Changes In Functional Gene Expression Research Articles

Transcriptome Analysis of Human Vascular Smooth Muscle Cells Cultured on a Polyglycolic Acid Mesh Scaffold

To construct tissue-engineered blood vessels (TEBVs) in vitro, it is necessary to transfer seed cells to three-dimensional (3D) scaffolds for culture. However, what happens to the behavior of the cells after they are transferred to the scaffold is unclear. Therefore, in this study, a transcriptome analysis was used to characterize the differentially expressed genes (DEGs) of vascular smooth muscle cells (VSMCs) before and after transfer to 3D polyglycolic acid (PGA) scaffolds and to understand the changes in functional gene expression in the early stage of 3D culture. Transcriptome sequencing results showed that DEGs in the seed cells were mainly enriched in cell proliferation and cell-cell adhesion. The DEGs of cells grown in a 3D PGA scaffold (PGA-VSMCs) were mainly enriched in signal transduction. Furthermore, we found that ERK1/2 was significantly activated in PGA-VSMCs and inhibiting the phosphorylation level of ERK 1/2 in PGA-VSMCs significantly increased the expression of elastin. In conclusion, the PGA scaffold material altered gene expression in VSMCs and affected the elastin production. This study advances our understanding of biomaterial-cell interactions and provides valuable insights for improving the cultivation of TEBVs.

Single-cell RNA sequencing reveals the local cell landscape in mouse epididymal initial segment during aging

BackgroundMorphological and functional alterations in aging reproductive organs result in decreased male fertility. The epididymis functions as the transition region for post-testicular sperm maturation. And we have previously demonstrated that the epididymal initial segment (IS), a region of the reproductive tract essential for sperm maturation and capacitation, undergoes considerable histological changes and chronic immune activation in mice during aging. However, the local aging-associated cellular and molecular changes in the aged epididymal IS are poorly understood.ResultsWe conducted single-cell RNA sequencing analysis on the epididymal IS of young (3-month-old) and old (21-month-old) mice. In total, 10,027 cells from the epididymal IS tissues of young and old mice were obtained and annotated. The cell composition, including the expansion of a principal cell subtype and Ms4a4bHiMs4a6bHi T cells, changed with age. Aged principal cells displayed multiple functional gene expression changes associated with acrosome reaction and sperm maturation, suggesting an asynchronous process of sperm activation and maturation during epididymal transit. Meanwhile, aging-related altered pathways in immune cells, especially the “cell chemotaxis” in Cx3cr1Hi epididymal dendritic cells (eDCs), were identified. The monocyte-specific expression of chemokine Ccl8 increased with age in eDCs. And the aged epididymal IS showed increased inflammatory cell infiltration and cytokine secretion. Furthermore, cell–cell communication analysis indicated that age increased inflammatory signaling in the epididymal IS.ConclusionContrary to the general pattern of lower immune responses in the male proximal genital tract, we revealed an inflammaging status in mouse epididymal initial segment. These findings will allow future studies to enable the delay of male reproductive aging via immune regulation.

Abstract 5458: TONSL is an immortalizing oncogene of the chromosome 8q24.3 amplicon and new therapeutic target in breast cancer

Abstract Study of genomic aberrations leading to immortalization of epithelial cells has been technically challenging due to lack of an appropriate isogenic model system. To address this technical challenge, we utilized primary breast luminal epithelial cells propagated from healthy donors of different genetic ancestry and their hTERT-immortalized counterparts to identify functional gene expression changes associated with immortalization. We identified elevated expression of TONSL (Tonsoku Like, DNA Repair Protein) as one of the earliest events during immortalization. TONSL is located on chromosome 8q24.3 and amplified in ~20% of breast cancers with significantly higher amplification in metastatic tumors. TONSL forms a complex with FACT and MMS22L1 to modulate multiple cellular pathways including DNA replication, repair through homologous recombination (HR) and functions as a post replicative histone/chromatin reader. TONSL alone immortalized primary breast epithelial cells and increased telomerase activity. While TONSL overexpression alone was insufficient for neoplastic transformation, TONSL-immortalized primary cells modified to overexpress defined oncogenes generated estrogen receptor-positive adenocarcinomas in NSG mice. Analysis of breast tumor microarray with ~500 tumors revealed poor overall and progression free survival of patients with TONSL-overexpressing tumors. TONSL increased chromatin accessibility to pro-oncogenic transcription factors including NF-κB and limited access to the tumor suppressor p53. Most importantly, TONSL overexpression resulted in significant changes in the expression of genes associated with DNA repair hubs, including upregulation of several genes in HR and Fanconi Anemia pathways. Consistent with the effects of TONSL on HR-associated genes, TONSL overexpressing primary cells exhibited upregulated DNA repair via HR. Moreover, TONSL was an essential gene for growth of TONSL-amplified breast cancer cell lines in vivo. Breast cancer cell lines with TONSL/chr8q24.3 amplification were sensitive to TONSL-FACT complex inhibitor CBL0137, both in vitro and in vivo. To our knowledge, TONSL is the only gene other than telomerase with immortalizing function and represents a new therapeutic target for breast cancer with chr8q24.3 amplification. Citation Format: Aditi S. Khatpe, Rebecca Dirks, Poornima Bhat-Nakshatri, Henry Mang, Katie Batic, Sarah Swiezy, Jacob Olson, Xi Rao, Yue Wang, Hiromi Tanaka, Sheng Liu, Jun Wan, Duojiao Chen, Yunlong Liu, Fang Fang, Sandra Althouse, Emily Hilsey, Maggie M. Granatir, Rebekah Addison, Constance J. Temm, George Sandusky, Audrey Lee-Gosselin, Kenneth Nephew Nephew, Kathy D. Miller, Harikrishna Nakshatri. TONSL is an immortalizing oncogene of the chromosome 8q24.3 amplicon and new therapeutic target in breast cancer. [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 5458.

Effects of multiple drivers of ocean global change on the physiology and functional gene expression of the coccolithophore Emiliania huxleyi.

Ongoing ocean global change due to anthropogenic activities is causing multiple chemical and physical seawater properties to change simultaneously, which may affect the physiology of marine phytoplankton. The coccolithophore Emiliania huxleyi is a model species often employed in the study of the marine carbon cycle. The effect of ocean acidification (OA) on coccolithophore calcification has been extensively studied; however, physiological responses to multiple environmental drivers are still largely unknown. Here we examined two-way and multiple driver effects of OA and other key environmental drivers-nitrate, phosphate, irradiance, and temperature-on the growth, photosynthetic, and calcification rates, and the elemental composition of E. huxleyi. In addition, changes in functional gene expression were examined to understand the molecular mechanisms underpinning the physiological responses. The single driver manipulation experiments suggest decreased nitrate supply being the most important driver regulating E. huxleyi physiology, by significantly reducing the growth, photosynthetic, and calcification rates. In addition, the interaction of OA and decreased nitrate supply (projected for year 2100) had more negative synergistic effects on E. huxleyi physiology than all other two-way factorial manipulations, suggesting a linkage between the single dominant driver (nitrate) effects and interactive effects with other drivers. Simultaneous manipulation of all five environmental drivers to the conditions of the projected year 2100 had the largest negative effects on most of the physiological metrics. Furthermore, functional genes associated with inorganic carbon acquisition (RubisCO, AEL1, and δCA) and calcification (CAX3, AEL1, PATP, and NhaA2) were most downregulated by the multiple driver manipulation, revealing linkages between responses of functional gene expression and associated physiological metrics. These findings together indicate that for more holistic projections of coccolithophore responses to future ocean global change, it is necessary to understand the relative importance of environmental drivers both individually (i.e., mechanistic understanding) and interactively (i.e., cumulative effect) on coccolithophore physiology.

The effect of commercial, natural and grape seed extract supplemented diets on gene expression signatures and survival of greenlip abalone (Haliotis laevigata) during heat stress

Summer mortality is a phenomenon associated with high temperature water spikes that can result in mass mortalities of abalone and other molluscs. This is a particular concern for aquaculture industries due to the economic impacts of such events. Diets containing algal supplements have been suggested as pre-emptive solutions for preventing these mass mortalities. The same has also been suggested for diets containing grape seed extract. This is due to their potential as a source of antioxidative compounds, which reduce the accumulation of harmful reactive oxygen species. This study aimed to identify functional genes associated with high survival in abalone fed diets high in antioxidative compounds during heat stress. Tentacle transcriptomes of 40 greenlip abalone (Haliotis laevigata) were investigated to determine the combined effects of differing diets and temperature on the gene expression responses by abalone. Here we compare the functional gene expression changes at 22°C and 25°C in abalone fed common commercial, live macroalgal (Ulva lactuca) and grape seed extract supplemented commercial diets as a means to understand the resulting high survival of abalone fed grape seed extract during heat stress. Twenty-four genes were differentially expressed between high survival promoting diets (macroalgae or grape seed extract supplemented commercial) relative to the purely commercial diet. Many of these genes have been suggested to be involved in antioxidant and innate immunity responses. The identification of these genes and their functional roles has enhanced our understanding of processes that contribute to summer stress resilience in abalone. Our study supports the hypothesis that diet and gene expression signatures may be indicative of the survival capabilities of abalone when exposed to heat stress.

The expression profile of angiotensin system on thawed murine ovaries.

Freezing and thawing is one of the most widely used tissue engineering techniques for the preservation of ovaries. Many cells and tissues demonstrate changes in functional gene expression after thawing. Several studies have reported the important roles of angiotensin (AT) system during the ovarian follicular growth. AT system consists of ATII, and ATII receptors type I (ATII-RI) and type II (ATII-RII). However, little is known whether frozen-thawed ovaries show any alteration of AT system member gene expression when treated with survival-enhancing factors. We aimed to investigate whether mass freezing and thawing with or without the use of Rho-associated kinase (ROCK) inhibitors up- or down-regulate the expression of ATII, ATII-RI, and ATII-RII genes on frozen-thawed ovarian tissues. Significant changes in the expression of ATII, ATII-RI, and ATII-RII genes were observed on thawed ovaries when compared to fresh control. The treatment with ROCK inhibitors did not significantly alter their expression. In conclusion, freezing and thawing of ovarian tissue may affect the mRNA expression levels of intra-ovarian AT system genes, and modulation of ROCK inhibitor activity may not regulate AT system on the frozenthawed ovarian tissue.

De novoassembled transcriptome of horned gall aphid,Schlechtendalia chinensisBell, suggest changes in functional gene expression during host alternation

The horned gall aphid, Schlechtendalia chinensis Bell, is the most economically valuable galling aphid. It accounts for approximately 75% of Chinese gallnut production, which is important for medical and chemical purposes. The horned gall aphid feeds on the Chinese sumac tree, Rhus chinensis, during the summer, induces galls, and overwinters on the moss Plagiomnium spp. However, the sequence information of S. chinensis is limited, and the functional gene expression changes during host alternation remain obscure. In this study, the transcriptome of the horned gall aphid was sequenced using high-throughput sequencing technology. Approximately 49 million reads were obtained and were assembled into 99 366 transcripts and 47 400 unigenes. Annotation was performed using a BLAST search against primary databases such as NCBI nr and Swiss-Prot, as well as enrichment analysis by GO, KOG and KEGG. Differentially expressed genes between spring and autumn migrant aphids were compared, and the expression levels of many genes related to detoxification, digestion and other functional genes were found to have changed, reflecting the adaptation ability of horned gall aphids in different seasons and hosts. Functional genes in wax biosynthesis were upregulated in spring migrant aphids. This study analyzed the expression profile difference between spring and autumn migrant aphids to approach the real functional genes change during host alternation. The transcriptome provides a basis to understanding the functional genes during gall aphid host alternation and the related physiological and molecular characteristics.

Mechanisms Underlying Latent Disease Risk Associated with Early-Life Arsenic Exposure: Current Research Trends and Scientific Gaps.

BackgroundMillions of individuals worldwide, particularly those living in rural and developing areas, are exposed to harmful levels of inorganic arsenic (iAs) in their drinking water. Inorganic As exposure during key developmental periods is associated with a variety of adverse health effects, including those that are evident in adulthood. There is considerable interest in identifying the molecular mechanisms that relate early-life iAs exposure to the development of these latent diseases, particularly in relationship to cancer.ObjectivesThis work summarizes research on the molecular mechanisms that underlie the increased risk of cancer development in adulthood that is associated with early-life iAs exposure.DiscussionEpigenetic reprogramming that imparts functional changes in gene expression, the development of cancer stem cells, and immunomodulation are plausible underlying mechanisms by which early-life iAs exposure elicits latent carcinogenic effects.ConclusionsEvidence is mounting that relates early-life iAs exposure and cancer development later in life. Future research should include animal studies that address mechanistic hypotheses and studies of human populations that integrate early-life exposure, molecular alterations, and latent disease outcomes.CitationBailey KA, Smith AH, Tokar EJ, Graziano JH, Kim KW, Navasumrit P, Ruchirawat M, Thiantanawat A, Suk WA, Fry RC. 2016. Mechanisms underlying latent disease risk associated with early-life arsenic exposure: current research trends and scientific gaps. Environ Health Perspect 124:170–175; http://dx.doi.org/10.1289/ehp.1409360

Prenatal Arsenic Exposure and the Epigenome: Identifying Sites of 5-methylcytosine Alterations that Predict Functional Changes in Gene Expression in Newborn Cord Blood and Subsequent Birth Outcomes

Prenatal Arsenic Exposure and the Epigenome: Identifying Sites of 5-methylcytosine Alterations that Predict Functional Changes in Gene Expression in Newborn Cord Blood and Subsequent Birth Outcomes

Permanent cardiac sarcomere changes in a rabbit model of intrauterine growth restriction.

BackgroundIntrauterine growth restriction (IUGR) induces fetal cardiac remodelling and dysfunction, which persists postnatally and may explain the link between low birth weight and increased cardiovascular mortality in adulthood. However, the cellular and molecular bases for these changes are still not well understood. We tested the hypothesis that IUGR is associated with structural and functional gene expression changes in the fetal sarcomere cytoarchitecture, which remain present in adulthood.Methods and ResultsIUGR was induced in New Zealand pregnant rabbits by selective ligation of the utero-placental vessels. Fetal echocardiography demonstrated more globular hearts and signs of cardiac dysfunction in IUGR. Second harmonic generation microscopy (SHGM) showed shorter sarcomere length and shorter A-band and thick-thin filament interaction lengths, that were already present in utero and persisted at 70 postnatal days (adulthood). Sarcomeric M-band (GO: 0031430) functional term was over-represented in IUGR fetal hearts.ConclusionThe results suggest that IUGR induces cardiac dysfunction and permanent changes on the sarcomere.

Prenatal arsenic exposure and the epigenome: identifying sites of 5-methylcytosine alterations that predict functional changes in gene expression in newborn cord blood and subsequent birth outcomes.

Prenatal exposure to inorganic arsenic (iAs) is detrimental to the health of newborns and increases the risk of disease development later in life. Here we examined a subset of newborn cord blood leukocyte samples collected from subjects enrolled in the Biomarkers of Exposure to ARsenic (BEAR) pregnancy cohort in Gómez Palacio, Mexico, who were exposed to a range of drinking water arsenic concentrations (0.456-236 µg/l). Changes in iAs-associated DNA 5-methylcytosine methylation were assessed across 424,935 CpG sites representing 18,761 genes and compared with corresponding mRNA expression levels and birth outcomes. In the context of arsenic exposure, a total of 2919 genes were identified with iAs-associated differences in DNA methylation. Site-specific analyses identified DNA methylation changes that were most predictive of gene expression levels where CpG methylation within CpG islands positioned within the first exon, the 5' untranslated region and 200 bp upstream of the transcription start site yielded the most significant association with gene expression levels. A set of 16 genes was identified with correlated iAs-associated changes in DNA methylation and mRNA expression and all were highly enriched for binding sites of the early growth response (EGR) and CCCTC-binding factor (CTCF) transcription factors. Furthermore, DNA methylation levels of 7 of these genes were associated with differences in birth outcomes including gestational age and head circumference.These data highlight the complex interplay between DNA methylation, functional changes in gene expression and health outcomes and underscore the need for functional analyses coupled to epigenetic assessments.

Rapid evolution of disease resistance is accompanied by functional changes in gene expression in a wild bird

Wild organisms are under increasing pressure to adapt rapidly to environmental changes. Predicting the impact of these changes on natural populations requires an understanding of the speed with which adaptive phenotypes can arise and spread, as well as of the underlying mechanisms. However, our understanding of these parameters is poor in natural populations. Here we use experimental and molecular approaches to investigate the recent emergence of resistance in eastern populations of North American house finches (Carpodacus mexicanus) to Mycoplasma galliseptum (MG), a severe conjunctivitis-causing bacterium. Two weeks following an experimental infection that took place in 2007, finches from eastern US populations with a 12-y history of exposure to MG harbored 33% lower MG loads in their conjunctivae than finches from western US populations with no prior exposure to MG. Using a cDNA microarray, we show that this phenotypic difference in resistance was associated with differences in splenic gene expression, with finches from the exposed populations up-regulating immune genes postinfection and those from the unexposed populations generally down-regulating them. The expression response of western US birds to experimental infection in 2007 was more similar to that of the eastern US birds studied in 2000, 7 y earlier in the epizootic, than to that of eastern birds in 2007. These results support the hypothesis that resistance has evolved by natural selection in the exposed populations over the 12 y of the epizootic. We hypothesize that host resistance arose and spread from standing genetic variation in the eastern US and highlight that natural selection can lead to rapid phenotypic evolution in populations when acting on such variation.

Functional Changes of Actin-Binding Proteins for Human Umbilical CD-105 Positive Stromal Cell Proliferation and Differentiation

Human umbilical Wharton's jelly cells (WJCs) possess the capacity of self-renewal and differentiation of mesenchymal stromal cells. In this study, human umbilical CD105-positive WJCs were cultured to investigate the functional roles of actin binding proteins in cell proliferation and adipogenic differentiation. Genistein, a tyrosine protein kinase inhibitor, lowered intracellular Ca2+ such as to attenuate cell proliferation and DNA synthesis through the β-catenin/ cyclin D1 pathway in the cells. Immunofluorescence confocal scanning microscopy indicated that changes in the subcellular distribution of tropomyosin (Tm), in which the diffuse cytosolic staining was shifted to show colocalization of Tm with actin stress fibers. Genistein treatment of cells also induced increases in the colocalization of caldesmon (CaD) and stress fibers. In contrast, genistein increased accumulation of the actin-nucleating protein formin-2 (FMN-2) and profilin in the peri-nuclear area. Silencing of FMN-2 by siRNA raised intracellular Ca2+ and rendered genistein resistance in decreasing intracellular Ca2+ in the cells. To define how actin filament assembly is regulated in the adipogenic differentiation, we determined functional changes in gene expression of actin binding proteins associated with morphological transformation in adipogenesis-induced WJCs. Adipogenic differentiation, as indicated by elevating expression of PPAR-γ mRNA, caused changes in β-actin mRNA expression and protein level. Gelsolin, an actin filament severing protein, also displayed a biphasic change of mRNA expression and protein level in the differentiation. During adiopogenesis mRNA expression levels for FMN-2 and Tm-1 were declined significantly, but no changes for Tm-2 and Tm-4. Taken together, our study resulted in the novel finding that actin-binding proteins act by modulating actin filament assembly for the proliferation and differentiation in human WJCs.

Anterior thalamic lesions produce chronic and profuse transcriptional de-regulation in retrosplenial cortex: A model of retrosplenial hypoactivity and covert pathology.

Anterior thalamic lesions are thought to produce 'covert pathology' in retrosplenial cortex, but the causes are unknown. Microarray analyses tested the hypothesis that thalamic damage causes a chronic, hypo-function of metabolic and plasticity-related pathways (Experiment 1). Rats with unilateral, anterior thalamic lesions were exposed to a novel environment for 20 minutes, and granular retrosplenial tissue sampled from both hemispheres 30 minutes, 2h, or 8h later. Complementary statistical approaches (analyses of variance, predictive patterning and gene set enrichment analysis) revealed pervasive gene expression differences between retrosplenial cortex ipsilateral to the thalamic lesion and contralateral to the lesion. Selected gene differences were validated by QPCR, immunohistochemistry (Experiment 1), and in situ hybridisation (Experiment 2). Following thalamic lesions, the retrosplenial cortex undergoes profuse cellular transcriptome changes including lower relative levels of specific mRNAs involved in energy metabolism and neuronal plasticity. These changes in functional gene expression may be largely driven by decreases in the expression of multiple transcription factors, including brd8, c-fos, fra-2, klf5, nfix, nr4a1, smad3, smarcc2, and zfp9, with a much smaller number (nfat5, neuroD1, RXRγ) showing increases. These findings have implications for conditions such as diencephalic amnesia and Alzheimer's disease, where both anterior thalamic pathology and retrosplenial cortex hypometabolism are prominent.

Environmental Chemicals Impacting the Thyroid: Targets and Consequences

Thyroid hormone (TH) is essential for normal brain development, but the specific actions of TH differ across developmental time and brain region. These actions of TH are mediated largely by a combination of thyroid hormone receptor (TR) isoforms that exhibit specific temporal and spatial patterns of expression during animal and human brain development. In addition, TR action is influenced by different cofactors, proteins that directly link the TR protein to functional changes in gene expression. Considering the importance of TH signaling in development, it is important to consider environmental chemicals that may interfere with this signaling. Recent research indicates that environmental chemicals can interfere with thyroid function and with TH signaling. The key issues are to understand the mechanism by which these chemicals act and the dose at which they act, and whether adaptive responses intrinsic to the thyroid system can ameliorate potential adverse consequences (i.e., compensate). In addition, several recent studies show that TRs may be unintended targets of chemicals manufactured for industrial purposes to which humans and wildlife are routinely exposed. Polychlorinated biphenyls, polybrominated diphenyl ethers, bisphenol-A, and specific halogenated derivatives and metabolites of these compounds have been shown to bind to TRs and perhaps have selective effects on TR functions. A number of common chemicals, including polybrominated biphenyls and phthalates, may also exert such effects. When we consider the importance of TH in brain development, it will be important to pursue the possibilities that these chemicals-or interactions among chemical classes-are affecting children's health by influencing TH signaling in the developing brain.