Genome Microarray Research Articles

TBR-760, a Dopamine-Somatostatin Compound, Arrests Growth of Aggressive Nonfunctioning Pituitary Adenomas in Mice.

TBR-760 (formerly BIM-23A760) is a chimeric dopamine (DA)-somatostatin (SST) compound with potent agonist activity at both DA type 2 (D2R) and SST type 2 (SSTR2) receptors. Studies have shown that chimeric DA-SST compounds are more efficacious than individual DA and/or SST analogues, either alone or combined, in inhibiting secretion from primary cultures of human somatotroph and lactotroph tumor cells. Nonfunctioning pituitary adenomas (NFPAs) express both D2R and SSTR2 and, consequently, may respond to TBR-760. We used a mouse model with the pro-opiomelanocortin (POMC) gene knocked out that spontaneously develops aggressive NFPAs. Genomic microarray and DA and SST receptor messenger RNA expression analysis indicate that POMC KO mouse tumors and human NFPAs have similar expression profiles, despite arising from different cell lineages, establishing POMC KO mice as a model for study of NFPAs. Treatment with TBR-760 for 8 weeks resulted in nearly complete inhibition of established tumor growth, whereas tumors from vehicle-treated mice increased in size by 890 ± 0.7%. Comparing TBR-760 with its individual DA and SST components, TBR-760 arrested tumor growth. Treatment with equimolar or 10×-higher doses of the individual SST or DA agonists, either alone or in combination, had no significant effect. One exception was the lower dose of DA agonist that induced modest suppression of tumor growth. Only the chimeric compound TBR-760 arrested tumor growth in this mouse model of NFPA. Further, significant tumor shrinkage was observed in 20% of the mice treated with TBR-760. These results support the development of TBR-760 as a therapy for patients with NFPA.

Gene expression profiling of tumor stroma interactions in retinoblastoma

We aimed to identify the critical molecular pathways altered upon tumor stroma interactions in retinoblastoma (RB). In vitro 2 D cocultures of RB tumor cells (Weri-Rb-1 and NCC-RbC-51) with primary bone marrow stromal cells (BMSC) was established. Global gene expression patterns in coculture samples were assessed using Affymetrix Prime view human gene chip microarray and followed with bioinformatics analyses. Key upregulated genes from Weri-Rb-1 + BMSC and NCC-RbC-51 + BMSC coculture were validated using qRT-PCR to ascertain their role in RB progression. Whole genome microarray experiments identified significant (P ≤ 0.05, 1.1 log 2 FC) transcriptome level changes induced upon coculture of RB cells with BMSC. A total of 1155 genes were downregulated and 1083 upregulated in Weri-Rb-1 + BMSC coculture. Similarly, 1865 genes showed downregulation and 1644 genes were upregulation in NCC-RbC-51 + BMSC coculture. The upregulated genes were significantly associated with pathways of focal adhesion, PI3K-Akt signalling, ECM-receptor interaction, JAK-STAT, TGF-β signalling thus contributing to RB progression. Validation of key genes by qRT-PCR revealed significant overexpression of IL8, IL6, MYC and SMAD3 in the case of Weri-Rb-1 + BMSC coculture and IL6 in the case of NCC-RbC-51 + BMSC coculture. The microarray expression study on in vitro RB coculture models revealed the pathways that could be involved in the progression of RB. The gene signature obtained in a stimulated model when a growing tumor interacts with its microenvironment may provide new horizons for potential targeted therapy in RB.

Low Molecular Weight Fucoidan Prevents Radiation-Induced Fibrosis and Secondary Tumors in a Zebrafish Model.

Radiotherapy often causes unwanted side effects such as radiation-induced fibrosis and second malignancies. Fucoidan, a sulfated polysaccharide extracted from brown seaweed, has many biological effects including anti-inflammation and anti-tumor. In the present study, we investigated the radioprotective effect of Oligo-Fucoidan (OF) using a zebrafish animal model. Adult zebrafish of wild-type and transgenic fish with hepatocellular carcinoma were orally fed with Oligo-Fucoidan before irradiation. Quantitative PCR, Sirius red stain, hematoxylin, and eosin stain were used for molecular and pathological analysis. Whole genomic microarrays were used to discover the global program of gene expression after Oligo-Fucoidan treatment and identified distinct classes of up- and downregulated genes/pathways during this process. Using Oligo-Fucoidan oral gavage in adult wild-type zebrafish, we found Oligo-Fucoidan pretreatment decreased irradiation-induced fibrosis in hepatocyte. Using hepatitis B virus X antigen (HBx), Src and HBx, Src, p53−/+ transgenic zebrafish liver cancer model, we found that Oligo-Fucoidan pretreatment before irradiation could lower the expression of lipogenic factors and enzymes, fibrosis, and cell cycle/proliferation markers, which eventually reduced formation of liver cancer compared to irradiation alone. Gene ontology analysis revealed that Oligo-Fucoidan pretreatment increased the expression of genes involved in oxidoreductase activity in zebrafish irradiation. Oligo-Fucoidan also decreased the expression of genes involved in transferase activity in wild-type fish without irradiation (WT), nuclear outer membrane-endoplasmic reticulum membrane network, and non-homologous end-joining (NHEJ) in hepatocellular carcinoma (HCC) transgenic fish. Rescue of those genes can prevent liver cancer formation. Conclusions: Our results provide evidence for the ability of Oligo-Fucoidan to prevent radiation-induced fibrosis and second malignancies in zebrafish.

Expression of long non-coding RNA SFTA1P and its function in non-small cell lung cancer

Non-small cell lung cancer (NSCLC) is a major type of lung cancer with high morbidity and mortality. Long non-coding RNAs (lncRNAs) have been reported to be important in development and progression of NSCLC. However, the role of lncRNA SFTA1P remains unclear. This study aims to explore the clinical roles, biological function, and mechanism of SFTA1P in NSCLC. SFTA1P expression was estimated by the quantitative real-time polymerase chain reaction (qRT-PCR) of 90 pairs of tissue samples, the Cancer Genome Atlas (TCGA) database and microarray. After overexpressing SFTA1P, NSCLC cell proliferation, cycle, and apoptosis were detected. We found that the expression of SFTA1P was significantly downregulated in NSCLC tissues with high diagnostic value (AUC = 0.87), which was consistent with the results of TCGA and microarray data. For the analysis of clinical features, the results revealed that SFTA1P expression was closely related to the pathological type (P < 0.01). Furthermore, the cell function results suggested that the overexpression of SFTA1P triggered cell cycle arrest in the S-phase (P < 0.05). From a mechanistic perspective, the results showed that the PI3K-AKT signaling pathway was inhibited after overexpression of SFTA1P in NSCLC. Taken together, this work supported that SFTA1P may play a suppressing role in the tumorigenesis of NSCLC by modulating PI3K-AKT signaling pathway to influence cell cycle, which provides a potential and prospective biomarker for NSCLC.

Detection of chromosomal abnormalities in spontaneous miscarriage by low‑coverage next‑generation sequencing.

Chromosomal abnormalities (CAs) can cause spontaneous miscarriage and increase the incidence of subsequent pregnancy loss and other complications. Presently, CAs are detected mainly by array comparative genomic hybridization (CGH) and single nucleotide polymorphism microarrays. The present study developed a low-coverage next-generation sequencing method to detect CAs in spontaneous miscarriage and assess its clinical performance. In total, 1,401 patients who had experienced an abortion were enrolled in the present study and divided into two groups. In group I, 437 samples that had been previously validated by array CGH were used to establish a method to detect CAs using a semiconductor sequencing platform. In group II, 964 samples, which were not verified, were assessed using established methods with respect to clinical significance. Copy number variant (CNV)-positive and euploidy samples were verified by array CGH and short tandem repeat profiling, respectively, based on quantitative fluorescent PCR. The low-coverage sequencing method detected CNVs >1 Mb in length and a total of 3.5 million unique reads. Similar results to array CGH were obtained in group I, except for six CNVs <1 Mb long. In group II, there were 341 aneuploidies, 195 CNVs, 25 mosaicisms and 403 euploidies. Overall, among the 1,401 abortion samples, there were 536 aneuploidies, 263 CNVs, 34 mosaicisms, and 568 euploidies. Trisomies were present in all autosomal chromosomes. The most common aneuploidies were T16, monosomy X, T22, T15, T21 and T13. Furthermore, one tetrasomy 21, one CNV associated with Wolf-Hirschhorn syndrome, one associated with DiGeorge syndrome and one associated with both Prader-Willi and Angelman syndromes were identified. These four cases were confirmed by short tandem repeat profiling and array CGH. Quantitative fluorescent PCR revealed nine polyploidy samples. The present method demonstrated equivalent efficacy to that of array CGH in detecting CNVs >1 Mb, with advantages of requiring less input DNA and lower cost.

Two Thalamic Regions Screened Using Laser Capture Microdissection with Whole Human Genome Microarray in Schizophrenia Postmortem Samples.

We used whole human genome microarray screening of highly enriched neuronal populations from two thalamic regions in postmortem samples from subjects with schizophrenia and controls to identify brain region-specific gene expression changes and possible transcriptional targets. The thalamic anterior nucleus is reciprocally connected to anterior cingulate, a schizophrenia-affected cortical region, and is also thought to be schizophrenia affected; the other thalamic region is not. Using two regions in the same subject to identify disease-relevant gene expression differences was novel and reduced intersubject heterogeneity of findings. We found gene expression differences related to miRNA-137 and other SZ-associated microRNAs, ELAVL1, BDNF, DISC-1, MECP2 and YWHAG associated findings, synapses, and receptors. Manual curation of our data may support transcription repression.

Six molecular patterns leading to hemophilia A phenotype in 18 females from Poland

IntroductionFemale hemophilia is an intriguing rare disorder and few larger reports on its genetic etiology are available. While historically the diagnosis was satisfactorily reached by factor VIII activity assays, the clinical and potentially therapeutic heterogeneity of female hemophilia calls for comprehensive molecular diagnosis in each case. Currently, the genetic investigations are not a part of routine, state-funded, diagnostics in Poland, and thus molecular epidemiological data are missing. AimWe set out to perform a comprehensive genetic analysis of Polish females with hemophilia A. Patients/methodsEighteen females with hemophilia A (including 2 with severe and 5 with moderate hemophilia phenotype) consented for genetic diagnostics. To establish F8 mutations, we used next-generation sequencing of a panel of genes associated with hematological disorders, standard assays for recurrent intragenic F8 inversions and MLPA when deletions were suspected. When appropriate we also used karyotyping, genomic microarrays and X chromosome inactivation assays. ResultsWhile abnormally skewed X-chromosome inactivation combined with a F8 variant on the active allele was, as expected, the most common genetic etiology, a number of other genetic scenarios were unraveled. This included: misdiagnosis (molecular diagnosis of vWd), Turner syndrome, compound heterozygosity and androgen insensitivity syndrome (a phenotypical 46,XY female with a novel androgen receptor gene mutation). We report 3 novel F8 mutations. ConclusionEvery case of female hemophilia warrants full genomic diagnostics, as this may change the diagnosis or reveal broader morbidity than a coagulation disorder (Turner syndrome, androgen insensitivity, or cardiovascular morbidity that we described previously in a SHAM syndrome carrier).

Minimum error calibration and normalization for genomic copy number analysis

BackgroundCopy number variations (CNV) are regional deviations from the normal autosomal bi-allelic DNA content. While germline CNVs are a major contributor to genomic syndromes and inherited diseases, the majority of cancers accumulate extensive “somatic” CNV (sCNV or CNA) during the process of oncogenetic transformation and progression. While specific sCNV have closely been associated with tumorigenesis, intriguingly many neoplasias exhibit recurrent sCNV patterns beyond the involvement of a few cancer driver genes. Currently, CNV profiles of tumor samples are generated using genomic micro-arrays or high-throughput DNA sequencing. Regardless of the underlying technology, genomic copy number data is derived from the relative assessment and integration of multiple signals, with the data generation process being prone to contamination from several sources. Estimated copy number values have no absolute or strictly linear correlation to their corresponding DNA levels, and the extent of deviation differs between sample profiles, which poses a great challenge for data integration and comparison in large scale genome analysis. ResultsIn this study, we present a novel method named “Minimum Error Calibration and Normalization for Copy Numbers Analysis” (Mecan4CNA). It only requires CNV segmentation files as input, is platform independent, and has a high performance with limited hardware requirements. For a given multi-sample copy number dataset, Mecan4CNA can batch-normalize all samples to the corresponding true copy number levels of the main tumor clones. Experiments of Mecan4CNA on simulated data showed an overall accuracy of 93% and 91% in determining the normal level and single copy alteration (i.e. duplication or loss of one allele), respectively. Comparison of estimated normal levels and single copy alternations with existing methods and karyotyping data on the NCI-60 tumor cell line produced coherent results. To estimate the method's impact on downstream analyses, we performed GISTIC analyses on the original and Mecan4CNA normalized data from the Cancer Genome Atlas (TCGA) where the normalized data showed prominent improvements of both sensitivity and specificity in detecting focal regions. ConclusionsMecan4CNA provides an advanced method for CNA data normalization, especially in meta-analyses involving large profile numbers and heterogeneous source data quality. With its informative output and visualization options, Mecan4CNA also can improve the interpretation of individual CNA profiles. Mecan4CNA is freely available as a Python package and through its code repository on Github.

OR15-04 Central Precocious Puberty without Central Nervous System Lesions: Is It Really Idiopathic?

Background: The etiological diagnosis of central precocious puberty (CPP) has been classically divided into causes with or without central nervous system (CNS) lesions. Among the cases without CNS lesions, most of them are classified as idiopathic. In clinical practice, about 90% of girls and 40% of boys with CPP are considered having the idiopathic form. In the last two decades, pioneering studies have revealed underlying genetic causes in patients with apparently idiopathic CPP.Objective: To describe the frequency of genetic causes identified in a large cohort of patients with CPP followed in a single research center and to evaluate its role in the distribution of the etiology of CPP.Patients and methods: A retrospective evaluation was performed analyzing the etiological diagnosis of 276 patients (246 girls, 30 boys) with CPP followed in a single university hospital outpatient clinic from 2006 to 2019. The great majority (230 patients) presented without CNS lesions, being classified as idiopathic CPP group. Among the idiopathic CPP group, 170 of them had DNA samples available and were included for genetic analysis. Patients included for genetic analysis were systematically investigated for genetic causes of CPP using standard methodologies of genetic-molecular analysis. Briefly, they were studied as follows: 120 by Sanger sequencing; 18 by target panel sequencing; 27 by whole-exome sequencing; 5 by whole-genome sequencing; 113 by specific DNA methylation analysis; and 38 by genomic microarray.Results: Among the 276 patients with CPP, 46 (16.7%) had pathological CNS lesions: 19 boys and 27 girls, indicating the prevalence of CPP with CNS lesions (organic) of 63.3% in boys and 11% in girls. The most common cause of organic CPP was hypothalamic hamartoma (20 cases). Meanwhile 230 patients (83.3%) encompassed the apparently idiopathic CPP group. Main characteristics of this idiopathic CPP group were: 219 girls and 11 boys; 158 sporadic (69%), 68 familial (29.5%) and 4 adopted (1.5%). In the subset of patients with DNA available (162 girls, 8 boys), the frequency of genetic causes was 11.8% (20 cases: 18 girls and 2 boys). Analyzing by sex, the frequency of genetic causes was higher in boys (25%) than in girls (11.1%). The identified genetic defects were the following: 9 cases with inactivating MKRN3 mutations (8 families), 6 cases with inactivating DLK1 mutations (2 families), 1 case with activating KISS1R mutation, 1 case with activating KISS1 mutation, 2 sporadic cases with maternal uniparental disomy of chromosome 14, and 1 sporadic case with epimutation at DLK1 locus.Conclusion: Pathogenic genetic defects were identified in 11.8% of patients with apparently idiopathic CPP involving four distinct genes. Altogether, these genetic findings indicate a context of changing in the distribution of the etiological diagnosis of CPP in both sexes, highlighting the genetic causes.

SUN-090 Investigation of Imprinting Defects in MKRN3 and DLK1 in Children with Idiopathic Central Precocious Puberty Through Specific DNA Methylation Analysis

Background: Loss of imprinting has been implicated in the pathogenesis of several human diseases. Monogenic causes of central precocious puberty (CPP) were identified in families with loss-of-function mutations affecting mainly the coding region of two paternally expressed imprinted genes: Makorin ring finger 3 (MKRN3) and Delta-like 1 homolog (DLK1). The role of imprinting defects involving these two genes in CPP has not been described so far.Objective: To investigate the methylation status at primary differentially methylated regions (DMR) of MKRN3 and DLK1 in a cohort of children with idiopathic CPP.Patients and methods: One-hundred and twenty CPP patients (112 sporadic, 8 familial; 115 females, 5 males) were selected for analysis. Leukocyte DNA was obtained from all patients. MKRN3 and DLK1 pathogenic allelic variants were first excluded by DNA sequencing analysis. Bisulfite treatment followed by Allele-Specific Methylated Multiplex Real-Time Quantitative PCR was performed with leukocyte DNA, analyzing separately the methylation index (MI) of MKRN3:TSS-DMR and DLK1/MEG3:IG-DMR for each patient. The MI results were compared with controls with normal pubertal development.Results: Mean age at puberty onset was 5.8 ±1.9yr for girls and 7.2 ±2.6yr for boys. Hypomethylation at DLK1/MEG3:IG-DMR was identified in 3 patients (I, II and III) with sporadic CPP: MI 10%, 16% and 11%, respectively. Interestingly, cases II and III were both girls who had been firstly referred to pediatric endocrinology for presenting precocious menarche; while case I was a boy who had been referred for presenting mild growth retardation, and developed CPP during monitoring. In addition, during follow-up, other clinical findings were noticed: being born small for gestational age, prominent forehead, small hands/feet, overweight/obesity and early onset type 2 diabetes in case III. Additional genetic investigation included SNP array in cases I and II, identifying a maternal uniparental disomy at chromosome 14 (upd(14)mat). Meanwhile, case III had normal genomic microarray and microsatellites analysis, excluding copy number variants and upd(14)mat, and indicating a mechanism of epimutation at DLK1/MEG3:IG-DMR. Uniparental disomy and epimutation are molecular mechanisms associated with the imprinting disorder known as Temple syndrome. In the remaining cases, mean MI for DLK1/MEG3:IG-DMR was 49±2%. In all cases, mean MI for MKRN3:TSS-DMR was 49±6%. There were no significant correlations between age at puberty onset and MI for MKRN3 (p=0.69) and DLK1(p=0.45).Conclusion: There was no leukocyte DNA methylation defect at MKRN3 imprinting control region in the idiopathic CPP cohort. DLK1/MEG3:IG-DMR hypomethylation was identified in 3 patients with CPP and additional findings of Temple syndrome, indicating that loss of effective imprinting of DLK1 locus is a mechanism leading to CPP.

SUN-081 High Throughput Genetic Analysis Revealed Novel Genomic Loci and Candidate Genes Involved in Central Precocious Puberty Associated with Complex Phenotypes

Background: Central precocious puberty (CPP) is mostly described as an isolated entity. Few studies have shown an association of CPP with complex cases or genetic syndromes, but without making inferences on molecular causalities.Objective: To genetically investigate a cohort of patients with CPP associated with complex phenotypes using high throughput methodologies.Patients and methods: From a large cohort of patients with idiopathic CPP followed at a university hospital outpatient clinic, thirty-eight patients were selected for high throughput genetic investigation for presenting at least 3 additional clinical features and conditions, characterizing complex phenotypes. All had normal brain MRI. Pathogenic allelic variants in CPP known genes were initially excluded. All patients were submitted to genomic microarray (SNP or CGH arrays). A subset of patients was also submitted to whole-exome sequencing (11 cases) or target panel sequencing (18 cases).Results: Among the group of 38 patients (35 girls, 4 boys; 21 sporadic, 17 familial), mean age at puberty onset was 5.8 ±2.1 and 8.3 ±3.0 yr in girls and boys, respectively. The more prevalent clinical features described included metabolic, growth and neurocognitive phenotypes; less prevalent features included dysmorphic features and congenital anomalies. Pathogenic or probably pathogenic genetic defects were identified in 9 cases: 5 sporadic (all identified as de novo) and 4 familial. Defects in sporadic cases were as follows: three cases with 7q11.23 deletion (Williams syndrome); one girl with ventricular arrhythmia presenting a rare 1p31.3 duplication, involving NFIA gene coding a transcription factor of NFI family with hypothalamic expression; and one girl with imperforate anus and learning difficulties with rare frameshift variants in AREL1 gene (p.Ser229Aspfs*3) coding an ubiquitin ligase, and TNRC6B gene (p.Gly665Leufs*35) coding a regulator of translational inhibition. In the four familial cases, the genetic defects segregated with CPP in a dominant inheritance mode. Three cases from unrelated families presented growth phenotypes and Xp22.33 deletions, including SHOX gene and other elements. One boy with maternal familial CPP and autism had two rare potentially pathogenic variants: a frameshift deletion in MKKS gene (p.Phe144Leufs*14); and a missense variant (p.Pro267Leu) in UGT2B4 gene. Interestingly, the later gene encodes a protein involved in estrogen hydroxylation and is associated to menarche timing in GWAS.Conclusion: Novel genetic defects were identified in 23% cases of CPP associated with complex phenotypes. Three chromosomal regions represented loci potentially implicated in CPP: Xp22.33, 7q11.23 and 1p31.3. Five genes were identified as candidate genes associated with CPP: NFIA, AREL1, TNRC6B, MKKS and UGT2B4.

Can adipose stromal cells replace retinal pericytes in diabetic retinopathy? In vitro comparison of pro-angiogenic capacities of human ASC and retinal pericytes

Background & Aim Pericyte dropout is a significant contribution to the microvascular complications leading to diabetic retinopathy (DR). The similarities with pericytes render adipose stromal cells (ASC) candidates to prevent vessel destabilization and control neoangiogenesis. In models of DR, ASC not only generate a cytoprotective and reparative environment by secretion of trophic factors acting on endothelial, neuronal and glial cells, but also engraft and integrate into the retina in a pericyte-like fashion. Concerns, however, are that AC may not withstand the hyperglycemic stress and may worsen DR by secretion of proangiogenic factors. Thus, we compared the angiogenic features of human ASC and retinal pericytes. Methods, Results & Conclusion We compared growth curves and marker expression of both cells. As angiogeneic features, we first assessed adhesion to endothelial extracellular matrix, modified by high-glucose. Next, we tested pro-angiogeneic properties of both cell types and their conditioned media on human retinal endothelial cells by means of vascular network formation. Further, we used whole genome microarrays to compare gene expression profiles. Based on multiplex cytokine results, inhibitors of certain cytokines used to assess their role in the angiogenic support. Although cells were not to be distinguished based on their phenotype, the pro-angiogenic activity was solely featured by ASC, whereas pericytes suppressed vascular network formation. Pericytes, in contrast to ASC, adhered and proliferated at reduced rates on high-glucose modified endothelial extracellular matrix. Differentially expressed genes clustered to cell adhesion and cell migration. Pericytes expressed predominantly genes related to vessel stabilisation, whereas ASC showed higher expression of genes related to angiogenesis. This was linked to cytokine secretion. In fact, VEGFR-2 was required for ASC angiogenic supportive capacities, whereas Ang-1 appeared not to be required for pericytes inhibitory action. Our results clearly document that the pro-angiogeneic activity discriminates ASC from retinal pericytes. Pericytes are marked by endothelial stabilizing properties whereas ASC rather show angiogenic supportive characteristics. These striking pro-angiogenic discrepancies prompts to investigate the ASC angiogeneic and potential pericyte replacement properties in more detail. Pericyte dropout is a significant contribution to the microvascular complications leading to diabetic retinopathy (DR). The similarities with pericytes render adipose stromal cells (ASC) candidates to prevent vessel destabilization and control neoangiogenesis. In models of DR, ASC not only generate a cytoprotective and reparative environment by secretion of trophic factors acting on endothelial, neuronal and glial cells, but also engraft and integrate into the retina in a pericyte-like fashion. Concerns, however, are that AC may not withstand the hyperglycemic stress and may worsen DR by secretion of proangiogenic factors. Thus, we compared the angiogenic features of human ASC and retinal pericytes. We compared growth curves and marker expression of both cells. As angiogeneic features, we first assessed adhesion to endothelial extracellular matrix, modified by high-glucose. Next, we tested pro-angiogeneic properties of both cell types and their conditioned media on human retinal endothelial cells by means of vascular network formation. Further, we used whole genome microarrays to compare gene expression profiles. Based on multiplex cytokine results, inhibitors of certain cytokines used to assess their role in the angiogenic support.

Intrarenal arteriosclerosis and telomere attrition associate with dysregulation of the cholesterol pathway.

Background: Recently, we demonstrated that arteriosclerosis in the smaller intrarenal arteries is associated with shorter telomere length, independently of history of cardiovascular events and calendar age. This suggests that intrarenal arteriosclerosis reflects replicative senescence, although the underlying molecular alterations remain unclear.Results: Shorter intrarenal telomere length associated significantly with the presence of renal arteriosclerosis (T/S ratio 0.91±0.15 vs. 1.20±0.23 with vs. without arteriosclerosis, p=0.007, test cohort; T/S ratio 0.98 ±0.26 vs. 1.03 ±0.18 with vs. without arteriosclerosis, p=0.02, validation cohort). The presence versus absence of intrarenal arteriosclerosis was associated with differential expression of 1472 transcripts. Pathway analysis revealed enrichment of molecules involved in the superpathway of cholesterol biosynthesis as the most significant. The differential expression of these genes was confirmed in the independent validation cohort. Furthermore, the specific mRNA expression of the molecules in the superpathway of cholesterol biosynthesis associated significantly with intrarenal telomere length, and with history of cardiovascular events.Interpretation: Our study illustrates that the superpathway of cholesterol biosynthesis interacts with the previously published association between shorter telomere length and arteriosclerosis.Methods: This study included a test cohort of 40 consecutive kidney donors (calendar age 48.0 ± 15), with biopsies obtained prior to transplantation. Intrarenal leucocyte telomere length content was assessed using quantitative RT-PCR. Whole genome microarray mRNA expression analysis was performed using Affymetrix Gene 2.0 ST arrays. We investigated the associations between mRNA gene expression, telomere length as marker of replicative senescence, and intrarenal arteriosclerosis (Banff “cv” score = vascular fibrous intimal thickening = intimal hyperplasia) using adjusted multiple regression models. For biological interpretation and pathway overrepresentation analysis, we used Ingenuity Pathway Analysis. The significant pathways and genes were validated in an independent validation cohort of 173 kidney biopsies obtained prior to transplantation.

Mating Enhances Expression of Hormonal and Trophic Factors in the Midbrain of Female Rats.

Among female rats, mating enhances neurosteroid formation in the midbrain ventral tegmental area (VTA; independent of peripheral steroid-secreting glands, ovaries, and adrenals). The sources/targets for these actions are not well understood. In Experiment 1, proestrous rats engaged in a mating paradigm, or did not, and the midbrains had been assessed via the Affymetrix rat genome microarrays. In Experiment 2, the influence of gonadal and adrenal glands on the expression of these genes was assessed in rats that were proestrous, ovariectomized (OVX), or OVX and adrenalectomized (ADX). The microarrays revealed 53 target genes that were significantly up-regulated (>2.0-fold change) in response to mating. Mating significantly enhanced the midbrain mRNA expression of genes involved in hormonal and trophic actions: Gh1, S100g, and Klk1b3 in proestrous, but not OVX and/or ADX, rats; Fshb in all but OVX/ADX rats; and lutenizing hormone β and thyroid-stimulating hormone (TSH) β in all rats. Thus, mating enhances midbrain gene expression independent and dependent of peripheral glands.

Variational Autoencoder-Based Dimensionality Reduction for High-Dimensional Small-Sample Data Classification

Classification problems in which the number of features (dimensions) is unduly higher than the number of samples (observations) is an essential research and application area in a variety of domains, especially in computational biology. It is also known as a high-dimensional small-sample-size (HDSSS) problem. Various dimensionality reduction methods have been developed, but they are not potent with the small-sample-sized high-dimensional datasets and suffer from overfitting and high-variance gradients. To overcome the pitfalls of sample size and dimensionality, this study employed variational autoencoder (VAE), which is a dynamic framework for unsupervised learning in recent years. The objective of this study is to investigate a reliable classification model for high-dimensional and small-sample-sized datasets with minimal error. Moreover, it evaluated the strength of different architectures of VAE on the HDSSS datasets. In the experiment, six genomic microarray datasets from Kent Ridge Biomedical Dataset Repository were selected, and several choices of dimensions (features) were applied for data preprocessing. Also, to evaluate the classification accuracy and to find a stable and suitable classifier, nine state-of-the-art classifiers that have been successful for classification tasks in high-dimensional data settings were selected. The experimental results demonstrate that the VAE can provide superior performance compared to traditional methods such as PCA, fastICA, FA, NMF, and LDA in terms of accuracy and AUROC.

Molecular Pathways Underlying Adaptive Repair of the Injured Kidney: Novel Donation After Cardiac Death and Acute Kidney Injury Platforms.

To test the hypothesis that gene expression profiling in peripheral blood from patients who have undergone kidney transplantation (KT) will provide mechanistic insights regarding graft repair and regeneration. Renal grafts obtained from living donors (LD) typically function immediately, whereas organs from donation after cardiac death (DCD) or acute kidney injury (AKI) donors may experience delayed function with eventual recovery. Thus, recipients of LD, DCD, and AKI kidneys were studied to provide a more complete understanding of the molecular basis for renal recovery. Peripheral blood was collected from LD and DCD/AKI recipients before transplant and throughout the first 30 days thereafter. Total RNA was isolated and assayed on whole genome microarrays. Comparison of longitudinal gene expression between LD and AKI/DCD revealed 2 clusters, representing 141 differentially expressed transcripts. A subset of 11 transcripts was found to be differentially expressed in AKI/DCD versus LD. In all recipients, the most robust gene expression changes were observed in the first day after transplantation. After day 1, gene expression profiles differed depending upon the source of the graft. In patients receiving LD grafts, the expression of most genes did not remain markedly elevated beyond the first day post-KT. In the AKI/DCD groups, elevations in gene expression were maintained for at least 5 days post-KT. In all recipients, the pattern of coordinate gene overexpression subsided by 28 to 30 days. Gene expression in peripheral blood of AKI/DCD recipients offers a novel platform to understand the potential mechanisms and timing of kidney repair and regeneration after transplantation.

Bioinformatics analysis of severe emphysema genome microarray based on GEO database

Objective: To investigate differential genes (DEGs) between no/mild and severe emphysema by bioinformatics analysis. Methods: The microarray dataset GSE1650, of lung tissue in no/mild and severe emphysema, was downloaded from the GEO database, and DEGs were obtained by t test. Analysis of DEGs based on DAVID database was used to obtain gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) pathway. The protein-protein interaction network (PPI) was established using STRING database to identify hub genes. Results: A total of 76 DEGs were obtained, of which 62 genes were up-regulated and 14 genes were down-regulated in severe emphysema group. Gene ontology showed that the DEGs were mainly involved in neutrophil chemotaxis, cellular response to interleukin-1, extracellular matrix organization, immune response, and KEGG pathway involved cytokine-cytokine receptor interaction, ECM-receptor interaction, PI3K-Akt signaling pathway, platelet activation. Seventeen hub genes were recognized by PPI analysis, including CXCL8, RRAD, CLU, TIMP1, SEPP1, ISLR, BGN, COL1A1, COLIA2, ACTA2, ACTN1, FIGF, TPM1, TPM2, LUM, COL6A3 and TAGLN. Among them, fifteen genes (CLU, TIMP1, SEPP1, ISLR, BGN, COLIA2, COL1A1, ACTA2, ACTN1, FIGF, TPM1, TPM2, LUM, COL6A3, TAGLN) were up-regulated and two genes (CXCL8, RRAD) were down-regulated. Conclusion: Bioinformatics analysis based on GEO database showed that there were DEGs between non/mild and severe emphysema patients.

In vitro and bioinformatics mechanistic-based approach for cadmium carcinogenicity understanding

Cadmium is a toxic metal able to enter the cells through channels and transport pathways dedicated to essential ions, leading, among others, to the dysregulation of divalent ions homeostasis. Despite its recognized human carcinogenicity, the mechanisms are still under investigation. A powerful tool for mechanistic studies of carcinogenesis is the Cell Transformation Assay (CTA). We have isolated and characterized by whole genome microarray and bioinformatics analysis of differentially expressed genes (DEGs) cadmium-transformed cells from different foci (F1, F2, and F3) at the end of CTA (6 weeks). The systematic analysis of up- and down-regulated transcripts and the comparison of DEGs in transformed cells evidence different functional targets and the complex picture of cadmium-induced transformation. Only 34 in common DEGs are found in cells from all foci, and among these, only 4 genes are jointly up-regulated (Ccl2, Ccl5, IL6 and Spp1), all responsible for cytokines/chemokines coding. Most in common DEGs are down-regulated, suggesting that the switching-off of specific functions plays a major role in this process. In addition, the comparison of dysregulated pathways immediately after cadmium treatment with those in transformed cells provides a valuable means to the comprehension of the overall process.

Intra-individual Genomic Variation Analysis in Tissues (Blood vs. Testis) Through SNP Microarray: A Case Report of Two Patients with Idiopathic Sertoli Cell Only Syndrome (SCOS)

Background:Sertoli cell only syndrome (SCOS) or germ cell aplasia is characterized by the existence of only sertoli cells in the seminiferous tubule without any germ cells. SCOS is a multifactorial disorder but genetic factors play a major role in pathogenesis of idiopathic SCOS.Case Presentation:Two cases of idiopathic SCOS had been reported with no non-genetic factor in their medical history that could play a role in aetiology of SCOS. Also, two normal fertile males were recruited as controls in this study. For evaluation of genomic imbalance, karyotyping (G-banding), FISH, STS-PCR and SNP microarray were carried out. SNP microarray was carried out in DNA of peripheral blood for cases as well as controls. However, for cases, SNP microarray was conducted in DNA of testicular Fine needle aspiration cytology (FNAC).Conclusion:No chromosome abnormality and Yq microdeletion was found in cases as well as in controls. Microarray detected many CNVs and LOH that cover genes with spermatogenesis related function and PAR CNVs in both cases. Differential genomic variations were found in blood and testis for cases. Therefore, the evaluation of pathogenesis of idiopathic SCOS might be dependent on both tissue samples. The evaluation of genomic imbalances at both tissue levels should be done for a large cohort of patients.

Specific immune landscapes and immune checkpoint expressions in histotypes and molecular subtypes of sarcoma

ABSTRACT Soft tissue sarcomas are a group of rare and aggressive connective tissue neoplasms for which curative therapeutic opportunities are limited in advanced phase. Clinical trials assessing immunotherapy in these tumors have so far reported limited efficacy. The objective of this study is to provide a description of the immunologic landscape of sarcomas to guide the next clinical trials of immunotherapy in these diseases. The gene expression profile of 93 immune checkpoint (ICP) and membrane markers (MM) of immune cells was analyzed in a series of 253 soft tissue sarcoma (synovial sarcoma, myxoid liposarcoma, sarcoma with complex genomic and GIST) using Agilent Whole Human Genome Microarrays. The unsupervised hierarchical clustering of gene expression level was found able to properly group patients according to the histological subgroup of sarcoma, indicating that each sarcoma subgroup is associated with a specific immune signature defined by its gene expression pattern. Using the prognostic impact of CIBERSORT signature on metastatic-free survival in each subgroup, specific target could be proposed for each of the four groups: Treg through ICOS and GITR in GIST, M0 macrophages in all four sarcoma subtypes, OX40 in SS, CD40 in GIST and SS. The immune landscape of sarcoma was found to be as heterogeneous as the histotypes and molecular subtypes, but strongly correlated to the histotype. Histotype adapted immunotherapeutic approaches in each sarcoma subtypes must be considered in view of these results, consistently with the already reported specific response of histotypes of ICPs.