Differences In mRNA Expression Levels Research Articles

Comprehensive gene expression analysis in gallbladder mucosal epithelial cells of dogs with gallbladder mucocele.

Gallbladder mucocele (GBM) is a common disease in the canine gallbladder. Although the pathogenesis of GBM remains unclear, we recently reported that the excessive accumulation of mucin in the gallbladder is not a result of overproduction by gallbladder epithelial cells (GBECs). Changes in the function of GBECs other than the production of mucin are associated with the pathogenesis of GBM. We performed an RNA sequencing (RNA-seq) analysis to comprehensively search for abnormalities in gene expression profiles of GBECs in dogs with GBM. Fifteen dogs with GBM and 8 dogs euthanized for reasons other than gallbladder disease were included. The GBECs were isolated from gallbladder tissues to extract RNA. The RNA-seq analysis was performed using the samples from 3 GBM cases and 3 dogs with normal gallbladders, and the gene expression profiles were compared between the 2 groups. Differences in mRNA expression levels of the extracted differentially expressed genes (DEGs) were validated by quantitative reverse transcription polymerase chain reaction (RT-qPCR) using samples of 15 GBM cases and 8 dogs with normal gallbladders. Comparison of gene expression profiles by RNA-seq extracted 367 DEGs, including ANO1, a chloride channel associated with changes in mucin morphology, and HTR4, which regulates the function of chloride channels. The ANO1 and HTR4 genes were confirmed to be downregulated in the GBM group by RT-qPCR. Our results suggest that GBM may be associated with decreased function of chloride channels expressed in GBECs.

Plasma exosomes from patients with active thyroid-associated orbitopathy induce inflammation and fibrosis in orbital fibroblasts

BackgroundThe pathogenesis of thyroid-associated orbitopathy (TAO) remains incompletely understand. The interaction between immunocytes and orbital fibroblasts (OFs) play a critical role in orbital inflammatory and fibrosis. Accumulating reports indicate that a significant portion of plasma exosomes (Pla-Exos) are derived from immune cells; however, their impact upon OFs function is unclear.MethodsOFs were primary cultured from inactive TAO patients. Exosomes isolated from plasma samples of patients with active TAO and healthy controls (HCs) were utilized for functional and RNA cargo analysis. Functional analysis in thymocyte differentiation antigen-1+ (Thy-1+) OFs measured expression of inflammatory and fibrotic markers (mRNAs and proteins) and cell activity in response to Pla-Exos. RNA cargo analysis was performed by RNA sequencing and RT-qPCR. Thy-1+ OFs were transfected with miR-144-3p mimics/inhibitors to evaluate its regulation of inflammation, fibrosis, and proliferation.ResultsPla-Exos derived from active TAO patients (Pla-ExosTAO−A) induced stronger production of inflammatory cytokines and hyaluronic acid (HA) in Thy-1+ OFs while inhibiting their proliferation. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and single sample gene set enrichment analysis (ssGSEA) suggested that the difference in mRNA expression levels between Pla-ExosTAO−A and Pla-ExosHC was closely related to immune cells. Differential expression analysis revealed that 62 upregulated and 45 downregulated miRNAs in Pla-ExosTAO−A, with the elevation of miR-144-3p in both Pla-Exos and PBMCs in active TAO group. KEGG analysis revealed that the target genes of differentially expressed miRNA and miR-144-3p enriched in immune-related signaling pathways. Overexpression of the miR-144-3p mimic significantly upregulated the secretion of inflammatory cytokines and HA in Thy-1+ OFs while inhibiting their proliferation.ConclusionPla-Exos derived from patients with active TAO were immune-active, which may be a long-term stimulus casual for inflammatory and fibrotic progression of TAO. Our finding suggests that Pla-Exos could be used as biomarkers or treatment targets in TAO patients.

Bioinformatics reveals diagnostic potential of cuproptosis-related genes in the pathogenesis of sepsis

BackgroundMultiple modes of cell death occur during the development of sepsis. Among these patterns, cuproptosis has recently been identified as a regulated form of cell death. However, its impact on the onset and progression of sepsis remains unclear. MethodWe screened a dataset of gene expression profiles from patients with sepsis using the GEO database. Survival analysis was performed to analyze the relationship between cuproptosis-related genes (CRGs) and prognosis. Hub genes were identified through univariate Cox regression analysis. The diagnostic value of hub genes in sepsis was tested in both training sets (GSE65682) and validation sets (GSE134347). To examine the association between hub genes and immune cells, single-sample gene set enrichment analysis (ssGSEA) and Pearson correlation analysis were employed. Additionally, the CRGs were validated in a septic mouse model using real-time quantitative PCR (qRT-PCR) and immunohistochemistry (IHC). ResultsIn sepsis, most CRGs were upregulated, with only DLD and MTF1 downregulated. High expression of three genes (GLE, LIAS, and PDHB) was associated with better prognosis, but only two hub genes (LIAS, PDHB) reached statistical significance. The receiver operating characteristic (ROC) analysis for diagnosing sepsis showed LIAS had a range of 0.793–0.906, while PDHB achieved values of 0.882 and 0.975 in the training and validation sets, respectively. ssGSEA analysis revealed a lower number of immune cells in the sepsis group, and there was a correlation between immune cell population and CRGs (LIAS, PDHB). Analysis in the septic mouse model demonstrated no significant difference in mRNA expression levels and IHC staining between LIAS and PDHB in heart and liver tissues, but up-regulation was observed in lung tissues. Furthermore, the mRNA expression levels and IHC staining of LIAS and PDHB were down-regulated in renal tissues. ConclusionsCuproptosis is emerging as a significant factor in the development of sepsis. LIAS and PDHB, identified as potential diagnostic biomarkers for cuproptosis-associated sepsis, are believed to play crucial roles in the initiation and progression of cuproptosis-induced sepsis.

Impaired autophagy activity-induced abnormal differentiation of bone marrow stem cells is related to adolescent idiopathic scoliosis osteopenia.

Osteopenia has been well documented in adolescent idiopathic scoliosis (AIS). Bone marrow stem cells (BMSCs) are a crucial regulator of bone homeostasis. Our previous study revealed a decreased osteogenic ability of BMSCs in AIS-related osteopenia, but the underlying mechanism of this phenomenon remains unclear. A total of 22 AIS patients and 18 age-matched controls were recruited for this study. Anthropometry and bone mass were measured in all participants. Bone marrow blood was collected for BMSC isolation and culture. Osteogenic and adipogenic induction were performed to observe the differences in the differentiation of BMSCs between the AIS-related osteopenia group and the control group. Furthermore, a total RNA was extracted from isolated BMSCs to perform RNA sequencing and subsequent analysis. A lower osteogenic capacity and increased adipogenic capacity of BMSCs in AIS-related osteopenia were revealed. Differences in mRNA expression levels between the AIS-related osteopenia group and the control group were identified, including differences in the expression of LRRC17 , DCLK1 , PCDH7 , TSPAN5 , NHSL2 , and CPT1B . Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed several biological processes involved in the regulation of autophagy and mitophagy. The Western blotting results of autophagy markers in BMSCs suggested impaired autophagic activity in BMSCs in the AIS-related osteopenia group. Our study revealed that BMSCs from AIS-related osteopenia patients have lower autophagic activity, which may be related to the lower osteogenic capacity and higher adipogenic capacity of BMSCs and consequently lead to the lower bone mass in AIS patients.

Clinical features and underlying mechanisms of KAT6B disease in a Chinese boy.

Lysine acetyltransferase 6B (KAT6B) encodes a highly conserved histone acetyltransferase that regulates the expression of multiple genes and is essential for human growth and development. We identified a novel frameshift variant c.3185del (p.leu1062Argfs*52) in a 5-year-old Chinese boy and further analyzed KAT6B expression and its interacting complexes and downstream products using real-time quantitative polymerase chain reaction (qPCR). Furthermore, we assessed its three-dimensional protein structure and compared the variant with other reported KAT6B variants. The deletion changed the leucine at position 1062 into an arginine, resulting in translation termination after base 3340, which may have affected protein stability and protein-protein interactions. KAT6B mRNA expression levels in this case were substantially different from those of the parents and controls in the same age range. There were also significant differences in mRNA expression levels among affected children's parents. RUNX2 and NR5A1, downstream products of the gene, affect the corresponding clinical symptoms. The mRNA expression levels of the two in children were lower than those of their parents and controls in the same age range. This deletion in KAT6B may affect protein function and cause corresponding clinical symptoms through interactions with key complexes and downstream products.

Polymorphisms and mRNA Expression Levels of IGF-1, FGF5, and KAP 1.4 in Tibetan Cashmere Goats.

The Tibetan cashmere goat is a precious breed in China and its cashmere is widely used in clothing and textiles. The genes IGF-1, FGF5, and KAP 1.4 have been shown to be crucial regulators of cashmere growth. In this study, we examined mRNA expression levels of these three genes and detected IGF-1, FGF5, and KAP 1.4 SNP loci in the Tibetan cashmere goat. After amplification and sequence alignment of the genes IGF-1, FGF5, and KAP 1.4 among 206 Tibetan cashmere goats, two new SNP loci were detected in gene KAP 1.4, while no SNP loci were found in amplified fragments of genes IGF-1 and FGF5. The expression levels of gene IGF-1 in Baingoin and Nyima counties were significantly higher than in other counties (p < 0.05). Moreover, the expression level of gene FGF5 in Gêrzê was significantly higher than in Rutog. The expression levels of mRNA in KAP 1.4 showed significant variation among seven counties. There were no significant differences in mRNA expression levels of IGF-1, FGF5, and KAP 1.4 in Tibetan cashmere goats when analysed by sex. The gene IGF-1 was slightly up-regulated in one to five-year-old cashmere goats, except in those that were 4 years old. The mRNA expression levels of FGF5 in one and two-year-old cashmere goats was lower compared with those in three to five-year-old cashmere goats. KAP 1.4 was up-regulated across one to five-year-old cashmere goats. In this study, SNP detection and mRNA expression analysis of IGF-1, FGF5, and KAP 1.4 genes was able to add data to genetic evolutionary analysis. Further studies should be carried out in SNPs to detect other fragments in genes IGF-1 and FGF5, as well as signal pathways and gene functions in protein levels of genes IGF-1, FGF5, and KAP 1.4 in the Tibetan cashmere goat.

Detecting Embryo Developmental Potential by Single Blastomere RNA-Seq.

Recent advances in preimplantation embryo diagnostics enable a wide range of applications using single cell biopsy and molecular-based selection techniques without compromising embryo production. This study was conducted to develop a single cell embryo biopsy technique and gene expression analysis method with a very low input volume to ensure normal embryo development and to see if there are differences in gene expression profiles between day-5 biopsied bovine embryos that developed into blastocysts and embryos arrested at morula stage. Out of the 65 biopsied morulae, 32 developed to blastocysts (49.2%). Out of the 13,580 successfully annotated genes, 1204 showed a difference in mRNA expression level. Out of these, 155 genes were expressed in embryos developing to blastocysts. The pathway enrichment analysis revealed significant enrichment in "organelle biogenesis and maintenance", "mRNA splicing" and "mitochondrial translation" pathways. These findings suggest principal differences in gene expression patterns and functional networks of embryos able to reach the blastocyst stage compared to embryos arrested in development. Our preliminary data suggest that single blastomere biopsy and selected gene expression profiles at morula stage could offer additional possibilities for early preimplantation embryo selection before transfer.

The influence of Interleukin-6, Interleukin-8, Interleukin-10, Interleukin-17, TNF-A, MIF, STAT3 on lung cancer risk in Moroccan population

To date, several studies have reported that key cytokines in the inflammatory system have important roles in the pathogenesis of cancer, notably in lung cancer. The aim of this case-control study, conducted for the first time in Moroccan population, was to investigate and to analyze the association of the following inflammatory cytokine genes Interleukin (IL)-6, Interleukin (IL)-8, Interleukin (IL)-10, Interleukin (IL)-17, Tumor Necrosis Factor-Alpha (TNFA), Macrophage migration Inhibitory Factor (MIF) and Signal Transducer and Activator of Transcription 3 (STAT3) with lung cancer risk in our patients. Firstly, the mRNA expression was assessed by a quantitative real time PCR in the peripheral blood of lung cancer patients and healthy subjects. Secondly, polymorphisms in the genes encoding cytokines were assessed in 160 lung cancer patients and 150 healthy controls. Genotyping analysis was performed with a Real-Time polymerase chain reaction using TaqMan® genotyping assays on a 7500 FAST Real-Time PCR System and Restriction Fragment Length PolymorphismPCR. Our results revealed a significant difference in mRNA expression levels of IL-6, IL-8, IL-10, IL-17 and TNFA genes in lung cancer patients compared to healthy subjects (P < 0.05). Among the studied genes, we found a significant association between lung cancer risk in our patients and the following polymorphisms IL-6 (rs1800795, rs1800796), IL-8 (rs4075, rs2227306), IL-17F (rs763780, rs2397084) and MIF (rs755622). In conclusion, the results of our study suggest that IL-6, IL-8, IL-10, IL-17 and MIF cytokine genes may aggravate lung cancer risk in the Moroccan population. However, further investigations are required to confirm our findings.

Expression of different genotypes of bovine TRDMT1 gene and its polymorphisms association with body measures in Qinchuan cattle (Bos Taurus)

DNA methyltransferase 2 (DNMT2) was renamed as tRNA aspartic acid methyltransferase 1 (TRDMT1) by catalyzing the methylation of tRNAAsp anti-codon loop C38. The development of sequencing of nucleic acids and protein detection techniques have prompted the demonstration that TRDMT1 mediated tRNA modification affects protein synthesis efficiency. This process affects the growth and development of animals. The DNA of 224 Qinchuan cattles aged 2–4 years old was collected in this experiment. The genetic variations of TRDMT1 exon and some intron regions were detected by mixed pool sequencing technology. qRT-PCR and Western Blot were used to detect the expression levels of mRNA and protein produced with the combination of different genetic variant loci. Three haplotypes were detected and the distribution ratios were different. Muscle tissue mRNA and protein testing showed that there were differences in mRNA expression levels among different genotypes (P < 0.05) and the protein expression levels between different genotypes show the same trend as mRNA. This study provides potential molecular materials for the improvement of Qinchuan cattle reproductivity and provides theoretical support for studying the effects of livestock TRDMT1 on animal growth and development.

Identification of two novel heterozygous SLC2A9 mutations in a Chinese woman and review of literature

ObjectiveThis study is aimed to describe the clinical and genetic characteristics of a Chinese woman diagnosed with renal hypouricemia type 2 (RHUC2). We also summarize the advances in research on RHUC2 by reviewing related literature. MethodsWe measured clinical parameters of a 57-year-old female and performed whole-exome sequencing to screen for mutations. Human embryonic kidney 293 cells were transiently transfected with plasmids containing wild-type or mutants. Relative mRNA quantification was determined by real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR). ResultsThis patient was diagnosed with diabetes and coronary heart disease. In addition, a decrease in 24-hour urinary chloride was observed. Two novel heterozygous variants of SLC2A9 (NM_020041.2): c.682-2_682-1insC and c.267C > G (p.Y89X) were identified. The mini-gene splicing assay revealed that c.682-2_682-1insC variant resulted in a frameshift mutation p. E228PfsX23. There was a statistically significant difference in mRNA expression level between the two mutants and the wild-type. ConclusionsThese findings strongly suggest that the two novel mutations are the causative agents of RHUC2. In particular, our findings provide further insights into the function of SLC2A9 and mechanisms of the complications.

Activation of Autophagy in Models of SF3B1 Mutant MDS

Background:SF3B1 is a key pre-mRNA splicing factor that is abundantly expressed in normal erythroid cells and whose mutation has been linked with high frequency to myelodysplastic syndromes with ringed sideroblasts (MDS with RS) implying that this gene may be an important driver of the pathogenesis of this subtype. Given that MDS with RS is characterized by ineffective erythropoiesis, we previously investigated the link between SF3B1 aberrations and the regulation of pathways that control erythroid maturation and iron homeostasis. Indeed, knockdown of SF3B1 led to significant impairment of the growth of erythroid cells and delayed erythroid differentiation. MDS erythroid cells were unable to properly process iron, resulting in its accumulation in mitochondria. Iron build-up inhibited the proliferation of erythroid progenitors and induced mitochondrial DNA-damage. During erythroid maturation, autophagy plays critical roles in the clearance of damaged mitochondria and maintaining iron homeostasis. Knockout of the essential autophagy gene, Atg7 leads to anemia due to a delayed clearance of mitochondria with a consequent increase in iron levels, ultimately resulting in increased reactive oxygen species formation. As such, we set out to determine if autophagy upregulation alleviates oxidative stress and thereby increases erythropoiesis in MDS with RS.Methods: Transmission electron microscopy (TEM) was performed to examine the cytoplasmic vacuolization, autophagosome content, and morphology of vacuoles and mitochondria in SF3B1 mutant (SF3B1MUT) vs. wild-type (SF3B1WT) cells. Immunoblotting was used to detect microtubule-associated protein 1 light chain 3 (LC3B), p62, and cathepsin D (marker of autophagic degradation). Whole exome sequencing (WES) was used to detect somatic alterations in autophagy genes and RNA-Sequencing and qPCR were conducted to evaluate differences in mRNA expression levels of autophagy genes. A missense mutation in SF3B1 resulting in K700E amino-acid substitution was introduced using EGE-CRISPR/Cas9-stimulated homology-mediated repair to generate heterozygous K562 cells expressing K700E.Transgenic heterozygous SF3B1 mice were used as an in vivo model. Temsirolimus (CCI-779), an mTOR inhibitor with autophagy-inducing properties, was tested in vitro and in vivo.Results: We identified numerous autophagosomes, double-membraned autophagic vacuoles, and single-membrane cytoplasmic structures in SF3B1MUTvs. SF3B1WT cells. LC3B protein was higher in primary SF3B1MUTvs. SF3B1WT cells. WES did not detect any somatic mutations in autophagy genes in the patients analyzed by TEM. RNA-Sequencing and qPCR showed that primary SF3B1MUT MDS with RS cells displayed increased expression levels of key genes of the ATG-autophagy pathway: [ATG2A/B, ATG3, ATG5 (FC=2), ATG9, (FC=5); P=.05], serine/threonine kinases [ULK1 (FC=2), ULK3 (FC=4); P=.05], and cathepsins [CTSB/D (FC=2), CTSE (FC=6); P=.01]. CRISPR/Cas9 K700E cells showed high autophagosome counts, increased basal expression of LC3B protein, and a 2-fold increase in autophagy genes (ATG5, ATG7, ULK1) compared to parental cells. Treatment with temsirolimus (10-100 nM) for 24 hours induced growth inhibition (IC50, 50 nM), enhanced the amount of autophagosomes containing degraded organelles, increased the percentage of dividing CD71+ cells and induced a 2-fold increase in LC3B in CRISPR/Cas9 K700E cells compared to parental cells. Temsirolimus (10 mg/kg i.p. 5d/wk) administered for two weeks to 6-8-month-old transgenic SF3B1 heterozygous mice (N=20) induced autophagy by increasing the number of autophagosomes and autophagolysosomes containing entrapped mitochondria, increased hemoglobin (7.5 vs. 6.6 g/dL; P=.05), and doubled the percentage of CD71+ erythroid cells (5-10%) in temsirolimus-treated vs. untreated SF3B1 mice.Conclusions: Basal autophagy is significantly upregulated in SF3B1MUT cells. Further stimulation of autophagic activity using FDA approved pathway-activating drugs may improve rates of erythrocyte production by SF3B1MUT clones and thus improve control of anemia in MDS with RS cases. DisclosuresAdvani:Takeda/ Millenium: Research Funding; Pfizer: Consultancy. Kelly:Pharmacyclics: Honoraria; Amgen: Honoraria; Abbvie: Honoraria; Jannsen: Honoraria. Sekeres:Celgene: Membership on an entity's Board of Directors or advisory committees. Carew:Millenium/ Takeda: Research Funding.

Research on feasibility of in vitro inflammatory wound microenvironment simulated by using inflammatory wound tissue homogenate of mice

Research on feasibility of in vitro inflammatory wound microenvironment simulated by using inflammatory wound tissue homogenate of mice

RFamide-related peptides' gene expression, polymorphism, and their association with reproductive traits in chickens

RFamide-related peptides (RFRP) are synthesized by the hypothalamus and have a regulatory role in gonad development. The goal of this study was to investigate the association between SNP of the RFRP gene and the reproductive traits and hormone levels of Zhenning yellow chickens. The mRNA expression levels were detected based on different tissues, ages, and genotypes. Eleven mutation sites were detected in the RFRP gene, 4 of which were significantly related to reproductive traits and hormone levels. Association analysis revealed that A276G was associated with egg production at 300 d of age (EP300) and amount of prehierarchical follicles (P < 0.05). G1396A was associated with egg weight at 300 d of age and luteinizing hormone (LH) and prolactin levels (P < 0.05). G1694A showed significant associations with fertilization rate and LH levels (P < 0.05), and A2659G was associated with EP300 (P < 0.05). The results of expression analysis showed that the RFRP mRNA expression levels in the hypothalamus were higher than those in other tissues (P < 0.01). The expression in immature individuals was higher than that in mature ones (P < 0.01). There were also differences in mRNA expression levels between different genotypes (P < 0.05). In summary, the results of this study might provide potential markers and a theoretical basis for the improvement of chicken reproductive traits.

Repeated social defeat exaggerates CaCl2-induced abdominal aortic aneurysm expansion by eliminating periaortic fibrosis in tissue repair phase: possible involvement of specific subtypes of macrophages

Abstract Background and objective Depression is an independent risk factor of cardiovascular disease (CVD) and significantly associated with the prevalence of abdominal aortic aneurysm (AAA). We have recently shown that repeated social defeat (RSD) precipitates depressive-like behaviors in apoE−/− mice and exaggerates atherosclerosis development by enhancing leukocyte activation. Here, we investigated the impact of RSD on AAA formation. Methods and results Eight-week-old male WT mice were exposed to RSD by housing with a larger CD-1 mouse in a shared home cage. They were subjected to vigorous physical contact daily for 10 consecutive days. Control mice were housed in the same gage without physical contact. After social interaction test to confirm depressive-like behaviors, defeated mice (28 of 48) and control mice (31 of 36) underwent application of 0.5 M calcium chloride (CaCl2) on the infrarenal aorta to induce AAA. At 1 week after application, maximum diameter and circumference of external elastic membrane were comparable between the two groups. The number of F-4/80, MMP-9, and TNF-α-positive cells in immunofluorescent images were also comparable. Further, in vitro bone marrow derived macrophages stimulation by LPS did not show any difference in mRNA expression levels of inflammatory cytokines, suggesting no discernable difference in acute inflammatory response between the two groups. In contrast, at 2 weeks after application, at the time point when MMP-9 and TNF-α-positive cells were scarcely observed, maximum diameter and circumference of external elastic membrane were significantly increased in defeated mice (0.72 mm vs. 0.90 mm, 1.59 mm vs. 2.00 mm, respectively, Control vs. Defeat, p&amp;lt;0.01). Intriguingly, periaortic fibrotic area in aneurysmal portion was markedly decreased in defeated mice (12.5×103 μm2 vs. 3.7×103 μm2, Control vs. Defeat, p&amp;lt;0.01). Consistently, accumulation of α-SMA-positive cells in adventitia of aneurysmal portion was much less in defeated mice than control mice (876 cells/mm2 vs. 319 cells/mm2, Control vs. Defeat, p&amp;lt;0.05), whereas those in tunica media of non-aneurysmal portion did not show any difference between the two groups. We next focused on the segregated nucleus-containing atypical monocyte (SatM), specific subtypes of monocytes/macrophages that are involved in fibrosis in injured tissues during the healing phase. We could observe SatM fraction in AAA tissue of control mice using flow cytometry. We also found that mRNA expression level of C/EBPβ, an essential regulator for SatM differentiation, was markedly decreased by 76% in BM cells of defeated mice compared with control mice (p&amp;lt;0.05). Conclusions Our findings demonstrate for the first time that RSD enhances AAA expansion by eliminating periaortic fibrosis in tissue repair phase, suggesting that the impaired resolution of acute inflammation after CaCl2 application contributes, at least in part, to the augmented expansion of AAA in defeated mice. Funding Acknowledgement Type of funding source: None

The critical role of BAP1 mutation in the prognosis and treatment selection of kidney renal clear cell carcinoma.

BackgroundThe BAP1 mutation is commonly found kidney renal clear cell carcinoma (KIRC) and a potential biomarker of individualized therapy. We evaluated the clinical significance of BAP1 mutation in the prognosis and treatment therapies for KIRC. Potential key pathways and related genes associated with these mechanisms were also identified in this investigation.MethodsWe identified the relevant data of patients BAP1 mutated on the cBioPortal and the compounds with significant selectivity to BAP1 mutations on the Genomics of Drug Sensitivity in Cancer (GDSC). And then, we identified the differences in mRNA expression levels of biological function annotation and pathways between mutated and wild type BAP1 patients by GSEA analysis. Furthermore, we screened the differentially expressed genes (DEGs) between BAP1 mutated and wild typed in KIRC patients and performed the GO and KEGG analysis. Finally, we conducted a protein-protein interaction (PPI) network to investigate the interaction between proteins encoded by candidate DEGs.ResultsReview of the TCGA data revealed 41 patients (10%) with KIRC displayed the BAP1 mutation. Further analysis led to the identification of 730 DEGs, while 617 genes were shown to be down-regulated, with 113 genes displaying upregulation. GO and KEGG pathway analysis indicated DEGs as enriched in metabolism, drug metabolism-cytochrome P450, and Drug-metabolizing enzymes. Subsequently, the top 10 hub genes, ranked by the degree in the PPI network were identified. Furthermore, our findings verify that the BAP1 mutation was associated with the deterioration of prognosis in patients with KIRC. Additionally, analysis of the GDSC database revealed that KIRC patients with BPP1 mutation are more prone to responding to Linsitinib.ConclusionsOur investigation identified the main pathways and relevant genes related to the BAP1 mutation in KIRC, which can contribute to the development of targeted treatment strategies for enhanced prognostic predictions of KIRC.

Gene expression analysis of activating and inhibitory receptors of natural killer cells in patients with acute myeloblastic leukemia

PurposeNatural killer (NK) cells are cytotoxic lymphocytes, which have long been known to play an essential role in immune surveillance of tumor cells. The results of several clinical studies imply evidence of impaired activity of NK cells in acute myeloblastic leukemia (AML). The aim of this study was to investigate the gene expression of activating and inhibitory receptors of NK cells in patients with newly diagnosed AML before and after induction therapy using 7 + 3 regimen in comparison to healthy donors. Materials and methodsSixteen AML patients aged 16–64 years as well as 16 matched healthy individuals were studied. Peripheral blood samples from patients were obtained in two steps, namely, in newly diagnosed patients and 28 days after receiving induction therapy. Real-time PCR was performed to evaluate the expression levels of activating receptors, including DNAM-1 and NKp46 as well as inhibitory receptors of KIR2DL1 and NKG2A. ResultsOur results demonstrated that the newly diagnosed patients showed over 50% decrease in NKp46 expression and a 6-fold increase in KIR2DL1 expression compared to healthy controls. The mRNA expression analysis in patients after induction therapy suggested a significant decrease in mRNA expressions of KIR2DL1 and NKG2A in comparison to newly diagnosed patients. ConclusionHerewith, we show a statistical difference in mRNA expression levels of activating (NKp46) and inhibitory receptors from NK cells in newly diagnosed AML patients when compared with healthy controls or patients who received induction therapy, supporting the findings of researchers who reported the impaired NK cells cytotoxicity in AML patients.

CYP3A5 Genotype as a Potential Pharmacodynamic Biomarker for Tacrolimus Therapy in Ulcerative Colitis in Japanese Patients.

Tacrolimus has been used to induce remission in patients with steroid-refractory ulcerative colitis. It poses a problem of large individual differences in dosage necessary to attain target blood concentration and, often, this leads to drug inefficacy. We examined the difference in mRNA expression levels of ATP binding cassette transporter B1 (ABCB1) between inflamed and non-inflamed tissues, and the influence of CYP3A5 genotype on tacrolimus therapy. The mRNA expression of CYP3A4 in colonic mucosa and that of cytochrome p450 3A5 (CYP3A5) and ABCB1 in inflamed and non-inflamed areas were examined in 14 subjects. The mRNA expression levels of CYP3A5 were higher than that of CYP3A4. The mRNA expression of ABCB1 was lower in the inflamed than in the non-inflamed mucosa, despite that of CYP3A5 mRNA level being not significantly changed. Hence, the deterioration of the disease is related to the reduction of the barrier in the inflamed mucosa. The relationship between CYP3A5 genotype and blood concentration, dose, and concentration/dose (C/D) ratio of tacrolimus in 15 subjects was studied. The tacrolimus dose to maintain equivalent blood concentrations was lower in CYP3A5*3/*3 than in CYP3A5*1 carriers, and the C/D ratio was significantly higher in the latter. Thus, CYP3A5 polymorphism information played a role in determining the initial dose of tacrolimus. Furthermore, since the effect of tacrolimus appears earlier in CYP3A5*3/*3 than in CYP3A5*1/*1 and *1/*3, it seems necessary to change the evaluation time of therapeutic effect by CYP3A5 genotype. Additionally, the relationship between CYP3A5 genotype and C/D ratio of tacrolimus in colonic mucosa was investigated in 10 subjects. Tacrolimus concentration in the mucosa was two-fold higher in CYP3A5*3/*3 than in CYP3A5*1 carriers, although no significant difference in tacrolimus-blood levels was observed. Therefore, the local concentration of tacrolimus affected by CYP3A5 polymorphism might be related to its therapeutic effect.

Evaluating macrophage migration inhibitory factor 1 expression as a prognostic biomarker in colon cancer.

Several studies indicate that macrophage migration inhibitory factor 1 plays a role for tumor progression in colon cancer. We investigated whether determination of migration inhibitory factor 1 mRNA expression levels in lymph nodes of colon cancer patients could be used as a prognostic marker. Expression levels of migration inhibitory factor 1 and carcinoembryonic antigen mRNAs were assessed in primary tumors and regional lymph nodes of 123 colon cancer patients (stages I-IV), and in colon cancer- and immune cell lines using quantitative reverse transcriptase-polymerase chain reaction. Expression of migration inhibitory factor 1 protein was investigated by two-color immunohistochemistry and immunomorphometry. Migration inhibitory factor 1 mRNA was expressed at 60 times higher levels in primary colon cancer tumors compared to normal colonic tissue (medians 8.2 and 0.2 mRNA copies/18S rRNA unit; p < .0001). A highly significant difference in mRNA expression levels was found between hematoxylin-eosin positive lymph nodes and hematoxylin-eosin negative lymph nodes (p < .0001). Migration inhibitory factor 1 and carcinoembryonic antigen proteins were simultaneously expressed in many colon cancer-tumor cells. Kaplan-Meier survival model and hazard ratio analysis, using a cutoff level at 2.19 mRNA copies/18S rRNA unit, revealed that patients with lymph nodes expressing high levels of migration inhibitory factor 1 mRNA had a 3.5-fold (p = .04) higher risk for recurrence, associated with a small, but significant, difference in mean survival time (7 months, p = .03) at 12 years of follow-up. Although migration inhibitory factor 1 mRNA expression levels were related to severity of disease and lymph node analysis revealed that colon cancer patients with high levels had a shorter survival time after surgery than those with low levels, the difference was small and probably not useful in clinical practice.

Constitutionally High Serotonin Tone Favors Obesity: Study on Rat Sublines With Altered Serotonin Homeostasis.

Central and peripheral pools of biogenic monoamine serotonin (5-hydroxytryptamine [5HT]) exert opposite effects on the body weight regulation: increase in brain 5HT activity is expected to decrease body weight, whereas increase in peripheral 5HT activity will increase body weight and adiposity. In a genetic model of rats with constitutionally high- or low-5HT homeostasis (hyperserotonergic/hyposerotonergic rats), we have studied how individual differences in endogenous 5HT tone modulate net energy balance of the organism. The high-5HT and low-5HT sublines of the model were developed by selective breeding toward extreme platelet activities of 5HT transporter, a key molecule determining 5HT bioavailability/activity. In animals from high-5HT and low-5HT sublines, we assessed physiological characteristics associated with body weight homeostasis and expression profile of a large scale of body weight–regulating genes in hypothalamus, a major brain region controlling energy balance. Results showed that under standard chow diet animals from the high-5HT subline, as compared to low-5HT animals, have lifelong increased body weight (by 12%), higher absolute daily food intake (by 9%), and different pattern of fat distribution (larger amount of white adipose tissue and lower amount of brown adipose tissue). A large number of body weight–regulating hypothalamic genes were analyzed for their mRNA expression: 24 genes by reverse transcription–quantitative polymerase chain reaction (n = 9–10 rats/subline) including neuropeptides and their receptors, growth factors, transcriptional factors, and receptors for peripheral signals, and a total of 84 genes of various classes by polymerase chain reaction array (pools of six rats/subline). Only few genes showed significant differences in mRNA expression levels between 5HT sublines (e.g. neuropeptide Y receptor, fibroblast growth factor 10), but high-5HT animals displayed a clear trend to upregulation of mRNAs for a number of orexigenic signaling peptides, their receptors, and other molecules with orexigenic activity. Receptors for peripheral signals (leptin, insulin) and molecules in their downstream signaling were not altered, indicating no changes in central insulin/leptin resistance. At the protein level, there were no differences in the content of hypothalamic leptin receptor between 5HT sublines, but significant sex and age effects were observed. Results show that higher constitutive/individual 5HT tone favors higher body weight and adiposity probably due to concurrent upregulation of several hypothalamic orexigenic pathways.

Inter-individual variability in freshwater tolerance is related to transcript level differences in gill and posterior kidney of European sea bass.

Acclimation to low salinities is a vital physiological challenge for euryhaline fish as the European sea bass Dicentrarchus labrax. This species undertakes seasonal migrations towards lagoons and estuaries where a wide range of salinity variations occur along the year. We have previously reported intraspecific differences in freshwater tolerance, with an average 30% mortality rate. In this study, we bring new evidence of mechanisms underlying freshwater tolerance in sea bass at gill and kidney levels. In fresh water (FW), intraspecific differences in mRNA expression levels of several ion transporters and prolactin receptors were measured. We showed that the branchial Cl-/HCO3- anion transporter (slc26a6c) was over-expressed in freshwater intolerant fish, probably as a compensatory response to low blood chloride levels and potential metabolic alkalosis. Moreover, prolactin receptor a (prlra) and Na+/Cl- cotransporter (ncc1) but not ncc-2a expression seemed to be slightly increased and highly variable between individuals in freshwater intolerant fish. In the posterior kidney, freshwater intolerant fish exhibited differential expression levels of slc26 anion transporters and Na+/K+/2Cl- cotransporter 1b (nkcc1b). Lower expression levels of prolactin receptors (prlra, prlrb) were measured in posterior kidney which probably contributes to the failure in ion reuptake at the kidney level. Freshwater intolerance seems to be a consequence of renal failure of ion reabsorption, which is not sufficiently compensated at the branchial level.