Gene Expression Patterns Research Articles

#1290 Adverse proinflammatory responses in the kidney after FGF23 administration in three murine kidney disease models

Abstract Background and Aims The hormone FGF23 is a biomarker associated with morbidity and mortality in individuals with and without kidney disease, but the role of FGF23 excess as a pathogenic factor is incompletely understood. Here, we investigated renal FGF23 signaling in kidney disease models. Method This study used three independent disease models: i) Male C57BL/6 mice (n = 16) were treated with Freud's adjuvant and nephrotoxic serum (NTS) to induce anti-glomerular basement membrane (anti-GBM) disease. ii) Female BALB/c mice (n = 8) were treated with adriamycin (doxorubicin) 10.5 mg/kg to induce focal and segmental glomerulosclerosis (FSGS). iii) Male DBA/2J mice (n = 20) were fed a diet containing adenine 0.2%. Control mice of the respective same strain and sex received vehicle injections. Mice of the anti-GBM and FSGS models and controls received intravenous injections of recombinant FGF23 1 µg or vehicle for six consecutive days (anti-GBM) or once (FSGS), with dissection 24 h after the last injection. Mice of the adenine model were dissected after 15 weeks. Following dissection, ex vivo precision-cut kidney slices (PCKS) were obtained from n = 4 mice and maintained for 24 at 37°C, 95% O2 and 5% CO2, followed by a 1 h treatment with recombinant FGF23 200 ng/ml or vehicle. Glomerular filtration rate (GFR) or renal retention parameters in serum and albuminuria were assessed. Kidneys underwent histological assessment using hematoxylin & eosin or Masson's trichrome. Renal RNA was isolated for bulk RNAseq. Differential gene expression was assessed to determine the effect of FGF23 treatment in disease-free controls, in each disease model, and the interaction between FGF23 X disease effect for the anti-GBM and FSGS groups. Gene set enrichment analysis was performed with a focus on the immune system. Results Anti-GBM mice showed a 45 ± 27% GFR decline (mean ± SD) compared to baseline, whereas controls showed an GFR increase of 11 ± 36% (p < 0.01). Kidney histology revealed an interstitial infiltrate. The FSGS model showed elevated serum creatinine and albuminuria, and hypercellularity in some glomeruli. Mice of the adenine model showed progressively increased blood urea nitrogen concentrations starting after 2 weeks, up to a 3-fold increase at week 14. Histology revealed interstitial fibrosis and tubular atrophy. Bulk RNAseq revealed proinflammatory transcriptional signatures after FGF23 treatment in all disease models, regardless of which timepoint or model: In the anti-GBM model, Hallmark gene sets of inflammatory response, interferon-α response, interferon-β response and allograft rejection were significantly increased after 6 days of FGF23 treatment, whereas disease-free controls showed no significantly changed immune gene sets after 6 days of FGF23. In FSGS mice, none of the Hallmark gene sets were changed after 1 FGF23 injection, but top individual gene expression affected by 1 FGF23 injection were an increased proinflammatory transcription factor Cebpb and an increased DNA damage transcript Dclre1b. Finally, the PCKS of adenine model revealed no significant Hallmark gene sets, but the two genes with differential expression were a proinflammatory macrophage/fibroblast chemokine Ccl4 (increased) and an immunoglobulin heavy variable Ighv2-2 (decreased). Conclusion FGF23-driven patterns of proinflammatory gene expression were observed in three experimental models of kidney disease, both in vivo and ex vivo assessment of FGF23 signaling, thus excluding effects of FGF23 on other organs. As these findings were limited to transcriptional analyses, the present data warrant further confirmation and exploration of FGF23 as a pathogenic agent in kidney disease.

Concordant Gene Expression and Alternative Splicing Regulation under Abiotic Stresses in Arabidopsis

The current investigation endeavors to identify differentially expressed alternatively spliced (DAS) genes that exhibit concordant expression with splicing factors (SFs) under diverse multifactorial abiotic stress combinations in Arabidopsis seedlings. SFs serve as the post-transcriptional mechanism governing the spatiotemporal dynamics of gene expression. The different stresses encompass variations in salt concentration, heat, intensive light, and their combinations. Clusters demonstrating consistent expression profiles were surveyed to pinpoint DAS/SF gene pairs exhibiting concordant expression. Through rigorous selection criteria, which incorporate alignment with documented gene functionalities and expression patterns observed in this study, four members of the serine/arginine-rich (SR) gene family were delineated as SFs concordantly expressed with six DAS genes. These regulated SF genes encompass cactin, SR1-like, SR30, and SC35-like. The identified concordantly expressed DAS genes encode diverse proteins such as the 26.5 kDa heat shock protein, chaperone protein DnaJ, potassium channel GORK, calcium-binding EF hand family protein, DEAD-box RNA helicase, and 1-aminocyclopropane-1-carboxylate synthase 6. Among the concordantly expressed DAS/SF gene pairs, SR30/DEAD-box RNA helicase, and SC35-like/1-aminocyclopropane-1-carboxylate synthase 6 emerge as promising candidates, necessitating further examinations to ascertain whether these SFs orchestrate splicing of the respective DAS genes. This study contributes to a deeper comprehension of the varied responses of the splicing machinery to abiotic stresses. Leveraging these DAS/SF associations shows promise for elucidating avenues for augmenting breeding programs aimed at fortifying cultivated plants against heat and intensive light stresses.

#1193 Tracking kidney cancer initiation via somatic mutation analysis of pre-cancer cells from Von Hippel Lindau cancer predisposition syndrome

Abstract Background and Aims Somatic mutations promote the transition from a normal cell to a cancer clone. Little is known about the factors that promote mutation in normal tissues, but whole genome sequencing of pre-cancer cells, followed by mutational pattern analyses, is a revolutionary tool to understand somatic mutation mechanisms active during an individual's lifetime. In the kidney, we have shown that normal kidney tubule epithelial cells (TEC) derived from damaged PT display an excess of somatic mutations and a peculiar enrichment of mutations in exons and highly transcribed DNA compared to other cell types [1]. However, the direct contribution of this PT-specific mutational process to carcinogenesis needs further demonstration. Here, we have analyzed normal TEC that are genetically predisposed to evolve into clear cell renal cell carcinoma (ccRCC), as they harbor a germline heterozygous mutation in the tumor suppressor Von Hippel Lindau, VHL. Using this genetic model of tumor predisposition, we have tracked the PT-specific mutational process from normal cells to overt ccRCC. This study sheds light on the etiology of this mutational process, as well as its causative role in ccRCC. Method We detected somatic mutations in single genomes from normal kidney TEC from 8 control individuals and 7 VHL-disease patients in the age range 24-70. Different from our previous study [1], we isolated kidney tubule cells from the urine. Multiple TECs per individual were subjected to in vitro clonal expansion, followed by whole genome sequencing (WGS), a golden-standard method to obtain high confidence somatic mutation data. We analyzed concomitant somatic mutation- and gene expression-data from 58 clones, and expression data from 154 TEC clones. Results First, we compared our newly generated dataset (TECs obtained from urines) with our previous dataset (TECs obtained from kidney biopsies). QPCR measurements of marker gene expression and somatic mutational pattern analyses showed that the same two populations could be clonally expanded from both urines and kidney biopsies. One population expressed markers of proximal tubule (AQP1, SLC17A3) and tubule damage (VCAM1, KIM1), and showed an excess of somatic single base substitutions (SBSs). This TEC population was defined: VCAM1-PT cells. We characterized the types of SBSs that are more frequently found in VCAM1-PT genomes. The mutation spectrum was different from that induced by exposure to common mutagens, e.g. aristolochic acid, reactive oxygen species and tobacco. Normal cells, including TEC, fat and blood progenitors, showed mutation depletion in highly transcribed genes, in agreement with more efficient repair. Instead, VCAM1-PT cells showed an enrichment of specific SBS types, distinct from those induced by another transcription-coupled mutational process described in the liver. In vitro exposure of TECs to the alkylating agent ENU recapitulates some features of the spectrum of mutations observed in vivo, suggesting that VCAM1-PT cells might fail to repair damage induced by endogenous alkylating agents. The VCAM1-PT-specific mutational signature was observed in ccRCC, but not found in a variety of non-kidney cell-types and cancers. Importantly, the impact of the mutational signature was more evident in VCAM1-PT genomes from VHL-disease patients compared to similar samples from control individuals. Moreover, VCAM1-PT cells were more common (8-fold increase, chi squared test P = .026) in the urines of VHL-disease patients than in the urines of controls. Conclusion Our data show that TECs derived from damaged PTs are subjected to a specific somatic mutation process during adult life. The process is a distinctive feature of kidney cancer (ccRCC) genomes, and is more evident in patients affected by VHL-cancer predisposition syndrome. These data suggest that heterozygous loss of VHL facilitates a PT-specific, somatic mutation process involved in cancer initiation.

A multi-view graph contrastive learning framework for deciphering spatially resolved transcriptomics data.

Spatially resolved transcriptomics data are being used in a revolutionary way to decipher the spatial pattern of gene expression and the spatial architecture of cell types. Much work has been done to exploit the genomic spatial architectures of cells. Such work is based on the common assumption that gene expression profiles of spatially adjacent spots are more similar than those of more distant spots. However, related work might not consider the nonlocal spatial co-expression dependency, which can better characterize the tissue architectures. Therefore, we propose MuCoST, a Multi-view graph Contrastive learning framework for deciphering complex Spatially resolved Transcriptomic architectures with dual scale structural dependency. To achieve this, we employ spot dependency augmentation by fusing gene expression correlation and spatial location proximity, thereby enabling MuCoST to model both nonlocal spatial co-expression dependency and spatially adjacent dependency. We benchmark MuCoST on four datasets, and we compare it with other state-of-the-art spatial domain identification methods. We demonstrate that MuCoST achieves the highest accuracy on spatial domain identification from various datasets. In particular, MuCoST accurately deciphers subtle biological textures and elaborates the variation of spatially functional patterns.

Blocking of amino acid transporter OsAAP7 promoted tillering and yield by determining basic and neutral amino acids accumulation in rice

BackgroundAmino acids are not only the main form of N in rice, but also are vital for its growth and development. These processes are facilitated by amino acid transporters within the plant. Despite their significance, only a few AAP amino acid transporters have been reported.ResultsIn this study, we observed that there were differences in the expression of amino acid transporter OsAAP7 among 521 wild cultivated rice varieties, and it directly negatively correlated with tillering and grain yield per plant. We revealed that OsAAP7 protein was localized to the endoplasmic reticulum and had absorption and transport affinity for amino acids such as phenylalanine (Phe), lysine (Lys), leucine (Leu), and arginine (Arg) using subcellular localization, yeast substrate testing, fluorescent amino acid uptake, and amino acid content determination. Further hydroponic studies showed that exogenous application of amino acids Phe, Lys and Arg inhibited the growth of axillary buds in the overexpression lines, and promoted the elongation of axillary buds in the mutant lines. Finally, RNA-seq analysis showed that the expression patterns of genes related to nitrogen, auxin and cytokinin pathways were changed in axillary buds of OsAAP7 transgenic plants.ConclusionsThis study revealed the gene function of OsAAP7, and found that blocking of amino acid transporter OsAAP7 with CRISPR/Cas9 technology promoted tillering and yield by determining basic and neutral amino acids accumulation in rice.

#2584 Mapping Progression of DKD in ReninAAV UNx db/db mice utilizing time-series RNA sequencing

Abstract Background and Aims The Renin adeno-associated virus (AAV) uninephrectomized (UNx) db/db mouse model of diabetic kidney disease (DKD) recapitulates hallmarks of DKD with hypertension, including albuminuria and glomerulosclerosis. Despite previous characterization of the model, gaps persist in our understanding regarding temporal patterns of gene expression and pathophysiology in the glomeruli. This longitudinal study characterizes isolated glomeruli from ReninAAV UNx db/db mice during progression of DKD with hypertension. Method Female db/db (BKS.Cg-Dock7m +/+ Leprdb/J) received a single i.v. dose of LacZAAV (control) or ReninAAV. Untreated db/m mice (BKS.Cg-Dock7m +/+ Leprdb/J) served as healthy controls. One week after AAV injection, ReninAAV mice underwent UNx, recovered for three weeks, and were subsequently randomized and stratified into 4 groups according to fed blood glucose and body weight. ReninAAV UNx mice were terminated at 4, 8, 12 and 16 weeks (w4-w16) after UNx. Control groups were terminated at 16 weeks. Endpoints included urine and plasma biochemistry, kidney histology (i.e. Collagen 1a1 and Glomerulosclerosis) and RNA sequencing of glomeruli isolated by laser capture microdissection. Results ReninAAV UNx db/db mice showed progressive kidney fibrosis (Col1a1%-area) and albuminuria (uACR) compared to LacZAAV db/db and db/m mice across all timepoints investigated. Furthermore, a significant increase in glomerulosclerosis was observed from w12 and onwards compared to LacZAAV and db/m mice. When compared to LacZAAV mice, more than 1,700 glomerular differentially regulated genes and more than 250 uniquely regulated genes were found at each timepoint, including markers of fibrosis, inflammation and glomerular injury. Several glomerular drug targets exhibited time-specific regulated in ReninAAV UNx db/db mice (e.g. Slc5a2, Egfr, Agtr1a). Regulated genes were segmented into nine clusters with distinct temporal patterns. Among these, a continuous increase in expression of genes associated with extracellular matrix (ECM), small molecule transport and temporal stimulation of metabolic pathways. Finally, a correlation analysis revealed strong associations between ECM and ECM-related pathways vs. glomerulosclerosis and albuminuria. Conclusion The ReninAAV UNx db/db mouse model of hypertensive DKD demonstrates a progressive increase in fibrosis and albuminuria paralleled by dynamic changes in glomerular gene expression signatures. Notably, the identification of temporal patterns of gene expression and pathway regulation provides novel insights into DKD pathophysiology and progression. This underscores the ReninAAV UNx db/db mouse as an applicable model of human DKD in preclinical target and drug discovery.

Endoplasmic reticulum protein ALTERED MERISTEM PROGRAM 1 negatively regulates senescence in Arabidopsis.

Plant senescence is a highly regulated developmental program crucial for nutrient reallocation and stress adaptation in response to developmental and environmental cues. Stress-induced and age-dependent natural senescence share both overlapping and distinct molecular responses and regulatory schemes. Previously, we have utilized a carbon-deprivation (C-deprivation) senescence assay using Arabidopsis (Arabidopsis thaliana) seedlings to investigate senescence regulation. Here we conducted a comprehensive time-resolved transcriptomic analysis of Arabidopsis wild type seedlings subjected to C-deprivation treatment at multiple time points, unveiling substantial temporal changes and distinct gene expression patterns. Moreover, we identified ALTERED MERISTEM PROGRAM 1 (AMP1), encoding an endoplasmic reticulum protein, as a potential regulator of senescence based on its expression profile. By characterizing loss-of-function alleles and overexpression lines of AMP1, we confirmed its role as a negative regulator of plant senescence. Genetic analyses further revealed a synergistic interaction between AMP1 and the autophagy pathway in regulating senescence. Additionally, we discovered a functional association between AMP1 and the endosome-localized ABNORMAL SHOOT3 (ABS3)-mediated senescence pathway and positioned key senescence-promoting transcription factors downstream of AMP1. Overall, our findings shed light on the molecular intricacies of transcriptome reprogramming during C-deprivation-induced senescence and the functional interplay among endomembrane compartments in controlling plant senescence.

#2566 Clinicopathological and molecular characteristics of plasma cell rich rejection in renal transplant biopsies

Abstract Background and Aims Plasma cell rich rejection (PCRR) is an uncommon, ill-defined type of renal allograft rejection in the literature considered as a subtype of T cell-mediated rejection (TCMR). PCRR has poorer clinical outcome and is often refractory to classic immunosuppressive therapy. Our study analyzed In this study, we analyzed PCRR in a large cohort of patients who underwent renal transplantation at the Amsterdam UMC. Our objective was to study clinical, histological and molecular signatures of PCRR in comparison to other types of rejection, especially late presentations of TCMR and ABMR. We hypothesized PCRR could be a specific subtype of allograft rejection with different molecular and cellular characteristics compared to (late) TCMR and ABMR with differences in clinical outcome. Method We retrospectively scored and reclassified the last known biopsy of 263 renal transplant recipients, morphologically classified as rejection according to the 2019 Banff classification. mRNA expression analysis was performed using the Nanostring B-HOT panel on a subset of cases. PCRR was compared to (late) TCMR, ABMR and mixed rejection for renal function follow-up and graft survival. Results mRNA analysis revealed uniquely expressed genes in PCRR including LOX, CPA3, IL4, IL17F, and MMP12. PCRR is enriched for genes related to mast cells, memory B- and T-cells and transcripts involved in NK cells and allograft fibrosis with heterogeneity in gene expression in biopsies with PCRR. PCRR might be a late event compared to late TCMR and ABMR, with a higher degree of total inflammation and fibrosis. Graft survival and kidney function was similar to late TCMR and ABMR during a 5-year follow-up period after renal biopsy Conclusion PCRR represents a distinct late-onset stage of inflammation displaying diverse gene expression patterns, with presence of mainly mast cells, NK cells and transcripts involved in renal allograft fibrosis. Such insights could enable a better and more tailored treatment for these patients and ultimately enhance long-term graft survival for patients affected by PCRR. Clinical outcomes in patients with PCRR appeared similar to late TCMR and ABMR.

Differential Antioxidant Enzyme Gene Expression and Functional Analysis of Pyridaben-Susceptible and -Resistant Strains of Tetranychus truncatus (Acari: Tetranychidae) under High Temperature Stress

Tetranychus truncatus (Acari: Tetranychidae) has caused serious economic losses on some crops (soybean, corn, and cotton) in China, and has developed resistance to most acaricides. Our laboratory study found that T. truncatus was resistant to pyridaben and also adapted to high temperature (34–40 °C). High temperature stress may cause arthropods to produce a large amount of reactive oxygen species (ROS), causing oxidative damage. Antioxidant enzymes, as the main antioxidants, can reduce the damage caused by excessive ROS in arthropods. In order to study the adaptation mechanism of the pyridaben-resistant strain of T. truncatus to high temperature and the role of antioxidant enzyme genes under high temperature stress, four antioxidant enzyme genes, TtSOD, TtPOD3, TtPOD4, and TtGSTs2, were screened according to the transcriptome sequencing data of pyridaben-susceptible and -resistant strains in T. truncatus. Firstly, the phylogeny and structure analyses of these four genes were carried out. Then, real-time quantitative PCR (RT-qPCR) technology was used to analyze the gene expression patterns of antioxidant enzymes in two strains of T. truncatus at three different high temperature ranges (34 °C, 38 °C, and 42 °C). The results showed that the expression levels of four antioxidant enzyme genes of two strains of T. truncatus were induced by high temperature stress, and the expression levels of antioxidant enzyme genes were significantly different in each development state. The gene expression of antioxidant enzyme genes in resistant strains at the adult stage was significantly higher than that in susceptible strains. After the TtSOD and TtPOD4 genes of adult mites of the resistant strain were silenced by RNA interference (RNAi) technology, the mortality rate of mites with TtPOD4 gene silencing reached 41.11% after 96 h at 34 °C, which was significantly higher than that of the control and TtSOD gene silencing. It has been confirmed that the TtPOD4 gene plays a key role in the adaptation of pyridaben-resistant strain of T. truncatus to high temperature. It lays a theoretical foundation for revealing the thermal adaptation mechanism of T. truncatus.

Cyclic Variations of Ovarian Development, Hormones and Sex Related Genes of Rainbow Trout (Oncorhynchus mykiss) During Different Growth Stages

This study aimed to investigate the reproductive biology of female rainbow trout (Oncorhynchus mykiss). Mature female (n.80) rainbow trout from different reproductive phases were collected. Through a transmission electron microscope (TEM), it was feasible to examine the oocyte at several developmental stages, namely the perinucleolus stage, cortical alveoli stage, vitellogenic stage, mature stage, and postovulatory stage. Progesterone and estradiol levels were measured at their lowest during the immature and spent phases, while reaching their highest levels during the maturing and mature stages. The total amount of saturated fatty acids (SFA), monounsaturated fatty acids (MUFA), and polyunsaturated fatty acids (PUFA) was greater in mature ovaries compared to immature and maturing ovaries. Gene transcripts related to the production of steroids, specifically star, cyp11a1, cyp17a1 and hsd3b were expressed at low levels during the immature stage and showed a significant rise during the mature stage. The ovarian gene expression patterns during oogenesis exhibited distinct dissimilarities. The fatty acid content, essential for the development of fish ovaries, and the sex steroid hormonal profile, which play a key role in regulating oogenesis, are particularly significant. These results will enhance our comprehension of the reproductive biology and sustainable management of rainbow trout in their natural environment.

Genome-wide identification and expression-pattern analysis of sulfate transporter (SULTR) gene family in cotton under multiple abiotic stresses and fiber development.

Sulfate transporter (SULTR) proteins are in charge of the transport and absorption on sulfate substances, and have been reported to play vital roles in the biological processes of plant growth and stress response. However, there were few reports of genome-wide identification and expression-pattern analysis of SULTRs in Hibiscus mutabilis. Gossypium genus is a ideal model for studying the allopolyploidy, therefore two diploid species (G. raimondii and G. arboreum) and two tetraploid species (G. hirsutum and G. barbadense) were chosen in this study to perform bioinformatic analyses, identifying 18, 18, 35, and 35 SULTR members, respectively. All the 106 cotton SULTR genes were utilized to construct the phylogenetic tree together with 11 Arabidopsis thaliana, 13 Oryza sativa, and 8 Zea mays ones, which was divided into Group1-Group4. The clustering analyses of gene structures and 10 conserved motifs among the cotton SULTR genes showed the consistent evolutionary relationship with the phylogenetic tree, and the results of gene-duplication identification among the four representative Gossypium species indicated that genome-wide or segment duplication might make main contributions to the expansion of SULTR gene family in cotton. Having conducted the cis-regulatory element analysis in promoter region, we noticed that the existing salicylic acid (SA), jasmonic acid (JA), and abscisic acid (ABA) elements could have influences with expression levels of cotton SULTR genes. The expression patterns of GhSULTR genes were also investigated on the 7 different tissues or organs and the developing ovules and fibers, most of which were highly expressed in root, stem, sepal, receptacel, ovule at 10 DPA, and fiber at 20 and 25 DPA. In addition, more active regulatory were observed in GhSULTR genes responding to multiple abiotic stresses, and 12 highly expressed genes showed the similar expression patterns in the quantitative Real-time PCR experiments under cold, heat, salt, and drought treatments. These findings broaden our insight into the evolutionary relationships and expression patterns of the SULTR gene family in cotton, and provide the valuable information for further screening the vital candidate genes on trait improvement.

Pan-transcriptome reveals a large accessory genome contribution to gene expression variation in yeast.

Gene expression is an essential step in the translation of genotypes into phenotypes. However, little is known about the transcriptome architecture and the underlying genetic effects at the species level. Here we generated and analyzed the pan-transcriptome of ~1,000 yeast natural isolates across 4,977 core and 1,468 accessory genes. We found that the accessory genome is an underappreciated driver of transcriptome divergence. Global gene expression patterns combined with population structure showed that variation in heritable expression mainly lies within subpopulation-specific signatures, for which accessory genes are overrepresented. Genome-wide association analyses consistently highlighted that accessory genes are associated with proportionally more variants with larger effect sizes, illustrating the critical role of the accessory genome on the transcriptional landscape within and between populations.

Widespread changes in gene expression accompany body size evolution in nematodes.

Body size is a fundamental trait that drives multiple evolutionary and ecological patterns. Caenorhabditis inopinata is a fig-associated nematode that is exceptionally large relative to other members of the genus, including C. elegans. We previously showed that C. inopinata is large primarily due to postembryonic cell size expansion that occurs during the larval-to-adult transition. Here, we describe gene expression patterns in C. elegans and C. inopinata throughout this developmental period to understand the transcriptional basis of body size change. We performed RNA-seq in both species across the L3, L4, and adult stages. Most genes are differentially expressed across all developmental stages, consistent with C. inopinata's divergent ecology and morphology. We also used a model comparison approach to identify orthologs with divergent dynamics across this developmental period between the two species. This included genes connected to neurons, behavior, stress response, developmental timing, and small RNA/chromatin regulation. Multiple hypodermal collagens were also observed to harbor divergent developmental dynamics across this period, and genes important for molting and body morphology were also detected. Genes associated with TGF-β signaling revealed idiosyncratic and unexpected transcriptional patterns given their role in body size regulation in C. elegans. Widespread transcriptional divergence between these species is unexpected and may be a signature of the ecological and morphological divergence of C. inopinata. Alternatively, transcriptional turnover may be the rule in the Caenorhabditis genus, indicative of widespread developmental system drift among species. This work lays the foundation for future functional genetic studies interrogating the bases of body size evolution in this group.

Biologically informed NeuralODEs for genome-wide regulatory dynamics

BackgroundGene regulatory network (GRN) models that are formulated as ordinary differential equations (ODEs) can accurately explain temporal gene expression patterns and promise to yield new insights into important cellular processes, disease progression, and intervention design. Learning such gene regulatory ODEs is challenging, since we want to predict the evolution of gene expression in a way that accurately encodes the underlying GRN governing the dynamics and the nonlinear functional relationships between genes. Most widely used ODE estimation methods either impose too many parametric restrictions or are not guided by meaningful biological insights, both of which impede either scalability, explainability, or both.ResultsWe developed PHOENIX, a modeling framework based on neural ordinary differential equations (NeuralODEs) and Hill-Langmuir kinetics, that overcomes limitations of other methods by flexibly incorporating prior domain knowledge and biological constraints to promote sparse, biologically interpretable representations of GRN ODEs. We tested the accuracy of PHOENIX in a series of in silico experiments, benchmarking it against several currently used tools. We demonstrated PHOENIX’s flexibility by modeling regulation of oscillating expression profiles obtained from synchronized yeast cells. We also assessed the scalability of PHOENIX by modeling genome-scale GRNs for breast cancer samples ordered in pseudotime and for B cells treated with Rituximab.ConclusionsPHOENIX uses a combination of user-defined prior knowledge and functional forms from systems biology to encode biological “first principles” as soft constraints on the GRN allowing us to predict subsequent gene expression patterns in a biologically explainable manner.

Analysis of common differential gene expression in synovial cells of osteoarthritis and rheumatoid arthritis.

To elucidate potential molecular mechanisms differentiating osteoarthritis (OA) and rheumatoid arthritis (RA) through a bioinformatics analysis of differentially expressed genes (DEGs) in patient synovial cells, aiming to provide new insights for clinical treatment strategies. Gene expression datasets GSE1919, GSE82107, and GSE77298 were downloaded from the Gene Expression Omnibus (GEO) database to serve as the training groups, with GSE55235 being used as the validation dataset. The OA and RA data from the GSE1919 dataset were merged with the standardized data from GSE82107 and GSE77298, followed by batch effect removal to obtain the merged datasets of differential expressed genes (DEGs) for OA and RA. Intersection analysis was conducted on the DEGs between the two conditions to identify commonly upregulated and downregulated DEGs. Enrichment analysis was then performed on these common co-expressed DEGs, and a protein-protein interaction (PPI) network was constructed to identify hub genes. These hub genes were further analyzed using the GENEMANIA online platform and subjected to enrichment analysis. Subsequent validation analysis was conducted using the GSE55235 dataset. The analysis of differentially expressed genes in the synovial cells from patients with Osteoarthritis (OA) and Rheumatoid Arthritis (RA), compared to a control group (individuals without OA or RA), revealed significant changes in gene expression patterns. Specifically, the genes APOD, FASN, and SCD were observed to have lower expression levels in the synovial cells of both OA and RA patients, indicating downregulation within the pathological context of these diseases. In contrast, the SDC1 gene was found to be upregulated, displaying higher expression levels in the synovial cells of OA and RA patients compared to normal controls.Additionally, a noteworthy observation was the downregulation of the transcription factor PPARG in the synovial cells of patients with OA and RA. The decrease in expression levels of PPARG further validates the alteration in lipid metabolism and inflammatory processes associated with the pathogenesis of OA and RA. These findings underscore the significance of these genes and the transcription factor not only as biomarkers for differential diagnosis between OA and RA but also as potential targets for therapeutic interventions aimed at modulating their expression to counteract disease progression. The outcomes of this investigation reveal the existence of potentially shared molecular mechanisms within Osteoarthritis (OA) and Rheumatoid Arthritis (RA). The identification of APOD, FASN, SDC1, TNFSF11 as key target genes, along with their downstream transcription factor PPARG, highlights common potential factors implicated in both diseases. A deeper examination and exploration of these findings could pave the way for new candidate targets and directions in therapeutic research aimed at treating both OA and RA. This study underscores the significance of leveraging bioinformatics approaches to unravel complex disease mechanisms, offering a promising avenue for the development of more effective and targeted treatments.

The Effects of Smoking on Telomere Length, Induction of Oncogenic Stress, and Chronic Inflammatory Responses Leading to Aging

Telomeres, potential biomarkers of aging, are known to shorten with continued cigarette smoke exposure. In order to further investigate this process and its impact on cellular stress and inflammation, we used an in vitro model with cigarette smoke extract (CSE) and observed the downregulation of telomere stabilizing TRF2 and POT1 genes after CSE treatment. hTERT is a subunit of telomerase and a well-known oncogenic marker, which is overexpressed in over 85% of cancers and may contribute to lung cancer development in smokers. We also observed an increase in hTERT and ISG15 expression levels after CSE treatment, as well as increased protein levels revealed by immunohistochemical staining in smokers’ lung tissue samples compared to non-smokers. The effects of ISG15 overexpression were further studied by quantifying IFN-γ, an inflammatory protein induced by ISG15, which showed greater upregulation in smokers compared to non-smokers. Similar changes in gene expression patterns for TRF2, POT1, hTERT, and ISG15 were observed in blood and buccal swab samples from smokers compared to non-smokers. The results from this study provide insight into the mechanisms behind smoking causing telomere shortening and how this may contribute to the induction of inflammation and/or tumorigenesis, which may lead to comorbidities in smokers.

Decoding Molecular Mechanisms Underlying Outcomes After Ischemic Stroke Thrombectomy by RNA Sequencing of Retrieved Clots.

Transcriptomic profiling has emerged as a powerful tool for exploring the molecular landscape of ischemic stroke clots and providing insights into the pathophysiological mechanisms underlying stroke progression and recovery. In this study, we aimed to investigate the relationship between stroke clot transcriptomes and stroke thrombectomy outcome, as measured by early neurological improvement (ENI) 30 (i.e., a 30% reduction in NIHSS at 24 h post-thrombectomy). We hypothesized that there exist distinct clot gene expression patterns between good and poor neurological outcomes. Transcriptomic analysis of 32 stroke clots retrieved by mechanical thrombectomy was conducted. Transcriptome data of these clots were analyzed to identify differentially expressed genes (DEGs), defined as those with a log(fold-change) ≥ 1.5 and q < 0.05 between samples with good and poor early neurological outcomes. Gene ontology and bioinformatics analyses were performed on genes with p < 0.01 to identify enriched biological processes and Ingenuity Pathway Analysis canonical pathways. Moreover, AUC analysis assessed the predictive power of DEGs for 90-day function outcome (mRS ≤ 2) and cellular composition of clot was predicted using CIBERSORT. We also assessed whether differential enrichment of immune cell types could indicate patient survival. A total of 41 DEGs were identified. Bioinformatics showed that enriched biological processes and pathways emphasized the chronic immune response and matrix metalloproteinase inhibition. Moreover, 25 of the DEGs were found to be significant predictors of 90-day mRS. These genes were indicative of monocytes enrichment and neutrophil depletion in patients with poorer outcomes. Our study revealed a distinct gene expression pattern and dysregulated biological pathways associated with ENI. This expression pattern was also predictive of long-term outcome, suggesting a biological link between those ENIs and 90-day mRS.

Centenarian hippocampus displays high levels of astrocytic metallothioneins.

The hippocampus is a brain area linked to cognition. The mechanisms that maintain cognitive activity in humans are poorly understood. Centenarians display extreme longevity which is generally accompanied by better quality of life, lower cognitive impairment, and reduced incidence of pathologies including neurodegenerative diseases. We performed transcriptomic studies in hippocampus samples from individuals of different ages (centenarians [≥97 years], old, and young) and identified a differential gene expression pattern in centenarians compared to the other two groups. In particular, several isoforms of metallothioneins (MTs) were highly expressed in centenarians. Moreover, we identified that MTs were mainly expressed in astrocytes. Functional studies in human primary astrocytes revealed that MT1 and MT3 are necessary for their homeostasis maintenance. Overall, these results indicate that the expression of MTs specifically in astrocytes is a mechanism for protection during aging.

Gene expression supports a single origin of horns and antlers in hoofed mammals

Horns, antlers, and other bony cranial appendages of even-toed hoofed mammals (ruminant artiodactyls) challenge traditional morphological homology assessments. Cranial appendages all share a permanent bone portion with family-specific integument coverings, but homology determination depends on whether the integument covering is an essential component or a secondary elaboration of each structure. To enhance morphological homology assessments, we tested whether juvenile cattle horn bud transcriptomes share homologous gene expression patterns with deer antlers relative to pig outgroup tissues, treating the integument covering as a secondary elaboration. We uncovered differentially expressed genes that support horn and antler homology, potentially distinguish them from non-cranial-appendage bone and other tissues, and highlight the importance of phylogenetic outgroups in homology assessments. Furthermore, we found differentially expressed genes that could support a shared cranial neural crest origin for horns and antlers and expression patterns that refine our understanding of the timing of horn and antler differentiation.

Monilinia fructicola genes involved in the cell wall-degrading process in early nectarine infection

Brown rot symptoms may be linked to alterations in the gene expression pattern of genes associated with cell wall degradation. In this study, we identify key carbohydrate-active enzymes (CAZymes) involved in cell wall degradation by Monilinia fructicola, including pme2 and pme3 (pectin methylesterases), cut1 (cutinase) and nep2 (necrosis-inducing factor). The expression of these genes is significantly modulated by red and blue light during early nectarine infection. The polygalacturonase gene pg1 and the cellulase gene cel1 also exhibit photoinduction albeit to a lesser extent. Red and blue light cause an acceleration in the initial stages of brown rot development caused by M. fructicola on nectarines. Disease symptoms like tissue maceration were evident after an incubation period of 24 h followed by 14 h of light exposition, in contrast to the usual incubation period of 48 to 72 h. Furthermore, the culture media exerts an impact on gene regulation, suggesting a complex interplay between light and nutrient signalling pathways in M. fructicola. In addition, we observe that red light promotes colony growth on a 12 h photoperiod and consistently reduces conidiation. In contrast, blue light hampers growth rate on both the 12 h and the 8 h photoperiod but only diminishes conidiation on the 12 h photoperiod. These findings enhance our comprehension of genes associated with cell wall degradation and the environmental factors influencing brown rot development.