Large Differences In Expression Research Articles

RNA-seq reproducibility of Pseudomonas aeruginosa in laboratory models of cystic fibrosis.

Reproducibility is a fundamental expectation in science and enables investigators to have confidence in their research findings and the ability to compare data from disparate sources, but evaluating reproducibility can be elusive. For example, generating RNA sequencing (RNA-seq) data includes multiple steps where variance can be introduced. Thus, it is unclear if RNA-seq data from different sources can be validly compared. While most studies on RNA-seq reproducibility focus on eukaryotes, we evaluate bias in bacteria using Pseudomonas aeruginosa gene expression data from five laboratory models of cystic fibrosis. We leverage a large data set that includes samples prepared in three different laboratories and paired data sets where the same sample was sequenced using at least two different sequencing pipelines. We report here that expression data are highly reproducible across laboratories. In addition, while samples sequenced with different sequencing pipelines showed significantly more variance in expression profiles than between labs, gene expression was still highly reproducible between sequencing pipelines. Further investigation of expression differences between two sequencing pipelines revealed that library preparation methods were the largest source of error, though analyses to identify the source of this variance were inconclusive. Consistent with the reproducibility of expression between sequencing pipelines, we found that different pipelines detected over 80% of the same differentially expressed genes with large expression differences between conditions. Thus, bacterial RNA-seq data from different sources can be validly compared, facilitating the ability to advance understanding of bacterial behavior and physiology using the wide array of publicly available RNA-seq data sets.IMPORTANCERNA sequencing (RNA-seq) has revolutionized biology, but many steps in RNA-seq workflows can introduce variance, potentially compromising reproducibility. While reproducibility in RNA-seq has been thoroughly investigated in eukaryotes, less is known about pipelines and workflows that introduce variance and biases in bacterial RNA-seq data. By leveraging Pseudomonas aeruginosa transcriptomes in cystic fibrosis models from different laboratories and sequenced with different sequencing pipelines, we directly assess sources of bacterial RNA-seq variance. RNA-seq data were highly reproducible, with the largest variance due to sequencing pipelines, specifically library preparation. Different sequencing pipelines detected overlapping differentially expressed genes, especially those with large expression differences between conditions. This study confirms that different approaches to preparing and sequencing bacterial RNA libraries capture comparable transcriptional profiles, supporting investigators' ability to leverage diverse RNA-seq data sets to advance their science.

Populations of Triple Negative and Hormone Receptor Positive HER2 Negative Breast Tumors Share Immune Gene Profiles

Background: Immune therapy has revolutionized the treatment of certain cancers including melanoma and lung cancer. Breast cancer has fewer tumors with high immune infiltrate and Immune Checkpoint Inhibitor (ICI) therapy has shown the most significant responses in the Triple Negative (TN) subtype although roles are emerging in the other subtypes. The presence of Tumor Infiltrating Lymphocytes (TIL) is predictive of response to ICI therapy in metastatic TN and associated with better survival in local TN disease. Hormone Receptor (HR) positive HER2 negative (HR+HER2-) breast tumors do not show improved prognosis with increasing TIL and only a small portion of HR+HER2- tumors respond to ICI in both metastatic and local disease. We therefore sought to identify genetic differences between TN and HR+HER2- tumors to identify how these may contribute to their differences in immune infiltrate. Methods: We contrasted immune-associated gene expression between 119 TN and 475 HR+HER2- breast tumors from The Cancer Genome Atlas (TCGA) and confirmed our findings from 299 TN and 1369 HR+HER2- breast tumors in METABRIC. Results: We found that TN and HR+HER2- tumors can be grouped into immune-high or -low tumors, with both subtypes represented in the immune-high group (40% HR+HER2- tumors of both Luminal A and Luminal B type and 71% TN tumors) in the TCGA. The genes upregulated in the immune-high cluster included GZMB, CXCL9, and IDO1 (Log2FC > 2; Adj. p < 10X10-40). The largest expression difference between the immune-high TN and HR+HER2- tumors was that TN tumors had more abundant Th1 and Th2 CD4+ T cells while HR+HER2- tumors had more abundant fibroblasts (Log2FC > 0.3; Adj p < 10X10-10). Conclusions: Our data suggest that an immune-high signature is not dictated by breast cancer subtype. However, fibroblasts, particularly fibroblast subsets associated with worse outcome, are more abundant in the immune-high HR+HER2- tumors.

Abstract 1822: Artemisia annua Lpolyphenols augment b-lapachone effects on oxaliplatin-resistant HCT 116 colorectal cancer cells by downregulating TERT, CD44, EGFR and oxaliplatin resistance-related proteins of OXP-R-Hct 116 cells

Abstract We previously demonstrated that β-lapachone (β-Lap) exerts stronger anticancer activity on oxaliplatin-resistant HCT116 colorectal cancer cells (Oxp-R-HCT 116 cells) than parental HCT116 cells (p-HCT 116 cells) by downregulating the oxaliplatin resistance-related upregulated proteins (Oxp-RR-Proteins) proteins in Oxp-R-HCT 116 cells, such as SOD1, MAPK, and nucelophosmin. We also demonstrated polyphenols extracted from Korean Artemisia annua L. (pKAL) exerts anticancer activity on radio-resistant MDA-MB-231 human breast cancer cells by suppressing stem cell phenotype, β-catenin, and MMP-9. In this study, we found that pKAL significantly enhanced the anticancer activity of β-lapachone (β-Lap) on oxaliplatin-resistant (Oxp-R) HCT116 colorectal cancer cells. The aim of this study is to elucidate how pKAL enhance the anticancer effects of β-Lap on Oxp-R-HCT 116 cells. CCK-8 assay, phase-contrast microscopy analysis, and morphological analysis with hematoxylin stain revealed that the anticancer effect of β-Lap is more enhanced by pKAL on Oxp-R-HCT 116 cells over 60 hr. This phenomenon was associated with suppression of oxaliplatin resistance-related upregulated proteins (Oxp-RR-Proteins) (p53, ERK, and β-catenin), and downregulation of cell survival- and stemness-related proteins (TERT, CD44 and EGFR) that were not up-regulated in Oxp-R-HCT 116 cells. Protein-protein interaction network analysis of the 21 proteins that showed large difference in expression between before and after the combined treatment of pKAL and β-Lap in HCT116-OxPt-R cells revealed that the enhanced anticancer effect of β-Lap by pKAL was related to the inhibition of negative regulation of apoptotic process and the induction of DNA damage through TERT, CD44, and EGFR-mediated multiple signaling networks. The detailed western blot analysis for anti-cancer effects of pKAL revealed that pKAL alone also suppressed the expression of TERT, CD44 and EGFR in p-HCT 116 cells as well as Oxp-R-HCT 116 cells while β-Lap alone did not influence the expression of them. In addition, for some of the Oxp-RR-Proteins of Oxp-R-HCT 116 cells (p53, ERK, and β-catenin) were suppressed by pKAL alone, but not others. However, some other Oxp-RR-Proteins of Oxp-R-HCT 116 cells that were not suppressed by pKAL alone were significantly suppressed by the combination treatment of pKAL and β-Lap. These findings suggest that pKAL enhanced the anti-cancer effects β-Lap by suppressing TERT, CD44, and EGFR-mediated multiple signaling networks as well as some of the Oxp-RR-Proteins of Oxp-R-HCT 116 cells. In conclusion, this study suggests that pKAL enhance the anticancer effects of β-Lap on OXP-R-Hct 116 cells by downregulating CD44, EGFR and some of the Oxp-RR-Proteins of Oxp-R-HCT 116 cells. Citation Format: Won Sup Lee, Eun Joo Jung, Hye Jung Kim, Sung Chul Shin, Gon Sup Kim, Jin-Myung Jung, Soon Chan Hong, Choong Won Kim. Artemisia annua Lpolyphenols augment b-lapachone effects on oxaliplatin-resistant HCT 116 colorectal cancer cells by downregulating TERT, CD44, EGFR and oxaliplatin resistance-related proteins of OXP-R-Hct 116 cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1822.

Global expression patterns of R-genes in tomato and potato.

As key-players of plant immunity, the proteins encoded by resistance genes (R-genes) recognize pathogens and initiate pathogen-specific defense responses. The expression of some R-genes carry fitness costs and therefore inducible immune responses are likely advantageous. To what degree inducible resistance driven by R-genes is triggered by pathogen infection is currently an open question. In this study we analyzed the expression of 940 R-genes of tomato and potato across 315 transcriptome libraries to investigate how interspecific interactions with microbes influence R-gene expression in plants. We found that most R-genes are expressed at a low level. A small subset of R-genes had moderate to high levels of expression and were expressed across many independent libraries, irrespective of infection status. These R-genes include members of the class of genes called NRCs (NLR required for cell death). Approximately 10% of all R-genes were differentially expressed during infection and this included both up- and down-regulation. One factor associated with the large differences in R-gene expression was host tissue, reflecting a considerable degree of tissue-specific transcriptional regulation of this class of genes. These results call into question the widespread view that R-gene expression is induced upon pathogen attack. Instead, a small core set of R-genes is constitutively expressed, imparting upon the plant a ready-to-detect and defend status.

Comparison of three DREADD agonists acting on Gq-DREADDs in the ventral tegmental area to alter locomotor activity in tyrosine hydroxylase:Cre male and female rats

RationaleDespite the increasingly pervasive use of chemogenetic tools in preclinical neuroscience research, the in vivo pharmacology of DREADD agonists remains poorly understood. The pharmacological effects of any ligand acting at receptors, engineered or endogenous, are influenced by numerous factors including potency, time course, and receptor selectivity. Thus, rigorous comparison of the potency and time course of available DREADD ligands may provide an empirical foundation for ligand selection. ObjectivesCompare the behavioral pharmacology of three different DREADD ligands clozapine-N-oxide (CNO), compound 21 (C21), and deschloroclozapine (DCZ) in a locomotor activity assay in tyrosine hydroxylase:cre recombinase (TH:Cre) male and female rats. MethodsLocomotor activity in nine adult TH:Cre Sprague-Dawley rats (5 female, 4 male) was monitored for two hours following administration of d-amphetamine (vehicle, 0.1–3.2 mg/kg, IP), DCZ (vehicle, 0.32–320 µg/kg, IP), CNO (vehicle, 0.32–10 mg/kg), and C21 (vehicle, 0.1–3.2 mg/kg, IP). Behavioral sessions were conducted twice per week prior to and starting three weeks after bilateral intra-VTA hM3Dq DREADD virus injection. Resultsd-Amphetamine significantly increased locomotor activity pre- and post-DREADD virus injection. DCZ, CNO, and C21 did not alter locomotor activity pre-DREADD virus injection. There was no significant effect of DCZ, CNO, and C21 on locomotor activity post-DREADD virus injection; however, large individual differences in both behavioral response and receptor expression were observed. ConclusionsLarge individual variability was observed in both DREADD agonist behavioral effects and receptor expression. These results suggest further basic research would facilitate the utility of these chemogenetic tools for behavioral neuroscience research.

A nuclear receptor HR96-related gene underlies large trans-driven differences in detoxification gene expression in a generalist herbivore

The role, magnitude, and molecular nature of trans-driven expression variation underlying the upregulation of detoxification genes in pesticide resistant arthropod populations has remained enigmatic. In this study, we performed expression quantitative trait locus (eQTL) mapping (n = 458) between a pesticide resistant and a susceptible strain of the generalist herbivore and crop pest Tetranychus urticae. We found that a single trans eQTL hotspot controlled large differences in the expression of a subset of genes in different detoxification gene families, as well as other genes associated with host plant use. As established by additional genetic approaches including RNAi gene knockdown, a duplicated gene with a nuclear hormone receptor HR96-related ligand-binding domain was identified as causal for the expression differences between strains. The presence of a large family of HR96-related genes in T. urticae may enable modular control of detoxification and host plant use genes, facilitating this species’ known and rapid evolution to diverse pesticides and host plants.

Abstract 553: SKP2 knockout induces macrophage infiltration in p53/Rb1 null transgenic mouse models of osteosarcoma and drives gene expression correlated with improved survival in patients

Abstract Background: Osteosarcoma (OS) is an aggressive cancer of the bone with a poor prognosis. OS often involve mutations of tumor suppressors RB1 and TP53. One putative proto-oncogene in OS is SKP2, which codes for a substrate-recognition factor of the SCF E3 ubiquitin ligase. We have demonstrated that germline knockout of SKP2 in a pre-clinical transgenic mouse model of OS doubly deficient in Rb1 and Trp53 improved survival, delayed tumorigenesis, reduced malignant cell proliferation, slowed tumor growth, diminished stemness, and induced apoptosis. However, the role that SKP2 plays in OS progression remains unclear. Method: We performed bulk RNA-sequencing on pre-clinical transgenic mouse models of OS. To model OS in mice, we generated a conditional double-knockout line of Trp53 and Rb1 mutations induced in cells of the bone-forming osteoblast lineage via Cre-Lox recombination (“DKO”: Osx1-Cre;Rb1lox/lox;p53lox/lox). We compared this with a triple-knockout model, which additionally features a germline Skp2 knockout (“TKO”: Osx1-Cre;Rb1lox/lox;p53lox/lox;SKP2-/-). We compared tumors from the TKO and DKO models via bulk RNA-sequencing (n=3 per group) to study differential expression and immune infiltration. We used immunohistochemistry (IHC) and quantification to validate differences in immune markers between genotypes. Using the transcriptomic results from the mouse models, we analyzed a human OS patient cohort of 83 participants (NCI TARGET OS) with RNA-seq and clinical data via survival analysis to infer the impact of modulating SKP2 in OS patients. Result: We found a large difference in gene expression between the TKO and DKO models. Surprisingly, we observed a dramatic increase in the expression of genes related to immune microenvironment infiltration in TKO tumors compared to DKO. Macrophage transcriptomic signatures were the strongest signal detected (P<0.001), but significant increases in B cells, endothelial cells and T cell signatures were also observed. IHC also showed macrophage markers were higher in TKO (P = 0.08). In the NCI TARGET OS cohort, high expression of genes up-regulated in TKO was significantly correlated with 5-year overall survival (p=0.02). This effect was driven by macrophage transcriptomic signatures. This finding was supported by an immune microenvironment deconvolution analysis, which showed that macrophages and T cells were associated with improved overall survival in the patient cohort (p=0.01). We are currently performing single-cell RNA-sequencing analysis to study immune infiltration and cellular heterogeneity in more detail. Conclusion: Taken together, our new findings indicate that SKP2 modulation in OS may induce a vigorous anti-tumor immune activation especially in the form of macrophage and lymphocyte infiltration into the tumor microenvironment. Citation Format: Alexander Ferrena, Jichuan Wang, Ranxin Zhang, Rui Yang, David Geller, Bang Hoang, Deyou Zheng. SKP2 knockout induces macrophage infiltration in p53/Rb1 null transgenic mouse models of osteosarcoma and drives gene expression correlated with improved survival in patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 553.

Identifying Genes Related to Acute Myocardial Infarction Based on Network Control Capability.

Identifying genes significantly related to diseases is a focus in the study of disease mechanisms. In this paper, from the perspective of integrated analysis and dynamic control, a method for identifying genes significantly related to diseases based on logic networks constructed by the LAPP method, referred to as NCCM, is proposed and applied to the study of the mechanism of acute myocardial infarction (AMI). It is found that 82.35% of 17 differential control capability genes (DCCGs) identified by NCCM are significantly correlated with AMI/MI in the literature and DISEASES database. The enrichment analysis of DCCGs shows that AMI is closely related to the positive regulation of vascular-associated smooth muscle cell proliferation and regulation of cytokine production involved in the immune response, in which HBEGF, THBS1, NR4A3, NLRP3, EDN1, and MMP9 play a crucial role. In addition, although the expression levels of CNOT6L and ACYP1 are not significantly different between the control group and the AMI group, NCCM shows that they are significantly associated with AMI. Although this result still needs further verification, it shows that the method can not only identify genes with large differences in expression but also identify genes that are associated with diseases but with small changes in expression.

The ATPase Inhibitory Factor 1 is a Tissue-Specific Physiological Regulator of the Structure and Function of Mitochondrial ATP Synthase: A Closer Look Into Neuronal Function.

The ATP synthase is an essential multifunctional enzyme complex of mitochondria that produces most of cellular ATP, shapes the structure of the inner membrane into cristae and regulates the signals that control cell fate or demise. The ATPase Inhibitory Factor 1 (IF1) functions in vivo as a physiological regulator of the ATP synthase and thereby controls mitochondrial structure and function, and the retrograde signaling pathways that reprogram nuclear gene expression. However, IF1 is not ubiquitously expressed in mammals, showing tissue-restricted expression in humans and mice and large expression differences between the two species in some tissues. Herein, we summarized key regulatory functions of IF1 for tissue homeostasis, with special emphasis on the deleterious effects that its genetic ablation in neurons has in learning. The development and characterization of tissue-specific mouse models with regulated expression of IF1 will be crucial to disentangle the contribution of the ATP synthase/IF1 axis in pathophysiology.

Immunological significance of alternative splicing prognostic signatures for bladder cancer

BackgroundBladder cancer (BLCA) is the most common malignant tumor in the genitourinary system, and the complex tumor microenvironment (TME) of BLCA is the main factor in its difficult treatment. Accumulated evidence supports that alternative splicing (AS) events frequently occur in cancer and are closely related to the TME. Therefore, there is an urgent need to comprehensively analyze the prognostic value of AS events in BLCA. MethodThe clinical, transcriptome and AS data of BLCA were downloaded from the Cancer Genome Atlas database, and a Cox proportional hazard regression model and LASSO regression were used to establish a prognostic signature. Then, the prognostic value of the signature was verified by clinical survival status, clinicopathologic features, tumor immune microenvironment (TIME), and immune checkpoint. Next, we screened the AS-related genes with the largest expression differences between tumor and normal samples by gene differential expression analysis. Finally, the regulatory network of AS-splicing factors (SFs) was established to unravel the potential regulatory mechanism of AS events in BLCA. ResultsA BLCA prognostic signature related to seven AS events was constructed, and the prognostic value of the signature was also verified from multiple perspectives. Moreover, there was significant abnormal expression of PTGER3, a gene implicated in AS events, the expression of which was associated with the survival, clinicopathological features, TIME, and immunotherapy of BLCA, suggesting that it has potential clinical application value. Furthermore, the AS-SF regulatory network indicated that splicing factors (PRPF39, LUC7L, HSPA8 and DDX21) might be potential biomarkers of BLCA. ConclusionsOur study revealed the potential role of AS events in the prognosis, TIME and immunotherapy of BLCA and yielded new insights into the molecular mechanisms of and personalized immunotherapy for BLCA.

Validation and genetic characterisation of a seed weight quantitative trait locus, qSW17.1, in progenies of cultivated and wild soybean

Context Seed weight is an important agronomic trait for determining yield and appearance quality of soybean (Glycine max (L.) Merr.). Understanding the genetic basis of seed weight might lead to improvement of these traits in soybean by optimising different genes or alleles controlling seed weight. Aims A major quantitative trait locus (QTL) for seed weight, qSW17.1, was identified previously. In this study, we used progenies of cultivated soybean and wild soybean (Glycine soja Sieb. and Zucc.) for further validation and characterisation of qSW17.1. Methods A BC4F2 population, a heterogeneous inbred family (HIF) population, and a pair of qSW17.1 near-isogenic lines (NILs) developed from progenies of a cross between cultivated soybean variety Jackson and wild soybean accession JWS156-1 were cultivated under field conditions. QTL analysis and candidate gene mining were conducted. Key results A QTL corresponding to qSW17.1, which explained 19.84% and 31.71% of the total phenotypic variance in BC4F2 and HIF populations, respectively, was detected. The NIL with the cultivated soybean allele showed higher shoot biomass than the NIL with the wild soybean allele under hydroponic growth conditions, suggesting that the large-seed-size allele of qSW17.1 might be beneficial in soybean seedling establishment. qSW17.1 was delimited to a physical interval of 2515 kb on chromosome 17. Glyma.17G108500 showed a large (~3.27-fold) difference in expression between the two NILs, and was considered a candidate gene underlying qSW17.1. Implications Our results provide valuable information regarding the genetic basis of seed weight control in soybean and its utilisation in soybean molecular breeding.

Toxicological transcriptome of human airway constructs after exposure to indoor air particulate matter: In search of relevant pathways of moisture damage-associated health effects

BackgroundMultiple health effects are associated with moisture damage in buildings. Studies explaining these associations and cell-level mechanisms behind the observed health effects are urgently called for. ObjectivesWe focused on characterizing gene expression in human airway epithelium after exposure to indoor air particulate matter (PM) sampled from houses with and without moisture damage, alongside determination of general toxicological markers. MethodsWe performed detailed technical building inspections in 25 residential houses and categorized them based on the detection of moisture damages and the probability of occupant exposure. PM sampling was complemented by microbiological and volatile organic compound assessment. We exposed human airway constructs to three dilutions (1:16, 1:8, 1:4) of collected PM from moisture-damaged (index) and non-moisture-damaged (reference) houses and imaged selected constructs with electron microscopy. We analyzed general toxicological markers and the RNA of exposed constructs was sequenced targeting genes associated with toxicological pathways. We did groupwise comparisons between index and reference houses and pairwise comparisons in matched index/reference houses. ResultsIn groupwise comparison, gene Cytochrome P450 Family 1 Subfamily A Member 1 (CYP1A1) was statistically significantly over-expressed in index houses at all dilutions of collected PM and Nuclear Factor Kappa B Subunit 1 (NFKB1) at dilution 1:4 of collected PM. In pairwise index/reference house comparison, several genes related to multiple toxicological pathways were activated, largest expression differences seen for CYP1A1. However, none of the genes was consistently expressed in all the matched pairs, and general toxicological markers did not differentiate index and reference houses. DiscussionThe exposure to PM from index houses activated toxicology -related genes in airway constructs. Differential expression was not consistent among all the index/reference pairs, possibly due to compositional differences of bioactive particles. Our study highlights CYP1A1 and NFKB1 as potential targets in moisture damage -associated cellular responses.

Investigating CXCR4 expression of tumor cells and the vascular compartment: A multimodal approach.

The C-X-C chemokine receptor 4 (CXCR4) is G protein-coupled receptor that upon binding to its cognate ligand, can lead to tumor progression. Several CXCR4-targeted therapies are currently under investigation, and with it comes the need for imaging agents capable of accurate depiction of CXCR4 for therapeutic stratification and monitoring. PET agents enjoy the most success, but more cost-effective and radiation-free approaches such as ultrasound (US) imaging could represent an attractive alternative. In this work, we developed a targeted microbubble (MB) for imaging of vascular CXCR4 expression in cancer. A CXCR4-targeted MB was developed through incorporation of the T140 peptide into the MB shell. Binding properties of the T140-MB and control, non-targeted MB (NT-MB) were evaluated in MDA-MB-231 cells where CXCR4 expression was knocked-down (via shRNA) through optical imaging, and in the lymphoma tumor models U2932 and SuDHL8 (high and low CXCR4 expression, respectively) by US imaging. PET imaging of [18F]MCFB, a tumor-penetrating CXCR4-targeted small molecule, was used to provide whole-tumor CXCR4 readouts. CXCR4 expression and microvessel density were performed by immunohistochemistry analysis and western blot. T140-MB were formed with similar properties to NT-MB and accumulated sensitively and specifically in cells according to their CXCR4 expression. In NOD SCID mice, T140-MB persisted longer in tumors than NT-MB, indicative of target interaction, but showed no difference between U2932 and SuDHL8. In contrast, PET imaging with [18F]MCFB showed a marked difference in tumor uptake at 40–60 min post-injection between the two tumor models (p<0.05). Ex vivo analysis revealed that the large differences in CXCR4 expression between the two models are not reflected in the vascular compartment, where the MB are restricted; in fact, microvessel density and CXCR4 expression in the vasculature was comparable between U2932 and SuDHL8 tumors. In conclusion, we successfully developed a T140-MB that can be used for imaging CXCR4 expression in the tumor vasculature.

Ontogeny of renal, hepatic, and placental expression of ATP-binding cassette and solute carrier transporters in the rat and the rabbit

Species differences in developmental toxicity can be due to varying expression of xenobiotic transporters. Hence, knowledge on the ontogeny of these transporters, especially in human, rat and rabbit, is pivotal. Two superfamilies of transporters, the ATP-binding cassette (ABC) and the solute carrier (SLC) transporters, are well known for their role in the absorption, distribution and/or elimination of xenobiotics and endogenous substances. The aim of this study was to compare the expression levels of these xenobiotic transporters in liver, kidney and placenta of man, Wistar rat and New Zealand White rabbit during pre- and postnatal development. For this purpose, qPCR experiments were performed for rat and rabbit tissues and the gene expression profiles were compared with literature data from man, rat and rabbit. Data analysis showed large differences in transporter expression in development and between species. These results can be used to better understand developmental toxicity findings in non-clinical species and their relevance for man.

Highly individual- and tissue-specific expression of glycoprotein group A and B blood antigens in the human kidney and liver

BackgroundCurrently, research on the quantitative distribution of ABO antigens in different organs and tissues remains limited. We aimed to examine the individual characteristics of blood group glycoprotein A and B antigen expression in human kidneys and livers.MethodsWe obtained human samples, including the renal artery, renal vein, renal tissue, hepatic artery, hepatic vein, portal vein, and hepatic tissue, from 24 deceased organ transplant donors. The expression of the blood group antigens glycoprotein A and B was analysed and compared by Western blotting.ResultsThere was no significant difference in the expression between blood group glycoprotein A and B antigens at any of the seven sites (p > 0.05). The expression of both A and B antigens was highest in renal tissue and the portal vein and was lowest in the renal artery. A large difference in glycoprotein antigen expression was observed among various donors or different regions of the same individual. Univariate analysis revealed that glycoprotein A/B antigens were affected by the age and sex of donors and were significantly higher in males and in young people.ConclusionsOur study found that blood group glycoprotein antigen expression showed certain trends and distinct distribution in the kidney, liver, and vessels among individuals and in different regions of the same individual, which may explain the different clinical outcomes of patients who received ABO-incompatible transplantation.

Expression of Urocortin 3 mRNA in the Central Nervous System of the Sea Lamprey Petromyzon marinus.

Simple SummaryNeuropeptides are small proteins produced and released by neurons. Neuropeptides are key mediators in the communication between neurons. Urocortin 3 is an important neuropeptide that is involved in stress-related behaviors. In this study, our aim was to determine in which regions of the lamprey brain urocortin 3 is expressed. The study of the distribution of neuroregulatory peptides in lamprey species helps in understanding their early evolution of neuropeptidergic systems in vertebrates because lampreys are one of the most ancient vertebrate groups. The sea lamprey life cycle lasts between five and nine years, and it includes a long larval stage and a transformation to the adult stage. We analyzed the organization of urocortin 3-expressing neuronal populations in the brain of larval and adult sea lampreys to establish whether this neuropeptide is expressed differentially in these two widely different phases of the sea lamprey life cycle. Our results revealed important differences between larval and adult stages. Moreover, comparing our results with the distribution of urocortin 3 reported in other vertebrate groups also revealed a poor evolutionary conservation of urocortin 3 expression in vertebrates. Our work sheds light on the evolution and role of urocortin 3 in vertebrates.In this study, we analyzed the organization of urocortin 3 (Ucn3)-expressing neuronal populations in the brain of the adult sea lamprey by means of in situ hybridization. We also studied the brain of larval sea lampreys to establish whether this prosocial neuropeptide is expressed differentially in two widely different phases of the sea lamprey life cycle. In adult sea lampreys, Ucn3 transcript expression was observed in neurons of the striatum, prethalamus, nucleus of the medial longitudinal fascicle, torus semicircularis, isthmic reticular formation, interpeduncular nucleus, posterior rhombencephalic reticular formation and nucleus of the solitary tract. Interestingly, in larval sea lampreys, only three regions showed Ucn3 expression, namely the prethalamus, the nucleus of the medial longitudinal fascicle and the posterior rhombencephalic reticular formation. A comparison with distributions of Ucn3 in other vertebrates revealed poor conservation of Ucn3 expression during vertebrate evolution. The large qualitative differences in Ucn3 expression observed between larval and adult phases suggest that the maturation of neuroregulatory circuits in the striatum, torus semicircularis and hindbrain chemosensory systems is closely related to profound life-style changes occurring after the transformation from larval to adult life.

The sex peptide receptor in the Asian gypsy moth, Lymantria dispar, is involved in development and stress resistance

The G protein-coupled receptor (GPCR) regulates downstream genes by binding to a heterotrimeric G protein. However, the function of sex peptide receptor (SPR) in lepidopteran species is mostly unknown. Understanding the physiological functions of SPR in insects is essential for exploring new insecticidal targets. In the present study, the functions of an SPR in Lymantria dispar (Asian gypsy moth; LdSPR) were investigated. The expression of LdSPR was the highest in the 6th instar larval stage, and there was a large difference in expression between male and female adults. After LdSPR gene silencing, L. dispar larvae showed increased sensitivity to high temperature, starvation, and oxidative stress, indicating that LdSPR enhances stress resistance. These results enrich our knowledge of the function of the insect SPRs, which will lead to a better understanding of other insect GPCR family members and the identification of new targets for the development of environmentally friendly pesticides.

Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger

Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.

MiR-373-3p Regulates Invasion and Migration Abilities of Trophoblast Cells via Targeted CD44 and Radixin.

Preterm labor (PTL) is one of the obstetric complications, and is known to be associated with abnormal maternal inflammatory response and intrauterine inflammation and/or infection. However, the expression of specific miRNAs associated with PTL is not clear. In this study, we performed combination analysis of miRNA array and gene array, and then selected one miRNA (miR-373-3p) and its putative target genes (CD44 and RDX) that exhibited large expression differences in term and PTL placentas with or without inflammation. Using qRT-PCR and luciferase assays, we confirmed that miR-373-3p directly targeted CD44 and RDX. Overexpression of miR-373-3p reduced the migration and invasion of trophoblast cells, while inhibition of miR-373-3p restored the migration and invasion abilities of trophoblast cells. Finally, we validated the expression of miR-373-3p and its target genes in clinical patients’ blood. miR-373-3p was increased in PTL patients’ blood, and was the most expressed in PTL patients’ blood with inflammation. In addition, by targeting the miR-373-3p, CD44 and RDX was decreased in PTL patients’ blood, and their expression were the lowest in PTL patients’ blood with inflammation. Taken together, these findings suggest that miR-373-3p and its target genes can be potential biomarkers for diagnosis of PTL.

PSGAN++: Robust Detail-Preserving Makeup Transfer and Removal.

In this paper, we address the makeup transfer and removal tasks simultaneously, which aim to transfer the makeup from a reference image to a source image and remove the makeup from the with-makeup image respectively. Existing methods have achieved much advancement in constrained scenarios, but it is still very challenging for them to transfer makeup between images with large pose and expression differences, or handle makeup details like blush on cheeks or highlight on the nose. In addition, they are hardly able to control the degree of makeup during transferring or to transfer a specified part in the input face. These defects limit the application of previous makeup transfer methods to real-world scenarios. In this work, we propose a Pose and expression robust Spatial-aware GAN (abbreviated as PSGAN++). PSGAN++ is capable of performing both detail-preserving makeup transfer and effective makeup removal. For makeup transfer, PSGAN++ uses a Makeup Distill Network (MDNet) to extract makeup information, which is embedded into spatial-aware makeup matrices. We also devise an Attentive Makeup Morphing (AMM) module that specifies how the makeup in the source image is morphed from the reference image, and a makeup detail loss to supervise the model within the selected makeup detail area. On the other hand, for makeup removal, PSGAN++ applies an Identity Distill Network (IDNet) to embed the identity information from with-makeup images into identity matrices. Finally, the obtained makeup/identity matrices are fed to a Style Transfer Network (STNet) that is able to edit the feature maps to achieve makeup transfer or removal. To evaluate the effectiveness of our PSGAN++, we collect a Makeup Transfer In the Wild (MT-Wild) dataset that contains images with diverse poses and expressions and a Makeup Transfer High-Resolution (MT-HR) dataset that contains high-resolution images. Experiments demonstrate that PSGAN++ not only achieves state-of-the-art results with fine makeup details even in cases of large pose/expression differences but also can perform partial or degree-controllable makeup transfer. Both the code and the newly collected datasets will be released at https://github.com/wtjiang98/PSGAN.