Brief Bioinform. 2021 Mar 29:bbab066. doi: 10.1093/bib/bbab066. Online ahead of print.

ABSTRACT

In network and systems medicine, active module identification methods (AMIMs) are widely used for discovering candidate molecular disease mechanisms. To this end, AMIMs combine network analysis algorithms with molecular profiling data, most commonly, by projecting gene expression data onto generic protein-protein interaction (PPI) networks. Although active module identification has led to various novel insights into complex diseases, there is increasing awareness in the field that the combination of gene expression data and PPI network is problematic because up-to-date PPI networks have a very small diameter and are subject to both technical and literature bias. In this paper, we report the results of an extensive study where we analyzed for the first time whether widely used AMIMs really benefit from using PPI networks. Our results clearly show that, except for the recently proposed AMIM DOMINO, the tested AMIMs do not produce biologically more meaningful candidate disease modules on widely used PPI networks than on random networks with the same node degrees. AMIMs hence mainly learn from the node degrees and mostly fail to exploit the biological knowledge encoded in the edges of the PPI networks. This has far-reaching consequences for the field of active module identification. In particular, we suggest that novel algorithms are needed which overcome the degree bias of most existing AMIMs and/or work with customized, context-specific networks instead of generic PPI networks.

PMID:33782690 | DOI:10.1093/bib/bbab066

Sci Rep. 2021 Mar 29;11(1):7077. doi: 10.1038/s41598-021-86490-x.

ABSTRACT

DNA damage activates cell cycle checkpoint proteins ATR and CHK1 to arrest cell cycle progression, providing time for repair and recovery. Consequently, inhibitors of ATR (ATRi) and CHK1 (CHK1i) enhance damage-induced cell death. Intriguingly, both CHK1i and ATRi alone elicit cytotoxicity in some cell lines. Sensitivity has been attributed to endogenous replications stress, but many more cell lines are sensitive to ATRi than CHK1i. Endogenous activation of the DNA damage response also did not correlate with drug sensitivity. Sensitivity correlated with the appearance of γH2AX, a marker of DNA damage, but without phosphorylation of mitotic markers, contradicting suggestions that the damage is due to premature mitosis. Sensitivity to ATRi has been associated with ATM mutations, but dysfunction in ATM signaling did not correlate with sensitivity. CHK1i and ATRi circumvent replication stress by reactivating stalled replicons, a process requiring a low threshold activity of CDK2. In contrast, γH2AX induced by single agent ATRi and CHK1i requires a high threshold activity CDK2. Hence, phosphorylation of different CDK2 substrates is required for cytotoxicity induced by replication stress plus ATRi/CHK1i as compared to their single agent activity. In summary, sensitivity to ATRi and CHK1i as single agents is elicited by premature hyper-activation of CDK2.

PMID:33782497 | DOI:10.1038/s41598-021-86490-x

Sci Rep. 2021 Mar 29;11(1):7046. doi: 10.1038/s41598-021-86480-z.

ABSTRACT

Understanding the interactions among agricultural processes, soil, and plants is necessary for optimizing crop yield and productivity. This study focuses on developing effective monitoring and analysis methodologies that estimate key soil and plant properties. These methodologies include data acquisition and processing approaches that use unmanned aerial vehicles (UAVs) and surface geophysical techniques. In particular, we applied these approaches to a soybean farm in Arkansas to characterize the soil-plant coupled spatial and temporal heterogeneity, as well as to identify key environmental factors that influence plant growth and yield. UAV-based multitemporal acquisition of high-resolution RGB (red-green-blue) imagery and direct measurements were used to monitor plant height and photosynthetic activity. We present an algorithm that efficiently exploits the high-resolution UAV images to estimate plant spatial abundance and plant vigor throughout the growing season. Such plant characterization is extremely important for the identification of anomalous areas, providing easily interpretable information that can be used to guide near-real-time farming decisions. Additionally, high-resolution multitemporal surface geophysical measurements of apparent soil electrical conductivity were used to estimate the spatial heterogeneity of soil texture. By integrating the multiscale multitype soil and plant datasets, we identified the spatiotemporal co-variance between soil properties and plant development and yield. Our novel approach for early season monitoring of plant spatial abundance identified areas of low productivity controlled by soil clay content, while temporal analysis of geophysical data showed the impact of soil moisture and irrigation practice (controlled by topography) on plant dynamics. Our study demonstrates the effective coupling of UAV data products with geophysical data to extract critical information for farm management.

PMID:33782488 | DOI:10.1038/s41598-021-86480-z

Sci Rep. 2021 Mar 29;11(1):7078. doi: 10.1038/s41598-021-86399-5.

ABSTRACT

Citrus limon (L.) Burm. F. is an important evergreen fruit crop whose rhizosphere and phyllosphere microbiota have been characterized, while seed microbiota is still unknown. Bacterial and fungal endophytes were isolated from C. limon surface-sterilized seeds. The isolated fungi-belonging to Aspergillus, Quambalaria and Bjerkandera genera-and bacteria-belonging to Staphylococcus genus-were characterized for indoleacetic acid production and phosphate solubilization. Next Generation Sequencing based approaches were then used to characterize the endophytic bacterial and fungal microbiota structures of surface-sterilized C. limon seeds and of shoots obtained under aseptic conditions from in vitro growing seedlings regenerated from surface-sterilized seeds. This analysis highlighted that Cutibacterium and Acinetobacter were the most abundant bacterial genera in both seeds and shoots, while Cladosporium and Debaryomyces were the most abundant fungal genera in seeds and shoots, respectively. The localization of bacterial endophytes in seed and shoot tissues was revealed by Fluorescence In Situ Hybridization coupled with Confocal Laser Scanning Microscopy revealing vascular bundle colonization. Thus, these results highlighted for the first time the structures of endophytic microbiota of C. limon seeds and the transmission to shoots, corroborating the idea of a vertical transmission of plant microbiota and suggesting its crucial role in seed germination and plant development.

PMID:33782436 | DOI:10.1038/s41598-021-86399-5

Mol Cancer Ther. 2021 Mar 29:molcanther.0907.2020. doi: 10.1158/1535-7163.MCT-20-0907. Online ahead of print.

ABSTRACT

ErbB3, a member of the ErbB receptor family, is a potent mediator in the development and progression of cancer, and its activation plays pivotal roles in acquired resistance against anti-EGFR therapies and other standard of care therapies. Upon ligand (NRG1) binding, ErbB3 forms heterodimers with other ErbB proteins (i.e., EGFR and ErbB2), which allows activation of downstream PI3K/Akt signaling. In this study, we developed a fully human anti-ErbB3 antibody, named ISU104, as an anti-cancer agent. ISU104 binds potently and specifically to the domain 3 of ErbB3. The complex structure of ErbB3-domain 3::ISU104-Fab revealed that ISU104 binds to the NRG1 binding region of the domain 3. The elucidated structure suggested that the binding of ISU104 to ErbB3 would hinder not only ligand binding but also the structural changes required for heterodimerization. Biochemical studies confirmed these predictions. ISU104 inhibited ligand binding and ligand-dependent heterodimerization and phosphorylation, and induced the internalization of ErbB3. As a result, downstream Akt phosphorylation and cell proliferation were inhibited. The anti-cancer efficacy of ISU104 was demonstrated in xenograft models of various cancers. In summary, a highly potent ErbB3 targeting antibody ISU104 is suitable for clinical development.

PMID:33782100 | DOI:10.1158/1535-7163.MCT-20-0907

J Bacteriol. 2021 Mar 29:JB.00037-21. doi: 10.1128/JB.00037-21. Online ahead of print.

ABSTRACT

To cope with sudden changes in their environment, bacteria can use a bet-hedging strategy by dividing the population into cells with different properties. This so-called bimodal or bistable cellular differentiation is generally controlled by positive feedback regulation of transcriptional activators. Due to the continuous increase in cell volume, it is difficult for these activators to reach an activation threshold concentration when cells are growing exponentially. This is one reason why bimodal differentiation is primarily observed from the onset of the stationary phase when exponential growth ceases. An exception is the bimodal induction of motility in Bacillus subtilis, which occurs early during exponential growth. Several mechanisms have been put forward to explain this, including double negative-feedback regulation and the stability of the mRNA molecules involved. In this study, we used fluorescence-assisted cell sorting to compare the transcriptome of motile and non-motile cells and noted that expression of ribosomal genes is lower in motile cells. This was confirmed using an unstable GFP reporter fused to the strong ribosomal rpsD promoter. We propose that the reduction in ribosomal gene expression in motile cells is the result of a diversion of cellular resources to the synthesis of the chemotaxis and motility systems. In agreement, single-cell microscopic analysis showed that motile cells are slightly shorter than non-motile cells, an indication of slower growth. We speculate that this growth rate reduction can contribute to the bimodal induction of motility during exponential growth.IMPORTANCETo cope with sudden environmental changes, bacteria can use a bet-hedging strategy and generate different types of cells within a population, so called bimodal differentiation. For example, a Bacillus subtilis culture can contain both motile and non-motile cells. In this study we compared the gene expression between motile and non-motile cells. It appeared that motile cells express less ribosomes. To confirm this, we constructed a ribosomal promoter fusion that enabled us to measure expression of this promoter in individual cells. This reporter fusion confirmed our initial finding. The re-allocation of cellular resources from ribosome synthesis towards synthesis of the motility apparatus results in a reduction in growth. Interestingly, this growth reduction has been shown to stimulate bimodal differentiation.

PMID:33782055 | DOI:10.1128/JB.00037-21

Pharmacol Res. 2021 Mar 26:105581. doi: 10.1016/j.phrs.2021.105581. Online ahead of print.

ABSTRACT

In-depth characterization of heart-brain communication in critically ill patients with severe acute respiratory failure is attracting significant interest in the COronaVIrus Disease 19 (COVID-19) pandemic era during intensive care unit (ICU) stay and after ICU or hospital discharge. Emerging research has provided new insights into pathogenic role of the deregulation of the heart-brain axis (HBA), a bidirectional flow of information, in leading to severe multiorgan disease syndrome (MODS) in patients with confirmed infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Noteworthy, HBA dysfunction may worsen the outcome of the COVID-19 patients. In this review, we discuss the critical role HBA plays in both promoting and limiting MODS in COVID-19. We also highlight the role of HBA as new target for novel therapeutic strategies in COVID-19 in order to open new translational frontiers of care. This is a translational perspective from the Italian Society of Cardiovascular Researches.

PMID:33781873 | DOI:10.1016/j.phrs.2021.105581

Methods. 2021 Mar 26:S1046-2023(21)00091-8. doi: 10.1016/j.ymeth.2021.03.017. Online ahead of print.

ABSTRACT

High-throughput RNA sequencing has enabled the extensive detection of circular RNAs (circRNAs) in eukaryotic organisms. However, most circRNAs are derived from exonic regions and possess sequences that are highly overlapped to their cognate linear mRNAs, which makes the reconstruction of the internal structure and full-length circular transcripts a challenging aspect in circRNA studies. To solve this problem, we provide a step-by-step protocol for the full-length reconstruction of circRNAs using CIRI-full and CIRI-long in Illumina and Nanopore RNA-seq libraries. By combining experimental and computational methods, we are able to effectively characterize the full-length landscape of circRNAs, which provide an important basis to explore the biogenesis and biological function of circRNAs.

PMID:33781864 | DOI:10.1016/j.ymeth.2021.03.017

Elife. 2021 Mar 30;10:e59187. doi: 10.7554/eLife.59187.

ABSTRACT

Despite recent improvements in microscope technologies, segmenting and tracking cells in three-dimensional time-lapse images (3D + T images) to extract their dynamic positions and activities remains a considerable bottleneck in the field. We developed a deep learning-based software pipeline, 3DeeCellTracker, by integrating multiple existing and new techniques including deep learning for tracking. With only one volume of training data, one initial correction, and a few parameter changes, 3DeeCellTracker successfully segmented and tracked ~100 cells in both semi-immobilized and 'straightened' freely moving worm's brain, in a naturally beating zebrafish heart, and ~1000 cells in a 3D cultured tumor spheroid. While these datasets were imaged with highly divergent optical systems, our method tracked 90-100% of the cells in most cases, which is comparable or superior to previous results. These results suggest that 3DeeCellTracker could pave the way for revealing dynamic cell activities in image datasets that have been difficult to analyze.

PMID:33781383 | DOI:10.7554/eLife.59187

Plant Methods. 2021 Mar 30;17(1):32. doi: 10.1186/s13007-021-00731-8.

ABSTRACT

BACKGROUND: We report a method to estimate carbon assimilation based on isotope ratio-mass spectrometry (IRMS) of 13CO2 labeled plant tissue. Photosynthetic carbon assimilation is the principal experimental observable which integrates important aspects of primary plant metabolism. It is traditionally measured through gas exchange. Despite its centrality in plant research, gas exchange performs poorly with rosette growth habits typical of Arabidopsis thaliana, mutant lines with limited biomass, and accounts poorly for leaf shading.

RESULTS: IRMS-based carbon assimilation values from plants labeled at different light intensities were compared to those obtained by gas exchange, and the two methods yielded similar values. Using this method, we observed a strong correlation between 13C content and labeling time (R2 = 0.999) for 158 wild-type plants labeled for 6 to 42 min. Plants cultivated under different light regimes showed a linear response with respect to carbon assimilation, varying from 7.38 nmol 13C mg-1 leaf tissue min-1 at 80 PAR to 19.27 nmol 13C mg-1 leaf tissue min-1 at 500 PAR. We applied this method to examine the link between inhibition of the 2C-methyl-D-erythritol-4-phosphate (MEP) pathway and suppression of photosynthesis. A significant decrease in carbon assimilation was observed when metabolic activity in the MEP pathway was compromised by mutation or herbicides targeting the MEP pathway. Mutants affected in MEP pathway genes 1-DEOXY-D-XYLULOSE 5-PHOSPHATE SYNTHASE (DXS) or 1-HYDROXY-2-METHYL-2-(E)-BUTENYL 4-DIPHOSPHATE SYNTHASE (HDS) showed assimilation rates 36% and 61% lower than wild type. Similarly, wild type plants treated with the MEP pathway inhibitors clomazone or fosmidomycin showed reductions of 52% and 43%, respectively, while inhibition of the analogous mevalonic acid pathway, which supplies the same isoprenoid intermediates in the cytosol, did not, suggesting inhibition of photosynthesis was specific to disruption of the MEP pathway.

CONCLUSIONS: This method provides an alternative to gas exchange that offers several advantages: resilience to differences in leaf overlap, measurements based on tissue mass rather than leaf surface area, and compatibility with mutant Arabidopsis lines which are not amenable to gas exchange measurements due to low biomass and limited leaf surface area. It is suitable for screening large numbers of replicates simultaneously as well as post-hoc analysis of previously labeled plant tissue and is complementary to downstream detection of isotopic label in targeted metabolite pools.

PMID:33781281 | DOI:10.1186/s13007-021-00731-8

Annu Rev Biochem. 2021 Mar 29. doi: 10.1146/annurev-biochem-072420-112431. Online ahead of print.

ABSTRACT

Optobiochemical control of protein activities allows the investigation of protein functions in living cells with high spatiotemporal resolution. Over the last two decades, numerous natural photosensory domains have been characterized and synthetic domains engineered and assembled into photoregulatory systems to control protein function with light.Here, we review the field of optobiochemistry, categorizing photosensory domains by chromophore, describing photoregulatory systems by mechanism of action, and discussing protein classes frequently investigated using optical methods. We also present examples of how spatial or temporal control of proteins in living cells has provided new insights not possible with traditional biochemical or cell biological techniques. Expected final online publication date for the Annual Review of Biochemistry, Volume 90 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

PMID:33781076 | DOI:10.1146/annurev-biochem-072420-112431

Nature. 2021 Mar 29. doi: 10.1038/s41586-021-03475-6. Online ahead of print.

ABSTRACT

Recent studies have provided insights into the pathology and immune response to coronavirus disease 2019 (COVID-19)1-8. However, thorough interrogation of the interplay between infected cells and the immune system at sites of infection is lacking. We use high parameter imaging mass cytometry9 targeting the expression of 36 proteins, to investigate at single cell resolution, the cellular composition and spatial architecture of human acute lung injury including SARS-CoV-2. This spatially resolved, single-cell data unravels the disordered structure of the infected and injured lung alongside the distribution of extensive immune infiltration. Neutrophil and macrophage infiltration are hallmarks of bacterial pneumonia and COVID-19, respectively. We provide evidence that SARS-CoV-2 infects predominantly alveolar epithelial cells and induces a localized hyper-inflammatory cell state associated with lung damage. By leveraging the temporal range of COVID-19 severe fatal disease in relation to the time of symptom onset, we observe increased macrophage extravasation, mesenchymal cells, and fibroblasts abundance concomitant with increased proximity between these cell types as the disease progresses, possibly as an attempt to repair the damaged lung tissue. This spatially resolved single-cell data allowed us to develop a biologically interpretable landscape of lung pathology from a structural, immunological and clinical standpoint. This spatial single-cell landscape enabled the pathophysiological characterization of the human lung from its macroscopic presentation to the single-cell, providing an important basis for the understanding of COVID-19, and lung pathology in general.

PMID:33780969 | DOI:10.1038/s41586-021-03475-6

PLoS One. 2021 Mar 29;16(3):e0248865. doi: 10.1371/journal.pone.0248865. eCollection 2021.

ABSTRACT

Dinoroseobacter shibae living in the photic zone of marine ecosystems is frequently exposed to oxygen that forms highly reactive species. Here, we analysed the adaptation of D. shibae to different kinds of oxidative stress using a GeLC-MS/MS approach. D. shibae was grown in artificial seawater medium in the dark with succinate as sole carbon source and exposed to hydrogen peroxide, paraquat or diamide. We quantified 2580 D. shibae proteins. 75 proteins changed significantly in response to peroxide stress, while 220 and 207 proteins were differently regulated by superoxide stress and thiol stress. As expected, proteins like thioredoxin and peroxiredoxin were among these proteins. In addition, proteins involved in bacteriochlophyll biosynthesis were repressed under disulfide and superoxide stress but not under peroxide stress. In contrast, proteins associated with iron transport accumulated in response to peroxide and superoxide stress. Interestingly, the iron-responsive regulator RirA in D. shibae was downregulated by all stressors. A rirA deletion mutant showed an improved adaptation to peroxide stress suggesting that RirA dependent proteins are associated with oxidative stress resistance. Altogether, 139 proteins were upregulated in the mutant strain. Among them are proteins associated with protection and repair of DNA and proteins (e. g. ClpB, Hsp20, RecA, and a thioredoxin like protein). Strikingly, most of the proteins involved in iron metabolism such as iron binding proteins and transporters were not part of the upregulated proteins. In fact, rirA deficient cells were lacking a peroxide dependent induction of these proteins that may also contribute to a higher cell viability under these conditions.

PMID:33780465 | DOI:10.1371/journal.pone.0248865

PLoS Comput Biol. 2021 Mar 29;17(3):e1008690. doi: 10.1371/journal.pcbi.1008690. Online ahead of print.

ABSTRACT

Candida albicans, an opportunistic fungal pathogen, is a significant cause of human infections, particularly in immunocompromised individuals. Phenotypic plasticity between two morphological phenotypes, yeast and hyphae, is a key mechanism by which C. albicans can thrive in many microenvironments and cause disease in the host. Understanding the decision points and key driver genes controlling this important transition and how these genes respond to different environmental signals is critical to understanding how C. albicans causes infections in the host. Here we build and analyze a Boolean dynamical model of the C. albicans yeast to hyphal transition, integrating multiple environmental factors and regulatory mechanisms. We validate the model by a systematic comparison to prior experiments, which led to agreement in 17 out of 22 cases. The discrepancies motivate alternative hypotheses that are testable by follow-up experiments. Analysis of this model revealed two time-constrained windows of opportunity that must be met for the complete transition from the yeast to hyphal phenotype, as well as control strategies that can robustly prevent this transition. We experimentally validate two of these control predictions in C. albicans strains lacking the transcription factor UME6 and the histone deacetylase HDA1, respectively. This model will serve as a strong base from which to develop a systems biology understanding of C. albicans morphogenesis.

PMID:33780439 | DOI:10.1371/journal.pcbi.1008690

EMBO Rep. 2021 Mar 29:e51573. doi: 10.15252/embr.202051573. Online ahead of print.

ABSTRACT

Fibroblasts are a major component of the microenvironment of most solid tumours. Recent research elucidated a large heterogeneity and plasticity of activated fibroblasts, indicating that their role in cancer initiation, growth and metastasis is complex and context-dependent. Here, we performed genome-wide expression analysis comparing fibroblasts in normal, inflammatory and tumour-associated skin. Cancer-associated fibroblasts (CAFs) exhibit a fibrotic gene signature in wound-induced tumours, demonstrating persistent extracellular matrix (ECM) remodelling within these tumours. A top upregulated gene in mouse CAFs encodes for PRSS35, a protease capable of collagen remodelling. In human skin, we observed PRSS35 expression uniquely in the stroma of high-grade squamous cell carcinomas. Ablation of PRSS35 in mouse models of wound- or chemically-induced tumorigenesis resulted in aberrant collagen composition in the ECM and increased tumour incidence. Our results indicate that fibrotic enzymes expressed by CAFs can regulate squamous tumour initiation by remodelling the ECM.

PMID:33780134 | DOI:10.15252/embr.202051573

J Exp Bot. 2021 Mar 29;72(7):2261-2265. doi: 10.1093/jxb/eraa600.

NO ABSTRACT

PMID:33779750 | DOI:10.1093/jxb/eraa600

Am J Respir Crit Care Med. 2021 Mar 29. doi: 10.1164/rccm.202009-3720OC. Online ahead of print.

ABSTRACT

RATIONALE Androgens are potentially beneficial in asthma, but androgen receptor (AR) has not been studied in human airways. OBJECTIVES To measure whether AR and its ligands are associated with human asthma outcomes. METHODS We compared AR expression to lung function, symptom scores and fractional of exhaled nitric oxide (FENO) in adults enrolled in the Severe Asthma Research Program (SARP). Further, asthma exacerbations, and emergency department (ED) visits were also evaluated in the SARP, with validation studies in the Cleveland Clinic Health System (CCHS) and the National Health and Nutrition Examination Survey (NHANES). MEASUREMENTS AND MAIN RESULTS In SARP (n=128), AR gene expression from bronchoscopic epithelial brushings was positively correlated with FEV1/FVC ratio (R2=0.135, p=0.0002) and total AQLQ score (R2=0.056, p=0.016); and was negatively associated with FENO (R2=0.178, p=9.8e-06) and NOS2 gene expression (R2=0.281, p=1.2e-10). In SARP (n=1,659), CCHS (n=32,527) and NHANES (n=2,629), women had more asthma exacerbations and ED visits than men. Levels of the AR ligand precursor dehydroepiandrosterone sulfate (DHEA-S) correlated positively with FEV1 in both women and men. CONCLUSIONS Higher AR expression in bronchial epithelial cells, and higher androgen levels, are associated with better lung function, fewer symptoms and lower FENO in human asthma. The role of androgens should be considered in asthma management.

PMID:33779531 | DOI:10.1164/rccm.202009-3720OC

Gut Microbes. 2021 Jan-Dec;13(1):1-19. doi: 10.1080/19490976.2021.1900995.

ABSTRACT

Oral antibiotics are commonly prescribed to non-hospitalized adults. However, antibiotic-induced changes in the human gut microbiome are often investigated in cohorts with preexisting health conditions and/or concomitant medication, leaving the effects of antibiotics not completely understood. We used a combination of omic approaches to comprehensively assess the effects of antibiotics on the gut microbiota and particularly the gut resistome of a small cohort of healthy adults. We observed that 3 to 19 species per individual proliferated during antibiotic treatment and Gram-negative species expanded significantly in relative abundance. While the overall relative abundance of antibiotic resistance gene homologs did not significantly change, antibiotic-specific gene homologs with presumed resistance toward the administered antibiotics were common in proliferating species and significantly increased in relative abundance. Virome sequencing and plasmid analysis showed an expansion of antibiotic-specific resistance gene homologs even 3 months after antibiotic administration, while paired-end read analysis suggested their dissemination among different species. These results suggest that antibiotic treatment can lead to a persistent expansion of antibiotic resistance genes in the human gut microbiota and provide further data in support of good antibiotic stewardship.Abbreviation: ARG - Antibiotic resistance gene homolog; AsRG - Antibiotic-specific resistance gene homolog; AZY - Azithromycin; CFX - Cefuroxime; CIP - Ciprofloxacin; DOX - Doxycycline; FDR - False discovery rate; GRiD - Growth rate index value; HGT - Horizontal gene transfer; NMDS - Non-metric multidimensional scaling; qPCR - Quantitative polymerase chain reaction; RPM - Reads per million mapped reads; TA - Transcriptional activity; TE - Transposable element; TPM - Transcripts per million mapped reads.

PMID:33779498 | DOI:10.1080/19490976.2021.1900995

Am J Physiol Renal Physiol. 2021 Mar 29. doi: 10.1152/ajprenal.00640.2020. Online ahead of print.

ABSTRACT

High-incidence regions of Leptospirosis caused by Leptospira spp., coincide with chronic kidney disease. This study investigates whether asymptomatic leptospirosis is an emerging culprit that predispose to progressive chronic kidney disease when superimposed on secondary nephrotoxic injury. Kidney histology/function and whole-transcriptomic profiles were evaluated for leptospira-infected C57/BL6 mice with adenine-induced kidney injury. The extent of tubulointerstitial kidney lesions and the expression of inflammation/fibrosis genes in infected mice with low-dose (0.1%) adenine, particularly in high-dose (0.2%) adenine-fed superimposed on leptospira-infected mice, were significantly increased compared with mice following infection or adenine diet alone and the findings are consistent with renal transcriptome analysis. Pathway enrichment findings showed integrin β- and fibronectin-encoding genes had distinct expression within the integrin-linked kinase signaling pathway which were up-regulated in 0.2% adenine-fed leptospira-infected mice but not in 0.2% adenine-fed mice, indicating background subclinical leptospiral infection indeed enhanced subsequent secondary nephrotoxic kidney injury and potential pathogenic molecules associated with secondary nephrotoxic leptospirosis. Comparative analysis of gene-expression patterns with UUO-induced mouse renal fibrosis and patients with chronic kidney disease showed that differentially expressed orthologous genes such as hemoglobin α, PDZ binding kinase and DNA topoisomerase II α were identified in infected mice fed with low-dose and high-dose adenine, respectively, revealing differentially expressed signatures identical to those found in the datasets and may serve as markers of aggravated kidney progression. This study indicates that background subclinical leptospirosis, when subjected to various degrees of subsequent secondary nephrotoxic injury, may predispose to exacerbated fibrosis, mimicking the pathophysiological process of progressive chronic kidney disease.

PMID:33779314 | DOI:10.1152/ajprenal.00640.2020

Am J Physiol Renal Physiol. 2021 Mar 29. doi: 10.1152/ajprenal.00064.2021. Online ahead of print.

ABSTRACT

The hormone aldosterone is essential for maintaining K+ and Na+ balance and controlling blood pressure. Aldosterone has different effects if it is secreted due to hypovolemia or hyperkalemia. The kidney distal convoluted tubule (DCT) is believed to play a central role in mediating the differential responses to aldosterone. To determine the alterations in the DCT that may be responsible for these effects, male mice with GFP expression specifically in the DCT were maintained on diets containing low NaCl (hypovolemic state) or high K citrate (hyperkalemic state) for 4 days and DCT cells isolated using fluorescence-activated cell sorting. This pure population of DCT cells were subjected to analysis by liquid chromatography-coupled tandem mass spectrometry. Over 3000 proteins were identified in the DCT, creating the first proteome of the mouse DCT. Of the identified proteins, 210 were altered in abundance following a low NaCl diet and 625 following the high K+ diet. Many of these changes were not detectable by analyzing whole kidney samples from the same animals. When comparing responses to high K+ versus low Na+ diets, protein translation, chaperone-mediated protein folding and protein ubiquitylation are likely to be significantly altered in the DCT subsequent to a high K+ diet. In conclusion, this study defines an in vivo protein landscape of the DCT in male mice following either a low NaCl or a high K+ diet and acts as an essential resource for the kidney research community.

PMID:33779313 | DOI:10.1152/ajprenal.00064.2021