Oligonucleotide Microarray Research Articles

Terminal microdeletion of chromosome 18 in a Malaysian boy characterized with few features of typical 18q- deletion syndrome: a case report

BackgroundThe 18q- deletion syndrome is a rare congenital chromosomal disorder caused by a partial deletion of the long arm of chromosome 18. The diagnosis of a patient with this syndrome relies on the family medical history, physical examination, developmental assessment, and cytogenetic findings. However, the phenotype of patients with 18q- deletion syndrome can be highly variable, ranging from almost normal to severe malformations and intellectual disability, and normal cytogenetic findings are common, thus complicating the diagnosis. Interestingly, only few characteristic features of typical 18q- deletion syndrome were found in the patient, despite sharing the same critical region. To our knowledge, this is the first report of a Malaysian individual with 18q- terminal microdeletion diagnosed with microarray-based technology.Case presentationHere we report a 16-year-old Malaysian Chinese boy, a product of a non-consanguineous marriage, who presented with intellectual disability, facial dysmorphism, high arched palate, congenital talipes equinovarus (clubfoot), congenital scoliosis, congenital heart defect, and behavioral problems. A routine chromosome analysis on 20 metaphase cells showed a normal 46, XY G-banded karyotype. Array-based comparative genomic hybridization was performed using a commercially available 244 K 60-mer oligonucleotide microarray slide according to the manufacturer’s protocol. This platform allows genome-wide survey and molecular profiling of genomic aberrations with an average resolution of about 10 kB. In addition, multiplex ligation-dependent probe amplification analysis was carried out using SALSA MLPA kit P320 Telomere-13 to confirm the array-based comparative genomic hybridization finding. Array-based comparative genomic hybridization analysis revealed a 7.3 MB terminal deletion involving chromosome band 18q22.3-qter. This finding was confirmed by multiplex ligation-dependent probe amplification, where a deletion of ten probes mapping to the 18q22.3-q23 region was detected, and further multiplex ligation-dependent probe amplification analysis on his parents showed the deletion to be de novo.ConclusionThe findings from this study expand the phenotypic spectrum of the 18q- deletion syndrome by presenting a variation of typical 18q- deletion syndrome features to the literature. In addition, this case report demonstrated the ability of the molecular karyotyping method, such as array-based comparative genomic hybridization, to assist in the diagnosis of cases with a highly variable phenotype and variable aberrations, such as 18q- deletion syndrome.

Los Polimorfismos en la Uteroglobina y en IL2R están asociados con el daño articular y/o la Cirugía articular en pacientes con Artritis Reumatoide

Introduction and Objectives. Of all clinical manifestations that mark prognosis of a patient with RA, radiological damaged is considered one of the most important variables. In addition to clinical and laboratory markers are increasingly studying the influence of genetic factors in the predictive ability of the RA forecast. Previous studies have reported misleading results about polymorphisms in different genes associated with radiological damage in RA. The aim of this study was to assess the involvement of the clinical, analytical and genetic variables in the radiological damage in a Spanish RA population. Methods. Six hundred thirty-two Spanish RA patients were included. SNP genotyping was performed using an oligonucleotide microarray. Allele and genotype association analyses with articular damage and a haplotype association test were performed. Results. This study includes retrospectively 604 Spanish RA patients with articular erosions and 616 with surgery due to RA. The A587G polymorphism (rs3741240) in uteroglobin gene was associated with increased radiological damage defined by phenotypes RX2 (multiple erosions on hands and feet) and surgery due to RA (OR 1.6 and 1.7 respectively). IL2R polymorphism was associated with RX2 phenotype (OR 2.95). Disease duration, painful joints, ESR, RF and ACPA are the analytical and clinical variables significantly associated with articular damage. Conclusions. These results demonstrate that the A587G and C4599T polymorphism in uteroglobin and IL2R genes respectively are associated with radiological damage in a Spanish RA population.

Transcriptional Profiling of Populations in the Clam Ruditapes decussatus Suggests Genetically Determined Differentiation in Gene Expression along Parallel Temperature Gradients and between Races of the Atlantic Ocean and West Mediterranean Sea

Ongoing ocean warming due to climate change poses new challenges for marine life and its exploitation. We have used transcriptomics to find genetically based responses to increased temperature in natural populations of the marine clam Ruditapes decussatus, which lives along parallel thermal gradients in southern Europe. Clams of the Atlantic and West Mediterranean races were collected in northern (cool) and a southern (warm) localities. The animals were kept in running seawater in the warm, southern Atlantic locality for a 15-week period. During this period, water temperature was raised to typical southern European summer values. After this period, an expression profile was obtained for a total of 34 clams and 11,025 probes by means of an oligonucleotide microarray. We found distinct transcriptional patterns for each population based on a total of 552 differentially expressed genes (DEGs), indicating innate differences which probably have a genetic basis. Race and latitude contributed significantly to gene expression differences, with very different sets of DEGs. A gene ontology analysis showed that races differed mainly in the genes involved in ribosomal function and protein biosynthesis, while genes related to glutathione metabolism and ATP synthesis in the mitochondria were the most outstanding with respect to north/south transcriptional differences.

Moritella viscosa early infection and transcriptional responses of intraperitoneal vaccinated and unvaccinated Atlantic salmon

Skin is the first line of defence against waterborne pathogens, such as Moritella viscosa, which is the causative agent of winter ulcer disease in Atlantic salmon (Salmo salar L.). The present study revealed that vaccination protects against both M. viscosa-induced mortality and skin ulceration, but protection varied according to the strain used in the vaccine formulation. Examination of skin tissue 4 days post M. viscosa challenge indicated that M. viscosa initiated infection by colonising the scale surface. Sequencing the transcripts of the variable region of the IgM heavy chain did not detect effect of vaccination or M. viscosa challenge on antibody repertoire and B cell trafficking from the lymphatic organs to skin. Skin layer-specific responses were examined with 44 K oligonucleotide microarray. Skin responded to vaccination and M. viscosa challenge by increasing transcription of structural genes, stimulating metabolism, and regulation of developmental processes. Immune responses to dead (vaccine) and live M. viscosa were very similar and no pathogen-specific changes were found. Combined use of skin transcriptional profiles and image analysis revealed differences in the infected skin layers between the study groups. M. viscosa was likely retained in the epidermis of vaccinated salmon, whereas the dermis was colonised in unvaccinated fish. Furthermore, decreased expression of lymphocyte-specific and antiviral genes in the dermis indicated possible evasion of immune-related cells from skin in salmon challenged with M. viscosa. Our data also indicated that intraperitoneal vaccination may prime the humoral innate response, which enables a rapid response in the dermis layer of skin during M. viscosa invasion.

Changes in the Expression Profile of Pyroptosis-Related Genes in Senescent Retinal Pigment Epithelial Cells after Lutein Treatment

Retinal pigment epithelium (RPE) is a specialized structure essential for proper vision, which is constantly exposed to oxidative damage. With aging, this damage accumulates within the RPE cells, causing various diseases, including age-related macular degeneration (AMD). Numerous antioxidant substances are used to prevent this process in humans, including lutein. This study aims to determine the differences in the expression patterns of pyroptosis genes in senescent human retinal pigment epithelial cell line ARPE-19 exposed to lutein. Changes in the expression of pyroptosis-related genes were assessed by oligonucleotide microarrays, and the results were validated by real-time RT-qPCR. The microarray analysis showed seven transcripts were differentially expressed both in the H2O2-treated cells versus the controls and in the lutein/H2O2-treated cells compared to the H2O2-treated cells (FC > 2.0). Depending on the used lutein, H2O2, or co-treatment of ARPE-19 cells, statistically significant differences in the expression of TXNIP, CXCL8, BAX, and CASP1 genes were confirmed by the RT-qPCR (p < 0.05). A STRING database analysis showed that the proteins encoded by the analyzed genes form a strong interaction network (p < 0.001). These data indicate that lutein modulates the expression level of pyroptosis-related genes, which may be useful for the development of new methods preventing pyroptosis pathway activation in the future.

Enzymatic Synthesis of High-Density RNA Microarrays.

Oligonucleotide microarrays are used to investigate the interactome of nucleic acids. DNA microarrays are commercially available, whereas equivalent RNA microarrays are not. This protocol describes a method to convert DNA microarrays of any density and complexity into RNA microarrays using only readily available materials and reagents. This simple conversion protocol will facilitate the accessibility of RNA microarrays to a wide range of researchers. In addition to general considerations for the design of a template DNA microarray, this procedure describes the experimental steps of hybridization of an RNA primer to the immobilized DNA, followed by its covalent attachment via psoralen-mediated photocrosslinking. The subsequent enzymatic processing steps comprise the extension of the primer with T7 RNA polymerase to generate complementary RNA, and finally the removal of the DNA template with TURBO DNase. Beyond the conversion process, we also describe approaches to detect the RNA product either by internal labeling with fluorescently labeled NTPs or via hybridization to the product strand, a step that can then be complemented by an RNase H assay to confirm the nature of the product. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Conversion of a DNA microarray to an RNA microarray Alternate Protocol: Detection of RNA via incorporation of Cy3-UTP Support Protocol 1: Detection of RNA via hybridization Support Protocol 2: RNase H assay.

The MAP2K2 Gene as Potential Diagnostic Marker in Monitoring Adalimumab Therapy of Psoriatic Arthritis.

MAP kinases are some of the cascades that are specialized in the cell's response to external stimuli. Their impaired functioning can be observed during the course of psoriatic arthritis. Currently, the best-known class of biological drugs is the inhibitors of the proinflammatory cytokine TNF-α, including adalimumab. The aim of this study was to assess changes in the expression of MAP kinase genes in patients with psoriatic arthritis treated with adalimumab, as well as to determine which of the analyzed transcripts could be used as a diagnostic or therapeutic target. An analysis was performed on the total RNA extracted from PBMCs of patients with psoriatic arthritis before and after three months of adalimumab therapy as well as from a control group. Changes in the expression of the mitogen-activated protein kinase genes were assessed using the HG-U133A 2.0 oligonucleotide microarray method, while the obtained results were validated using the real-time RT-qPCR method. Using the oligonucleotide microarray method, 14 genes coded for proteins from the MAPK group were identified with at least a two-fold change of expression in the control group and during adalimumab therapy. Validation of the results confirmed a statistically significant decrease in the transcriptional activity of the MAP2K2 gene in the group of patients three months after the administration of adalimumab relative to the control group. Adalimumab therapy alters the expression of MAPK-coding genes. The assessment of the number of MAP2K2 mRNA molecules can potentially be used in diagnostic analyses or in monitoring adalimumab therapy.

The landscape of N6-methyladenosine modification patterns and altered transcript profiles in the cardiac-specific deletion of natriuretic peptide receptor A.

The atrial natriuretic peptide (ANP) and the brain natriuretic peptide (BNP) are critical biological makers and regulators of cardiac functions. Our previous results show that NPRA (natriuretic peptide receptor A)-deficient mice have distinct metabolic patterns and expression profiles compared with the control. Still, the molecular mechanism that could account for this observation remains to be elucidated. Here, methylation alterations were detected by mazF-digestion, and differentially expressed genes of transcriptomes were detected by a Genome Oligo Microarray using the myocardium from NPRA-deficient (NPRA-/-) mice and wild-type (NPRA+/+) mice as the control. Comprehensive analysis of m6A methylation data gave an altered landscape of m6A modification patterns and altered transcript profiles in cardiac-specific NPRA-deficient mice. The m6A "reader" igf2bp3 showed a clear trend of increase, suggesting a function in altered methylation and expression in cardiac-specific NPRA-deficient mice. Intriguingly, differentially m6A-methylated genes were enriched in the metabolic process and insulin resistance pathway, suggesting a regulatory role in cardiac metabolism of m6A modification regulated by NPRA. Notably, it was confirmed that the pyruvate dehydrogenase kinase 4 (Pdk4) gene upregulated the gene expression and the hypermethylation level simultaneously, which may be the key factor for the cardiac metabolic imbalance and insulin resistance caused by natriuretic peptide signal resistance. Taken together, cardiac metabolism might be regulated by natriuretic peptide signaling, with decreased m6A methylation and a decrease of Pdk4.

An advanced and efficient asymmetric PCR method for microarray applications.

The sensitivity of a PCR based biochip assay relies on the efficiency of PCR amplicons in binding to the microarray spots. The essential factor determining the sensitivity is the amount of single stranded (ss) amplicons available for biochip hybridization. Asymmetric PCR can generate ss-amplicons depending on the ratio of primers used in the amplification process, but this process is often inefficient. We report a novel variant of PCR called the Asymmetric Exponential and Linear Amplification (AELA) which can overcome these issues and generate large amounts of single stranded amplicons. AELA-PCR introduces an amplification strategy that makes use of both exponential and linear amplification of the target nucleic acid. This is done by specifically designed primers and choice of adequate thermal profiles. In conventional PCR with a classical thermal profile, these specifically designed primers will work normally and contribute to an exponential increase of amplicons. A designed sequence extension of one of the primers and a very specific thermal profile, will result in a situation that the extended primer will be the only functional one for amplification, resulting in a linear phase of the amplification process. That is why during this step only one of the two strands of the target is amplified linearly and no longer exponentially. The result of the whole process is an amplification product enriched very strongly in one of the two single strands of the target. These adaptions in PCR are particularly favorable where the generation of ss-DNA/RNA is required. We demonstrate the higher biochip sensitivity of AELA-PCR compared to conventional amplification methods with an example of the Staphylococcus aureus detection on a DNA oligonucleotide microarray.

Penalized logistic regression with prior information for microarray gene expression classification.

Cancer classification and gene selection are important applications in DNA microarray gene expression data analysis. Since DNA microarray data suffers from the high-dimensionality problem, automatic gene selection methods are used to enhance the classification performance of expert classifier systems. In this paper, a new penalized logistic regression method that performs simultaneous gene coefficient estimation and variable selection in DNA microarray data is discussed. The method employs prior information about the gene coefficients to improve the classification accuracy of the underlying model. The coordinate descent algorithm with screening rules is given to obtain the gene coefficient estimates of the proposed method efficiently. The performance of the method is examined on five high-dimensional cancer classification datasets using the area under the curve, the number of selected genes, misclassification rate and F-score measures. The real data analysis results indicate that the proposed method achieves a good cancer classification performance with a small misclassification rate, large area under the curve and F-score by trading off some sparsity level of the underlying model. Hence, the proposed method can be seen as a reliable penalized logistic regression method in the scope of high-dimensional cancer classification.

Laboratory and clinical evaluation of a microarray for the detection of ATP7B mutations in Wilson disease in China.

Wilson disease (WD) is an autosomal recessive copper metabolic disorder caused by mutations in ATP7B. Sanger sequencing is currently used for ATP7B variant identification. However, the ATP7B gene contains 21 exons, which makes sequencing of the entire gene both complex and time-consuming. Therefore, a simpler assay is urgently needed. We performed a laboratory and clinical evaluation of an oligonucleotide microarray for the detection of 24 ATP7B recurrent mutations (except p.P992L) in Chinese patients with WD. The accuracy of the microarray was evaluated by screening for ATP7B mutations in 126 patients including 106 suspected WD samples and 20 patients with other liver diseases as negative control. Results were confirmed by Sanger sequencing. We established a reliable microarray system for the rapid detection of the 24 ATP7B mutations, with a sensitivity of 30 ng/test genomic DNA and specificity of 100% for all loci; the coefficient of variation in repeatability tests was <10%. Clinical evaluation showed an overall concordance between the microarray detection and sequencing of 100%, and 81.13% (86/106) of suspected WD cases showed ATP7B mutations by microarray detection. Microarray and Sanger sequencing identified p.R778L (50.94%), p.A874V (17.92%), p.P992L (11.32%), p.V1106I (11.32%), and p.I1148T (6.60%) as the most common mutations in WD patients. Our microarray system is customizable and easily used for high-throughput detection of certain recurrent ATP7B mutations, providing a simpler method suitable for WD genetic diagnosis in China.

Abstract 5170: Coding and non-coding gene meta-features predict outcome in pediatric rhabdomyosarcomas

Abstract INTRODUCTION: Pediatric rhabdomyosarcoma (RMS) has varying outcomes, particularly in intermediate-risk disease (IR-RMS) due to the limited ability of clinical staging to accurately risk-stratify a large proportion of patients. This study aimed to identify prognostic signatures in IR-RMS, the clinical subgroup with the most heterogeneous outcomes, which can potentially improve risk stratification compared with routine clinicopathologic metrics. Signature performance was validated on an independent set of RMS patients. METHODS: Prospectively obtained primary tumor specimens from 80 IR-RMS patients on Children’s Oncology Group clinical trial protocols formed the training set. Tumors from 54 RMS patients across all clinical risk groups formed the validation set. Whole transcriptome profiling was performed using oligonucleotide microarrays employing nearly 1.4 million probe selection regions (PSRs) and used to derive weighted meta-features. Accuracies of protein-coding and non-coding meta-features to predict overall (OS) and event-free (EFS) survival were compared using areas under receiver operating characteristic curves. Associated biological processes were analyzed using curated pathway analysis tools. RESULTS: PAX-FKHR status was able to predict OS (p=0.041) and EFS (p=0.008) in the validation set, but not in the training set. Histologic subtype followed a similar predictive pattern. Cox regression on over 17,000 coding genes on the training set identified a prognostic 30-coding gene meta-feature (gMF; OS p=0.001, EFS p=0.012). A similar analysis on non-coding transcripts identified a 39-PSR meta-feature (ncMF; OS, EFS p&amp;lt;0.001). Both gMF and ncMF were able to predict OS and EFS (p≤0.023) in the validation cohort. Based on OS, predictive accuracy of ncMF was higher than gMF (96% vs. 71%, p&amp;lt;0.001). Analysis of biological processes using gMF showed enrichment for functions associated with musculoskeletal development and signaling pathways. Similar analysis of non-coding meta-features revealed enrichment for cellular assembly, cell cycle, apoptosis, and cancer-associated functions. CONCLUSIONS: A non-coding RNA meta-feature was able to better predict outcome in IR-RMS than a coding gene meta-feature, where most standard clinical prognosticators failed. The meta-features were independently validated in IR and non-IR RMS. This suggests that non-coding transcripts can regulate and determine RMS biology and aggressiveness, and be used as novel prognostic indicators. Citation Format: Anirban P. Mitra, Sheetal A. Mitra, Jonathan D. Buckley, Stephen X. Skapek, Douglas S. Hawkins, Timothy J. Triche. Coding and non-coding gene meta-features predict outcome in pediatric rhabdomyosarcomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5170.

A versatile CRISPR Cas12a-based point-of-care biosensor enabling convenient glucometer readout for ultrasensitive detection of pathogen nucleic acids

Pathogen nucleic acid detection is of great significance to control the spread of diseases caused by the viruses. Nevertheless, traditional methods for nucleic acid detection such as polymerase chain reaction (PCR) and oligonucleotide microarrays require bulky instruments, which restrain their point-of-care (POC) testing application. Here, we proposed a POC method enabling sensitive detection of pathogen nucleic acids by combining the clustered regularly interspaced short palindromic repeat (CRISPR) Cas12a-based assay and personal glucometer readout (PGM). The quantification of target pathogen DNA by PGM was achieved based on pathogen DNA activates Cas12a ssDNase to cleave magnetic bead-DNA-invertase reporter probe, and separated free invertase to catalyze hydrolysis of sucrose to glucose. Without using nucleic acid amplification technology, we demonstrated here dual signal amplifications based on Cas12a and invertase-mediated catalytic reactions, making it possible to sensitively detect HIV-related DNA or SARS-CoV-2 pseudovirus with the limits of detection of 11.0 fM and 50 copies/μL, respectively. This strategy also showed excellent selectivity as well as potential applicability for detection of HIV in human serum samples or of SARS-CoV-2 in saliva samples. Therefore, our CRISPR-PGM-based dual signal amplifications detection platform might offer a great promise in POC diagnosis of pathogen nucleic acids.

ATF4/TXNIP/REDD1/mTOR signaling mediates the antitumor activities of liver X receptor in pancreatic cancers.

Limited by difficulties in early detection and availabilities of effective treatments, pancreatic cancer is a highly malignant disease with poor prognosis. Nuclear receptors are a family of ligand-dependent transcription factors that are highly druggable therapeutic targets playing critical roles in human physiological and pathological development, including cancer. In this study, we explored the therapeutic potential as well as the molecular mechanisms of liver X receptor (LXR) agonist GW3965 in pancreatic cancer. Soft-agar colony formation assay, xenograft tumors, Oligonucleotide microarray, Reverse transcription real-time polymerase chain reaction, Western immunoblotting and Immunohistochemistry were used in this study. We demonstrated pleotropic in vitro activities of GW3965 in pancreatic cell lines MIA PaCa-2 and BXPC3 including reduction of cell viability, inhibition of cell proliferation, stimulation of cell death, and suppression of colony formation, which translated to significant inhibition of xenograft tumor growth in vitro. By mapping the gene expression profiles, we identified the up-regulations of 188 and the down-regulations of 92 genes common to both cell lines following GW3965 treatment. Genes responsive to GW3965 represent a variety of biological pathways vital for multiple cellular functions. Specifically, we identified that the activating transcription factor 4/thioredoxin-interacting protein/regulated in development and DNA damage responses 1/mechanistic target of rapamycin (ATF4/TXNIP/REDD1/mTOR) signaling critically controls GW3965-mediated regulation of cell proliferation/death. The significance of the ATF4/TXNIP/REDD1/mTOR pathway was further supported by associated expressions in xenograft tumors as well as human pancreatic cancer samples. This study provides the pre-clinical evidence that LXR agonist is a promising therapy for pancreatic cancer.

Elucidation of the Potential Hair Growth-Promoting Effect of Botryococcus terribilis, Its Novel Compound Methylated-Meijicoccene, and C32 Botryococcene on Cultured Hair Follicle Dermal Papilla Cells Using DNA Microarray Gene Expression Analysis.

A person’s quality of life can be adversely affected by hair loss. Microalgae are widely recognized for their abundance and rich functional components. Here, we evaluated the hair growth effect of a green alga, Botryococcus terribilis (B. terribilis), in vitro using hair follicle dermal papilla cells (HFDPCs). We isolated two types of cells from B. terribilis—green and orange cells, obtained from two different culture conditions. Microarray and real time-PCR results revealed that both cell types stimulated the expression of several pathways and genes associated with different aspect of the hair follicle cycle. Additionally, we demonstrated B. terribilis’ effect on collagen and keratin synthesis and inflammation reduction. We successfully isolated a novel compound, methylated-meijicoccene (me-meijicoccene), and C32 botryococcene from B. terribilis to validate their promising effects. Our study revealed that treatment with the two compounds had no cytotoxic effect on HFDPCs and significantly enhanced the gene expression levels of hair growth markers at low concentrations. Our study provides the first evidence of the underlying hair growth promoting effect of B. terribilis and its novel compound, me-meijicoccene, and C32 botryococcene.

P693. Protein-Coding Transcriptome in Major Depressive Disorder and Suicidality: Transcription Factors Regulate Distinct Genes in Oligodendrocyte Function, Lipid Biogenesis, Myelination and Extracellular Matrix Pathways

Gene expression profiling studies in the brains of individuals who died by suicide and had depression-using oligonucleotide microarrays have often failed to distinguish MDD and suicide. However, the biological mechanisms underlying MDD and suicide remain elusive. To address these knowledge gaps, we applied next-generation sequencing technology to evaluate protein coding transcriptome changes in MDD and suicide and its effect in males vs females.

Differences in the Expression Patterns of TGFβ Isoforms and Associated Genes in Astrocytic Brain Tumors.

Simple SummaryNumerous molecular changes are observed during tumor progression. Genes associated with TGFβ isoforms are involved in many cancers, including brain cancer. Using molecular techniques to evaluate 43 brain tumor sections from patients at different stages of astrocytic brain tumor, we assessed differences in the expression patterns of genes associated with TGFβ isoforms and quantified the mRNA of three TGFβ isoforms. Our study confirmed significant differences in the expression of genes associated with TGFβ isoforms as well as differences in isoform expression and the identification of 16 genes that differentiate between disease grades. Database analysis revealed interactions between the products of these genes, some of which are associated with tumorigenesis. Differences in the expression patterns of transcripts associated with TGFβ isoforms confirm that they are involved in astrocytic brain tumor transformation. Quantitative assessment of TGFβ2 mRNA may be a useful method in the future to facilitate the diagnosis of disease grade.Genes associated with the TGFβ isoforms are involved in a number of different cancers, and their effect on the progression of brain tumors is also being discussed. Using an oligonucleotide microarray method, we assessed differences in expression patterns of genes in astrocytic brain tumor sections from 43 patients at different stages of disease. Quantitative mRNA assessment of the three TGFβ isoforms was also performed by real-time RT-qPCR. Oligonucleotide microarray data were analyzed using the PL-Grid Infrastructure. The microarray analysis showed a statistically significant (p < 0.05) increase in TGFβ1 and TGFβ2 expression in G3/G4 stage relative to G2, whereas real-time RT-qPCR validation confirmed this change only for the TGFβ2 isoform (p < 0.05). The oligonucleotide microarray method allowed the identification of 16 differential genes associated with TGFβ isoforms. Analysis of the STRING database showed that the proteins encoded by the analyzed genes form a strong interaction network (p < 0.001), and a significant number of proteins are involved in carcinogenesis. Differences in expression patterns of transcripts associated with TGFβ isoforms confirm that they play a role in astrocytic brain tumor transformation. Quantitative assessment of TGFβ2 mRNA may be a valuable method to complement the diagnostic process in the future.

AltWOA: Altruistic Whale Optimization Algorithm for feature selection on microarray datasets

The data-driven modern era has enabled the collection of large amounts of biomedical and clinical data. DNA microarray gene expression datasets have mainly gained significant attention to the research community owing to their ability to identify diseases through the “bio-markers” or specific alterations in the gene sequence that represent that particular disease (for example, different types of cancer). However, gene expression datasets are very high-dimensional, while only a few of those are “bio-markers”. Meta-heuristic-based feature selection effectively filters out only the relevant genes from a large set of attributes efficiently to reduce data storage and computation requirements. To this end, in this paper, we propose an Altruistic Whale Optimization Algorithm (AltWOA) for the feature selection problem in high-dimensional microarray data. AltWOA is an improvement on the basic Whale Optimization Algorithm. We embed the concept of altruism in the whale population to help efficient propagation of candidate solutions that can reach the global optima over the iterations. Evaluation of the proposed method on eight high dimensional microarray datasets reveals the superiority of AltWOA compared to popular and classical techniques in the literature on the same datasets both in terms of accuracy and the final number of features selected. The relevant codes for the proposed approach are available publicly at https://github.com/Rohit-Kundu/AltWOA.

3q27.1 microdeletion causes prenatal and postnatal growth restriction and neurodevelopmental abnormalities

BackgroundOverlapping microdeletions of chromosome 3q26-3q28 have been reported in eight individuals. The common phenotype observed in these individuals include intrauterine growth restriction, short stature, microcephaly, feeding difficulties, facial dysmorphisms, limb abnormalities and developmental delay. The most striking clinical features shared among all reported cases is prenatal and postnatal growth restriction and neurodevelopmental abnormalities.Case presentationWe identified two additional individuals with overlapping deletions and shared clinical features by high-resolution SNP oligonucleotide microarray, and refined the smallest region of overlap (SRO) to a 1.2 Mb genomic location in chromosome 3q27.1 by reviewing and comparing all published cases. We evaluated the SRO using ACMG/ClinGen current recommendations for classifying copy number variants (CNVs), and discussed the contribution of the genes deleted in the SRO to the abnormal phenotype observed in these individuals.ConclusionsThis study provides further evidence supporting the existence of a novel 3q27.1 microdeletion syndrome and suggests that haploinsufficiency of potential candidate genes, DVL3, AP2M1, and PARL in the SRO in 3q27.1 is responsible for the phenotype.

Identifying Drug Candidates for Pancreatic Neuroendocrine Tumors Based on Differently Expressed Genes

Introduction: Prognosis of patients with pancreatic neuroendocrine tumors(pNET) is variable and there is a paucity of effective drugs to treat pNET. Genome-wide analyses may allow for identification of potential drugs based on differentially expressed genes(DEGs). Methods: Oligo microarray data from RNA expression profiling of pNET and normal pancreas tissues was downloaded from the Gene Expression Omnibus. Functional and pathway enrichment information of the DEGs was obtained using the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases. Corresponding homologous proteins were analyzed and potential therapeutic drugs for pNET were identified using the Connectivity Map and Drug-Gene Interaction Database. Results: RNA expression information from 63 non-functional pNET samples and 9 normal pancreatic tissue samples was obtained. Assessment of raw data from 12,610 genes demonstrated that 1,082 and 380 genes were upregulated and downregulated, respectively. Of note, tumor and normal tissue had different expression profiles(Figure). Upregulated pathways were associated with nitrogen metabolism, GABAergic synapse and graft-versus-host disease, whereas downregulated pathways include C-type leptin receptor signaling pathway, pertussis and AMPK signaling pathway. In particular, upregulated genes included DYNLL1, GNB5, GNB2, GNG4, GNAI2, GNAI1, HIST2H2BE, NUP107, NUP133 and SNAP25, while downregulated genes include CXCL8, F2, CXCL2, GCG, SST, INS, GALR3, CCL20, ADRA2B and CXCL6. Using the Drug-Gene Interaction Database, candidate drugs for pNET treatment included canertinib, acarbose, AG-592, lonidamine, azacytidine, erlotinib, rottlerin and HU-211. Conclusions: Drug candidates targeted against pNET were identified based on differentially expressed genes. Available genetic atlas data may help identify agents with therapeutic efficacy to treat pNET patients using a more targeted approach.