-1718, kept under prolonged exposure to the PI3Kδ inhibitor idelalisib until acquisition of resistance, or with no drug. Cells underwent transcriptome, miRNA and methylation profiling, whole exome sequencing, and pharmacological screening which led to the identification of the overexpression of ERBB4 and its ligands HBEGF and NRG2 in the resistant cells. Cellular and genetic experiments demonstrated the involvement of this axis in blocking the anti-tumor activity of various BTK and PI3K inhibitors, currently used in the clinical setting. Addition of recombinant HBEGF induced resistance to BTK and PI3K inhibitors in parental cells but also in additional lymphoma models. Combination with the ERBB inhibitor lapatinib was beneficial in resistant cells and in other lymphoma models already expressing the identified resistance factors. Multi-omics analysis underlined that an epigenetic reprogramming affected the expression of the resistance-related factors, and pretreatment with demethylating agents or EZH2 inhibitors overcame the resistance. Resistance factors were shown to be expressed in clinical samples, further extending the findings of the study.

In conclusions, we identified a novel ERBB4-driven mechanism of resistance to BTK and PI3K inhibitors and treatments that appear to overcome it.

Key points

A mechanism of secondary resistance to the PI3Kδ and BTK inhibitors in B cell neoplasms driven by secreted factors.

Resistance can be reverted by targeting ERBB signaling.
KLRG1 marks tumor-infiltrating CD4 T cell subsets associated with tumor progression and immunotherapy response
Authors: Ager Casey R. , Zhang Mingxuan , Chaimowitz Matthew , Bansal Shruti , Obradovic Aleksandar , Rogava Meri , Melms Johannes C. , McCann Patrick , Spina Catherine , Drake Charles G. , Dallos Matthew C. , Izar Benjamin
Published: January 2023

Current methods for biomarker discovery and target identification in immuno-oncology rely on static snapshots of tumor immunity. To thoroughly characterize the temporal nature of antitumor immune responses, we developed a 34-parameter spectral flow cytometry panel and performed high-throughput analyses in critical contexts. We leveraged two distinct preclinical models that recapitulate cancer immunoediting (NPK-C1) and immune checkpoint blockade (ICB) response (MC38), respectively, and profiled multiple relevant tissues at and around key inflection points of immune surveillance and escape and/or ICB response. Machine learning-driven data analysis revealed a pattern of KLRG1 expression that uniquely identified intratumoral effector CD4 T cell populations that constitutively associate with tumor burden across tumor models, and are lost in tumors undergoing regression in response to ICB. Similarly, a Helios-KLRG1+subset of tumor-infiltrating regulatory T cells (Tregs) was associated with tumor progression from immune equilibrium to escape, and were also lost in tumors responding to ICB. Validation studies confirmed KLRG1 signatures in human tumorinfiltrating CD4 T cells associate with disease progression in renal cancer. These findings nominate KLRG1+CD4 T cell populations as subsets for further investigation in cancer immunity and demonstrate the utility of longitudinal spectral flow profiling as an engine of dynamic biomarker and/or target discovery.
Screening of herbal molecules for the management of Alzheimer’s Disorder through molecular docking andin-vitroinvestigation
Authors: Nagu Priyanka , Pathan Amjad Khan A , Mehta Vineet
Published: January 2023

At present, there is not a single disease-modifying drug available for the management of Alzheimer’s disease (AD) pathogenesis. The exact pathology of AD is still not known, which opens up the wide scope of research for developing some novel therapeutic strategies for AD management. In the present study, 100 herbal molecules were identified through the literature survey which could be beneficial for Acetylcholinesterase (AChE), Butyrylcholinesterase (BChE), β-Secretase inhibition, and neurodegeneration. AutoDock Tools-1.5.6 docking software is used to screen the herbal molecules against AChE, BChE, and β-Secretase with Protein Data Bank (PDB) ID 1B41, 1P0I, and 1FKN respectively. Based on the docking parameters quercetin, rutin, vitisinol-C, dihydrotanshinone-I, and β-carotene were found to be the best molecules against their respective proteins receptors. Moreover,in-vitroAChE and BChE assay demonstrated that quercetin and rutin could modulate cholinergic pathways during AD and thereby could impart beneficial effects during AD. Further, our results forin-vitroneurodegeneration studies also support the neuroprotective effect of quercetin and rutin against HgCl2-induced neurodegeneration and suggested the protective role of these molecules against neurodegeneration during AD. However, a preclinical investigation is required to support the potential effect on AD pathogenesis.
Regulated Induced Proximity Targeting Chimeras (RIPTACs): a Novel Heterobifunctional Small Molecule Therapeutic Strategy for Killing Cancer Cells Selectively
Authors: Raina Kanak , Forbes Chris D. , Stronk Rebecca , Rappi Jonathan P. , Eastman Kyle J. , Gerritz Samuel W. , Yu Xinheng , Li Hao , Bhardwaj Amit , Forgione Mia , Hundt Abigail , King Madeline P. , Posner Zoe M. , Denny Allison , McGovern Andrew , Puleo David E. , Garvin Ethan , Chenard Rebekka , Zaware Nilesh , Mousseau James J. , Macaluso Jennifer , Martin Michael , Bassoli Kyle , Jones Kelli , Garcia Marco , Howard Katia , Smith Levi M. , Chen Jinshan M. , De Leon Cesar A. , Hines John , Kayser-Bricker Katherine J. , Crews Craig M.
Published: January 2023

While specific cell signaling pathway inhibitors have yielded great success in oncology, directly triggering cancer cell death is one of the great drug discovery challenges facing biomedical research in the era of precision oncology. Attempts to eradicate cancer cells expressing unique target proteins, such as antibody-drug conjugates (ADCs), T-cell engaging therapies, and radiopharmaceuticals have been successful in the clinic, but they are limited by the number of targets given the inability to target intracellular proteins. More recently, heterobifunctional small molecules such as Proteolysis Targeting Chimera (PROTACs) have paved the way for protein proximity inducing therapeutic modalities.

Here, we describe a proof-of-concept study using novel heterobifunctional small molecules calledRegulatedInducedProximityTargetingChimeras or RIPTACs, which elicit a stable ternary complex between a target protein selectively expressed in cancer tissue and a pan-expressed protein essential for cell survival. The resulting cooperative protein:protein interaction (PPI) abrogates the function of the essential protein, thus leading to cell death selectively in cells expressing the target protein. This approach not only opens new target space by leveraging differentially expressed intracellular proteins but also has the advantage of not requiring the target to be a driver of disease. Thus, RIPTACs can address non-target mechanisms of resistance given that cell killing is driven by inactivation of the essential protein.

Using the HaloTag7-FKBP model system as a target protein, we describe RIPTACs that incorporate a covalent or non-covalent target ligand connected via a linker to effector ligands such as JQ1 (BRD4), BI2536 (PLK1), or multi-CDK inhibitors such as TMX3013 or dinaciclib. We show that these RIPTACs exhibit positive co-operativity, accumulate selectively in cells expressing HaloTag7-FKBP, form stable target:RIPTAC:effector trimers in cells, and induce an anti-proliferative response in target-expressing cells. We propose that RIPTACs are a novel heterobifunctional therapeutic modality to treat cancers that are known to selectively express a specific intracellular protein.
HSV-1 Oncolytic Virus Targeting CEACAM6-Expressing Tumors Using a Bispecific T-Cell Engager
Authors: Murad Yanal M. , Lee I-Fang , Liu Xiaohu , Delwar Zahid , Ding Jun , Liu Guoyu , Tatsiy Olga , Chouljenko Dmitry , Hussack Gregory , Van Faassen Henk , Jia William Wei-Guo
Published: January 2023

VG21306 is a novel oncolytic virus (OV) that encodes a secretable bispecific T-cell engager targeting Carcinoembryonic antigen cell adhesion molecule 6 (CEACAM6)-expressing tumors. Delivering a T-cell engager locally to a tumor mass will circumvent physical barriers that prevent antibodies from penetrating the tumor, and will mitigate the off-tumor, on-target toxicity risk. Both in vitro and in vivo testing demonstrated the expression of a functional T-cell engager capable of binding both targets. The efficacy of the engager was demonstrated in vitro, where addition of the engager payload to the OV enhanced anti-tumor efficacy against tumor cells overexpressing CEACAM6. Moreover, we have demonstrated the engager’s ability to induce bystander killing in cells lacking CEACAM6 expression, as well as engaging exhausted T cells and inducing tumor cell death. The safety of the engager was demonstrated by the lack of binding to normal human tissue or normal tissue adjacent to tumors, as well as the absence of any measurable leakage of the expressed engager into the blood of mice treated by intratumoral OV injection.
Extracellular succinate induces spatially organized biofilm formation inClostridioides difficile
Authors: Auria Emile , Deschamps Julien , Briandet Romain , Dupuy Bruno
Published: January 2023

Clostridioides difficileis the major cause of nosocomial diarrhea, which are associated with gut microbiome dysbiosis. Biofilms ofC. difficilehave been progressively linked to the pathogenesis of this bacterium and the recurrences of its infections. Though the number of conditions in whichC. difficilebiofilms are being produced is increasing, little is known about how and when biofilms are formed in the gut. Here we report that succinate, a metabolite abundantly produced by the dysbiotic gut microbiota, inducesin vitrobiofilm formation ofC. difficilestrains. We characterized the morphology and spatial composition of succinate-induced biofilms, and compared to non-induced or deoxycholate-induced biofilms, biofilms induced by succinate are significantly thicker, structurally more complex, and poorer in proteins and exopolysaccharides (EPS). We then applied transcriptomics and genetics to characterize the early stages of succinate-induced biofilm formation and we showed that succinate-induced biofilm results from major metabolic shifts and cell-wall composition changes. Similar to deoxycholate-induced biofilms, biofilms induced by succinate depend on the presence of a rapidly metabolized sugar. Finally, although succinate can be consumed by the bacteria, we found that the extracellular succinate is in fact responsible for the induction of biofilm formation through complex regulation involving global metabolic regulators and the osmotic stress response. In the context of human gut dysbiosis, succinate can limit bacterial infections through the control of innate immune responses. Collectively, our results suggest that succinate is an intestinal signal which can drive the biofilm formation and persistence ofC. difficilein the gut and increase the risk of relapse.