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OSF-Builder: A New Tool for Constructing and Representing Evolutionary Histories Involving Introgression

Introgression is an evolutionary process which provides an important source of innovation for evolution. Although various methods have been used to detect introgression, very few methods are currently available for constructing evolutionary histories involving introgression. In this article, we propose a new method for constructing such evolutionary histories whose starting point is a species forest (consisting of a collection of lineage trees, usually arising as a collection of clades or monophyletic groups in a species tree), and a gene tree for a specific allele of interest, or allele tree for short. Our method is based on representing introgression in terms of a certain "overlay" of the allele tree over the lineage trees, called an overlaid species forest (OSF). OSFs are similar to phylogenetic networks although a key difference is that they typically have multiple roots because each monophyletic group in the species tree has a different point of origin. Employing a new model for introgression, we derive an efficient algorithm for building OSFs called OSF-Builder that is guaranteed to return an optimal OSF in the sense that the number of potential introgression events is minimized. As well as using simulations to assess the performance of OSF-Builder, we illustrate its use on a butterfly data set in which introgression has been previously inferred. The OSF-Builder software is available for download from https://www.uea.ac.uk/computing/software/OSF-Builder.

The population genetics of structural variants in grapevine domestication

Structural variants (SVs) are a largely unexplored feature of plant genomes. Little is known about the type and size of SVs, their distribution among individuals and, especially, their population dynamics. Understanding these dynamics is critical for understanding both the contributions of SVs to phenotypes and the likelihood of identifying them as causal genetic variants in genome-wide associations. Here, we identify SVs and study their evolutionary genomics in clonally propagated grapevine cultivars and their outcrossing wild progenitors. To catalogue SVs, we assembled the highly heterozygous Chardonnay genome, for which one in seven genes is hemizygous based on SVs. Using an integrative comparison between Chardonnay and Cabernet Sauvignon genomes by whole-genome, long-read and short-read alignment, we extended SV detection to population samples. We found that strong purifying selection acts against SVs but particularly against inversion and translocation events. SVs nonetheless accrue as recessive heterozygotes in clonally propagated lineages. They also define outlier regions of genomic divergence between wild and cultivated grapevines, suggesting roles in domestication. Outlier regions include the sex-determination region and the berry colour locus, where independent large, complex inversions have driven convergent phenotypic evolution.

Improving our mechanistic understanding of the indirect effects of CMV infection in transplant recipients

Cytomegalovirus (CMV) is an immunomodulatory virus that indirectly increases the risk for bacterial, fungal, and viral infections. However, the pathogenesis of this phenomenon is poorly understood. We determined whether inflammatory responses to different Toll-like receptor (TLR) ligands are blunted during CMV infection in solid-organ transplant (SOT) patients. Peripheral blood mononuclear cells from 38 SOT patients with and without CMV were incubated in the presence of various viral, fungal, and bacterial TLR ligands. Cytokines were measured in the supernatant by multiplex enzyme-linked immunosorbent assay. Patients had blunted cytokine responses to bacterial, fungal, and viral ligands during CMV infection when compared to the absence of CMV infection. This was independent of viral load, clinical presentation of CMV infection or immunosuppression, supporting the clinical observation in SOT recipients that CMV infection increases susceptibility to bacterial, fungal, and other viral infections. Moreover, in the absence of CMV infection, patients with subsequent CMV infection had lower cytokines in response to TLR ligands compared to those without subsequent CMV infection, suggesting that inherent differences in patients not directly related to CMV also contribute to this increased susceptibility. In summary, these data provide novel ex vivo evidence to support indirect effects of CMV.

Serum cytokine, chemokine, and growth factor profiles and their modulation in inflammatory bowel disease

Ulcerative colitis (UC) and Crohn disease (CD) are the most common forms of inflammatory bowel disease (IBD). Because these subtypes of IBD are characterized by periods of activity and remission, an understanding of the modulation of biochemical markers with the clinical features of IBD or its treatment, may be useful for determining the correct treatment protocol.This study aimed to evaluate the serum levels of 27 protein biomarkers to determine their association with IBD, correlation with clinical findings of disease, and modulation according to the pharmacologic therapy.A case-control study was carried out in Zacatecas, Mexico. The 27 protein profiles of serum from 53 participants (23 UC, 11 CD, and 19 controls) were evaluated using the Pro Human Cytokine 27-Plex immunoassay (Bio-Rad).Considering the controls as a reference, the group with IBD endoscopic activity showed higher serum levels of granulocyte colony-stimulating factor (G-CSF), interleukin 1 receptor antagonist (IL-1Ra), and platelet-derived growth factor BB (PDGF-BB) (P < .05). Interferon-induced protein 10 (IP-10) was associated with extraintestinal symptoms of disease (P = .041). Both PDGF-BB and interleukin 6 (IL-6) showed the strongest correlations with clinical features of IBD. Levels of IL-6, IL-7, and monocyte chemoattractant protein 1 were higher with 5-aminosalicylic acid (5-ASA) + Azathioprine therapy than controls (P < .05). Combined therapy with 5-ASA + Adalimumab led to the strongest changes in marker modulation: IL-4, IL-5, IL-15, and PDGF-BB, were upregulated (P < .05).Elevated serum levels of G-CSF, IL-1Ra, and PDGF-BB were associated with IBD endoscopic activity, and of IP-10 with extraintestinal manifestations of IBD. Combined therapy of 5-ASA + Adalimumab produced significant upregulation of IL-4, IL-5, IL-15, and PDGF-BB. This information may be useful for deciding on the course of pharmacologic therapy for patients with IBD and for generating new therapy alternatives to improve the outcome of patients with IBD.

Differential Impact of Subtherapeutic Antibiotics and Ionophores on Intestinal Microbiota of Broilers

Antimicrobial growth promoters (AGPs) are commonly used in the livestock industry at subtherapeutic levels to improve production efficiency, which is achieved mainly through modulation of the intestinal microbiota. However, how different classes of AGPs, particularly ionophores, regulate the gut microbiota remains unclear. In this study, male Cobb broiler chickens were supplemented for 14 days with or without one of five commonly used AGPs including three classical antibiotics (bacitracin methylene disalicylate, tylosin, and virginiamycin) and two ionophores (monensin and salinomycin) that differ in antimicrobial spectrum and mechanisms. Deep sequencing of the V3-V4 region of the bacterial 16S rRNA gene revealed that two ionophores drastically reduced a number of rare bacteria resulting in a significant decrease in richness and a concomitant increase in evenness of the cecal microbiota, whereas three antibiotics had no obvious impact. Although each AGP modulated the gut microbiota differently, the closer the antibacterial spectrum of AGPs, the more similarly the microbiota was regulated. Importantly, all AGPs had a strong tendency to enrich butyrate- and lactic acid-producing bacteria, while reducing bile salt hydrolase-producing bacteria, suggestive of enhanced metabolism and utilization of dietary carbohydrates and lipids and improved energy harvest, which may collectively be responsible for the growth-promoting effect of AGPs.

Two bifunctional inositol pyrophosphate kinases/phosphatases control plant phosphate homeostasis

Many eukaryotic proteins regulating phosphate (Pi) homeostasis contain SPX domains that are receptors for inositol pyrophosphates (PP-InsP), suggesting that PP-InsPs may regulate Pi homeostasis. Here we report that deletion of two diphosphoinositol pentakisphosphate kinases VIH1/2 impairs plant growth and leads to constitutive Pi starvation responses. Deletion of phosphate starvation response transcription factors partially rescues vih1 vih2 mutant phenotypes, placing diphosphoinositol pentakisphosphate kinases in plant Pi signal transduction cascades. VIH1/2 are bifunctional enzymes able to generate and break-down PP-InsPs. Mutations in the kinase active site lead to increased Pi levels and constitutive Pi starvation responses. ATP levels change significantly in different Pi growth conditions. ATP-Mg2+ concentrations shift the relative kinase and phosphatase activities of diphosphoinositol pentakisphosphate kinases in vitro. Pi inhibits the phosphatase activity of the enzyme. Thus, VIH1 and VIH2 relay changes in cellular ATP and Pi concentrations to changes in PP-InsP levels, allowing plants to maintain sufficient Pi levels.

Composition of bacterial and archaeal communities in the rumen of dromedary camel using cDNA-amplicon sequencing

The camel is known to survive in harsh environmental conditions, due to its higher digestive efficiency of high-fiber diets compared with other ruminants. However, limited data are available on the microbial community in the rumen of a camel. In this study, the Illumina sequencing of V4 region of 16S rRNA genes based on RNA isolation was employed to get insight into the bacterial and archaeal communities associated with liquid and solid rumen fractions in eight camels under different feeding systems. Camels in group C1 were fed Egyptian clover hay plus concentrates mixture and camels of group C2 were fed fresh Egyptian clover. The results showed that liquid fraction has higher operational taxonomic units (OTUs) than solid fraction, and camel group C1 showed a higher microbial diversity than C2. The UniFrac analysis indicated that the microbial communities in camel groups are distinct. Moreover, phylum Firmicutes and Bacteroidetes dominated the bacterial community and Candidatus Methanomethylophilus dominated the archaeal community with a significant difference in the relative abundance between camel groups. Dominant bacterial genera were Prevotella, Fibrobacteres, Ruminococcus, and Butyrivibrio. There were many negative and positive correlations between and within bacterial and archaeal genera. The composition of microbial community in the rumen of a camel is similar to other ruminants with differences in the abundance.

Rhodanese domain-containing sulfurtransferases: multifaceted proteins involved in sulfur trafficking in plants

Sulfur is an essential element for the growth and development of plants, which synthesize cysteine and methionine from the reductive assimilation of sulfate. Besides its incorporation into proteins, cysteine is the building block for the biosynthesis of numerous sulfur-containing molecules and cofactors. The required sulfur atoms are extracted either directly from cysteine by cysteine desulfurases or indirectly after its catabolic transformation to 3-mercaptopyruvate, a substrate for sulfurtransferases (STRs). Both enzymes are transiently persulfidated in their reaction cycle, i.e. the abstracted sulfur atom is bound to a reactive cysteine residue in the form of a persulfide group. Trans-persulfidation reactions occur when sulfur atoms are transferred to nucleophilic acceptors such as glutathione, proteins, or small metabolites. STRs form a ubiquitous, multigenic protein family. They are characterized by the presence of at least one rhodanese homology domain (Rhd), which usually contains the catalytic, persulfidated cysteine. In this review, we focus on Arabidopsis STRs, presenting the sequence characteristics of all family members as well as their biochemical and structural features. The physiological functions of particular STRs in the biosynthesis of molybdenum cofactor, thio-modification of cytosolic tRNAs, arsenate tolerance, cysteine catabolism, and hydrogen sulfide formation are also discussed.

Characterization of novel small RNAs (sRNAs) contributing to the desiccation response of Salmonella enterica serovar Typhimurium

Noncoding RNA (ncRNA) modulation of gene expression has now been ubiquitously observed across all domains of life. An increasingly apparent role of ncRNAs is to coordinate changes in gene expressions in response to environmental stress. Salmonella enterica, a common food-born pathogen, is known for its striking ability to survive, adapt, and thrive in various unfavourable environments which makes it a particularly difficult pathogen to eliminate as well as an interesting model in which to study ncRNA contributions to cellular stress response. Mounting evidence now suggests that small RNAs (sRNAs) represent key regulators of Salmonella stress adaptation. Approximately 50-500 nucleotides in length, sRNAs regulate gene expression through complementary base pairing with molecular targets and have recently been suggested to outnumber protein-coding genes in bacteria. In this work, we employ small RNA transcriptome sequencing to characterize changes in the sRNA profiles of Salmonella in response to desiccation. In all, we identify 102 previously annotated sRNAs significantly differentially expressed during desiccation; and excitingly, 71 novel sRNAs likewise differentially expressed. Small transcript northern blotting and qRT-PCRs confirm the identities and expressions of several of our novel sRNAs, and computational analyses indicate the majority are highly conserved and structurally related to characterized sRNAs. Predicted sRNA targets include several proteins necessary for desiccation survival and this, in part, suggests a role for desiccation-regulated sRNAs in this stress response. Furthermore, we find individual knock-outs of two of the novel sRNAs identified herein, either sRNA1320429 or sRNA3981754, significantly impairs the ability of Salmonella to survive desiccation, confirming their involvements (and suggesting the potential involvements of other sRNAs we identify in this work) in the Salmonella response to desiccation.

The Small RNA Repertoire of Small Extracellular Vesicles Isolated From Donor Kidney Preservation Fluid Provides a Source for Biomarker Discovery for Organ Quality and Posttransplantation Graft Function

Supplemental Digital Content is available in the text.

Delayed graft function (DGF) after kidney transplantation is negatively associated with long-term graft function and survival. Kidney function after transplantation depends on multiple factors, both donor- and recipient-associated. Prediction of posttransplantation graft function would allow timely intervention to optimize patient care and survival. Currently, graft-based predictions can be made based on histological and molecular analyses of 0-hour biopsy samples. However, such analyses are currently not implemented, as biopsy samples represent only a very small portion of the entire graft and are not routinely analyzed in all transplantation centers. Alternatives are thus required.

Secondary crest myofibroblast PDGFRα controls the elastogenesis pathway via a secondary tier of signaling networks during alveologenesis

Postnatal alveolar formation is the most important and the least understood phase of lung development. Alveolar pathologies are prominent in neonatal and adult lung diseases. The mechanisms of alveologenesis remain largely unknown. We inactivated Pdgfra postnatally in secondary crest myofibroblasts (SCMF), a subpopulation of lung mesenchymal cells. Lack of Pdgfra arrested alveologenesis akin to bronchopulmonary dysplasia (BPD), a neonatal chronic lung disease. The transcriptome of mutant SCMF revealed 1808 altered genes encoding transcription factors, signaling and extracellular matrix molecules. Elastin mRNA was reduced, and its distribution was abnormal. Absence of Pdgfra disrupted expression of elastogenic genes, including members of the Lox, Fbn and Fbln families. Expression of EGF family members increased when Tgfb1 was repressed in mouse. Similar, but not identical, results were found in human BPD lung samples. In vitro, blocking PDGF signaling decreased elastogenic gene expression associated with increased Egf and decreased Tgfb family mRNAs. The effect was reversible by inhibiting EGF or activating TGFβ signaling. These observations demonstrate the previously unappreciated postnatal role of PDGFA/PDGFRα in controlling elastogenic gene expression via a secondary tier of signaling networks composed of EGF and TGFβ.

Vasculogenic mimicry is associated with trastuzumab resistance of HER2-positive breast cancer

Background

Trastuzumab is a drug that targets the receptor tyrosine kinase HER2 and is essential for the treatment of HER2-positive breast cancer. Resistance to the drug leads to severe consequences, including disease recurrence, tumor enlargement, and metastasis. We hypothesized that trastuzumab treatment might be associated with phenotypic switching in HER2-positive breast cancer cells (BCCs), enabling them to escape and survive the effect of trastuzumab.

Methods

We conducted comprehensive immunophenotyping to detect phenotypic changes in HER2-positive BCCs treated with trastuzumab, based on criteria determined a priori. Based on immunophenotyping results, we characterized the vascular phenotypes of HER2-positive BCCs by western blotting, real-time RT-PCR, and tube formation assay. The vascular phenotype of tumor cells from clinical samples was evaluated by staining with periodic acid-Schiff and an anti-CD31 antibody. We explored small molecule inhibitors that suppress tube formation and determined the inhibitory mechanism.

Results

Out of 242 cell surface antigens, 9 antigens were significantly upregulated and 3 were significantly downregulated by trastuzumab treatment. All upregulated antigens were related to endothelial and stem cell phenotypes, suggesting that trastuzumab treatment might be correlated to switching to a vascular phenotype, namely, vasculogenic mimicry (VM). Several VM markers were upregulated in trastuzumab-treated cells, but these cells did not form tubes on Matrigel, a functional hallmark of VM. Upon analysis of three trastuzumab-resistant HER2-positive cell lines, we found that all three cell lines showed tube formation on Matrigel in the presence of angiogenic growth factors including EGF, FGF2, IGF1, or VEGF. Clinically, VM channels significantly increased in surviving cancer cell clusters of surgically removed tumors pretreated with trastuzumab and chemotherapy compared to both surgically removed tumors without prior systemic treatment and tumors biopsied before presurgical treatment with trastuzumab. Finally, we found that salinomycin completely suppressed VM in all three trastuzumab-resistant cell lines through disruption of actin cytoskeletal integrity.

Conclusions

VM promotes metastasis and worsens patient outcomes. The present study indicates that HER2-positive BCCs can exhibit VM in an angiogenic microenvironment after eventually acquiring trastuzumab resistance. The clinical finding supports this in vitro observation. Thus, targeting VM might provide a therapeutic benefit to patients with HER2-positive breast cancer.

Electronic supplementary material

The online version of this article (10.1186/s13058-019-1167-3) contains supplementary material, which is available to authorized users.

HNF4 factors control chromatin accessibility and are redundantly required for maturation of the fetal intestine

As embryos mature, cells undergo remarkable transitions that are accompanied by shifts in transcription factor regulatory networks. Mechanisms driving developmental transitions are incompletely understood. The embryonic intestine transitions from a rapidly proliferating tube with pseudostratified epithelium prior to murine embryonic day (E) 14.5 to an exquisitely folded columnar epithelium in fetal stages. We sought to identify factors driving mouse fetal intestinal maturation by mining chromatin accessibility data for transcription factor motifs. ATAC-seq accessible regions shift during tissue maturation, with CDX2 transcription factor motifs abundant at chromatin-accessible regions of the embryo. Hepatocyte nuclear factor 4 (HNF4) transcription factor motifs are the most abundant in the fetal stages (>E16.5). Genetic inactivation of Hnf4a and its paralog Hnf4g revealed that HNF4 factors are redundantly required for fetal maturation. CDX2 binds to and activates Hnf4 gene loci to elevate HNF4 expression at fetal stages. HNF4 and CDX2 transcription factors then occupy shared genomic regulatory sites to promote chromatin accessibility and gene expression in the maturing intestine. Thus, HNF4 paralogs are key components of an intestinal transcription factor network shift during the embryonic to fetal transition.

Diverse picornaviruses are prevalent among free-living and laboratory rats (Rattus norvegicus) in Hungary and can cause disseminated infections

In this study, the full length genomes of three phylogenetically distant picornaviruses (family Picornaviridae) belonging to the genus Rosavirus (rat08/rRoB/HUN, MN116648), Kobuvirus (rat08/rAiA/HUN, MN116647), and Cardiovirus (rat08/rCaB/HUN, MN116646) were obtained from a single faecal sample of a free-living Norway rat (Rattus norvegicus) in Hungary using viral metagenomics and RT-PCR/Sanger sequencing. The acquired complete genomes were in silico analyzed in detail revealing the presence of a second minor open reading frame encoding an alternative Leader peptide (L*) in rat08/rCaB/HUN and a ca. 222 nt-long sequence repeat with compact secondary RNA structure in the 3' UTR of rat08/rRoB/HUN. The studied rat picornaviruses were frequently detectable by RT-PCR with relatively high viral loads ranged between 8.99E+02 and 1.29E+06 copies/ml in rat faecal samples collected from five geographically distant locations throughout Hungary. The VP1 sequence-based phylogenetic analyses show the presence of multiple, mostly location-specific lineages for all three picornaviruses. Rat rosavirus and rat cardiovirus were identified in spleen while rat cardiovirus was also detected in liver, muscle and kidney samples with variable copy numbers (6.42E+01-1.90E+05 copies/μg total RNA) suggesting extra-intestinal dissemination. Both viruses were also prevalent (70.0% and 18.2%) among two populations of laboratory rats ("Wistar-type" and "hooded-type") held in different, isolated laboratory animal units.

Essential role of GEXP15, a specific Protein Phosphatase type 1 partner, in Plasmodium berghei in asexual erythrocytic proliferation and transmission

The essential and distinct functions of Protein Phosphatase type 1 (PP1) catalytic subunit in eukaryotes are exclusively achieved through its interaction with a myriad of regulatory partners. In this work, we report the molecular and functional characterization of Gametocyte EXported Protein 15 (GEXP15), a Plasmodium specific protein, as a regulator of PP1. In vitro interaction studies demonstrated that GEXP15 physically interacts with PP1 through the RVxF binding motif in P. berghei. Functional assays showed that GEXP15 was able to increase PP1 activity and the mutation of the RVxF motif completely abolished this regulation. Immunoprecipitation assays of tagged GEXP15 or PP1 in P. berghei followed by immunoblot or mass spectrometry analyses confirmed their interaction and showed that they are present both in schizont and gametocyte stages in shared protein complexes involved in the spliceosome and proteasome pathways and known to play essential role in parasite development. Phenotypic analysis of viable GEXP15 deficient P. berghei blood parasites showed that they were unable to develop lethal infection in BALB/c mice or to establish experimental cerebral malaria in C57BL/6 mice. Further, although deficient parasites produced gametocytes they did not produce any oocysts/sporozoites indicating a high fitness cost in the mosquito. Global proteomic and phosphoproteomic analyses of GEXP15 deficient schizonts revealed a profound defect with a significant decrease in the abundance and an impact on phosphorylation status of proteins involved in regulation of gene expression or invasion. Moreover, depletion of GEXP15 seemed to impact mainly the abundance of some specific proteins of female gametocytes. Our study provides the first insight into the contribution of a PP1 regulator to Plasmodium virulence and suggests that GEXP15 affects both the asexual and sexual life cycle.

In the absence of an effective vaccine and the emerging resistance to artemisinin combination therapy, malaria is still a significant threat to human health. Increasing our understanding of the specific mechanisms of the biology of Plasmodium is essential to propose new strategies to control this infection. Here, we demonstrated that GEXP15, a specific protein in Plasmodium, was able to interact with the Protein Phosphatase 1 and regulate its activity. We showed that both proteins are implicated in common protein complexes involved in the mRNA splicing and proteasome pathways. We reported that the deletion of GEXP15 leads to a loss of parasite virulence during asexual stages and a total abolishment of the capacity of deficient parasites to develop in the mosquito. We also found that this deletion affects both protein phosphorylation status and significantly decreases the expression of essential proteins in schizont and gametocyte stages. This study characterizes for the first time a novel molecular pathway through the control of PP1 by an essential and specific Plasmodium regulator, which may contribute to the discovery of new therapeutic targets to control malaria.

Phylotypic Characterization of Mycobionts and Photobionts of Rock Tripe Lichen in East Antarctica

Saxicolous rock ripe lichens that grow on rocks in the East Antarctic fellfields were sampled for phylotypic characterization of its constituent mycobionts (fungi) and photobionts (algae and cyanobacteria). The rock tripe lichen-forming fungal and algal phylotypes were classified under the common lichen-forming genera of ascomycetes, namely, Umbilicaria, and green algae, namely, Trebouxia and Coccomyxa. However, phylotypes of the green algal chloroplasts and the lichen-associated cyanobacteria showed unexpectedly high diversity. The detected chloroplast phylotypes were not fully affiliated with the green algal genera Trebouxia or Coccomyxa. The predominant chloroplast phylotype demonstrated maximum resemblance to Neglectella solitaria, which is neither a known Antarctic species nor a typical lichen photobiont. Another dominant chloroplast phylotype belonged to the atypical Antarctic green algae family. Cyanobacterial phylotypes were dominated by those affiliated with the Microcoleus species rather than the well-known lichen-associates, Nostoc species. The occurrences of these Microcoleus-affiliated cyanobacterial phylotypes were specifically abundant within the Yukidori Valley site, one of the Antarctic Specially Protected Areas (ASPA). The ASPA site, along with another 50 km-distant site, yielded most of the cryptic diversity in the phylotypes of chloroplasts and cyanobacteria, which may contribute to the phenotypic variability within the rock tripe lichen photobionts.

Clostridioides difficile LuxS mediates inter-bacterial interactions within biofilms

The anaerobic gut pathogen, Clostridioides difficile, forms adherent biofilms that may play an important role in recurrent C. difficile infections. The mechanisms underlying C. difficile community formation and inter-bacterial interactions are nevertheless poorly understood. C. difficile produces AI-2, a quorum sensing molecule that modulates biofilm formation across many bacterial species. We found that a strain defective in LuxS, the enzyme that mediates AI-2 production, is defective in biofilm development in vitro. Transcriptomic analyses of biofilms formed by wild type (WT) and luxS mutant (luxS) strains revealed a downregulation of prophage loci in the luxS mutant biofilms compared to the WT. Detection of phages and eDNA within biofilms may suggest that DNA release by phage-mediated cell lysis contributes to C. difficile biofilm formation. In order to understand if LuxS mediates C. difficile crosstalk with other gut species, C. difficile interactions with a common gut bacterium, Bacteroides fragilis, were studied. We demonstrate that C. difficile growth is significantly reduced when co-cultured with B. fragilis in mixed biofilms. Interestingly, the absence of C. difficile LuxS alleviates the B. fragilis-mediated growth inhibition. Dual species RNA-sequencing analyses from single and mixed biofilms revealed differential modulation of distinct metabolic pathways for C. difficile WT, luxS and B. fragilis upon co-culture, indicating that AI-2 may be involved in induction of selective metabolic responses in B. fragilis. Overall, our data suggest that C. difficile LuxS/AI-2 utilises different mechanisms to mediate formation of single and mixed species communities.

Decreased synthesis of ribosomal proteins in tauopathy revealed by non-canonical amino acid labelling

Tau is a scaffolding protein that serves multiple cellular functions that are perturbed in neurodegenerative diseases, including Alzheimer's disease (AD) and frontotemporal dementia (FTD). We have recently shown that amyloid-β, the second hallmark of AD, induces de novo protein synthesis of tau. Importantly, this activation was found to be tau-dependent, raising the question of whether FTD-tau by itself affects protein synthesis. We therefore applied non-canonical amino acid labelling to visualise and identify newly synthesised proteins in the K369I tau transgenic K3 mouse model of FTD. This revealed massively decreased protein synthesis in neurons containing pathologically phosphorylated tau, a finding confirmed in P301L mutant tau transgenic rTg4510 mice. Using quantitative SWATH-MS proteomics, we identified changes in 247 proteins of the de novo proteome of K3 mice. These included decreased synthesis of the ribosomal proteins RPL23, RPLP0, RPL19 and RPS16, a finding that was validated in both K3 and rTg4510 mice. Together, our findings present a potential pathomechanism by which pathological tau interferes with cellular functions through the dysregulation of ribosomal protein synthesis.

Loss of the transcription factor RBPJ induces disease-promoting properties in brain pericytes

Sufficient vascular supply is indispensable for brain development and function, whereas dysfunctional blood vessels are associated with human diseases such as vascular malformations, stroke or neurodegeneration. Pericytes are capillary-associated mesenchymal cells that limit vascular permeability and protect the brain by preserving blood-brain barrier integrity. Loss of pericytes has been linked to neurodegenerative changes in genetically modified mice. Here, we report that postnatal inactivation of the Rbpj gene, encoding the transcription factor RBPJ, leads to alteration of cell identity markers in brain pericytes, increases local TGFβ signalling, and triggers profound changes in endothelial behaviour. These changes, which are not mimicked by pericyte ablation, imperil vascular stability and induce the acquisition of pathological landmarks associated with cerebral cavernous malformations. In adult mice, loss of Rbpj results in bigger stroke lesions upon ischemic insult. We propose that brain pericytes can acquire deleterious properties that actively enhance vascular lesion formation and promote pathogenic processes.

Pericytes are perivascular cells essential for blood-brain barrier maintenance. Here Diéguez-Hurtado et al. show that depletion of the transcription factor RBPJ in pericytes affects their molecular identity and disturbs endothelial cell behaviour, inducing the formation of vascular lesions in the brain.

One-time nitrogen fertilization shifts switchgrass soil microbiomes within a context of larger spatial and temporal variation

Soil microbiome responses to short-term nitrogen (N) inputs remain uncertain when compared with previous research that has focused on long-term fertilization responses. Here, we examined soil bacterial/archaeal and fungal communities pre- and post-N fertilization in an 8 year-old switchgrass field, in which twenty-four plots received N fertilization at three levels (0, 100, and 200 kg N ha^-1 as NH₄NO₃) for the first time since planting. Soils were collected at two depths, 0–5 and 5–15 cm, for DNA extraction and amplicon sequencing of 16S rRNA genes and ITS regions for assessment of microbial community composition. Baseline assessments prior to fertilization revealed no significant pre-existing divergence in either bacterial/archaeal or fungal communities across plots. The one-time N fertilizations increased switchgrass yields and tissue N content, and the added N was nearly completely removed from the soil of fertilized plots by the end of the growing season. Both bacterial/archaeal and fungal communities showed large spatial (by depth) and temporal variation (by season) within each plot, accounting for 17 and 12–22% of the variation as calculated from the Sq. root of PERMANOVA tests for bacterial/archaeal and fungal community composition, respectively. While N fertilization effects accounted for only ~4% of overall variation, some specific microbial groups, including the bacterial genus Pseudonocardia and the fungal genus Archaeorhizomyces, were notably repressed by fertilization at 200 kg N ha^-1. Bacterial groups varied with both depth in the soil profile and time of sampling, while temporal variability shaped the fungal community more significantly than vertical heterogeneity in the soil. These results suggest that short-term effects of N fertilization are significant but subtle, and other sources of variation will need to be carefully accounted for study designs including multiple intra-annual sampling dates, rather than one-time “snapshot” analyses that are common in the literature. Continued analyses of these trends over time with fertilization and management are needed to understand how these effects may persist or change over time.

A six-inhibitor culture medium for improving naïve-type pluripotency of porcine pluripotent stem cells

Understanding essential signaling network requirements and making appropriate adjustments in culture conditions are crucial if porcine pluripotent stem cells (PSC) are to achieve their full potential. Here, we first used two protein factors (LIF and FGF2) and kinase inhibitor combinations in attempts to convert primed type lentiviral-reprogrammed porcine induced PSC (Lv-piPSC) into naïve-like state and developed a medium called FL6i. In addition to FGF2 and LIF, this medium contained inhibitors of MAPK14, MAPK8, TGFB1, MAP2K1, GSK3A and BMP. Crucially, the usual TGFB1 and BMP4 protein components of many stem cell media were replaced in FL6i with inhibitors of TGFB1 and BMP. With this medium, Lv-piPSC were readily transformed from their original primed state into cells that formed colonies with typical features of naïve-state stem cells. The FL6i medium also assisted generation of naïve-type piPSC lines from porcine embryonic fibroblasts with non-integrating episomal plasmids (Epi-piPSC). These lines, despite retaining variable amounts of vector DNA, expressed higher endogenous pPOU5F1 and pSOX2 than Lv-piPSC. They have been cultured without obvious morphological change for >45 passages and retained pluripotent phenotypes in terms of upregulation of genes associated with pluripotency, low expression of genes linked to emergence of somatic cell lineages, and ability to generate well differentiated teratomas in immune-compromised mice. FL6i conditions, therefore, appear to support elevated pluripotent phenotypes. However, FL6i was less able to support the generation of embryonic stem cells from porcine blastocysts. Although colonies with dome-shaped morphologies were evident and the cells had some gene expression features linked to pluripotency, the phenotypes were ultimately not stable. Pathway analysis derived from RNAseq data performed on the various cell lines generated in this study suggest the benefits of employing the FL6i medium on porcine cells reside in its ability to minimize TGFB1 and BMP signaling, which would otherwise de-stabilize the stem cell state.

Sporadic Creutzfeldt-Jakob disease prion infection of human cerebral organoids

For the transmissible, neurogenerative family of prion diseases, few human models of infection exist and none represent structured neuronal tissue. Human cerebral organoids are self-organizing, three-dimensional brain tissues that can be grown from induced pluripotent stem cells. Organoids can model aspects of neurodegeneration in Alzheimer's Disease and Down's Syndrome, reproducing tau hyperphosphorylation and amyloid plaque pathology. To determine whether organoids could be used to reproduce human prion infection and pathogenesis, we inoculated organoids with two sporadic Creutzfeldt-Jakob Disease prion subtypes. Organoids showed uptake, followed by clearance, of the infectious inoculum. Subsequent re-emergence of prion self-seeding activity indicated de novo propagation. Organoid health assays, prion titer, prion protein electrophoretic mobility and immunohistochemistry demonstrated inoculum-specific differences. Our study shows, for the first time, that cerebral organoids can model aspects of human prion disease and thus offer a powerful system for investigating different human prion subtype pathologies and testing putative therapeutics.

Dissecting the Stromal Signaling and Regulation of Myeloid Cells and Memory Effector T Cells in Pancreatic Cancer

PURPOSE

Myeloid cells are a prominent immunosuppressive component within the stroma of pancreatic ductal adenocarcinoma (PDAC). Previously, targeting myeloid cells has had limited success. Here, we sought to target the myeloid cells through modifying a specific stromal component.

EXPERIMENTAL DESIGN

A murine model of metastatic PDAC treated with an irradiated whole-cell PDAC vaccine and PDAC specimens from patients treated with the same type of vaccine were used to assess the immune-modulating effect of stromal hyaluronan (HA) degradation by PEGPH20.

RESULTS

Targeting stroma by degrading HA with PEGPH20 in combination with vaccine decreases CXCL12/CXCR4/CCR7 immunosuppressive signaling axis expression in cancer-associated fibroblasts, myeloid, and CD8⁺ T cells, respectively. This corresponds with increased CCR7^- effector memory T-cell infiltration, an increase in tumor-specific IFNγ, and improved survival. In the stroma of human PDACs treated with the same vaccine, decreased stromal CXCR4 expression significantly correlated with decreased HA and increased cytotoxic activities, suggesting CXCR4 is an important therapeutic target.

CONCLUSIONS

This study represents the first to dissect signaling cascades following PDAC stroma remodeling via HA depletion, suggesting this not only overcomes a physical barrier for immune cell trafficking, but alters myeloid function leading to downstream selective increases in effector memory T-cell infiltration and antitumor activity.

Replication of Crohn's Disease Mucosal E. coli Isolates inside Macrophages Correlates with Resistance to Superoxide and Is Dependent on Macrophage NF-kappa B Activation

Mucosa-associated Escherichia coli are increased in Crohn’s disease (CD) and colorectal cancer (CRC). CD isolates replicate within macrophages but the specificity of this effect for CD and its mechanism are unclear. Gentamicin exclusion assay was used to assess E. coli replication within J774.A1 murine macrophages. E. coli growth was assessed following acid, low-nutrient, nitrosative, oxidative and superoxide stress, mimicking the phagolysosome. Twelve of 16 CD E. coli isolates replicated >2-fold within J774.A1 macrophages; likewise for isolates from 6/7 urinary tract infection (UTI), 8/9 from healthy subjects, compared with 2/6 ulcerative colitis, 2/7 colorectal cancer and 0/3 laboratory strains. CD mucosal E. coli were tolerant of acidic, low-nutrient, nitrosative and oxidative stress. Replication within macrophages correlated strongly with tolerance to superoxide stress (rho = 0.44, p = 0.0009). Exemplar CD E. coli HM605 and LF82 were unable to survive within Nfκb1^-/- murine bone marrow-derived macrophages. In keeping with this, pre-incubation of macrophages with hydrocortisone (0.6 µM for 24 h) caused 70.49 ± 12.11% inhibition of intra-macrophage replication. Thus, CD mucosal E. coli commonly replicate inside macrophages, but so do some UTI and healthy subject strains. Replication correlates with resistance to superoxide and is highly dependent on macrophage NF-κB signalling. This may therefore be a good therapeutic target.

Annotation and Expression of IDN2-like and FDM-like Genes in Sexual and Aposporous Hypericum perforatum L. accessions

The protein IDN2, together with the highly similar interactors FDM1 and FDM2, is required for RNA-directed DNA methylation (RdDM) and siRNA production. Epigenetic regulation of gene expression is required to restrict cell fate determination in A. thaliana ovules. Recently, three transcripts sharing high similarity with the A. thaliana IDN2 and FDM1-2 were found to be differentially expressed in ovules of apomictic Hypericum perforatum L. accessions. To gain further insight into the expression and regulation of these genes in the context of apomixis, we investigated genomic, transcriptional and functional aspects of the gene family in this species. The H. perforatum genome encodes for two IDN2-like and 7 FDM-like genes. Differential and heterochronic expression of FDM4-like genes was found in H. perforatum pistils. The involvement of these genes in reproduction and seed development is consistent with the observed reduction of the seed set and high variability in seed size in A. thaliana IDN2 and FDM-like knockout lines. Differential expression of IDN2-like and FDM-like genes in H. perforatum was predicted to affect the network of potential interactions between these proteins. Furthermore, pistil transcript levels are modulated by cytokinin and auxin but the effect operated by the two hormones depends on the reproductive phenotype.

Spinal neural tube closure depends on regulation of surface ectoderm identity and biomechanics by Grhl2

Lack or excess expression of the surface ectoderm-expressed transcription factor Grainyhead-like2 (Grhl2), each prevent spinal neural tube closure. Here we investigate the causative mechanisms and find reciprocal dysregulation of epithelial genes, cell junction components and actomyosin properties in Grhl2 null and over-expressing embryos. Grhl2 null surface ectoderm shows a shift from epithelial to neuroepithelial identity (with ectopic expression of N-cadherin and Sox2), actomyosin disorganisation, cell shape changes and diminished resistance to neural fold recoil upon ablation of the closure point. In contrast, excessive abundance of Grhl2 generates a super-epithelial surface ectoderm, in which up-regulation of cell-cell junction proteins is associated with an actomyosin-dependent increase in local mechanical stress. This is compatible with apposition of the neural folds but not with progression of closure, unless myosin activity is inhibited. Overall, our findings suggest that Grhl2 plays a crucial role in regulating biomechanical properties of the surface ectoderm that are essential for spinal neurulation.

Loss or over-expression of Grainyhead-like transcription factors (Grhl) prevents closure of the neural tube but the mechanism underlying this is unclear. Here, the authors show that Grhl2 regulates murine posterior-neuropore closure via changes in the identity and biomechanics of the non-neural, surface ectoderm cells.

Unraveling the role of the transcriptional regulator VirS in low pH-induced responses of Mycobacterium tuberculosis and identification of VirS inhibitors

The ability of Mycobacterium tuberculosis to respond and adapt to various stresses such as oxygen/nitrogen radicals and low pH inside macrophages is critical for the persistence of this human pathogen inside its host. We have previously shown that an AraC/XylS-type transcriptional regulator, VirS, which is induced in low pH, is involved in remodeling the architecture of the bacterial cell envelope. However, how VirS influences gene expression to coordinate these pH responses remains unclear. Here, using a genetic biosensor of cytoplasmic pH, we demonstrate that VirS is required for the intracellular pH maintenance in response to acidic stress and inside acidified macrophages. Furthermore, we observed that VirS plays an important role in blocking phagosomal-lysosomal fusions. Transcriptomics experiments revealed that VirS affects the expression of genes encoding metabolic enzymes, cell-wall envelope proteins, efflux pumps, ion transporters, detoxification enzymes, and transcriptional regulators expressed under low-pH stress. Employing electrophoretic mobility-shift assays, DNA footprinting, and in silico analysis, we identified a DNA sequence to which VirS binds and key residues in VirS required for its interaction with DNA. A significant role of VirS in M. tuberculosis survival in adverse conditions suggested it as a potential anti-mycobacterial drug target. To that end, we identified VirS inhibitors in a virtual screen; the top hit compounds inhibited its DNA-binding activity and also M. tuberculosis growth in vitro and inside macrophages. Our findings establish that VirS mediates M. tuberculosis responses to acidic stress and identify VirS-inhibiting compounds that may form the basis for developing more effective anti-mycobacterial agents.

Inhibition of the cardiac myocyte mineralocorticoid receptor ameliorates doxorubicin-induced cardiotoxicity

Aim

Anthracyclines such as doxorubicin are widely used in cancer therapy but their use is limited by cardiotoxicity. Up to date there is no established strategy for the prevention of anthracyclin-induced heart failure. In this study, we evaluated the role of the cardiac myocyte mineralocorticoid receptor (MR) during doxorubicin-induced cardiotoxicity.

Methods and results

A single high-dose or repetitive low-dose doxorubicin administration lead to markedly reduced left ventricular function in mice. Treatment with the MR antagonist eplerenone prevented doxorubicin-induced left ventricular dysfunction. In order to identify the cell types and molecular mechanisms involved in this beneficial effect we used a mouse model with cell type-specific MR deletion in cardiac myocytes. Cardiac myocyte MR deletion largely reproduced the effect of pharmacological MR inhibition on doxorubicin-induced cardiotoxicity. RNAseq from isolated cardiac myocytes revealed a repressive effect of doxorubicin on gene expression which was prevented by MR deletion.

Conclusions

We show here that (i) eplerenone prevents doxorubicin-induced left ventricular dysfunction in mice, and (ii) this beneficial effect is related to inhibition of MR in cardiac myocytes. Together with present clinical trial data our findings suggest that MR antagonism may be appropriate for the prevention of doxorubicin-induced cardiotoxicity.

Skeletal-muscle-derived mesenchymal stem/stromal cells from patients with osteoarthritis show superior biological properties compared to bone-derived cells

Mesenchymal stem/stromal cells (MSCs) are being exploited for patient-derived stem-cell therapies. As the biological properties of MSCs derived from skeletal muscle of osteoarthritis patients are poorly understood, the aim of this study was to compare muscle MSCs with well-recognized bone and bone marrow-derived MSCs from these patients. Paired samples of skeletal muscle and trabecular bone tissue were obtained from 21 patients with osteoarthritis. Isolated cells were compared using ex vivo immunophenotyping and detailed in vitro analyses. These included the colony forming unit fibroblast assay, growth kinetics, senescence, multilineage potential, immunophenotyping, and MSC marker gene expression profiling. Freshly isolated MSCs from muscle showed improved viability over bone-derived MSCs, with similar mesenchymal fraction. Muscle-derived MSCs showed superior clonogenicity, higher growth rates, and lower doubling times. Muscle-derived MSCs also showed superior osteogenic and myogenic properties and a positive correlation between CD271 expression and adipogenesis. Senescence rate as well as adipogenic and chondrogenic potentials were similar. Skeletal muscle-derived MSCs of osteoarthritis patients have superior clonogenicity and growth kinetics compared to bone-derived MSCs, making them a good candidate for autologous stem-cell therapies. Moreover, the positive correlation between CD271 and adipogenesis suggest that CD271 expressing muscle MSCs might contribute to muscle steatosis observed in osteoarthritis.

Distinct amino acid and lipid perturbations characterize acute versus chronic malaria

Chronic malaria is a major public health problem and significant challenge for disease eradication efforts. Despite its importance, the biological factors underpinning chronic malaria are not fully understood. Recent studies have shown that host metabolic state can influence malaria pathogenesis and transmission, but its role in chronicity is not known. Here, with the goal of identifying distinct modifications in the metabolite profiles of acute versus chronic malaria, metabolomics was performed on plasma from Plasmodium-infected humans and nonhuman primates with a range of parasitemias and clinical signs. In rhesus macaques infected with Plasmodium coatneyi, significant alterations in amines, carnitines, and lipids were detected during a high parasitemic acute phase and many of these reverted to baseline levels once a low parasitemic chronic phase was established. Plasmodium gene expression, studied in parallel in the macaques, revealed transcriptional changes in amine, fatty acid, lipid and energy metabolism genes, as well as variant antigen genes. Furthermore, a common set of amines, carnitines, and lipids distinguished acute from chronic malaria in plasma from human Plasmodium falciparum cases. In summary, distinct host-parasite metabolic environments have been uncovered that characterize acute versus chronic malaria, providing insights into the underlying host-parasite biology of malaria disease progression.

Integrated approaches to study the drought tolerance mechanism in hot pepper (Capsicum annuum L.)

Drought is one of the predominant abiotic stresses which have phenomenal impact on crop productivity. Alterations in aquaporin gene expressions are part of complex molecular responses by plant in response to drought. To better understand the role of aquaporins in economically important crop chilli (Capsicum annuum), drought induced gene expression of twelve aquaporins was determined in drought tolerant-KCa-4884 and drought susceptible-G-4 genotypes. Conjointly, the effect of drought on leaf water status and photosynthetic parameters were evaluated. Gene expression of all examined 12 aquaporins was up-regulated in KCa-4884 and in contrast, all the aquaporin genes were down-regulated in G-4 under drought stress. Significant variations among two chilli genotypes have been recorded in photosynthetic rate (P _n ), stomatal conductance (G _s ), and relative water content (RWC), sub-stomatal CO₂ concentration (C _i ). KCa-4884 revealed significantly high rates of P _n and RWC and decreased G _s under water deficit conditions providing evidence for superior drought adaptive strategies. Differences in physiological parameters illustrate prevention of water loss during drought. Up-regulation of aquaporins in drought tolerant genotype implicates their possible role in water relations and photosynthetic performance even under extended drought conditions.

RNA-seq analysis of the salivary glands and midgut of the Argasid tick Ornithodoros rostratus

Ornithodoros rostratus is a South American argasid tick which importance relies on its itchy bite and potential as disease vector. They feed on a wide variety of hosts and secrete different molecules in their saliva and intestinal content that counteract host defences and help to accommodate and metabolize the relatively large quantity of blood upon feeding. The present work describes the transcriptome profile of salivary gland (SG) and midgut (MG) of O. rostratus using Illumina sequencing. A total of 8,031 contigs were assembled and assigned to different functional classes. Secreted proteins were the most abundant in the SG and accounted for ~67% of all expressed transcripts with contigs with identity to lipocalins and acid tail proteins being the most representative. On the other hand, immunity genes were upregulated in MG with a predominance of defensins and lysozymes. Only 10 transcripts in SG and 8 in MG represented ~30% of all RNA expressed in each tissue and one single contig (the acid tail protein ORN-9707) represented ~7% of all expressed contigs in SG. Results highlight the functional difference of each organ and identified the most expressed classes and contigs of O. rostratus SG and MG.

Identification and comparative analysis of the CIPK gene family and characterization of the cold stress response in the woody plant Prunus mume

Prunus mume is an important ornamental woody plant that grows in tropical and subtropical regions. Freezing stress can adversely impact plant productivity and limit the expansion of geographical locations. Understanding cold-responsive genes could potentially bring about the development of new ways to enhance plant freezing tolerance. Members of the serine/threonine protein kinase (CIPK) gene family play important roles in abiotic stress. However, the function of CIPK genes in P. mume remains poorly defined. A total of 16 CIPK genes were first identified in P. mume. A systematic phylogenetic analysis was conducted in which 253 CIPK genes from 12 species were divided into three groups. Furthermore, we analysed the chromosomal locations, molecular structures, motifs and domains of CIPK genes in P. mume. All of the CIPK sequences had NAF domains and promoter regions containing cis-acting regulatory elements of the related stress response. Three PmCIPK genes were identified as Pmu-miR172/167-targeted sites. Transcriptome data showed that most PmCIPK genes presented tissue-specific and time-specific expression profiles. Nine genes were highly expressed in flower buds in December and January, and 12 genes were up-regulated in stems in winter. The expression levels of 12 PmCIPK genes were up-regulated during cold stress treatment confirmed by qRT-PCR. Our study improves understanding of the role of the PmCIPK gene family in the low temperature response in woody plants and provides key candidate genes and a theoretical basis for cold resistance molecular-assisted breeding technology in P. mume.

A reinforcing HNF4-SMAD4 feed-forward module stabilizes enterocyte identity

BMP/SMAD signaling is a crucial regulator of intestinal differentiation^1–4. However, the molecular underpinnings of the BMP pathway in this context are unknown. Here, we characterize the mechanism by which BMP/SMAD signaling drives enterocyte differentiation. We establish that the transcription factor HNF4A acts redundantly with an intestine-restricted HNF4 paralog, HNF4G, to activate enhancer chromatin and upregulate the majority of transcripts enriched in the differentiated epithelium; cells fail to differentiate upon double knockout of both HNF4 paralogs. Furthermore, we show that SMAD4 and HNF4 function via a reinforcing feed-forward loop, activating each other’s expression and co-binding to regulatory elements of differentiation genes. This feed-forward regulatory module promotes and stabilizes enterocyte cell identity; disruption of the HNF4-SMAD4 module results in loss of enterocyte fate in favor of progenitor and secretory cell lineages. This intersection of signaling and transcriptional control provides a framework to understand regenerative tissue homeostasis, particularly in tissues with inherent cellular plasticity⁵.

Characterization of donor and recipient CD8+ tissue-resident memory T cells in transplant nephrectomies

Tissue-resident memory T (T_RM) cells are characterized by their surface expression of CD69 and can be subdivided in CD103+ and CD103− T_RM cells. The origin and functional characteristics of T_RM cells in the renal allograft are largely unknown. To determine these features we studied T_RM cells in transplant nephrectomies. T_RM cells with a CD103+ and CD103− phenotype were present in all samples (n = 13) and were mainly CD8+ T cells. Of note, donor-derived T_RM cells were only detectable in renal allografts that failed in the first month after transplantation. Grafts, which failed later, mainly contained recipient derived T_RM cells. The gene expression profiles of the recipient derived CD8+ T_RM cells were studied in more detail and showed a previously described signature of tissue residence within both CD103+ and CD103− T_RM cells. All CD8+ T_RM cells had strong effector abilities through the production of IFNγ and TNFα, and harboured high levels of intracellular granzyme B and low levels of perforin. In conclusion, our results demonstrate that donor and recipient T_RM cells reside in the rejected renal allograft. Over time, the donor-derived T_RM cells are replaced by recipient T_RM cells which have features that enables these cells to aggressively respond to the allograft.

TGF-β activation impairs fibroblast ability to support adult lung epithelial progenitor cell organoid formation

Transforming growth factor-β (TGF-β)-induced fibroblast-to-myofibroblast differentiation contributes to remodeling in chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis, but whether this impacts the ability of fibroblasts to support lung epithelial repair remains little explored. We pretreated human lung fibroblasts [primary (phFB) or MRC5 cells] with recombinant human TGF-β to induce myofibroblast differentiation, then cocultured them with adult mouse lung epithelial cell adhesion molecule-positive cells (EpCAM⁺) to investigate their capacity to support epithelial organoid formation in vitro. While control phFB and MRC5 lung fibroblasts supported organoid formation of mouse EpCAM⁺ cells, TGF-β pretreatment of both phFB and MRC5 impaired organoid-supporting ability. We performed RNA sequencing of TGF-β-treated phFB, which revealed altered expression of key Wnt signaling pathway components and Wnt/β-catenin target genes, and modulated expression of secreted factors involved in mesenchymal-epithelial signaling. TGF-β profoundly skewed the transcriptional program induced by the Wnt/β-catenin activator CHIR99021. Supplementing organoid culture media recombinant hepatocyte growth factor or fibroblast growth factor 7 promoted organoid formation when using TGF-β pretreated fibroblasts. In conclusion, TGF-β-induced myofibroblast differentiation results in Wnt/β-catenin pathway skewing and impairs fibroblast ability to support epithelial repair likely through multiple mechanisms, including modulation of secreted growth factors.

Addiction to DUSP1 protects JAK2V617F-driven polycythemia vera progenitors against inflammatory stress and DNA damage, allowing chronic proliferation

Inflammatory and oncogenic signaling converge in disease evolution of BCR–ABL-negative myeloproliferative neoplasms, clonal hematopoietic stem cell disorders characterized by gain-of-function mutation in JAK2 kinase (JAK2V617F), with highest prevalence in patients with polycythemia vera (PV). Despite the high risk, DNA-damaging inflammatory microenvironment, PV progenitors tend to preserve their genomic stability over decades until their progression to post-PV myelofibrosis/acute myeloid leukemia. Using induced pluripotent stem cells-derived CD34⁺ progenitor-enriched cultures from JAK2V617F⁺ PV patient and from JAK2 wild-type healthy control, CRISPR-modified HEL cells and patients’ bone marrow sections from different disease stages, we demonstrate that JAK2V617F induces an intrinsic IFNγ- and NF-κB-associated inflammatory program, while suppressing inflammation-evoked DNA damage both in vitro and in vivo. We show that cells with JAK2V617F tightly regulate levels of inflammatory cytokines-induced reactive oxygen species, do not fully activate the ATM/p53/p21waf1 checkpoint and p38/JNK MAPK stress pathway signaling when exposed to inflammatory cytokines, suppress DNA single-strand break repair genes’ expression yet overexpress the dual-specificity phosphatase (DUSP) 1. RNAi-mediated knock-down and pharmacological inhibition of DUSP1, involved in p38/JNK deactivation, in HEL cells reveals growth addiction to DUSP1, consistent with enhanced DNA damage response and apoptosis in DUSP1-inhibited parental JAK2V617F⁺ cells, but not in CRISPR-modified JAK2 wild-type cells. Our results indicate that the JAK2V617F⁺ PV progenitors utilize DUSP1 activity as a protection mechanism against DNA damage accumulation, promoting their proliferation and survival in the inflammatory microenvironment, identifying DUSP1 as a potential therapeutic target in PV.

Identification and expression analysis of the Spodoptera exigua neuropeptidome under different physiological conditions

Neuropeptides are small signalling molecules acting as neurohormones, neurotransmitters and neuromodulators. Being part of the chemical communication system between cells within an organism, they are involved in the regulation of different aspects of animal physiology and behaviour such as feeding, reproduction, development and locomotion. Transcriptomic data from larval and adult tissues have been obtained and mined to generate a comprehensive neuropeptidome for the polyphagous insect pest Spodoptera exigua. Sixty-three neuropeptides have been identified and described based on their tissue specificity and their regulation in response to different abiotic perturbations. Expression analyses have identified those neuropeptides involved in ingestive and digestive behaviour of S. exigua larvae and revealed a general pattern of upregulation in the midgut during larval starvation. Our results represent a comprehensive neuropeptidome of a lepidopteran species that will be highly relevant to future studies and provide novel information of the insect's perception of its environment.

miR-147b-mediated TCA cycle dysfunction and pseudohypoxia initiate drug tolerance to EGFR inhibitors in lung adenocarcinoma

Drug-tolerance is an acute defense response prior to a fully drug-resistant state and tumor relapse, however there are few therapeutic agents targeting drug-tolerance in the clinic. Here we show that miR-147b initiates a reversible tolerant-state to the EGFR inhibitor osimertinib in non-small cell lung cancer. With miRNA-seq analysis we find that miR-147b is the most upregulated microRNA in osimertinib-tolerant and EGFR mutated lung cancer cells. Whole transcriptome analysis of single-cell derived clones reveals a link between osimertinib-tolerance and pseudohypoxia responses irrespective of oxygen levels. Further metabolomics and genetic studies demonstrate that osimertinib-tolerance is driven by miR-147b repression of VHL and succinate dehydrogenase linked to the tricarboxylic acid cycle and pseudohypoxia pathways. Finally, pretreatment with a miR-147b inhibitor delays osimertinib-associated drug tolerance in patient-derived three-dimensional (3D) structures. This link between miR-147b and tricarboxylic acid cycle may provide promising targets for preventing tumor relapse.

RNA-seq analysis reveals resistome genes and signalling pathway associated with vancomycin-intermediate Staphylococcus aureus

Context

Vancomycin-intermediate Staphylococcus aureus remains one of the most prevalent multidrug-resistant pathogens causing healthcare infections that are difficult to treat.

Aims

This study uses a comprehensive computational analysis to systematically investigate various gene expression profiles of resistant and sensitive S. aureus strains on exposure to antibiotics.

Settings and Design

The transcriptional changes leading to the development of multiple antibiotic resistance were examined by an integrative analysis of nine differential expression experiments under selected conditions of vancomycin-intermediate and -sensitive strains for four different antibiotics using publicly available RNA-Seq datasets.

Materials and Methods

For each antibiotic, three experimental conditions for expression analysis were selected to identify those genes that are particularly involved in the development of resistance. The results were further scrutinised to generate a resistome that can be analysed for their role in the development or adaptation to antibiotic resistance.

Results

The 99 genes in the resistome are then compiled to create a multiple drug resistome of 25 known and novel genes identified to play a part in antibiotic resistance. The inclusion of agr genes and associated virulence factors in the identified resistome supports the role of agr quorum sensing system in multiple drug resistance. In addition, enrichment analysis also identified the kyoto encyclopedia of genes and genomes (KEGG) pathways - quorum sensing and two-component system pathways - in the resistome gene set.

Conclusion

Further studies on understanding the role of the identified molecular targets such as SAA6008_00181, SAA6008_01127, agrA, agrC and coa in adapting to the pressure of antibiotics at sub-inhibitory concentrations can help in learning the molecular mechanisms causing resistance to the pathogens as well as finding other potential therapeutics.

Transcriptomics-based validation of the relatedness of heterogeneous nuclear ribonucleoproteins to chronic lymphocytic leukemia as potential biomarkers of the disease aggressiveness

OBJECTIVES

To use independent transcriptomics data sets of cancer patients with prognostic information from public repositories to validate the relevance of our previously described chronic lymphocytic leukemia (CLL)-related proteins at the level of transcription (mRNA) to the prognosis of CLL.  Methods: This is a validation study that was conducted at Majmaah University, Kingdom of Saudi Arabia between January-2017 and July-2018. Two independent data sets of CLL transcriptomics from Gene Expression Omnibus (GEO) with time-to-first treatment (TTFT) data (GSE39671; 130 patients) and information about overall survival (OS) (GSE22762; 107 patients) were used for the validation analyses. To further investigate the relatedness of a transcript of interest to other neoplasms, 6 independent data sets of cancer transcriptomics with prognostic information (1865 patients) from the cancer genomics atlas (TCGA) were used. Pathway-enrichment analyses were conducted using Reactome; and correlation analyses of gene expression were performed using Pearson score. Results: Nine of the CLL-related proteins exhibited transcript expression that predicted TTFT and 7 of the CLL-related proteins showed mRNA levels that predicted OS in CLL patients (p≤0.05). Of these transcripts, 8 were different types of heterogeneous nuclear ribonucleoproteins (HNRNPs); and 2 (HNRNPUL2 and HIST1C1H) retained prognostic significance in the 2 independent data sets. Furthermore, genes that enriched CLL-related pathways (p≤0.05; false discovery rate [FDR] ≤0.05) were found to correlate with the expression of HNRNPUL2 (Pearson score: ≥0.50; p lessthan 0.00001). Finally, increased expression of HNRNPUL2 was indicative of poor prognosis of various types of cancer other than CLL (p less than 0.05). Conclusion: The cognate transcripts of 14 of our CLL-related proteins significantly predicted CLL prognosis.

Vitamin D supplementation alters the expression of genes associated with hypertension and did not induce DNA damage in rats

Vitamin D3 deficiency has been correlated with altered expression of genes associated with increased blood pressure (BP); however, the role of vitamin D3 supplementation in the genetic mechanisms underlying hypertension remains unclear. Thus, the aim of this study was investigate the consequences of vitamin D3 supplemented (10,000 IU/kg) or deficient (0 IU/kg) diets on regulation of expression of genes related to hypertension pathways in heart cells of spontaneously hypertensive rats (SHR) and normotensive Wistar Kyoto (WKY) controls. An additional aim was to assess the impact of vitamin D3 on DNA damage and oxidative stress markers. The gene expression profiles were determined by PCR array, DNA damage was assessed by an alkaline comet assay, and oxidative stress markers by measurement of thiobarbituric acid reactive substances (TBARS) and glutathione (GSH) levels. In SHR rats data showed that the groups of genes most differentially affected by supplemented and deficient diets were involved in BP regulation and renin-angiotensin system. In normotensive WKY controls, the profile of gene expression was similar between the two diets. SHR rats were more sensitive to changes in gene expression induced by dietary vitamin D3 than normotensive WKY animals. In addition to gene expression profile, vitamin D3 supplemented diet did not markedly affect DNA or levels of TBARS and GSH levels in both experimental groups. Vitamin D3 deficient diet produced lipid peroxidation in SHR rats. The results of this study contribute to a better understanding of the role of vitamin D3 in the genetic mechanisms underlying hypertension. Abbreviations: AIN, American Institute of Nutrition; EDTA, disodium ethylenediaminetetraacetic acid; GSH, glutathione; PBS, phosphate buffer solution; SHR, spontaneously hypertensive rats; TBARS, thiobarbituric acid reactive substances; WKY, Wistar Kyoto.

Evidence of mitochondrial DNA in the chloroplast genome of Convallaria keiskei and its subsequent evolution in the Asparagales

DNA transfer between internal organelles such as the nucleus, mitochondrion, and plastid is a well-known phenomenon in plant evolution, and DNA transfer from the plastid and mitochondrion to the nucleus, from the plastid to the mitochondrion, and from the nucleus to the mitochondrion has been well-documented in angiosperms. However, evidence of the transfer of mitochondrial DNA (mtDNA) to the plastid has only been found in three dicotyledons and one monocotyledon. In the present study, we characterised and analysed two chloroplast (cp) genome sequences of Convallaria keiskei and Liriope spicata, and found that C. keiskei has the largest cp genome (162,109 bp) in the Asparagaceae. Interestingly, C. keiskei had a ~3.3-kb segment of mtDNA in its cp genome and showed similarity with the mt gene rpl10 as a pseudogene. Further analyses revealed that mtDNA transfer only occurred in C. keiskei in the Nolinoideae, which diverged very recently (7.68 million years ago (mya); 95% highest posterior density (HPD): 14.55–2.97 mya). These findings indicate that the C. keiskei cp genome is unique amongst monocotyledon land plants, but further work is necessary to understand the direction and mechanism involved in the uptake of mtDNA by the plastid genome of C. keiskei.

The VQ motif-containing proteins in the diploid and octoploid strawberry

The plant VQ motif-containing proteins are a recently discovered class of plant regulatory proteins interacting with WRKY transcription factors capable of modulate their activity as transcriptional regulators. The short VQ motif (FxxhVQxhTG) is the main element in the WRKY-VQ interaction, whereas a newly identified variable upstream amino acid motif appears to be determinant for the WRKY specificity. The VQ family has been studied in several species and seems to play important roles in a variety of biological processes, including response to biotic and abiotic stresses. Here, we present a systematic study of the VQ family in both diploid (Fragaria vesca) and octoploid (Fragaria x ananassa) strawberry species. Thus, twenty-five VQ-encoding genes were identified and twenty-three were further confirmed by gene expression analysis in different tissues and fruit ripening stages. Their expression profiles were also studied in F. ananassa fruits affected by anthracnose, caused by the ascomycete fungus Colletotrichum, a major pathogen of strawberry, and in response to the phytohormones salicylic acid and methyl-jasmonate, which are well established as central stress signals to regulate defence responses to pathogens. This comprehensive analysis sheds light for a better understanding of putative implications of members of the VQ family in the defence mechanisms against this major pathogen in strawberry.