bluuebunny/crossref_metadata_2025 huggingface dataset:
ACDA: Implementation of an Augmented Drug Synergy Prediction Algorithm
Authors: Domanskyi Sergii , Jocoy Emily L. , Srivastava Anuj , Bult Carol J.
Published: October 2022

Motivation

Drug synergy prediction is a complex problem typically approached with machine learning techniques using molecular data, pharmacological data, and knowledge of biological-interaction networks. The recently published Cancer Drug Atlas (CDA) uses a logistic regression model to predict a binary synergy outcome in cell-line models by utilizing drug target information, knowledge of genes mutated in each model, and the models’ monotherapy drug sensitivity. However, we observed low performance, 0.33, of the CDA measured by Pearson correlation of predicted versus measured sensitivity when we evaluated datasets from six studies that were not considered during the development of the CDA. Here we describe improvements to the CDA algorithm, the Augmented CDA, that improved performance by 71% and robustness to dataset variations in drug response values.

Results

We augmented the drug-synergy prediction-modeling approach CDA described in Narayan et al. by applying a random forest regression and optimization via cross-validation hyper-parameter tuning. We benchmarked the performance of our Augmented CDA (ACDA) compared to the original CDA algorithm using datasets from DrugComb, an open-access drug-combination screening data resource. The ACDA’s performance is 71% higher than that of the CDA when trained and validated on the same dataset spanning ten tissues. The ACDA performs marginally better (6% increase) than the CDA when trained on one dataset and validated on another dataset in 22 cases that cover seven tissues. We also compared the performance of ACDA to one of the winners of the DREAM Drug Combination Prediction Challenge (Mikhail Zaslavskiy’s algorithm which we denoted as EN). The performance of EN was smaller than that of the ACDA in 15 out of 19 cases. In addition to data from cell lines, we also trained the ACDA algorithm on Novartis Institutes for BioMedical Research PDX encyclopedia (NIBR PDXE) data and generated sensitivity predictions for the cases where drug-combination tumor-volume measurements were unavailable. Finally, we developed an approach to visualize synergy-prediction data using dendrograms and heatmaps instead of the Voronoi diagrams used in the CDA. The latter has a complex algorithmic realization and no publicly available implementation, whereas the ACDA visualization approach is more transparent and has open access. We implemented and wrapped the ACDA algorithm in an easy-to-use python package available from PyPI.

Availability

The source code is available athttps://github.com/TheJacksonLaboratory/drug-synergy, and the software package can be installed directly from PyPI using pip.

Contact

Anuj.Srivastava@jax.org,Carol.Bult@jax.org
Uncovering transcriptional regulatory network during regeneration for boosting wheat transformation
Authors: Liu Xuemei , Bie Xiaomin , Lin Xuelei , Li Menglu , Wang Hongzhe , Zhang Xiaoyu , Yang Yiman , Zhang Chunyan , Zhang Xiansheng , Xiao Jun
Published: October 2022

Genetic transformation is important for gene functional study and crop breeding. Though it is available in many plant species, the transformation efficiency in wheat is generally low, which greatly restricts the genetic manipulation in wheat. Here, we use multi-omic analysis strategy to uncover core transcriptional regulatory network (TRN) driving wheat shoot regeneration and identify key factors that boost the transformation efficiency. RNA-seq, ATAC-seq and CUT&Tag were used to profile the transcriptome and chromatin dynamic during regeneration process from immature embryo of wheat variety Fielder. Sequential expression of gene clusters that mediating cell fate transition during regeneration is induced by auxin signaling, in coordination with changes of chromatin accessibility, H3K27me3 and H3K4me3 status. The TRN driving wheat shoot regeneration was built-up and 446 key transcriptional factors (TFs) occupied the core of network were identified, including functionally tested regeneration factors in other species. We further compared the regeneration process between wheat andArabidopsisand found that DNA binding with one finger (DOF) TFs show distinct patterns in two species. Furthermore, we found thatTaDOF5.6(TraesCS6A02G274000) andTaDOF3.4(TraesCS2B02G592600) can significantly improve the transformation efficiency of different wheat varieties. Thus, our data uncovers the molecular regulatory insights for wheat shoot regeneration process and provides potential novel targets for improving transformation efficiency in wheat.
The nanopore sequencing of a Chinese rhesus macaque revealed patterns of methylation, recombination, and selection for structural variations
Authors: Chen Jianhai , Zhong Jie , He Xuefei , Jakovlić Ivan , Zhang Yong , Yang Hao , Chen Younan , Yang Guang , Fan Chuanzhu , Shen Bairong
Published: October 2022

Rhesus macaques (Macaca mulatta) are the most extensively studied nonhuman primate species for human biomedical modeling. However, little is known about the biological pattern of genome-wide structural variations (SVs) and the evolutionary forces underlying SVs. Here, we conducted genomic sequencing and analyses based on Nanopore long reads and Illumina short reads technology. We called SVs between the two subspecies (China vs. India), using three methods of assembly-based and long-reads-based algorithms. Interestingly, we found significantly more SVs in X-chromosome than in autosomes, consistent with the expectation of the faster-X divergence at the subspecies level. With the fine-scale methylation frequencies and recombination rates, we found duplications with significantly lower methylation frequencies while higher recombination rates than other types of SVs, suggesting a higher level of transcriptional and evolutionary potential for duplications than for other SVs types. A genome-wide scan of selective sweep revealed that over 3% of SVs are under positive selection. Moreover, X chromosome showed significantly higher number of positively selected SVs than do autosomes, suggesting the “faster-X effect” of SVs. Our study revealed a different evolutionary importance for duplications compared with other SVs forms. We also revealed the “faster-X effect” of SVs, which could provide raw material upon which positive selection can further play.
ViReaDB: A user-friendly database for compactly storing viral sequence data and rapidly computing consensus genome sequences
Authors: Moshiri Niema
Published: October 2022

Motivation

In viral molecular epidemiology, reconstruction of consensus genomes from sequence data is critical for tracking mutations and variants of concern. However, storage of the raw sequence data can become prohibitively large, and computing consensus genome from sequence data can be slow and requires bioinformatics expertise.

Results

ViReaDB is a user-friendly database system for compactly storing viral sequence data and rapidly computing consensus genome sequences. From a dataset of 1 million trimmed mapped SARS-CoV-2 reads, it is able to compute the base counts and the consensus genome in 16 minutes, store the reads alongside the base counts and consensus in 50 MB, and optionally store just the base counts and consensus (without the reads) in 300 KB.

Availability

ViReaDB is freely available on PyPI (https://pypi.org/project/vireadb) and on GitHub (https://github.com/niemasd/ViReaDB) as an open-source Python software project.

Contact

niema@ucsd.edu
DNA methylation restricts coordinated germline and neural fates in embryonic stem cell differentiation
Authors: Schulz Mathieu , Teissandier Aurélie , de la Mata Elena , Armand Mélanie , Iranzo Julian , El Marjou Fatima , Gestraud Pierre , Walter Marius , Kinston Sarah , Göttgens Berthold , Greenberg Maxim V.C. , Bourc’his Deborah
Published: October 2022

Somatic DNA methylation is established early during mammalian development, as embryonic cells transition from naive to primed pluripotency. This precedes the emergence of the three somatic germ layers, but also the segregation of the germline that undergoes genome-wide DNA demethylation after specification. While DNA methylation is essential for embryogenesis, the point at which it becomes critical during differentiation and whether all lineages equally depend on it is unclear. Using culture modeling of cellular transitions, we found that DNA methylation-free embryonic stem cells (ESCs) with a triple DNA methyltransferase knockout (TKO) normally progressed through the continuum of pluripotency states, but demonstrated skewed differentiation abilities towards neural versus other somatic lineages. More saliently, TKO ESCs were fully competent for establishing primordial germ cell-like cells (PGCLCs), even showing temporally extended and self-sustained capacity for the germline fate. By mapping chromatin states, we found that the neural and germline lineages are linked by a similar enhancer dynamics during priming, defined by common sets of methyl-sensitive transcription factors that fail to be decommissioned in absence of DNA methylation. We propose that DNA methylation controls the temporality of a coordinated neural-germline axis of preferred differentiation route during early development.
Species-wide genomics of kākāpō provides transformational tools to accelerate recovery
Authors: Guhlin Joseph , Lec Marissa F. Le , Wold Jana , Koot Emily , Winter David , Biggs Patrick , Galla Stephanie J. , Urban Lara , Foster Yasmin , Cox Murray P. , Digby Andrew , Uddstrom Lydia , Eason Daryl , Vercoe Deidre , Davis Tāne ,   Kākāpō Recovery Team, Howard Jason T , Jarvis Erich , Robertson Fiona E. , Robertson Bruce C. , Gemmell Neil , Steeves Tammy E. , Santure Anna W. , Dearden Peter K.
Published: October 2022

The kākāpō is a critically endangered, intensively managed, long-lived nocturnal parrot endemic to Aotearoa New Zealand. We generated and analyzed whole-genome sequence data for nearly all individuals living in early 2018 (169 individuals) to generate a high-quality species-wide genetic variant callset. We leverage extensive long-term metadata to quantify genome-wide diversity of the species over time and present new approaches using probabilistic programming, combined with a phenotype dataset spanning five decades, to disentangle phenotypic variance into environmental and genetic effects while quantifying uncertainty in small populations. We find associations for growth, disease susceptibility, clutch size, and egg fertility within genic regions previously shown to influence these traits in other species. Finally, we generate breeding values to predict phenotype and illustrate that active management over the past 45 years has maintained both genome-wide diversity and diversity in breeding values, and hence, evolutionary potential. We provide new pathways for informing future conservation management decisions for kākāpō, including prioritizing individuals for translocation and monitoring individuals with poor growth or high disease risk. Overall, by explicitly addressing the challenge of small sample size, we provide a template for the inclusion of genomic data that will be transformational for species recovery efforts around the globe.
Role of DEAD Box RNA helicases in low temperature adapted growth of AntarcticPseudomonas syringaeLz4W
Authors: Hussain Ashaq , Ray Malay Kumar
Published: October 2022

Nucleic acid metabolism plays an important role in adaptation of organisms to environment. For adaptation to cold environment, organisms need to overcome the impediments in complex RNA secondary structures that are highly stabilized at low temperature affecting metabolism and growth of the organisms. Employing gene disruption through homologous recombination, we investigated the role of all major DEAD box RNA helicases (rhlE, srmB, csdA, dbpAandrhlB) in cold adapted growth ofPseudomonas syringae. Our findings concluded thatsrmBanddbpAgenes are important for cold adapted growth, whereascsdAis indispensable for growth at low temperature. Helicase genesrhlBandrhlEhave no appreciable role in cold adapted growth ofPseudomonas syringae. Functional complementation studies revealed that RNA helicases don’t have any redundant functions, as the roles performed by different helicases are individual and specific.
Neglected no longer: Phylogenomic resolution of higher-level relationships in Solifugae
Authors: Kulkarni Siddharth S. , Steiner Hugh G. , Garcia Erika L. , Iuri Hernán , Jones R. Ryan , Ballesteros Jesús A. , Gainett Guilherme , Graham Matthew R. , Harms Danilo , Lyle Robin , Ojanguren-Affilastro Andrés A. , Santibañez-López Carlos E. , de Miranda Gustavo Silva , Cushing Paula E. , Gavish-Regev Efrat , Sharma Prashant P.
Published: October 2022

Considerable progress has been achieved in resolving higher-level relationships of Arthropoda in the past two decades, largely precipitated by advances in sequencing technology. Yet, dark branches persist in the arthropod tree of life, principally among groups that are difficult to collect, occur in cryptic habitats, or are characterized by minute body size. Among chelicerates, the mesodiverse order Solifugae (commonly called camel spiders or sun spiders) is one of the last orders of Arachnida that lacks a higher-level phylogeny altogether and has long been characterized as one of the “neglected cousins”, a lineage of arachnid orders that are comparatively poorly studied with respect to evolutionary relationships. Though renowned for their aggression, remarkable running speed, and adaptation to arid habitats, inferring solifuge relationships has been hindered by inaccessibility of diagnostic characters in most ontogenetic stages for morphological datasets, whereas molecular investigations to date have been limited to one of the 12 recognized families. In this study we generated a phylogenomic dataset via capture of ultraconserved elements (UCEs) and sampled all extant families. We recovered a well-resolved phylogeny of solifuge families, with two distinct groups of New World taxa nested within a broader Paleotropical radiation. To provide a temporal context to solifuge diversification, we estimated molecular divergence times using fossil calibrations within a least-squares framework. Solifugae were inferred to have radiated by the Permian, with divergences of most families dating to the post Paleogene-Cretaceous extinction. These results accord with a diversification history largely driven by vicariance as a result of continental breakup.
The matrisome of the murine and human dorsal root ganglion: a transcriptomal approach
Authors: Vroman Robin , Hunter Rahel , Wood Matthew J. , Davis Olivia C. , Malfait Zoë , George Dale S. , Ren Dongjun , Tavares-Ferreira Diana , Price Theodore J. , Malfait Anne-Marie , Malfait Fransiska , Miller Rachel E. , Syx Delfien
Published: October 2022

The extracellular matrix (ECM) is a dynamic structure composed of a large number of molecules that can be divided into six different categories and are collectively called the matrisome. The ECM plays pivotal roles in physiological and pathological processes in many tissues, including the nervous system. Intriguingly, alterations in ECM molecules/pathways are often associated with painful human conditions and murine experimental pain models. Nevertheless, mechanistic insight into the interplay of normal or defective ECM and pain is largely lacking. To expand the knowledge on ECM composition and synthesis in the peripheral nervous system, we used a transcriptomal approach to investigate the expression and cellular origin of matrisome genes in murine and human dorsal root ganglia (DRG), containing the cell bodies of sensory neurons. Bulk RNA sequencing data showed that over 60% of all matrisome genes were expressed in both murine and human DRG, with proportionally more core matrisome genes (glycoproteins, collagens, and proteoglycans) expressed compared to matrisome-associated genes (ECM-affiliated genes, ECM regulators and secreted factors). Examination of the cellular origin of matrisome expression by single cell RNA sequencing on murine DRG revealed that core matrisome genes, especially collagens, were expressed by vascular leptomeningeal-like (fibroblast) cell types whereas matrisome-associated genes were mainly expressed by neuronal cell types. We analyzed cell-cell communication networks with the CellChat R package and predicted an important role for the Collagen signaling pathway in connecting vascular cell types and nociceptors in murine tissue, which we confirmed by analysis of spatial transcriptomic data from human DRG. RNAscopein situhybridization and immunohistochemistry confirmed expression of collagens in fibroblasts surrounding nociceptors in human DRG. This study supports the idea that the DRG matrisome may contribute to neuronal signaling in both mouse and human. The identification of the cellular distribution of murine and human matrisome genes provides a framework to study the role of the ECM in peripheral nervous tissue and its effects on pain signaling.

Highlights

Transcriptomal analyses of mouse and human dorsal root ganglia (DRG) revealed that over 60% of matrisome genes are expressed by murine and human dorsal root ganglia (DRG), with over 85% of the genes with orthologues overlapping between both species.

Matrisome-associated genes had the highest expression in both species and included conserved expression of annexins, S100 calcium binding proteins and cathepsins.

Collagens and collagen receptors are expressed by distinct cell types in murine and human DRG, suggesting that the collagen signaling pathway could be involved in cell-cell signaling.
Structural Basis for Selective Proteolysis of ADAM10 Substrates at Membrane-Proximal Sites
Authors: Lipper Colin H. , Egan Emily D. , Gabriel Khal-Hentz , Blacklow Stephen C.
Published: October 2022

The endopeptidase ADAM10 is a critical catalyst for regulated proteolysis of key drivers of mammalian development and physiology, and for non-amyloidogenic cleavage of the Alzheimer’s precursor protein as the primary α-secretase. ADAM10 functionin vivorequires formation of a complex with a C8-tetraspanin protein, with different ADAM10-C8-tetraspanin complexes having distinct substrate selectivity, yet the basis for such selectivity remains elusive. We present here a cryo-EM structure of a vFab-ADAM10-Tspan15 complex, which shows that Tspan15 binding relieves ADAM10 autoinhibition and positions the enzyme active site about 20 Å from the plasma membrane for membrane-proximal substrate cleavage. Cell-based assays of N-cadherin shedding establish that the positioning of the active site by the interface between the ADAM10 catalytic domain and the bound tetraspanin influences selection of the preferred cleavage site. Together, these studies reveal the molecular mechanism underlying selective ADAM10 proteolysis at membrane-proximal sites and offer a roadmap for its modulation in disease.
Antibody avidity and multi-specificity combined to confer protection against SARS-CoV-2 and resilience against viral escape
Authors: Aschner Clare Burn , Muthuraman Krithika , Kucharska Iga , Cui Hong , Prieto Katherine , Nair Manoj S. , Wang Maple , Huang Yaoxing , Christie-Holmes Natasha , Poon Betty , Lam Jessica , Sultana Azmiri , Kozak Robert , Mubareka Samira , Rubinstein John L. , Rujas Edurne , Treanor Bebhinn , Ho David D. , Jetha Arif , Julien Jean-Philippe
Published: October 2022

SARS-CoV-2, the causative agent of COVID-19, has been responsible for a global pandemic. Monoclonal antibodies have been used as antiviral therapeutics, but have been limited in efficacy by viral sequence variability in emerging variants of concern (VOCs), and in deployment by the need for high doses. In this study, we leverage the MULTI-specific, multi-Affinity antiBODY (Multabody, MB) platform, derived from the human apoferritin protomer, to drive the multimerization of antibody fragments and generate exceptionally potent and broad SARS-CoV-2 neutralizers. CryoEM revealed a high degree of homogeneity for the core of these engineered antibody-like molecules at 2.1 Å resolution. We demonstrate that neutralization potency improvements of the MB over corresponding IgGs translates into superiorin vivoprotection: in the SARS-CoV-2 mouse challenge model, comparablein vivoprotection was achieved for the MB delivered at 30x lower dose compared to the corresponding IgGs. Furthermore, we show how MBs potently neutralize SARS-CoV-2 VOCs by leveraging augmented avidity, even when corresponding IgGs lose their ability to neutralize potently. Multiple mAb specificities could also be combined into a single MB molecule to expand the neutralization breadth beyond SARS-CoV-2 to other sarbecoviruses. Our work demonstrates how avidity and multi-specificity combined can be leveraged to confer protection and resilience against viral diversity that exceeds that of traditional monoclonal antibody therapies.
Therapy Induced Tumor Senescence Model
Authors: Singh Ghanendra
Published: October 2022

Senescent cell accumulation and defective clearance of the senescent cells by the immune system occur with aging and increase the prevalence of diseases like cancer. Anti-tumor therapies can induce senescence in the tumor cells. Senescence Associated Secretory Phenotypes (SASP) secretion by these senescent tumor cells activates the innate NK cells which can detect and eliminate them. Mechanisms are unclear about how does it occur? A combination of immunotherapy and senotherapy has shown the possibility to reduce the tumor burden and increase the health span. The temporal and intensity dynamics of the therapeutic dose regimen remains to be studied. Therefore, a simplified therapy-induced senescence (TIS) phenomenological model is proposed to explain the mechanism of senescent tumor cell clearance by the NK immune cells and understand the possibility of a two-punch therapy technique in regulating tumors. Interaction strength changes for the cellular population within a healthy and an aged tumor microenvironment. The simulation result shows an oscillatory behavior existing between the tumor and immune cells. Tumor heterogeneity acts as inherent noise in sustaining the tumor for relapse emergence despite therapeutic clearance. The model indicates the formation of a robust oscillatory loop between the tumor, immune, and senescence cells which they can tune by modifying the phenotypic fitness landscape through secreted factors making them resistant despite selective removal of the sensitive populations by various therapies. The model highlights the importance of modified and aged tumor microenvironment by senescence tumor cells in obstructing clearance of both senescence and tumor cells by the innate immune system. Cancer therapies along with senolytics may have a robust and effective regulatory potential over tumor and senescence cells. The model also provides a preliminary analysis of the therapy temporal and intensity dosage regimen causing a therapeutic shift in tumors.
Transforming growth factor-β promotes the postselection thymic development and peripheral function of interferon-γ-producing invariant natural killer T cells
Authors: Morgan Roxroy C. , Frank Cameron , Greger Munmun , Sigvardsson Mikael , Bartom Elizabeth T. , Kee Barbara L.
Published: October 2022

Interferon-γ producing invariant natural killer T (iNKT1) cells are lipid reactive innate-like lymphocytes that are resident in the thymus and peripheral tissues where they protect against pathogenic infection. The thymic functions of iNKT1 cells are not fully elucidated but subsets of thymic iNKT cells modulate CD8 T cell, dendritic cell, B cell and thymic epithelial cell numbers or function. Here we show that a subset of thymic iNKT1 cells require transforming growth factor (TGF)-β induced signals for their development and for expression of residency associated adhesion receptors. Liver and spleen iNKT1 cells do not share this TGF-β gene signature but nonetheless TGF-β is required for optimal liver iNKT1 cell function. Our findings provide insight into the heterogeneity of mechanisms guiding iNKT1 cell development in different tissues and suggest a close association between a subset of iNKT1 cells and TGF-β producing cells in the thymus.
Patterns of chemotherapy use and outcomes in advanced non-small-cell lung cancer in relation to age in England: A retrospective analysis of the population-based Systemic Anti-Cancer Treatment (SACT) dataset
Authors: Pilleron S. , Morris EJA. , Dodwell D. , Franks K.N.
Published: October 2022

Objective

We described the patterns of chemotherapy use and outcomes in patients diagnosed with stage III or IV non-small cell lung cancer (NSCLC) in England.

Method

In this retrospective population-based study, we included 20,716 (62% stage IV) patients with NSCLC diagnosed in 2014-17 treated with chemotherapy. We used the Systemic Anti-Cancer Treatment (SACT) dataset to describe changes in treatment plan and estimated 30 and 90-day mortality rates and median, 6- and 12-month overall survival (OS) using Kaplan Meier estimator for patients aged <75 and ≥ 75 by stage. Using flexible hazard regression models we assessed the impact of age, stage, treatment intent (stage III) and performance status on survival.

Results

Patients aged ≥ 75 years were less likely to receive 2 or more regimens, more likely to have their treatment modified because of comorbidities and their doses reduced compared to younger patients. However, early mortality rates and overall survival were similar across ages, apart from the oldest patients with stage III disease.

Conclusion

This observational study demonstrates that age is associated with treatment choices in an older population with advanced NSCLC in England. Although this reflecting a pre-immunotherapy period, given the median age of NSCLC patients and increasingly older population, these results suggest older patients (>75yrs) may need additional support to access more intense treatments that may influence overall survival.
Epigenetic and transcriptomic reprogramming in monocytes of severe COVID-19 patients reflects alterations in myeloid differentiation and the influence of inflammatory cytokines
Authors: Godoy-Tena Gerard , Barmada Anis , Morante-Palacios Octavio , de la Calle-Fabregat Carlos , Martins-Ferreira Ricardo , Ferreté-Bonastre Anna G. , Ciudad Laura , Ruiz-Sanmartín Adolfo , Martínez-Gallo Mónica , Ferrer Ricard , Ruiz-Rodriguez Juan Carlos , Rodríguez-Ubreva Javier , Vento-Tormo Roser , Ballestar Esteban
Published: October 2022

COVID-19 manifests with a wide spectrum of clinical phenotypes, ranging from asymptomatic and mild to severe and critical. Severe and critical COVID-19 patients are characterized by marked changes in the myeloid compartment, especially monocytes. However, little is known about the epigenetic alterations that occur in these cells during hyperinflammatory responses in severe COVID-19 patients. In this study, we obtained the DNA methylome and transcriptome of peripheral blood monocytes from severe COVID-19 patients. DNA samples extracted from CD14+CD15-monocytes of 48 severe COVID-19 patients and 11 healthy controls were hybridized on MethylationEPIC BeadChip arrays. In parallel, single-cell transcriptomics of 10 severe COVID-19 patients were generated. CellPhoneDB was used to infer changes in the crosstalk between monocytes and other immune cell types. We observed DNA methylation changes in CpG sites associated with interferon-related genes and genes associated with antigen presentation, concordant with gene expression changes. These changes significantly overlapped with those occurring in bacterial sepsis, although specific DNA methylation alterations in genes specific to viral infection were also identified. We also found these alterations to comprise some of the DNA methylation changes occurring during myeloid differentiation and under the influence of inflammatory cytokines. A progression of DNA methylation alterations in relation to the Sequential Organ Failure Assessment (SOFA) score was found to be related to interferon-related genes and T-helper 1 cell cytokine production. CellPhoneDB analysis of the single-cell transcriptomes of other immune cell types suggested the existence of altered crosstalk between monocytes and other cell types like NK cells and regulatory T cells. Our findings show the occurrence of an epigenetic and transcriptional reprogramming of peripheral blood monocytes, which could be associated with the release of aberrant immature monocytes, increased systemic levels of pro-inflammatory cytokines, and changes in immune cell crosstalk in these patients.
Peptides that Mimic RS repeats modulate phase separation of SRSF1, revealing a reliance on combined stacking and electrostatic interactions
Authors: Fargason Talia , De Silva Naiduwadura Ivon Upekala , King Erin , Zhang Zihan , Paul Trenton , Shariq Jamal , Zaharias Steve , Zhang Jun
Published: October 2022

Phase separation plays crucial roles in both sustaining cellular function and perpetuating disease states. Despite extensive studies, our understanding of this process is hindered by low solubility of phase-separating proteins. One example of this is found in SR proteins. These proteins are characterized by domains rich in arginine and serine (RS domains), which are essential to alternative splicing,in vivophase separation, and a low solubility that has made these proteins difficult to study for decades. Here, we solubilize the founding member of the SR family, SRSF1, by introducing a peptide mimicking RS repeats as a co-solute. We find that this RS-mimic peptide forms interactions similar to those of the protein’s RS domain. Both interact with a combination of surface-exposed aromatic residues and acidic residues on SRSF1’s RNA Recognition Motifs (RRMs) through electrostatic and cation-pi interactions. Analysis of RRM domains spanning the human proteome indicates that RRM domains involved in phase separation have more exposed aromatic residues and that in phase-separating proteins containing RS repeats, such residues are frequently surrounded by acidic residues. In addition to opening an avenue to previously unavailable proteins, our work provides insight into how SR proteins phase separate and participate in nuclear speckles.
A Compartmentalized Model to Directional Sensing: How can an Amoeboid Cell Unify Pointwise External Signals as an Integrated Entity?
Authors: Eidi Zahra , Sadeghi Mehdi
Published: October 2022

After being exposed to an external chemical attractant, several internal cellular downstream signal transduction pathways control the chemotactic machinery of eukaryotes. The spatial activation of these pathways ultimately leads to some sort of symmetry breaking around the cell periphery in the form of redistribution of several biochemicals,e.g., polymerized actin at one side of the cell for propulsion and the assembly of myosin II at nearly opposite side for retraction. In this study, we revisit the modeling of this process, which is called directional sensing, with a compartment-based design. In our model, we consider a network of excitable elements around cell circumference which are stimulated occasionally with local colored noise. The exciting elements are capable of sharing information with their close neighbors. We show that the dynamic can distinguish a temporary but enough long-lasting direction, statistically, pointing towards the gradient of external stimulants that can be deemed as the preferred orientation of the cell periphery during the directional sensing process in eukaryotes.
Allelic diversity uncovers protein domains contributing to the emergence of antimicrobial resistance
Authors: Grant Trudy-Ann , López-Pérez Mario , Almagro-Moreno Salvador
Published: October 2022

Antimicrobial resistance (AMR) remains a major threat to global health. To date, tractable approaches that decipher how AMR emerges within a bacterial population remain limited. Here, we developed a framework that exploits genetic diversity from environmental bacterial populations to decode emergent phenotypes such as AMR. OmpU, is a porin that makes up to 60% of the outer membrane ofVibrio cholerae, the cholera pathogen. This porin is directly associated with the emergence of the bacterium and confers resistance to numerous host antimicrobials. In this study, we examined naturally occurring allelic variants of OmpU in environmentalV. choleraeand established associations that connected genotypic variation with phenotypic outcome. We covered the landscape of gene variability and found that the porin forms two major phylogenetic clusters with striking genetic diversity. We generated 14 isogenic mutant strains, each encoding a uniqueompUallele, and found that divergent genotypes lead to convergent antimicrobial resistance profiles. We identified and characterized functional domains in OmpU unique to variants conferring AMR-associated phenotypes. Specifically, we identified four conserved domains that are linked with resistance to bile and host-derived antimicrobial peptides. Mutant strains for these domains exhibit differential susceptibility patterns to these and other antimicrobials. Interestingly, a mutant strain in which we exchanged the four domains of the clinical allele for those of a sensitive strain exhibits a resistance profile closer to a porin deletion mutant. Finally, using phenotypic microarrays, we uncovered novel functions of OmpU and their connection with allelic variability. Our findings highlight the suitability of our approach towards dissecting the specific protein domains associated with the emergence of AMR and can be naturally extended to other bacterial pathogens and biological processes.

AUTHOR SUMMARY

Antimicrobial resistance (AMR) is one of the major threats to global health. To date, tractable approaches that decipher how AMR emerges within a bacterial population remain limited. Here we developed an approach that uses genetic diversity from environmental populations to decode emergent phenotypes such as AMR. Specifically, we examined naturally occurring allelic variants of an outer membrane porin, OmpU, inVibrio choleraeand established associations between genotype and phenotype. Using this approach, we identified and characterized the functional domains in OmpU unique to variants conferring AMR-associated phenotypes. Our perspective towards disentangling the emergence of AMR can be naturally extended to other proteins and bacterial pathogens.
Deletion of the ion channelTrpm4increases cardiac inflammatory markers and fibrosis after myocardial infarction in mice
Authors: Boukenna Mey , Rougier Jean-Sébastien , Aghagolzadeh Parisa , Pradervand Sylvain , Guichard Sabrina , Hämmerli Anne-Flore , Pedrazzini Thierry , Abriel Hugues
Published: October 2022

BACKGROUND

The first cause of mortality worldwide is ischemic heart disease. In myocardial infarction (MI), the ischemic event causes cell death, which triggers a large inflammatory response responsible for removing necrotic material and inducing tissue repair. Endothelial cells, immune cells and fibroblasts play a key role in orchestrating this healing process. TRPM4 is a Ca2+-activated ion channel permeable to monovalent cations and its silencing or knocking out was shown to critically modify cellular functions of these non-myocytic cell types.

OBJECTIVE

Our aims were to 1) evaluate the role of TRPM4 on mice survival and cardiac function after MI; and 2) investigate the role of TRPM4 in the post-MI acute and chronic inflammatory response.

METHODS

We performed ligation of the left anterior descending coronary artery or sham intervention on 154Trpm4WT or KO male mice and monitored survival for up to 5 weeks as well as cardiac function using echocardiography at 72h and five weeks. We drew blood at different acute time points (6h, 12h, 24h) and performed time-of-flight mass spectrometry to analyze the sera proteomes. Further, we sacrificed sub-groups of mice at 24h and 72h after surgery and performed single-cell RNA sequencing on the non-myocytic cells. Lastly, we assessed fibrosis and angiogenesis at five weeks using type I collagen and CD31 immunostaining respectively.

RESULTS

We observed no significant differences in survival or cardiac function post-MI between both genotypes. However, our serum proteomics data showed significantly decreased tissue injury markers such as creatine kinase M and VE-Cadherin in KO compared to WT 12h after MI. On the other hand, inflammation characterized by serum amyloid P component in the serum, as well as higher number of recruited granulocytes, M1 macrophages, M1 monocytes, Mac-6 macrophages, and expression of pro-inflammatory genes such asIl1b, Lyz2andS100a8/a9was significantly higher in endothelial cells, macrophages and fibroblasts of KO than of WT. This correlated with increased cardiac fibrosis and angiogenesis 5 weeks after MI in KO.

CONCLUSION

Our data suggest that knocking outTrpm4drastically increases acute inflammation post-MI, is associated with increased chronic fibrosis and does not improve survival at 5 weeks post-MI. Thus, targeting TRPM4 in the context of MI should be pondered carefully and approaches that nuance the timing of the inhibition or cellular target may be required.
Knockout of ribosomal protein RpmJ leads to zinc resistance inEscherichia coli
Authors: Shirakawa Riko , Ishikawa Kazuya , Furuta Kazuyuki , Kaito Chikara
Published: October 2022

Zinc is an essential metal for cells, but excess amounts are toxic. Other than by regulating the intracellular zinc concentration by zinc uptake or efflux, the mechanisms underlying bacterial resistance to excess zinc are unknown. In the present study, we searched for zinc-resistant mutant strains from the Keio collection, a gene knockout library ofEscherichia coli, a model gram-negative bacteria. We found that knockout mutant of RpmJ, a 50S ribosomal protein, exhibited zinc resistance. TherpmJmutant was sensitive to protein synthesis inhibitors and had altered translation fidelity, indicating ribosomal dysfunction. In therpmJmutant, the intracellular zinc concentration was decreased under excess zinc conditions. RNA sequence analysis revealed thatrpmJknockout decreased the expression of synthetic genes for iron-sulfur cluster proteins, which are toxic targets for zinc. These findings suggest that knocking out RpmJ causes zinc resistance by decreasing zinc targets and lowering the intracellular zinc concentration. Knockouts of other ribosomal proteins, including RplA, RpmE, RpmI, and RpsT, also led to a zinc-resistant phenotype, suggesting that deletion of ribosomal proteins is closely related to zinc resistance.
Quantifying metal ion specificity of the nickel-binding proteinCcNikZ-II fromClostridium carboxidivoransin the presence of competing metal ions
Authors: Diep Patrick , Kell Brayden , Yakunin Alexander , Hilfinger Andreas , Mahadevan Radhakrishnan
Published: October 2022

Many proteins bind transition metal ions as cofactors to carry out their biological functions. Despite binding affinities for divalent transition metal ions being predominantly dictated by the Irving-Williams series for wild-type proteins,in vivometal ion binding specificity is ensured by intracellular mechanisms that regulate free metal ion concentrations. However, a growing area of biotechnology research considers the use of metal-binding proteinsin vitroto purify specific metal ions from wastewater, where specificity is dictated by the protein’s metal binding affinities. A goal of metalloprotein engineering is to modulate these affinities to improve a protein’s specificity towards a particular metal; however, the quantitative relationship between the affinities and the equilibrium metal-bound protein fractions depends on the underlying binding kinetics. Here we demonstrate a high-throughput intrinsic tryptophan fluorescence quenching method to validate kinetic models in multi-metal solutions forCcNikZ-II, a nickel-binding protein fromClostridium carboxidivorans. Using our validated models, we quantify the relationship between binding affinity and specificity in different classes of metal-binding models forCcNikZ-II. We further demonstrate that principles for improving specificity through changes in binding affinity are qualitatively different depending on the competing metals, highlighting the power of mechanistic models to guide metalloprotein engineering targets.
Citrus genomic resources unravel putative genetic determinants of Huanglongbing, a pathogen-triggered immune disease
Authors: Gao Yuxia , Xu Jin , Li Zhilong , Zhang Yunzeng , Riera Nadia , Xiong Zhiwei , Ouyang Zhigang , Liu Xinjun , Lu Zhanjun , Seymour Danelle , Zhong Balian , Wang Nian
Published: October 2022

Citrus is one of the most important tree crops worldwide and citrus production is threatened by Huanglongbing (HLB), a devasting citrus disease caused byCandidatusLiberibacter. HLB is a pathogen-triggered immune disease, in which the pathogen initiates systemic and chronic immune responses including the excessive production of reactive oxidative species, which subsequently lead to cell death of phloem tissues and HLB disease symptoms. Here, we identified putative genetic determinants of HLB pathogenicity by integrating citrus genomic resources to characterize the pan-genome of accessions that differ in their response to HLB. Genome-wide association mapping and analysis of allele-specific expression between susceptible, tolerant, and resistant accessions further refined candidates underlying the response to HLB. To enable these analyses we first developed a phased diploid assembly ofCitrus sinensis‘Newhall’ genome and produced resequencing data for 91 citrus accessions that differ in their response to HLB. These data were combined with previous resequencing data from 356 sequenced accessions for genome-wide association mapping of the HLB response. Genes with HLB pathogenicity were associated with the host immune response, ROS production, and antioxidants. Overall, this study has provided a significant recourse of citrus genomic data and we have identified candidate genes to be further explored to understand the genetic determinants of HLB pathogenicity and to generate HLB resistant/tolerant citrus varieties.
Metformin attenuates hyperglycaemia-stimulated pro-fibrotic gene expression in vascular adventitial fibroblasts via inhibition of Discoidin Domain Receptor 2
Authors: Titus Allen Sam , Ushakumary Mereena George , Venugopal Harikrishnan , Wang Mingyi , Lakatta Edward G. , Kailasam Shivakumar
Published: October 2022

Molecular mechanisms underlying the diverse therapeutic effects of anti-diabetic metformin, beyond its anti-hyperglycaemic effects, remain largely unclear. Metformin is reported to reduce the long-term complications of diabetes, including cardiovascular fibrosis and remodelling. Our recent investigations show that Discoidin Domain Receptor 2 (DDR2), a collagen receptor tyrosine kinase, has an obligate regulatory role in collagen type I gene expression in cardiac and vascular adventitial fibroblasts, and that it may be a molecular link between arterial fibrosis and metabolic syndrome in rhesus monkeys. Using gene knockdown and over-expression approaches, the present study examined whether DDR2 is a target of metformin, and whether, by targeting DDR2, it inhibits fibronectin and collagen expression in vascular adventitial fibroblasts exposed to hyperglycaemic conditions. Metformin was found to attenuate hyperglycaemia-induced increase in DDR2 mRNA and protein expression by inhibiting TGF-β1/ Smad2/3 signalling that mediates the stimulatory effect of hyperglycaemia on DDR2 expression. Metformin also inhibited DDR2-dependent expression of fibronectin and collagen, indicating that it regulates these matrix proteins via DDR2 inhibition. The findings identify DDR2, a major mediator of cardiovascular remodelling, as a molecular target of metformin, thereby uncovering the molecular basis of its protective role in vascular fibrosis, and possibly, cardiac fibrosis associated with diabetic cardiomyopathy.
Genes associated with depression and coronary artery disease are enriched for inflammation and cardiomyopathy-associated pathways
Authors: Singh Kritika , Lee Hyunjoon , Sealock Julia M , Miller-Flemming Tyne , Straub Peter , Cox Nancy J. , Wells Quinn S. , Smoller Jordan W. , Hodges Emily C. , Davis Lea K.
Published: October 2022

Background

Depression and Coronary Artery Disease (CAD) are highly comorbid conditions. Approximately 40% of individuals who have one diagnosis will also develop the other within their lifetime. Prior research indicates that polygenic risk for depression increases the odds of developing CAD even in the absence of clinical depression. However, the specific genes and pathways involved in comorbid depression-CAD remain unknown.

Results

We identified genes that are significantly associated with both depression and CAD, and are enriched for pathways involved in inflammation and for previous association with cardiomyopathy. We observed increased rate of prevalent, but not incident, cardiomyopathy cases in individuals with comorbid depression-CAD compared to those with CAD alone in three electronic large health record (EHR) datasets.

Conclusions

The results of our study implicate genetically regulated inflammatory mechanisms in depression-CAD. Our results also raise the hypothesis that depression-associated CAD may be enriched for cardiomyopathy.

Clinical Perspective

What’s New?

Gene associations shared between depression and CAD are enriched for prior association with cardiomyopathy phenotypes.

Cardiomyopathy is significantly more prevalent in individuals with comorbid depression-CAD than in CAD or depression alone.

What are the Clinical Implications?

Our work suggests that individuals with comorbid depression-CAD may benefit from screening for cardiomyopathy.
East Asian-specific and cross-ancestry genome-wide meta-analyses provide mechanistic insights into peptic ulcer disease
Authors: He Yunye , Koido Masaru , Sutoh Yoichi , Shi Mingyang , Otsuka-Yamasaki Yayoi , Munter Hans Markus , Morisaki Takayuki , Nagai Akiko , Murakami Yoshinori , Tanikawa Chizu , Hachiya Tsuyoshi , Matsuda Koichi , Shimizu Atsushi , Kamatani Yoichiro
Published: October 2022

Peptic ulcer disease (PUD) refers to acid-induced injury of the digestive tract, occurring mainly in the stomach (gastric ulcer; GU) or duodenum (duodenal ulcer; DU). We conducted a large-scale cross-ancestry meta-analysis of PUD combining genome-wide association studies with four Japanese and two European studies (52,032 cases and 905,344 controls), and discovered 25 novel loci highly concordant across ancestries. Based on these loci, an examination of similarities and differences in genetic architecture between GU and DU demonstrated that GU shared the same risk loci as DU, although with smaller genetic effect sizes and higher polygenicity than DU, indicating higher heterogeneity of GU.H. pylori(HP)-stratified analysis found an HP-related host genetic locus, marking its role in HP-mediated PUD etiology. Integrative analyses using bulk and single-cell transcriptome profiles highlighted the genetic factors of PUD to be enriched in the highly expressed genes in stomach tissues, especially in somatostatin-producing D cells. Our results provide genetic evidence that gastrointestinal cell differentiations and hormone regulations are critical in PUD etiology.