Identification Of Gene Expression Patterns Research Articles

Liquid Biopsy in Whole Blood for Identification of Gene Expression Patterns (mRNA and miRNA) Associated with Recurrence of Glioblastoma WHO CNS Grade 4.

GBM WHO CNS Grade 4 represents a major challenge for oncology due to its aggressive behavior. Conventional imaging has restrictions in detecting tumor recurrence. This prospective study aims to identify gene-based biomarkers in whole blood instead of isolating exosomes for the early detection of tumor recurrence. Blood samples (n = 33) were collected from seven GBM patients at time points before and after surgery as well as upon tumor recurrence. Four tumor tissue samples were assessed in parallel. Next-generation sequencing (NGS), including mRNA-seq and small RNA-seq, was used to analyze gene expression profiles in blood samples and tumor tissues. A novel filtering pipeline was invented to narrow down potential candidate genes. In total, between 6-93 mRNA and 1-19 small RNA candidates could be identified among the seven patients. The overlap of genes between the patients was minimal, indicating significant inter-individual variance among GBM patients. In summary, this prospective study supports the applicability of gene expression measurements in whole blood for the detection of tumor recurrence. It might provide an alternative to the challenging workflow of liquid biopsy after laborious exosome isolation from whole blood.

Comparative profile of transcripts from anthers of hybrid plants and parental lines of sunflower

Most heterosis research over the years has focused on increasing vigour and productivity, and less on the multitude of biochemical and molecular phenotypes as an expression of hybrid superiority under favourable or stressful conditions. Plant productivity depends on the microsporogenesis and microgametogenesis processes highly sensitive to unfavorable environmental conditions and other stress factors that often induce the androsterility. The paper presents the results of the expression polymorphism analysis (by RT-qPCR) of candidate genes with functions in DNA replication, recombination, repair, and mitochondrial morpho-functional organization processes in anthers of homozygous and heterozygous sunflower plants with phenotypic differences in male gametophyte (fertile/sterile). A particular interest in this research represented the identification of gene expression patterns in hybrid (F1) plants in norm, for possible associations of transcriptional response with heterozygous effect, and under conditions of induced stress (gibberellin treatment) as a factor in irreversible phenotype change of anthers from fertile to sterile. Thus, the high proportion of different non-additive and transgressive expression patterns in hybrid plants was established, revealing genetic divergence and expression polymorphisms in parental lines. The sterile anther phenotype of hybrid plants obtained by gibberellin treatment of the inflorescence at the buttoning phase is causally related to changes in allelic gene expression patterns at different phases of microsporogenesis.

Single-cell transcriptome sequencing of plant leaf expressing anti-HER2 VHH–FcK cancer therapeutic protein

The transgenic plant is a promising strategy for the production of highly valuable biotherapeutic proteins such as recombinant vaccines and antibodies. To achieve an efficient level of protein production, codon sequences and expression cassette elements need to be optimized. However, the systematical expression of recombinant proteins in plant biomass can generally be controlled for the production of therapeutic proteins after the generation of transgenic plants. Without understanding the transgene expression patterns in plant tissue, it is difficult to enhance further production levels. In this study, single-cell RNA-sequencing (scRNA-seq) analysis of transgenic tobacco (Nicotiana tabacum) leaf, expressing an immunotherapeutic llama antibody against breast cancer, anti-HER2 VHH–Fc, was conducted to obtain data on the expression pattern of tissue-specific cells. These high-quality scRNA-seq data enabled the identification of gene expression patterns by cell types, which can be applied to select the best cell types or tissues for the high production of these recombinant antibodies. These data provide a foundation to elucidate the mechanisms that regulate the biosynthesis of recombinant proteins in N. tabacum.

Antimony resistance and gene expression in Leishmania: spotlight on molecular and proteomic aspects.

Leishmaniasis is a vector-borne parasitic disease caused by Leishmania parasites with a spectrum of clinical manifestations, ranging from skin lesions to severe visceral complications. Treatment of this infection has been extremely challenging with the concurrent emergence of drug resistance. The differential gene expression and the discrepancies in protein functions contribute to the appearance of 2 distinct phenotypes: resistant and sensitive, but the current diagnostic tools fail to differentiate between them. The identification of gene expression patterns and molecular mechanisms coupled with antimony (Sb) resistance can be leveraged to prompt diagnosis and select the most effective treatment methods. The present study attempts to use comparative expression of Sb resistance-associated genes in resistant and sensitive Leishmania, to disclose their relative abundance in clinical or in vitro selected isolates to gain an understanding of the molecular mechanisms of Sb response/resistance. Data suggest that the analysis of resistance gene expression would verify the Sb resistance or susceptibility only to a certain extent; however, none of the individual expression patterns of the studied genes was diagnostic as a biomarker of Sb response of Leishmania. The findings highlighted will be useful in bridging the knowledge gap and discovering innovative diagnostic tools and novel therapeutic targets.

Development of a diagnostic and risk prediction model for Alzheimer's disease through integration of single-cell and bulk transcriptomic analysis of glutamine metabolism.

In this study, we present a novel system for quantifying glutamine metabolism (GM) to enhance the effectiveness of Alzheimer's disease (AD) diagnosis and risk prediction. Single-cell RNA sequencing (scRNA-seq) analysis was utilized to comprehensively assess the expression patterns of GM. The WGCNA algorithm was applied to investigate the most significant genes related to GM. Subsequently, three machine learning algorithms (Boruta, LASSO, and SVM-RFE) were employed to identify GM-associated characteristic genes and develop a risk model. Patients were divided into high- and low-risk groups based on this model. Moreover, we explored biological properties, distinct signaling pathways, and immunological characteristics of AD patients at different risk levels. Finally, in vitro and in vivo models of AD were constructed to validate the characteristics of the feature genes. Both scRNA-seq and bulk transcriptomic analyses revealed increased GM activity in AD patients, specifically in certain cell subsets (pDC, Tem/Effector helper T cells (LTB), and plasma cells). Cells with higher GM scores demonstrated more significant numbers and strengths of interactions with other cell types. The WGCNA algorithm identified 360 genes related to GM, and a risk score was constructed based on nine characteristic genes (ATP13A4, PIK3C2A, CD164, PHF1, CES2, PDGFB, LCOR, TMEM30A, and PLXNA1) identified through multiple machine learning algorithms displayed reliable diagnostic efficacy for AD onset. Nomograms, calibration curves, and decision curve analysis (DCA) based on these characteristic genes provided significant clinical benefits for AD patients. High-risk AD patients exhibited higher levels of immune-related functions and pathways, increased immune cell infiltration, and elevated expressions of immune modulators. RT-qPCR analysis revealed that the majority of the nine characteristic genes were differentially expressed in AD-induced rat neurons. Knocking down PHF1 could protect against neurite loss and alleviate cell injury in AD neurons. In vivo, down-regulation of PHF1 in AD models decreases GM metabolism levels and modulates the immunoinflammatory response in the brain. This comprehensive identification of gene expression patterns contributes to a deeper understanding of the underlying pathological mechanisms driving AD pathogenesis. Furthermore, the risk model based on the nine-gene signature offers a promising theoretical foundation for developing individualized treatments for AD patients.

Expression of Apoptotic and Ubiquitin-Proteasome Genes Are Altered in Blastocoel Fluid From Preimplantation Euploid IVF Embryos That Result in Miscarriage [ID: 1365769

INTRODUCTION: Infertility is one of the leading causes of recurrent miscarriage, affecting approximately 14% of reproductive-aged patients. Recurrent miscarriages are presumed to be the result of embryonic chromosomal abnormalities such as aneuploidy. Literature has indicated that apoptotic mechanisms may play a role in selective elimination of aneuploid cells during preimplantation embryo development. This study aims to identify the expression patterns of an apoptotic gene and a gene encoding a ubiquitin ligase within blastocoel fluid-conditioned media from preimplantation euploid in vitro fertilization (IVF) embryos that resulted in miscarriage to identify specific genes associated with poor implantation outcomes. METHODS: Candidate genes were identified through whole-transcriptome (RNA-seq) analysis of blastocoel fluid from euploid IVF embryos that resulted in successful or unsuccessful implantation. Blastocoel fluid from euploid IVF embryos resulting in miscarriage or successful implantation was selected for specific gene expression analysis using RT-qPCR and Taqman-specific primers. BCL2L12 and SHARPIN gene expression was assessed, compared to GAPDH control. RESULTS: Expression of BCL2L12, an antiapoptotic gene, and SHARPIN, a gene that encodes an ubiquitin ligase, was altered in blastocoel fluid samples associated with miscarriage. Initial studies indicate that SHARPIN has a higher expression in blastocoel fluid from samples associated with negative implantation outcomes. CONCLUSION: Identification of gene expression patterns during preimplantation development that are associated with miscarriage may allow for an additional embryo quality metric to improve the success of each IVF embryo transfer potentially reducing the number of miscarriages. Additionally, these metrics could be expanded to allow for the identification of potential high-risk pregnancies soon after implantation, without any harm to the fetus.

"Dorsal-Ventral" Genes Are Part of an Ancient Axial Patterning System: Evidence from Trichoplax adhaerens (Placozoa).

Placozoa are a morphologically simplistic group of marine animals found globally in tropical and subtropical environments. They consist of two named species, Trichoplax adhaerens and more recently Hoilungia hongkongensis, both with roughly six morphologically distinct cell types. With a sequenced genome, a limited number of cell types, and a simple flattened morphology, Trichoplax is an ideal model organism from which to explore the biology of an animal with a cellular complexity analagous to that of the earliest animals. Using a new approach for identification of gene expression patterns, this research looks at the relationship of Chordin/TgfΒ signaling and the axial patterning system of Placozoa. Our results suggest that placozoans have an oral–aboral axis similar to cnidarians and that the parahoxozoan ancestor (common ancestor of Placozoa and Cnidaria) was likely radially symmetric.

Abstract 42: Identification of gene expression patterns distinguishing responders and non-responders to induction chemotherapy in sinonasal undifferentiated carcinoma

Abstract Background: Sinonasal undifferentiated carcinoma (SNUC) is a rare, highly aggressive cancer that arises in the nasal cavity and paranasal sinuses. Despite aggressive multimodal therapy the prognosis remains poor, and the median survival time is less than 18 months. Because of its locally advanced nature, cisplatin-based induction chemotherapy has been used in our institution to downstage unresectable tumors before definitive surgery or radiation therapy. Interestingly, our previous study showed that response to induction chemotherapy is a prognostic indicator and may be used to select patients for definitive local treatment. In this study, we performed gene expression analysis on SNUC specimens to identify molecular markers to predict/distinguish between responders and non-responders to induction chemotherapy. Materials and Methods: Twenty-seven formalin-fixed paraffin-embedded samples from 24 patients treated at MD Anderson Cancer Center between 1999 to 2016 were used in this study. Among them, 12 specimens were treatment-naïve. Gene expression analysis was performed on an HTG EdgeSeq Oncology Biomarker Panel. Unsupervised clustering analysis and Mann-Whitney test were performed using JMP software and IBM SPSS Statistics 23, previously. Pathway analysis was performed using Ingenuity Pathway Analysis. Results: First, we attempted to identify a set of genes which could predict response to induction chemotherapy. Unfortunately, unsupervised clustering analysis on treatment-naïve specimen was incapable of distinguishing between responders and non-responders. However, using discriminant analysis we succeeded in finding genes classifying patients into responders and non-responders. Then we studied the tumor specimens harvested after induction chemotherapy; differentially expressed genes between the two groups (Mann-Whitney test; p<0.05) were analyzed for pathway analysis. Multiple upstream regulators related to cell survival and proliferation including Transforming growth factor beta 1 were predicted to be activated in the non-responders' specimens. Conclusions: Our study revealed the possibility that cell survival and proliferation pathways are upregulated in non-responders to induction chemotherapy in SNUC. This finding suggests that non-responders to induction chemotherapy might be treated by inhibiting those pathways. Our comprehensive gene expression study is a significant step towards developing new therapeutic approaches in SNUC. Citation Format: Yoko Takahashi, Diana Bell, Frederico O. Gleber-Netto, Tong-Xin Xie, Dianna Roberts, Curtis Pickering, Jeffrey N. Myers, Ehab Y. Hanna. Identification of gene expression patterns distinguishing responders and non-responders to induction chemotherapy in sinonasal undifferentiated carcinoma [abstract]. In: Proceedings of the AACR-AHNS Head and Neck Cancer Conference: Optimizing Survival and Quality of Life through Basic, Clinical, and Translational Research; April 23-25, 2017; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(23_Suppl):Abstract nr 42.

Expression Pattern of ERF Gene Family under Multiple Abiotic Stresses in Populus simonii × P. nigra

Identification of gene expression patterns of key genes across multiple abiotic stresses is critical for mechanistic understanding of stress resistance in plant. In the present study, we identified differentially expressed genes (DEGs) in di-haploid Populus simonii × P. nigra under respective stresses of NaCl, KCl, CdCl2, and PEG. On the basis of RNA-Seq, we detected 247 DEGs that are shared by the four stresses in wild type poplar, and mRNA abundance of the DEGs were validated in transgenic poplar overexpressing ERF76 gene by RNA-Seq and RT-qPCR. Results from gene ontology analysis indicated that these genes are enriched in significant pathways, such as phenylpropanoid biosynthesis, phenylalanine metabolism, starch and sucrose metabolism, and plant hormone signal transduction. Ethylene response factor (ERF) gene family plays significant role in plant abiotic stress responses. We also investigated expression pattern of ERF gene family under the four stresses. The ERFs and DEGs share similar expression pattern across the four stresses. The transgenic poplar is superior to WT in morphologic, physiological and biochemical traits, which demonstrated the ERF76 gene plays a significant role in stress resistance. These studies will give a rise in understanding the stress response mechanisms in poplar.

Midbrain Gene Screening Identifies a New Mesoaccumbal Glutamatergic Pathway and a Marker for Dopamine Cells Neuroprotected in Parkinson's Disease.

The ventral tegmental area (VTA) and substantia nigra pars compacta (SNc) of the midbrain are associated with Parkinson’s disease (PD), schizophrenia, mood disorders and addiction. Based on the recently unraveled heterogeneity within the VTA and SNc, where glutamate, GABA and co-releasing neurons have been found to co-exist with the classical dopamine neurons, there is a compelling need for identification of gene expression patterns that represent this heterogeneity and that are of value for development of human therapies. Here, several unique gene expression patterns were identified in the mouse midbrain of which NeuroD6 and Grp were expressed within different dopaminergic subpopulations of the VTA, and TrpV1 within a small heterogeneous population. Optogenetics-coupled in vivo amperometry revealed a previously unknown glutamatergic mesoaccumbal pathway characterized by TrpV1-Cre-expression. Human GRP was strongly detected in non-melanized dopaminergic neurons within the SNc of both control and PD brains, suggesting GRP as a marker for neuroprotected neurons in PD. This study thus unravels markers for distinct subpopulations of neurons within the mouse and human midbrain, defines unique anatomical subregions within the VTA and exposes an entirely new glutamatergic pathway. Finally, both TRPV1 and GRP are implied in midbrain physiology of importance to neurological and neuropsychiatric disorders.

A point mutation in the extracellular domain of L1 blocks its capacity to confer metastasis in colon cancer cells via CD10.

The neural L1 transmembrane cell adhesion receptor of the immunoglobulin-like family is a target gene of Wnt-β-catenin signaling in human colorectal cancer (CRC) cells and is expressed at the invasive edge of the tumor tissue. L1 overexpression in cultured CRC cells confers enhanced proliferation, motility and liver metastasis. We have analyzed the mechanisms of L1-mediated signaling in CRC cells by using various point mutations in the L1 ectodomain that are known to cause severe genetically inherited mental retardation disorders in patients. We found that all such L1 ectodomain mutations abolish the ability of L1 to confer metastatic properties in CRC cells. Using gene array analysis, we identified L1-mutation-specific gene expression signatures for the L1/H210Q and L1/D598N mutations. We identified CD10, a metalloprotease (neprilysin, neutral endopeptidase) and a gene that is specifically induced in CRC cells by L1 in an L1/H210Q mutation-specific manner. CD10 expression was required for the L1-mediated induction of cell proliferation, motility and metastasis, as suppression of CD10 levels in L1-expressing CRC cells abolished the L1 effects on CRC progression. The signaling from L1 to CD10 was mediated through the L1-ezrin-NF-κB pathway. In human CRC tissue L1 and CD10 were localized in partially overlapping regions in the more invasive areas of the tumor tissue. The results suggest that CD10 is a necessary component conferring the L1 effects in CRC cells. The identification of gene expression patterns of L1-domain-specific point mutations may provide novel markers and targets for interfering with L1-mediated CRC progression.

Identification of gene expression patterns crucially involved in experimental autoimmune encephalomyelitis and multiple sclerosis.

ABSTRACTAfter encounter with a central nervous system (CNS)-derived autoantigen, lymphocytes leave the lymph nodes and enter the CNS. This event leads only rarely to subsequent tissue damage. Genes relevant to CNS pathology after cell infiltration are largely undefined. Myelin-oligodendrocyte-glycoprotein (MOG)-induced experimental autoimmune encephalomyelitis (EAE) is an animal model of multiple sclerosis (MS), a chronic autoimmune disease of the CNS that results in disability. To assess genes that are involved in encephalitogenicity and subsequent tissue damage mediated by CNS-infiltrating cells, we performed a DNA microarray analysis from cells derived from lymph nodes and eluted from CNS in LEW.1AV1 (RT1av1) rats immunized with MOG 91-108. The data was compared to immunizations with adjuvant alone or naive rats and to immunizations with the immunogenic but not encephalitogenic MOG 73-90 peptide. Here, we show involvement of Cd38, Cxcr4 and Akt and confirm these findings by the use of Cd38-knockout (B6.129P2-Cd38tm1Lnd/J) mice, S1P-receptor modulation during EAE and quantitative expression analysis in individuals with MS. The hereby-defined underlying pathways indicate cellular activation and migration pathways mediated by G-protein-coupled receptors as crucial events in CNS tissue damage. These pathways can be further explored for novel therapeutic interventions.

Central dogma alchemy.

Central dogma alchemy.

Identification of Gene Expression Pattern Related to Breast Cancer Survival Using Integrated TCGA Datasets and Genomic Tools.

Several large-scale human cancer genomics projects such as TCGA offered huge genomic and clinical data for researchers to obtain meaningful genomics alterations which intervene in the development and metastasis of the tumor. A web-based TCGA data analysis platform called TCGA4U was developed in this study. TCGA4U provides a visualization solution for this study to illustrate the relationship of these genomics alternations with clinical data. A whole genome screening of the survival related gene expression patterns in breast cancer was studied. The gene list that impacts the breast cancer patient survival was divided into two patterns. Gene list of each of these patterns was separately analyzed on DAVID. The result showed that mitochondrial ribosomes play a more crucial role in the cancer development. We also reported that breast cancer patients with low HSPA2 expression level had shorter overall survival time. This is widely different to findings of HSPA2 expression pattern in other cancer types. TCGA4U provided a new perspective for the TCGA datasets. We believe it can inspire more biomedical researchers to study and explain the genomic alterations in cancer development and discover more targeted therapies to help more cancer patients.

BM-22 * BOC AND MAP2 ARE OPERATIVE IN BREAST CANCER METASTASIS TO BRAIN

Approximately 40% of patients with systemic cancer will develop central nervous system (CNS) metastasis. In adults, metastases to the brain arise most commonly from primary tumors of the lung, breast, skin and gastrointestinal tract. Breast cancer is the second most common cause of brain metastasis occurring in ∼20% of patients. Current systemic treatments have failed to prevent the development of CNS metastasis of these malignancies. CNS involvement is almost always fatal, even in case the primary tumor is under control. Therefore, preventing the development of CNS metastases would be a great step forward in the treatment of patients with potentially disseminating, or disseminated tumors. The molecular basis of breast cancer metastasis to brain is largely unknown and no therapeutic agents preventing tumor cells to colonize the brain are available. Our study aims at the identification of gene expression patterns of breast primary tumors which are involved in the formation of cerebral metastases. To this aim, gene expression profiles of patients with metastasized breast cancers with and without cerebral metastases were compared. All tumors were negative for ER/PR/her2neu. Among various genes the cell adhesion associated, oncogene regulated (BOC) and microtubule associated protein 2 (MAP2) were prominently present. These genes were validated by RT-PCR and immunohistochemistry. Currently, we are carrying out functional studies to reveal the specific involvement of BOC and MAP2 in the formation of brain metastasis.

Dynamic agglomerative clustering of gene expression profiles

The increasing use of microarray technologies is generating a large amount of data that must be processed to extract underlying gene expression patterns. Existing clustering methods could suffer from certain drawbacks. Most methods cannot automatically separate scattered, singleton and mini-cluster genes from other genes. Inclusion of these types of genes into regular clustering processes can impede identification of gene expression patterns. In this paper, we propose a general clustering method, namely a dynamic agglomerative clustering (DAC) method. DAC can automatically separate scattered, singleton and mini-cluster genes from other genes and thus avoid possible contamination to the gene expression patterns caused by them. For DAC, the scattered gene filtering step is no longer necessary in data pre-processing. In addition, we propose a criterion for evaluating clustering results for a dataset which contains scattered, singleton and/or mini-cluster genes. DAC has been applied successfully to two real datasets for identification of gene expression patterns. Our numerical results indicate that DAC outperforms other clustering methods, such as the quality-based and model-based clustering methods, in clustering datasets which contain scattered, singleton and/or mini-cluster genes.

Identification of gene expression patterns using planned linear contrasts

BackgroundIn gene networks, the timing of significant changes in the expression level of each gene may be the most critical information in time course expression profiles. With the same timing of the initial change, genes which share similar patterns of expression for any number of sampling intervals from the beginning should be considered co-expressed at certain level(s) in the gene networks. In addition, multiple testing problems are complicated in experiments with multi-level treatments when thousands of genes are involved.ResultsTo address these issues, we first performed an ANOVA F test to identify significantly regulated genes. The Benjamini and Hochberg (BH) procedure of controlling false discovery rate (FDR) at 5% was applied to the P values of the F test. We then categorized the genes with a significant F test into 4 classes based on the timing of their initial responses by sequentially testing a complete set of orthogonal contrasts, the reverse Helmert series. For genes within each class, specific sequences of contrasts were performed to characterize their general 'fluctuation' shapes of expression along the subsequent sampling time points. To be consistent with the BH procedure, each contrast was examined using a stepwise Studentized Maximum Modulus test to control the gene based maximum family-wise error rate (MFWER) at the level of αnew determined by the BH procedure. We demonstrated our method on the analysis of microarray data from murine olfactory sensory epithelia at five different time points after target ablation.ConclusionIn this manuscript, we used planned linear contrasts to analyze time-course microarray experiments. This analysis allowed us to characterize gene expression patterns based on the temporal order in the data, the timing of a gene's initial response, and the general shapes of gene expression patterns along the subsequent sampling time points. Our method is particularly suitable for analysis of microarray experiments in which it is often difficult to take sufficiently frequent measurements and/or the sampling intervals are non-uniform.

Cloning and Expression Analysis of Salt Responsive Gene from Kandelia candel

Identification of gene expression patterns in mangroves grown under salinity will help to reveal the molecular mechanisms of salt tolerance. Here, 10 cDNAs of genes were isolated from Kandelia candel and identified by representational difference analysis of cDNA (cDNA RDA) under different NaCl concentrations. Of five genes expressed preferentially under salt condition, two were unknown, three were two kinds of low molecular mass heat-shock proteins (sHSPs) and ADP-ribosylation factor, respectively. The expressions of other five genes were repressed under NaCl stress, two encoded cyclophilins, three were tonoplast intrinsic protein, early light-induced protein and 60S ribosomal protein, respectively.

Immunocytochemistry as a tool for zebrafish developmental neurobiology.

Two methods are presented here that allow clear visualization of antibody localization in zebrafish whole mount preparations, both for immunocytochemistry (ICC) alone and in combination with in situ hybridization (ISH). The first protocol describes ICC performed using a modified permeabilization technique and the chromogen AEC (3-Amino-9-ethylcarbazole). The second protocol describes the co-localization of transcriptional and translational products using a combined ISH/ICC protocol. A fluorescing chromogen (Fast Red, FR) is used to detect mRNA transcripts by ISH, and is combined with ICC that uses a secondary antibody conjugated to a different fluorescent molecule (Alexa 488). These procedures allow the identification of gene expression patterns in cell types identifiable with known antibodies.

Application of DNA microarray technology to study genes controlled by progesterone in human endometrial stromal cells in vitro

Application of DNA microarray technology to study genes controlled by progesterone in human endometrial stromal cells in vitro