Regulatory Modules of Human Thermogenic Adipocytes: Functional Genomics of Meta-Analyses Derived Marker-Genes

SummaryRecently, ProFAT and BATLAS scores have been offered to determine thermogenic status of adipocytes using expression pattern of brown and white marker-genes. In this work, we investigated the functional context of these genes. Although the two meta-analyses based marker-gene lists have little overlap, their enriched pathways show strong coincides suggesting they may better characterize adipocytes. We demonstrate that functional genomics of the annotated genes in common pathways enables an extended analysis of thermogenesis regulation, generates testable hypotheses supported by experimental results in human adipocytes with different browning potential and may lead to more global conclusions than single-state studies. Our results imply that different biological processes shape brown and white adipocytes with presumed transitional states. We propose that the thermogenic adipocyte phenotype require both repression of whitening and induction of browning. These simultaneous actions and hitherto unnoticed regulatory modules, such as the exemplified HIF1A that may directly act at UCP1 promoter, can set new direction in obesity research.HighlightsIntegrated pathways better characterize brown adipocytes than marker-genesDifferent processes shape the brown and white adipocyte phenotypesThermogenic phenotype may require simultaneous repression of whitening and induction of browningProtein network analyses reveals unnoticed regulatory modules of adipocyte phenotypeHIF1A may regulate thermogenesis by direct control of UCP1 gene-expressionGraphical Abstract

Download Full-text

Regulatory modules of human thermogenic adipocytes: functional genomics of large cohort and Meta-analysis derived marker-genes

BMC Genomics ◽

10.1186/s12864-021-08126-8 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Beáta B. Tóth ◽

Zoltán Barta ◽

Ákos Barnabás Barta ◽

László Fésüs

Keyword(s):

Functional Genomics ◽

Meta Analysis ◽

Interaction Network ◽

Regulatory Elements ◽

Integrative Approach ◽

Marker Genes ◽

Biological Processes ◽

White Adipocyte ◽

Regulatory Modules ◽

White Adipocytes

Abstract Background Recently, ProFAT and BATLAS studies identified brown and white adipocytes marker genes based on analysis of large databases. They offered scores to determine the thermogenic status of adipocytes using the gene-expression data of these markers. In this work, we investigated the functional context of these genes. Results Gene Set Enrichment Analyses (KEGG, Reactome) of the BATLAS and ProFAT marker-genes identified pathways deterministic in the formation of brown and white adipocytes. The collection of the annotated proteins of the defined pathways resulted in expanded white and brown characteristic protein-sets, which theoretically contain all functional proteins that could be involved in the formation of adipocytes. Based on our previously obtained RNA-seq data, we visualized the expression profile of these proteins coding genes and found patterns consistent with the two adipocyte phenotypes. The trajectory of the regulatory processes could be outlined by the transcriptional profile of progenitor and differentiated adipocytes, highlighting the importance of suppression processes in browning. Protein interaction network-based functional genomics by STRING, Cytoscape and R-Igraph platforms revealed that different biological processes shape the brown and white adipocytes and highlighted key regulatory elements and modules including GAPDH-CS, DECR1, SOD2, IL6, HRAS, MTOR, INS-AKT, ERBB2 and 4-NFKB, and SLIT-ROBO-MAPK. To assess the potential role of a particular protein in shaping adipocytes, we assigned interaction network location-based scores (betweenness centrality, number of bridges) to them and created a freely accessible platform, the AdipoNET (https//adiponet.com), to conveniently use these data. The Eukaryote Promoter Database predicted the response elements in the UCP1 promoter for the identified, potentially important transcription factors (HIF1A, MYC, REL, PPARG, TP53, AR, RUNX, and FoxO1). Conclusion Our integrative approach-based results allowed us to investigate potential regulatory elements of thermogenesis in adipose tissue. The analyses revealed that some unique biological processes form the brown and white adipocyte phenotypes, which presumes the existence of the transitional states. The data also suggests that the two phenotypes are not mutually exclusive, and differentiation of thermogenic adipocyte requires induction of browning as well as repressions of whitening. The recognition of these simultaneous actions and the identified regulatory modules can open new direction in obesity research.

Download Full-text

ZFP982 confers mouse embryonic stem cell characteristics by regulating expression of Nanog, Zfp42 and Dppa3

10.1101/2020.06.03.131847 ◽

2020 ◽

Author(s):

Fariba Dehghanian ◽

Patrick Piero Bovio ◽

Zohreh Hojati ◽

Tanja Vogel

Keyword(s):

Stem Cells ◽

Stem Cell ◽

Embryonic Stem Cells ◽

Neural Differentiation ◽

Marker Gene ◽

Embryonic Stem ◽

Mouse Embryonic Stem Cells ◽

Stem Cell Marker ◽

Marker Genes ◽

List Type

AbstractWe here used multi-omics analyses to identify and characterize zinc finger protein 982 (Zfp982) that confers stemness characteristics by regulating expression of Nanog, Zfp42 and Dppa3 in mouse embryonic stem cells (mESC). Network-based expression analyses comparing the transcriptional profiles of mESC and differentiated cells revealed high expression of Zfp982 in stem cells. Moreover, Zfp982 showed transcriptional overlap with Yap1, the major co-activator of the Hippo pathway. Quantitative proteomics and co-immunoprecipitation revealed interaction of ZFP982 with YAP1. ZFP982 used a GCAGAGKC motif to bind to chromatin, for example near the stemness conferring genes Nanog, Zfp42 and Dppa3 as shown by ChIP-seq. Loss-of-function experiments in mESC established that expression of Zfp982 is necessary to maintain stem cell characteristics. Zfp982 expression decreased with progressive differentiation, and knockdown of Zfp982 resulted in neural differentiation of mESC. ZFP982 localized to the nucleus in mESC and translocated to the cytoplasm upon neuronal differentiation. Similarly, YAP1 localized to the cytoplasm upon differentiation, but in mESC YAP1 was present in the nucleus and cytoplasm.Graphical AbstractZFP982 is a regulator of stemness of mouse embryonic stem cells and acts as transcription factor by activating expression of stem cell genes including Nanog, Dppa3 and Zfp42.HighlightsZfp982 is a new mouse stem cell defining marker gene.Zfp982 is co-expressed with Yap1 and stem cell marker genes in mESC.ZFP982 binds to DNA and induces expression of master genes of stemness in mESC.Expression of Zfp982 gene prevents neural differentiation and maintains stem cell characteristics.ZFP982 and YAP1 interact in mESC and translocate to the cytoplasm upon neural differentiation.

Download Full-text

Multi-view feature selection for identifying gene markers: a diversified biological data driven approach

BMC Bioinformatics ◽

10.1186/s12859-020-03810-0 ◽

2020 ◽

Vol 21 (S18) ◽

Author(s):

Sudipta Acharya ◽

Laizhong Cui ◽

Yi Pan

Keyword(s):

Gene Expression ◽

Feature Selection ◽

Gene Selection ◽

Marker Gene ◽

Biological Data ◽

Protein Interaction Data ◽

Marker Genes ◽

Data Sets ◽

Gene Markers ◽

Multi Objective

Abstract Background In recent years, to investigate challenging bioinformatics problems, the utilization of multiple genomic and proteomic sources has become immensely popular among researchers. One such issue is feature or gene selection and identifying relevant and non-redundant marker genes from high dimensional gene expression data sets. In that context, designing an efficient feature selection algorithm exploiting knowledge from multiple potential biological resources may be an effective way to understand the spectrum of cancer or other diseases with applications in specific epidemiology for a particular population. Results In the current article, we design the feature selection and marker gene detection as a multi-view multi-objective clustering problem. Regarding that, we propose an Unsupervised Multi-View Multi-Objective clustering-based gene selection approach called UMVMO-select. Three important resources of biological data (gene ontology, protein interaction data, protein sequence) along with gene expression values are collectively utilized to design two different views. UMVMO-select aims to reduce gene space without/minimally compromising the sample classification efficiency and determines relevant and non-redundant gene markers from three cancer gene expression benchmark data sets. Conclusion A thorough comparative analysis has been performed with five clustering and nine existing feature selection methods with respect to several internal and external validity metrics. Obtained results reveal the supremacy of the proposed method. Reported results are also validated through a proper biological significance test and heatmap plotting.

Download Full-text

PPIT: an R package for inferring microbial taxonomy from nifH sequences

Bioinformatics ◽

10.1093/bioinformatics/btab100 ◽

2021 ◽

Author(s):

Bennett J Kapili ◽

Anne E Dekas

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Query Sequence ◽

Marker Gene ◽

R Package ◽

Supplementary Information ◽

Marker Genes ◽

Pairwise Identity ◽

Metabolic Marker ◽

Microbial Taxonomy

Abstract Motivation Linking microbial community members to their ecological functions is a central goal of environmental microbiology. When assigned taxonomy, amplicon sequences of metabolic marker genes can suggest such links, thereby offering an overview of the phylogenetic structure underpinning particular ecosystem functions. However, inferring microbial taxonomy from metabolic marker gene sequences remains a challenge, particularly for the frequently sequenced nitrogen fixation marker gene, nitrogenase reductase (nifH). Horizontal gene transfer in recent nifH evolutionary history can confound taxonomic inferences drawn from the pairwise identity methods used in existing software. Other methods for inferring taxonomy are not standardized and require manual inspection that is difficult to scale. Results We present Phylogenetic Placement for Inferring Taxonomy (PPIT), an R package that infers microbial taxonomy from nifH amplicons using both phylogenetic and sequence identity approaches. After users place query sequences on a reference nifH gene tree provided by PPIT (n = 6317 full-length nifH sequences), PPIT searches the phylogenetic neighborhood of each query sequence and attempts to infer microbial taxonomy. An inference is drawn only if references in the phylogenetic neighborhood are: (1) taxonomically consistent and (2) share sufficient pairwise identity with the query, thereby avoiding erroneous inferences due to known horizontal gene transfer events. We find that PPIT returns a higher proportion of correct taxonomic inferences than BLAST-based approaches at the cost of fewer total inferences. We demonstrate PPIT on deep-sea sediment and find that Deltaproteobacteria are the most abundant potential diazotrophs. Using this dataset we show that emending PPIT inferences based on visual inspection of query sequence placement can achieve taxonomic inferences for nearly all sequences in a query set. We additionally discuss how users can apply PPIT to the analysis of other marker genes. Availability PPIT is freely available to non-commercial users at https://github.com/bkapili/ppit. Installation includes a vignette that demonstrates package use and reproduces the nifH amplicon analysis discussed here. The raw nifH amplicon sequence data have been deposited in the GenBank, EMBL, and DDBJ databases under BioProject number PRJEB37167. Supplementary information Supplementary data are available at Bioinformatics online.

Download Full-text

Abstract 1372: Characterization Of The Rejuvenation Of Cardiac Sympathetic Nerves In Cardiac Hypertrophy

Circulation ◽

10.1161/circ.116.suppl_16.ii_281-d ◽

2007 ◽

Vol 116 (suppl_16) ◽

Author(s):

Kensuke Kimura ◽

Masaki Ieda ◽

Hideaki Kanazawa ◽

Takahide Arai ◽

Takashi Kawakami ◽

...

Keyword(s):

Cardiac Hypertrophy ◽

Fluorescent Protein ◽

Sympathetic Neurons ◽

Weight Ratio ◽

Sympathetic Nerves ◽

Marker Genes ◽

List Type ◽

Stellate Ganglia ◽

Immature Neuron

Background : Cardiac hypertrophy induces the fetal isoform of genes (rejuvenation), including contractile proteins, ion channels, and natriuretic peptides. Cardiac sympathetic nerve function is known to be altered in cardiac hypertrophy and congestive heart failure. We recently reported that alteration of cardiac sympathetic nerves (CSN) was caused by their rejuvenation (Circ Res, 2007). The present study was designed to examine the precise characterization of the rejuvenation of CSN in cardiac hypertrophy. Methods and Results : RV hypertrophy was produced by consistent hypoxia (10% O 2 ) in C57/BL6 mice. RV pressure increased to 47 mmHg, and RV/(body weight) ratio increased by 1.6 fold. Nerve growth factor protein was augmented in hypertrophic RV, but was unchanged in LV. Double-transgenic mice, which specifically express eGFP (enhanced green fluorescent protein) in the sympathetic neurons, was generated by crossing dopamine β-hydroxylase (DBH)-Cre mice with Floxed-eGFP mice. The eGFP-positive CSN were markedly increased in hypertrophic RV, but not in LV. Nerve density, quantitated by immunostained area with eGFP and GAP43 (growth-associated corn marker), increased by 8.1 and 9.3 fold, respectively, in RV, but not in LV. (4) Catecholamine content was attenuated in RV. (5) Western blot revealed that tyrosine hydroxylase was markedly down-regulated in RV. (6) Immunostaining clearly demonstrated that the immature neuron markers, PSA-NCAM (highly polysialylated neural cell adhesion molecule) and Ulip-1 (Unc-33-like phosphoprotein 1), were expressed in CSN in hypertrophic RV and stellate ganglia. Basic helix-loop-helix transcription factor, Mash-1 (mammalian achaete-scute complex homolog 1) was strongly expressed in the stellate ganglia. (7) Immature neuron marker-immunopositive cells in stellate ganglia had a markedly decreased TH expression. Conclusion : The rejuvenated CSN showed various immature and fetal neuron marker genes at not only the peripheral axons but also the cellular bodies at the stellate ganglia. Rejuvenation of CSN might be critically involved in the alteration of sympathetic neuronal function in cardiac hypertrophy, including depressed norepinephrine synthesis and hyperinnervation.

Download Full-text

Recombination and deletion of sequences in shuttle vector plasmids in mammalian cells

Molecular and Cellular Biology ◽

10.1128/mcb.5.9.2265-2271.1985 ◽

1985 ◽

Vol 5 (9) ◽

pp. 2265-2271

Author(s):

S Chakrabarti ◽

S Joffe ◽

M M Seidman

Keyword(s):

Shuttle Vector ◽

Marker Gene ◽

Simian Virus 40 ◽

Repeated Sequences ◽

Marker Genes ◽

Insertion Mutagenesis ◽

Direct Repeats ◽

African Green Monkey Kidney ◽

Alu Sequence ◽

Insertion Mutants

Shuttle vector plasmids were constructed with directly repeated sequences flanking a marker gene. African green monkey kidney (AGMK) cells were infected with the constructions, and after a period of replication, the progeny plasmids were recovered and introduced into bacteria. Those colonies with plasmids that had lost the marker gene were identified, and the individual plasmids were purified and characterized by restriction enzyme digestion. Recombination between the repeated elements generated a plasmid with a precise deletion and a characteristic restriction pattern, which distinguished the recombined molecules from those with other defects in the marker gene. Recombination among the following different sequences was measured in this assay: (i) the simian virus 40 origin and enhancer region, (ii) the AGMK Alu sequence, and (iii) a sequence from plasmid pBR322. Similar frequencies of recombination among these sequences were found. Recombination occurred more frequently in Cos1 cells than in CV1 cells. In these experiments, the plasmid population with defective marker genes consisted of the recombined molecules and of the spontaneous deletion-insertion mutants described earlier. The frequency of the latter class was unaffected by the presence of the option for recombination represented by the direct repeats. Both recombination and deletion-insertion mutagenesis were stimulated by double-strand cleavage between the repeated sequences and adjacent to the marker, and the frequency of the deletion-insertion mutants in this experiment was again independent of the presence of the direct repeats. We concluded that although recombination and deletion-insertion mutagenesis were both stimulated by double-strand cleavage, the molecules which underwent the two types of change were drawn from separate pools.

Download Full-text

The effect of including the Nordic Hamstring exercise on sprint and jump performance in athletes: protocol of a systematic review and meta-analyses

10.1101/2020.04.01.20048686 ◽

2020 ◽

Author(s):

Kasper Krommes ◽

Mathias F. Nielsen ◽

Laura Krohn ◽

Birk M. Grønfeldt ◽

Kristian Thorborg ◽

...

Keyword(s):

Systematic Review ◽

High Speed ◽

Data Extraction ◽

Force Production ◽

List Type ◽

Jump Performance ◽

Production Studies ◽

Hamstring Strain ◽

Data Extraction Form ◽

Meta Analyses

AbstractThe Nordic Hamstring exercise reduces hamstring strain injuries in football and other sports, but the exercise is not well adopted in practice. Barriers from practitioners include fear of performance decrements, due to lack of specificity of the exercise with high speed running. However, in theory, increased eccentric hamstring strength could transfer to faster sprinting due to higher horizontal force production. Studies on the effect of the Nordic Hamstring exercise on performance have been conflicting and no synthesis of the evidence exists. We therefore pose the following question: does including the Nordic Hamstring exercise hamper sprint or jump performance in athletes? We will answer this question by performing a systematic review of the literature, critically appraise relevant studies, and GRADE the evidence across key outcomes and perform meta-analyses, meta-regression and subgroup analyses. In this protocol we outline the planned methods and procedures.Progress reportBesides this protocol, our data extraction form and the process of data extraction has been piloted on 3 relevant studies, along with familiarization with the Risk of Bias 2.0 tool. We have also comprised a preliminary search strategy for PubMed.Supplementary filesData Extraction Form (.pdf)Populated PRISMA-P checklist (.pdf)

Download Full-text

Cellular resolution anatomical and molecular atlases for prenatal human brains

10.1101/2021.07.14.452297 ◽

2021 ◽

Author(s):

Song-Lin Ding ◽

Joshua J. Royall ◽

Phil Lesnar ◽

Benjamin A.C. Facer ◽

Kimberly A. Smith ◽

...

Keyword(s):

Human Brain ◽

Hippocampal Formation ◽

Marker Gene ◽

Brain Structures ◽

Marker Genes ◽

Subcortical Structures ◽

Cellular Resolution ◽

Reliable Marker ◽

Human Brains ◽

Developmental Features

Increasing interest in studies of prenatal human brain development, particularly using new single-cell genomics and anatomical technologies to create cell atlases, creates a strong need for accurate and detailed anatomical reference atlases. In this study, we present two cellular-resolution digital anatomical atlases for prenatal human brain at post-conceptional weeks (PCW) 15 and 21. Both atlases were annotated on sequential Nissl-stained sections covering brain-wide structures on the basis of combined analysis of cytoarchitecture, acetylcholinesterase staining and an extensive marker gene expression dataset. This high information content dataset allowed reliable and accurate demarcation of developing cortical and subcortical structures and their subdivisions. Furthermore, using the anatomical atlases as a guide, spatial expression of 37 and 5 genes from the brains respectively at PCW 15 and 21 was annotated, illustrating reliable marker genes for many developing brain structures. Finally, the present study uncovered several novel developmental features, such as the lack of an outer subventricular zone in the hippocampal formation and entorhinal cortex, and the apparent extension of both cortical (excitatory) and subcortical (inhibitory) progenitors into the prenatal olfactory bulb. These comprehensive atlases provide useful tools for visualization, targeting, imaging and interpretation of brain structures of prenatal human brain, and for guiding and interpreting the next generation of cell census and connectome studies.

Download Full-text

Hypertrophy of Adipose Tissues in Quail Embryos by in ovo Injection of All-Trans Retinoic Acid

Frontiers in Physiology ◽

10.3389/fphys.2021.681562 ◽

2021 ◽

Vol 12 ◽

Author(s):

Dong-Hwan Kim ◽

Joonbum Lee ◽

Sanggu Kim ◽

Hyun S. Lillehoj ◽

Kichoon Lee

Keyword(s):

Retinoic Acid ◽

Vitamin A ◽

Marker Gene ◽

Marker Genes ◽

Health Issues ◽

Fat Cell ◽

In Ovo ◽

Adipose Tissues ◽

Trans Retinoic Acid ◽

All Trans Retinoic Acid

Excessive adipose accretion causes health issues in humans and decreases feed efficiency in poultry. Although vitamin A has been known to be involved in adipogenesis, effects of all-trans retinoic acid (atRA), as a metabolite of vitamin A, on embryonic adipose development have not been studied yet. Avian embryos are developing in confined egg environments, which can be directly modified to study effects of nutrients on embryonic adipogenesis. With the use of quail embryos, different concentrations of atRA (0 M to 10 μM) were injected in ovo at embryonic day (E) 9, and adipose tissues were sampled at E14. Percentages of fat pad weights in embryo weights were significantly increased in the group injected with 300 nM of atRA. Also, among three injection time points, E5, E7, or E9, E7 showed the most significant increase in weight and percentage of inguinal fat at E14. Injection of atRA at E7 increased fat cell size in E14 embryos with up-regulation of pro-adipogenic marker genes (Pparγ and Fabp4) and down-regulation of a preadipocyte marker gene (Dlk1) in adipose tissues. These data demonstrate that atRA promotes hypertrophic fat accretion in quail embryos, implying important roles of atRA in embryonic development of adipose tissues.

Download Full-text

A New Genome-to-Genome Comparison Approach for Large-Scale Revisiting of Current Microbial Taxonomy

Microorganisms ◽

10.3390/microorganisms7060161 ◽

2019 ◽

Vol 7 (6) ◽

pp. 161 ◽

Cited By ~ 1

Author(s):

Ming-Hsin Tsai ◽

Yen-Yi Liu ◽

Von-Wun Soo ◽

Chih-Chieh Chen

Keyword(s):

Microbial Diversity ◽

Large Scale ◽

Gene Selection ◽

Marker Gene ◽

Genome Comparison ◽

Marker Genes ◽

Species Classification ◽

Genome Wide ◽

A Genome ◽

Comparison Approach

Microbial diversity has always presented taxonomic challenges. With the popularity of next-generation sequencing technology, more unculturable bacteria have been sequenced, facilitating the discovery of additional new species and complicated current microbial classification. The major challenge is to assign appropriate taxonomic names. Hence, assessing the consistency between taxonomy and genomic relatedness is critical. We proposed and applied a genome comparison approach to a large-scale survey to investigate the distribution of genomic differences among microorganisms. The approach applies a genome-wide criterion, homologous coverage ratio (HCR), for describing the homology between species. The survey included 7861 microbial genomes that excluded plasmids, and 1220 pairs of genera exhibited ambiguous classification. In this study, we also compared the performance of HCR and average nucleotide identity (ANI). The results indicated that HCR and ANI analyses yield comparable results, but a few examples suggested that HCR has a superior clustering effect. In addition, we used the Genome Taxonomy Database (GTDB), the gold standard for taxonomy, to validate our analysis. The GTDB offers 120 ubiquitous single-copy proteins as marker genes for species classification. We determined that the analysis of the GTDB still results in classification boundary blur between some genera and that the marker gene-based approach has limitations. Although the choice of marker genes has been quite rigorous, the bias of marker gene selection remains unavoidable. Therefore, methods based on genomic alignment should be considered for use for species classification in order to avoid the bias of marker gene selection. On the basis of our observations of microbial diversity, microbial classification should be re-examined using genome-wide comparisons.

Download Full-text