scholarly journals Transcriptomic analysis investigating the interaction between peripheral serotonin and high-fat diet feeding on mammary gene expression in midlactation mice

2020 ◽  
Vol 52 (1) ◽  
pp. 47-55
Author(s):  
A. A. Cheng ◽  
W. Li ◽  
L. L. Hernandez

To understand the role of peripheral serotonin and its interaction with diet in midlactation mammary gene expression, our study uses tryptophan hydroxylase 1 knockout ( Tph1-KO) mice fed a high-fat diet (HFD). It has previously been demonstrated that HFD feeding increases inflammatory and immune pathways in peak lactation mammary glands of mice and increases pup mortality in wild-type (WT) mice compared with dams fed a low-fat diet (LFD). Peripheral serotonin inhibition has been associated with resistance to obesity in male mice fed an HFD. Little is known about the function of Tph1 and how peripheral serotonin affects mammary gland function during pregnancy and lactation. In this study, WT and Tph1-KO models were used to investigate global transcriptomic changes in peak lactation mammary glands when dams were fed either an HFD or LFD. WT and Tph1-KO female mice were assigned to either an LFD or HFD beginning at 3 wk of age ( n = 4/group). Dams were euthanized on lactation day 11. Differentially expressed genes (DEGs) were first filtered by adjusted P value (cutoff ≤ 0.05) and fold-change (FC, cutoff ≥2). Genes were further filtered by mean normalized read count with a cutoff 310. We did not observe many differentially expressed genes in WT and Tph1-KO dams fed LFD. However, 3,529 DEGs were observed between WT-HFD and Tph1-KO-HFD mice, including cell cycle regulation and MAPK pathways being significantly enriched. Further research is required to completely understand the physiological significance of our results on peak lactation mammary physiology and the contribution of serotonin.

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0255770
Author(s):  
Adrienne A. Cheng ◽  
Wenli Li ◽  
Laura L. Hernandez

Little attention has been given to the effect of positional variation of gene expression in the mammary gland. However, more research is shedding light regarding the physiological differences that mammary gland location can have on the murine mammary gland. Here we examined the differentially expressed genes between mammary gland positions under either a low-fat diet (LFD) or a high-fat diet (HFD) in the mid-lactation mammary gland (lactation day 11; L11). Three-week old WT C57BL/6 mice were randomly assigned to either a low-fat diet (LFD) or high fat diet (HFD) (n = 3/group) and either the right thoracic mammary gland (TMG) or inguinal mammary gland (IMG) was collected from each dam for a total of 12 unique glands. Within each diet, differentially expressed genes (DEGs) were first filtered by adjusted p-value (cutoff ≤ 0.05) and fold-change (FC, cutoff ≥2). Genes were further filtered by mean normalized read count with a cutoff≥10. We observed that mammary gland position had a significant impact on mammary gland gene expression with either LFD or HFD diet, with 1264 DEGs in LFD dams and 777 DEGs in HFD dams. We found that genes related to snRNP binding and translation initiation were most significantly altered between the TMG and IMG. Although we were not able to discern a molecular mechanism, many small nuclear RNAs and small nucleolar RNAs were differentially expressed between the TMG and IMG responsible for cellular functions such as splicing and ribosome biogenesis, which provides and interesting avenue for future research. Our study supports the hypothesis that collection of the mammary gland from a particular location influences mammary gland gene expression, thereby highlighting the importance for researchers to be vigilant in documenting and reporting which mammary gland they are using for their studies.


2020 ◽  
Vol 26 (Supplement_1) ◽  
pp. S32-S32
Author(s):  
Reza Yarani ◽  
Oana Palasca ◽  
Nadezhda Tsankova Doncheva ◽  
Christian Anthon ◽  
Bartosz Pilecki ◽  
...  

Abstract Background Dextran sulfate sodium (DSS) ulcerative colitis (UC) murine models have long been used for in vivo studies. DSS is a negatively charged polysaccharide with colitogenic properties. Although the mechanisms by which DSS induces intestinal inflammation are not fully understood, there are several good reasons why the DSS chemical colitis model for investigating the immunopathogenesis mechanism of UC is widely used. These include strong phenotypic clinical manifestations which emulate numerous clinical and histopathological features of human UC, ease of use, low mortality rate and high reproducibility. Here, by using high-throughput RNA sequencing analysis we set to investigate the major predicted gene regulators (GRs) affected by differentially expressed genes in the DSS treated UC model in order to obtain regulatory insights into the pathogenic mechanisms of UC development. Methods A DSS-induced mouse model of UC was established. Total RNA from colon tissue and blood of 3 healthy and 3 DSS-treated mice was extracted and sequenced by Illumina HiSeq 4000. Gene expression levels were obtained by mapping and quantification to the annotated mouse genome. Subsequently, differential gene expression analysis between DSS-treated and control mice both in colon and blood was performed. Ingenuity pathway analysis software (IPA®, Qiagen) was used to predict/identify major GRs affected by significantly differentially expressed genes (SDEGs, FC > |2|, p ≤0.05) in both colon and blood. Results Our analysis revealed how many and which major GRs are affected in DSS-treated mice and also the direction of change as compared to healthy (untreated) mice. In colon, 595 activated and 198 inhibited major GRs (p-value of overlap ≤0.05) in relation to ∼ 3180 SDEGs were identified, while in blood, we identified 205 activated and 62 inhibited GRs (in relation to ∼650 SDEGs). Colon and blood share 181 activated and 41 inhibited GRs. Identified GRs include transcription regulators, cytokines, transmembrane receptors and enzymes that mainly contribute to the development of inflammatory/immune responses. In colon and blood, the top 10 activated and inhibited regulators with the highest positive and negative activation z-score with target molecules as well as expression in the datasets are indicated in Figure 1a and 1b, respectively. Conclusion In this study, we analyzed linkage of GRs to SDEGs through coordinated expression and identified potential major regulators that have significant effect on UC pathogenic-related gene expression. These GRs seem to be the key regulators of transcriptomic changes induced by inflammation. These findings expand our molecular understanding of putative new targets that may be important in the pathophysiology of UC and provide biological insights into the observed expression changes between the UC and healthy controls.


2019 ◽  
Vol 123 (3) ◽  
pp. 308-318 ◽  
Author(s):  
Tianyun Shao ◽  
Qiuhong Yu ◽  
Tingshuo Zhu ◽  
Anhong Liu ◽  
Xiumei Gao ◽  
...  

AbstractThe rate of hyperglycaemia in people around the world is increasing at an alarming rate at present, and innovative methods of alleviating hyperglycaemia are needed. The effects of Jerusalem artichoke inulin on hyperglycaemia, liver-related genes and the intestinal microbiota in mice fed a high-fat diet (HFD) and treated with streptozotocin (STZ) to induce hyperglycaemia were investigated. Inulin-treated hyperglycaemic mice had decreased average daily food consumption, body weight, average daily water consumption and relative liver weight and blood concentrations of TAG, total cholesterol, HDL-cholesterol and fasting blood glucose. Liver-related gene expressions in hyperglycaemic (HFD-fed and STZ-treated) compared with control mice showed eighty-four differentially expressed genes (forty-nine up-regulated and thirty-five down-regulated). In contrast, hyperglycaemic mice treated with inulin had twenty-two differentially expressed genes compared with control ones. Using Illumina high-throughput sequencing technology, the rarefaction and the rank abundance curves as well as the α diversity indices showed the treatment-induced differences in bacterial diversity in intestine. The linear discriminant analysis of effect size showed that the inulin treatment improved intestinal microbiota; in particular, it significantly increased the number of Bacteroides in the intestine of mice. In conclusion, inulin is potentially an effective functional food for the prevention and/or treatment of hyperglycaemia.


2022 ◽  
Vol 82 ◽  
Author(s):  
L. S. Santos ◽  
R. J. B. Matos ◽  
G. S. Cordeiro ◽  
G. S. Perez ◽  
D. A. E. Santo ◽  
...  

Abstract Exposure to the hight-fat diet may alter the control of food intake promoting hyperphagia and obesity. The objective of this study was to investigate the effects of this diet on dopamine receptors (drd1 and drd2), proopiomelanocortin (pomc), neuropeptideY (npy) genes expression, and preference food in adult rats. Wistar female rats were fed a hight-fat or control diet during pregnancy and lactation. The offspring were allocated into groups: Lactation – Control (C) and High-fat (H). Post-weaning – Control Control (CC), offspring of mothers C, fed a control diet after weaning; Control Hight-fat (CH), offspring of mothers C, fed a hight-fat diet after weaning; Hight-fat Control (HC), offspring of mothers H, fed with control diet after weaning; and Hight-fat Hight-fat (HH), offspring of mothers H, fed a H diet after weaning. The groups CH and HH presented greater expression of drd1 in comparison to the CC. The drd2 of CH and HC presented higher gene expression than did CC. HH presented higher pomc expression in comparison to the other groups. HC also presented greater expression in comparison to CH. The npy of HH presented greater expression in relation to CH and HC. HH and HC have had a higher preference for a high-fat diet at 102º life’s day. The high-fat diet altered the gene expression of the drd1, drd2, pomc and npy, and influencing the food preference for high-fat diet.


Stroke ◽  
2020 ◽  
Vol 51 (Suppl_1) ◽  
Author(s):  
Gina Sykes ◽  
Yusra Batool ◽  
Joseph Kamtchum Tatuene ◽  
Sarah Zehnder ◽  
Glen C Jickling

Introduction: Immune system dysregulation occurs with age. This includes an increase in inflammation, and immunosenescence, the inability to efficiently respond to new immune challenges. These changes are evident in various diseases but have yet to be evaluated in a population with ischemic stroke. Age is an important factor in stroke, contributing to stroke risk, outcome and risk of hemorrhagic transformation. This study aimed to assess the changes that occur with age in the leukocyte gene expression of patients with ischemic stroke. Methods: Two cohorts of acute ischemic stroke patients were analyzed; cohort 1 (n=94) and cohort 2 (n=79). RNA was isolated from PAXgene tubes and processed on Affymetrix microarrays. Differentially expressed genes associated with age quartiles were identified by ANCOVA, adjusted for sex and batch. Functional analysis identified age-associated pathways. Differentially expressed genes were compared with previous non-stroke aging studies in whole blood. Results: There were 61 and 442 age-associated genes in cohorts 1 and 2 respectively (FDR-corrected p<0.05, partial correlation coefficient ≥ |0.3|). Nineteen genes, including CR2, CCR6 and CXCR5 , were found in common and decreased with age among both cohorts (max-log10(p value) = 17). Functional analysis of the 61 and 442 genes revealed with advancing age there is a change in the humoral immune system, including antibody production and B cell proliferation. When compared to aging gene expression studies in controls, 52% of age-associated genes in cohort 1 and 31% of cohort 2 age-associated genes overlapped with those found in controls, and 16 of the 19 common genes to both cohorts overlapped in controls (max-log10(p value) = 15). Conclusion: In patients with acute stroke there is a change in leukocyte gene expression with advancing age. Changes included a shift in humoral immune response with a potentially impaired B cell response. While many of the age-associated alterations in gene expression present in stroke are similar to non-stroke controls, these changes warrant further investigation for their impact on stroke outcome and risk.


Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 3795-3795
Author(s):  
Monika Belickova ◽  
Jaroslav Cermak ◽  
Alzbeta Vasikova ◽  
Eva Budinska

Abstract Abstract 3795 Poster Board III-731 Gene expression profiles of CD34+ cells were compared between a cohort of 51 patients with MDS or AML from MDS and 7 healthy controls. The patients were classified according to the WHO criteria as follows: 5q- syndrome (n=7), RA (n=3), RARS (n=2), RCMD (n=10), RAEB-1 (n=7), RAEB-2 (n=15), and AML with MLD (multilineage dysplasia) (n=7). HumanRef-8 v2 Expression Bead Chips (Illumina) were used to generate expression profiles of the samples for >22,000 transcripts. The raw data were normalized data with the R software, lumi package. Normalized data were filtered by detection p-value <0.01, resulting in total number of 9811genes. To identify differentially expressed genes we performed two parallel statistical hypothesis testings: Analysis of Variance (ANOVA) together with Tukey test and empirical bayesian thresholding correction for multiple testing problem; and Significance Analysis of Microarrays (SAM). The results were confirmed by real-time quantitative PCR for six genes (TaqMan Gene Expression Assays). Hierarchical clustering of significantly differentially expressed genes clearly separated patients and controls, 5q-syndrome and RAEB-1 as a separate entities confirming usefulness of WHO classification subgroups. The most up-regulated genes in all patients included HBG2, HBG1, CYBRD1, HSPA1B, ANGPT1, and MYC. We assume that expression changes in globin genes, both fetal and adult globins (HBG2, HBG1 and HBA1, HBB) may play role not only in dysregulation of erythropoiesis but also in the disease progression or leukemic transformation of MDS. Among the most down-regulated genes, 13 genes related to B-lymphopoiesis (e.g. POU2AF1, VPREB1, VPREB3, CD79A, EBF1, LEF1, BCL3, IRF8 & IRF4) were detected, suggesting the abnormal development of B-cell progenitors in all MDS patients. Some of these genes (e.g. VPREB3, LEF1) showed decreasing trend in expression level from early to advanced MDS with the lowest expression in AML with MLD. Patients with advanced MDS had significantly decreased expression of genes involved in in the mitotic cell cycle, DNA replication, and chromosome segregation compared to early MDS where these gene subsets were up-regulated. The DAVID database also identified de-regulation in the cell cycle pathway through its 7 genes (CDC25C, CDC7, CDC20, ORC1L, CCNB2, BUB1, & CCNA2). On the other hand, advanced MDS patients showed significant up-regulation of proto-oncogenes (BMI1, MERTK) and genes related to angiogenesis (ANGPT1), anti-apoptosis (VNN1). The results confirm on molecular basis that increased cell proliferation and resistance to apoptosis together with a loss of cell cycle control, damaged DNA repair and altered immune response may play an important role in the expansion of malignant clone in MDS patients. The study was supported by Grant NR-9235 obtained from the Ministry of Health, Czech Republic. Disclosures: No relevant conflicts of interest to declare.


2017 ◽  
Vol 6 (4) ◽  
pp. 327-339 ◽  
Author(s):  
Pili Zhang ◽  
Tianjiao Chu ◽  
N. Dedousis ◽  
Benjamin S. Mantell ◽  
Ian Sipula ◽  
...  

Viruses ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2374
Author(s):  
Joanna Sajewicz-Krukowska ◽  
Jan Paweł Jastrzębski ◽  
Maciej Grzybek ◽  
Katarzyna Domańska-Blicharz ◽  
Karolina Tarasiuk ◽  
...  

Astrovirus infections pose a significant problem in the poultry industry, leading to multiple adverse effects such as a decreased egg production, breeding disorders, poor weight gain, and even increased mortality. The commonly observed chicken astrovirus (CAstV) was recently reported to be responsible for the “white chicks syndrome” associated with an increased embryo/chick mortality. CAstV-mediated pathogenesis in chickens occurs due to complex interactions between the infectious pathogen and the immune system. Many aspects of CAstV–chicken interactions remain unclear, and there is no information available regarding possible changes in gene expression in the chicken spleen in response to CAstV infection. We aim to investigate changes in gene expression triggered by CAstV infection. Ten 21-day-old SPF White Leghorn chickens were divided into two groups of five birds each. One group was inoculated with CAstV, and the other used as the negative control. At 4 days post infection, spleen samples were collected and immediately frozen at −70 °C for RNA isolation. We analyzed the isolated RNA, using RNA-seq to generate transcriptional profiles of the chickens’ spleens and identify differentially expressed genes (DEGs). The RNA-seq findings were verified by quantitative reverse-transcription PCR (qRT-PCR). A total of 31,959 genes was identified in response to CAstV infection. Eventually, 45 DEGs (p-value < 0.05; log2 fold change > 1) were recognized in the spleen after CAstV infection (26 upregulated DEGs and 19 downregulated DEGs). qRT-PCR performed on four genes (IFIT5, OASL, RASD1, and DDX60) confirmed the RNA-seq results. The most differentially expressed genes encode putative IFN-induced CAstV restriction factors. Most DEGs were associated with the RIG-I-like signaling pathway or more generally with an innate antiviral response (upregulated: BLEC3, CMPK2, IFIT5, OASL, DDX60, and IFI6; downregulated: SPIK5, SELENOP, HSPA2, TMEM158, RASD1, and YWHAB). The study provides a global analysis of host transcriptional changes that occur during CAstV infection in vivo and proves that, in the spleen, CAstV infection in chickens predominantly affects the cell cycle and immune signaling.


Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 26-26
Author(s):  
Manishkumar S. Patel ◽  
Ellen K. Kendall ◽  
Sarah Ondrejka ◽  
Agrima Mian ◽  
Yazeed Sawalha ◽  
...  

Background Diffuse large B cell lymphoma (DLBCL) is curable in ~60-70% of patients using standard chemoimmunotherapy, but the prognosis is poor for relapsed/refractory (R/R) DLBCL. Therefore, understanding the underlying molecular mechanisms will facilitate early prediction and effective management of resistance to therapy. Recent studies of paired diagnostic-relapse biopsies from patients have relied on a single "omics" approach, examining either gene expression or epigenetic evolution. Here we present a combined analysis of gene expression and DNA methylation profiles of paired diagnostic-relapse DLBCL biopsies to identify changes responsible for relapse after R-CHOP. Methods Biopsies from 23 DLBCL patients were obtained at the time of diagnosis and relapse following frontline R-CHOP chemoimmunotherapy. The cohort had 18 (78.3%) male patients with median age of 62 (range, 35-86) years and median IPI of 2.5 (range, 1-5). The median time from diagnosis to relapse was 7 (range, 0-57) months. DNA and RNA were extracted simultaneously from formalin-fixed paraffin embedded (FFPE) biopsy samples. DNA methylation levels were measured through Illumina 850k Methylation Array for 22 pairs of diagnostic-relapse biopsies. RNA from diagnostic-relapse paired biopsies from 6 patients was sequenced using Illumina HiSeq4000. Differentially methylated probes were identified using the DMRcate package, and differentially expressed genes were identified using the DESeq2 package. Gene set enrichment analysis was performed using canonical pathway gene sets from MSigDB. Pearson's correlation with a Bonferroni correction to the p-value was used to calculate the correlation between regularized log transformed gene expression counts and methylation beta values. Results In a pairwise comparison of gene expression between diagnostic and R/R biopsy pairs, we found 14 differentially expressed genes (FDR&lt;0.1 & Log2FC&gt;|1|) consistent across all pairs. Compared to gene expression at diagnosis, five genes (CYP1B1, LGR4, ATXN1, CTSC, ZMAT3) were downregulated, and eight genes (ERBB3, CD19, CARD11, MT-RNR2, IGHG3, CCDC88C, ATP2A3, CENPE, and PCNT) were up-regulated in the R/R samples. Many of these genes have been previously implicated in oncogenesis, such as ERBB3, a member of the epidermal growth receptor family. Importantly, some of these genes have known roles in DLBCL biology, such as CD19, a member of the B-cell receptor complex, and CARD11, a gene in which several oncogenic mutations have been identified in DLBCL as a mediator of NF-KB activation. Gene set enrichment analysis revealed overexpression of immune signatures such as cytokine-cytokine receptor interaction, chemokine receptor-chemokine binding, and the IL-12-STAT4 pathway at diagnosis. At relapse, cell cycle, B-cell receptor, and NOTCH signaling pathways were overexpressed. Interestingly, in a pairwise comparison of methylation between diagnostic and R/R biopsy pairs, there were no differentially methylated probes (FDR&lt;0.05), suggesting no coordinated epigenetic evolution between diagnostic and R/R pairs. For biopsy pairs that had both gene expression and methylation data (5 pairs), we correlated gene expression and methylation values. We found that none of the differentially expressed genes between the diagnostic and R/R biopsies were significantly correlated with methylation status (adjusted p-value&lt;0.05). Conclusions By analyzing paired diagnostic and relapse DLBCL biopsies, we found that at the time of relapse, there are significant transcriptomic changes but no significant epigenetic changes when compared to diagnostic biopsies. Activation of B-cell receptor and NOTCH signaling, as well as the loss of immune signaling at relapse, cannot be attributed to coordinated epigenetic changes in methylation. As the epigenetic profile of the biopsies did not consistently evolve, these data emphasize the need for better understanding of the baseline methylation profiles at the time of diagnosis, as well as acquired somatic mutations that may contribute to the emergence of therapeutic resistance. Future studies are needed to focus on how activation of signaling pathways triggered by genomic alterations can be targeted in relapsed/refractory DLBCL. Disclosures Hsi: Seattle Genetics: Consultancy, Honoraria; Miltenyi: Consultancy, Honoraria; Abbvie: Research Funding; Eli Lilly: Research Funding; CytomX: Consultancy, Honoraria. Hill:Takeda: Research Funding; Genentech: Consultancy, Honoraria, Research Funding; Karyopharm: Consultancy, Honoraria, Research Funding; Celgene: Consultancy, Honoraria, Research Funding; Abbvie: Consultancy, Honoraria, Research Funding; Pharmacyclics: Consultancy, Honoraria, Research Funding; Beigene: Consultancy, Honoraria, Research Funding; AstraZenica: Consultancy, Honoraria, Research Funding; Kite, a Gilead Company: Consultancy, Honoraria, Research Funding; Novartis: Consultancy, Honoraria; BMS: Consultancy, Honoraria, Research Funding.


Nutrients ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 2885
Author(s):  
Dawid Gawliński ◽  
Kinga Gawlińska ◽  
Irena Smaga

In recent years, strong evidence has emerged that exposure to a maternal high-fat diet (HFD) provokes changes in the structure, function, and development of the offspring’s brain and may induce several neurodevelopmental and psychiatric illnesses. The aims of this study were to evaluate the effects of a maternal HFD during pregnancy and lactation on depressive-like behavior and Cnr1 gene expression (encoding the CB1 receptor) in brain structures of rat offspring and to investigate the epigenetic mechanism involved in this gene expression. We found that a maternal HFD during pregnancy and lactation induced a depressive-like phenotype at postnatal days (PNDs) 28 and 63. We found that a maternal HFD decreased the Cnr1 mRNA levels in the prefrontal cortex with the increased levels of miR-212-5p and methylation of CpG islands at the Cnr1 promoter and reduced the level of Cnr1 gene expression in the dorsal striatum with an increased level of miR-154-3p in adolescent male offspring. A contrasting effect of a maternal HFD was observed in the hippocampus, where upregulation of Cnr1 gene expression was accompanied by a decrease of miR-154-3p (at PNDs 28 and 63) and miR-212-5p (at PND 63) expression and methylation of CpG islands at the Cnr1 promoter in male offspring. In summary, we showed that a maternal HFD during pregnancy and lactation triggered several epigenetic mechanisms in the brains of rat offspring, which may be related to long-lasting alterations in the next generation and produce behavioral changes in offspring, including a depressive-like phenotype.


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