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At least 163 records · Page 9Linked to original sources
PubMed2025

Molecular hallmarks of excitatory and inhibitory neuronal resilience to Alzheimer's disease.

BACKGROUND: A significant proportion of individuals maintain cognition despite extensive Alzheimer's disease (AD) pathology, known as cognitive resilience. Understanding the molecular mechanisms that protect these individuals could reveal therapeutic targets for AD. METHODS: This study defines molecular and cellular signatures of cognitive resilience by integrating bulk RNA and single-cell transcriptomic data with genetics across multiple brain regions. We analyzed data from the Religious Order Study and the Rush Memory and Aging Project (ROSMAP), including bulk RNA sequencing (n = 631 individuals) and multiregional single-nucleus RNA sequencing (n = 48 individuals). Subjects were categorized into AD, resilient, and control based on β-amyloid and tau pathology, and cognitive status. We identified and prioritized protected cell populations using whole-genome sequencing-derived genetic variants, transcriptomic profiling, and cellular composition. RESULTS: Transcriptomics and polygenic risk analysis position resilience as an intermediate AD state. Only GFAP and KLF4 expression distinguished resilience from controls at tissue level, whereas differential expression of genes involved in nucleic acid metabolism and signaling differentiated AD and resilient brains. At the cellular level, resilience was characterized by broad downregulation of LINGO1 expression and reorganization of chaperone pathways, specifically downregulation of Hsp90 and upregulation of Hsp40, Hsp70, and Hsp110 families in excitatory neurons. MEF2C, ATP8B1, and RELN emerged as key markers of resilient neurons. Excitatory neuronal subtypes in the entorhinal cortex (ATP8B+ and MEF2Chigh) exhibited unique resilience signaling through activation of neurotrophin (BDNF-NTRK2, modulated by LINGO1) and angiopoietin (ANGPT2-TEK) pathways. MEF2C+ inhibitory neurons were over-represented in resilient brains, and the expression of genes associated with rare genetic variants revealed vulnerable somatostatin (SST) cortical interneurons that survive in AD resilience. The maintenance of excitatory-inhibitory balance emerges as a key characteristic of resilience. CONCLUSIONS: We have defined molecular and cellular hallmarks of cognitive resilience, an intermediate state in the AD continuum. Resilience mechanisms include preserved neuronal function, balanced network activity, and activation of neurotrophic survival signaling. Specific excitatory neuronal populations appear to play a central role in mediating cognitive resilience, while a subset of vulnerable interneurons likely provides compensation against AD-associated hyperexcitability. This study offers a framework to leverage natural protective mechanisms to mitigate neurodegeneration and preserve cognition in AD.

Humans↗
PubMed2005

Mast cell-specific genes--new drug targets/pathogenesis.

It has become possible to see all the expressed genes present in a cell (transcriptome) at once using microarray. We have applied microarray technology in various studies involving allergic diseases. Although we and others have discovered various novel molecules crucially involved in the pathogenesis of the disease, transcriptome assay is now expected as a tool for understanding the whole molecule balancing, i.e., system biology. Here I introduce examples of our trials for understanding the whole functional roles of mast cells as has been published in the web database for transcriptomes expressed by several mast cell types and various cell types. In the near future, we will be able to construct human mast cell models in silico (in a computer) by analyzing integrative information regarding the genome, transcriptome and proteome of mast cells, and will be able to test our hypotheses without having to perform in vitro tests.

Animals↗
PubMed2005

Applications of DNA tiling arrays for whole-genome analysis.

DNA microarrays are a well-established technology for measuring gene expression levels. Microarrays designed for this purpose use relatively few probes for each gene and are biased toward known and predicted gene structures. Recently, high-density oligonucleotide-based whole-genome microarrays have emerged as a preferred platform for genomic analysis beyond simple gene expression profiling. Potential uses for such whole-genome arrays include empirical annotation of the transcriptome, chromatin-immunoprecipitation-chip studies, analysis of alternative splicing, characterization of the methylome (the methylation state of the genome), polymorphism discovery and genotyping, comparative genome hybridization, and genome resequencing. Here we review different whole-genome microarray designs and applications of this technology to obtain a wide variety of genomic scale information.

Animals↗
PubMed2003

Proteomics as a functional genomics tool.

To understand the function of all the genes in an organism, one needs to know not only which genes are expressed, when, and where, but also what the protein end products are and under which conditions they accumulate in certain tissues. Proteomics aims at describing the whole protein output of the genome and complements transcriptomic and metabolomic studies. Proteomics depends on extracting, separating, visualizing, identifying, and quantifying the proteins and their interactions present in an organism or tissue at any one time. All of these stages have limitations. Therefore, it is, at present, impossible to describe the whole proteome of any organism. Plants might synthesize many thousands of proteins at one time, and the whole potentially synthesized proteome certainly exceeds the number of estimated genes for that genome. This occurs because the gene products of one gene can differ due to alternative splicing and a variety of possible posttranslational modifications. It is, therefore, essential to optimize every step towards detecting the whole proteome while realizing the limitations. We concentrate here on the most commonly used steps in high-throughput plant proteomics with the techniques we have found most reproducible and with the highest resolution and quality.

Coloring Agents↗
PubMed2006

Global transcriptomic analysis of Desulfovibrio vulgaris on different electron donors.

Whole-genome microarrays of Desulfovibrio vulgaris were used to determine relative transcript levels in cells grown to exponential or stationary phase on a medium containing either lactate or formate as electron donor. The results showed that 158 and 477 genes were differentially expressed when comparing exponential to stationary phase in lactate- or formate-based media, respectively; and 505 and 355 genes were responsive to the electron donor used at exponential or stationary phase, respectively. Functional analyses suggested that the differentially regulated genes were involved in almost every aspect of cellular metabolism, with genes involved in protein synthesis, carbon, and energy metabolism being the most regulated. The results suggested that HynBA-1 might function as a primary periplasmic hydrogenase responsible for oxidation of H2 linked to the proton gradient in lactate-based medium, while several periplasmic hydrogenases including HynBA-1 and Hyd might carry out this role in formate-based medium. The results also indicated that the alcohol dehydrogenase and heterodisulfide reductase catalyzed pathway for proton gradient formation might be actively functioning for ATP synthesis in D. vulgaris. In addition, hierarchical clustering analysis using expression data across different electron donors and growth phases allowed the identification of the common electron donor independent changes in gene expression specifically associated with the exponential to stationary phase transition, and those specifically associated with the different electron donors independent of growth phase. The study provides the first global description and functional interpretation of transcriptomic response to growth phase and electron donor in D. vulgaris.

Bacterial Proteins↗
PubMed2024

Pterostilbene Targets Hallmarks of Aging in the Gene Expression Landscape in Blood of Healthy Rats.

SCOPE: Polyphenols from the phytoestrogen group, including pterostilbene (PTS), are known for their antioxidant, anti-inflammatory, and anti-cancer effects. In recent reports, phytoestrogens attenuate age-related diseases; however, their pro-longevity effects in healthy models in mammals remain unknown. As longevity research demonstrates age-related transcriptomic signatures in human blood, the current study hypothesizes that phytoestrogen-supplemented diet may induce changes in gene expression that ultimately confer pro-longevity benefits. METHODS AND RESULTS: In the present study, RNA sequencing is conducted to determine transcriptome-wide changes in gene expression in whole blood of healthy rats consuming diets supplemented with phytoestrogens. Ortholog cell deconvolution is applied to analyze the omics data. The study discovered that PTS leads to changes in the gene expression landscape and PTS-target genes are associated with functions counteracting hallmarks of aging, including genomic instability, epigenetic alterations, compromised autophagy, mitochondrial dysfunction, deregulated nutrient sensing, altered intercellular interaction, and loss of proteostasis. These functions bridge together under anti-inflammatory effects through multiple pathways, including immunometabolism, where changes in cellular metabolism (e.g., ribosome biogenesis) impact the immune system. CONCLUSION: The findings provide a rationale for pre-clinical and clinical longevity studies and encourage investigations on PTS in maintaining cellular homeostasis, decelerating the process of aging, and improving conditions with chronic inflammation.

Animals↗
PubMed2006

Expression profiling by whole-genome interspecies microarray hybridization reveals differential gene expression in procyclic promastigotes, lesion-derived amastigotes, and axenic amastigotes in Leishmania mexicana.

We examined the Leishmania mexicana transcriptome to identify differentially regulated mRNAs using high-density whole-genome oligonucleotide microarrays designed from the genome data of a closely related species, Leishmania major. Statistical analysis on array hybridization data representing 8156 predicted coding regions revealed 288 genes (3.5% of all genes) whose steady-state mRNA levels meet criteria for differential regulation between promastigotes and lesion-derived amastigotes. Interestingly, sample comparison of promastigotes to axenic amastigotes resulted in only 17 genes (0.2%) that meet the same statistical criteria for differential regulation. The reduced number of regulated genes is a consequence of an increase in the magnitude of the transcript levels in cells under axenic conditions. The expression data for a subset of genes was validated by quantitative PCR. Our studies show that interspecies hybridization on microarrays can be used to analyze closely related protozoan parasites, that axenic culture conditions may alter amastigote transcript abundance, and that there is only a relatively modest change in abundance of a few mRNAs between morphologically distinct promastigote and amastigote cultured cells. Leishmania may represent an alternative paradigm for eukaryotic differentiation with minimal contributions from changes in mRNA abundance.

Animals↗
PubMed2026

Genome-wide identification and expression analysis of the CREB/ATF family and its potential role in melanogenesis in the Manila clam (Ruditapes philippinarum).

Ruditapes philippinarum is an economically important bivalve species in China, and shell color is a trait of ecological and commercial significance. Melanin is a key determinant of shell color, and members of the CREB/ATF family have been reported to participate in melanogenesis in other organisms. In this study, members of the CREB/ATF family were systematically identified at the whole-genome level based on genomic and transcriptomic datasets, followed by analyses of their phylogenetic relationships, gene structures, and expression patterns. A total of six CREB/ATF family members were identified and classified into five subfamilies. Expression profiling and RT-qPCR validation revealed that most CREB/ATF genes were highly expressed in the mantle and displayed clear differences among shell-color phenotypes. Except for RpATF4 and RpCREBZF, most members exhibited relatively high expression levels in dark-colored shell strains, particularly in black and zebra-striped clams. Moreover, most genes showed low expression during early embryonic and larval stages but increased expression at the single-siphon spat and juvenile stages. These results suggest that the CREB/ATF family may be involved in melanin-associated shell-color regulation in R. philippinarum, providing important candidate genes and a theoretical basis for further elucidating the molecular mechanisms of shell-color formation in mollusks.

Animals↗
PubMed2006

Transcriptional response of Candida albicans to hypoxia: linkage of oxygen sensing and Efg1p-regulatory networks.

The major human fungal pathogen, Candida albicans, colonizes different body sites, differing greatly in oxygen levels. Using whole-genome DNA microarrays, we analysed the transcriptomal response of C. albicans to hypoxia. In this condition, transcripts of genes involved in fermentative metabolism, including glycolytic genes, as well as hypha-specific genes, were up-regulated; in contrast, genes regulating oxidative metabolism were down-regulated. Although the morphogenetic and metabolic regulator Efg1p regulates these genes during normoxia, we found that Efg1p is not involved in their hypoxic regulation. Instead, Efg1p was specifically required for hypoxic expression or repression of subsets of genes. One class of hypoxia-regulated genes, encoding proteins involved in fatty acid biosynthesis, was dependent on Efg1p for maximal hypoxic expression, requiring Efg1p for transcriptional activation. During hypoxia, efg1 mutants contained lower levels of unsaturated fatty acids, while hyphal morphogenesis on solid media was significantly increased at temperatures <37 degrees C. These results suggest that during oxygen-limitation, Efg1p acts as a repressor of filamentation and as a positive regulator of fatty acid desaturation. We discuss that C. albicans responds to hypoxia largely by different mechanisms compared to budding yeast and that hypoxic adaptation requiring Efg1p is crucial for successful infection of human cells and tissues.

Candida albicans↗
PubMed2026

The current and future perspective of ChickenGTEx project and its applications in precision breeding.

The Chicken Genotype-Tissue Expression (ChickenGTEx) project was established to systematically characterize the regulatory landscape of the chicken genome and to accelerate the translation of functional genomics into precision breeding. By integrating whole-genome sequencing with multi-tissue transcriptomic profiling, ChickenGTEx provides a comprehensive atlas of gene expression regulation across diverse tissues and physiological systems. Current findings demonstrate that complex production traits are governed by coordinated regulatory networks rather than isolated loci, with substantial contributions from tissue-specific gene expression, structural variation, and genotype-by-sex interactions. Sex-dependent regulatory effects further refine the genetic architecture of metabolic, immune, and reproductive traits, highlighting the importance of incorporating sex as a biological variable in genomic analyses. Application of integrative omics frameworks within elite layer populations has revealed multilayer regulatory mechanisms underlying extended laying performance, feed efficiency, metabolic health, and eggshell quality. By partitioning phenotypic variance into genetic, regulatory, and host-microbiome components, these approaches move beyond association-based mapping toward causal inference and biological interpretation. Importantly, validated regulatory loci identified through ChickenGTEx and related analyses provide actionable markers for genomic selection and rational targets for precision genome modification. Looking forward, continued expansion of regulatory atlases, incorporation of single-cell and longitudinal data in diverse environmental conditions, and integration of functional annotation into breeding pipelines will further enhance prediction accuracy and sustainable genetic improvement. The ChickenGTEx project thus represents a foundational platform bridging functional genomics and practical poultry breeding.

Animals↗
PubMed2003

The math of making mutant mice.

More than ten large-scale mutagenesis projects are now generating hundreds of novel mouse mutants. Projects employ a wide variety of strategies and screens: targeting as much as the whole genome, part of a chromosome or just single genes. In this commentary, we consider the pros and cons of different tactics. We highlight issues of cost, efficiency and defend the impact of this mutagenesis program in an era of sophisticated conditional knockouts and advanced transgenic lines. Given the significant difficulties of adequately phenotyping and mapping randomly generated mutations that cover the whole genome, we tend to favor regional and gene-targeted screens. Whatever the choice of method, whole genome sequence data combined with detailed transcriptome and proteome surveys promise to significantly improve the efficiency with which series of mutations in a large subset of mammalian genes can be generated and cloned.

Animals↗
PubMed2005

Region-specific saturation germline mutagenesis in mice using the Sleeping Beauty transposon system.

Recent consolidation of the whole-genome sequence with genome-wide transcriptome profiling revealed the existence of functional units within the genome in specific chromosomal regions, as seen in the coordinated expression of gene clusters and colocalization of functionally related genes. An efficient region-specific mutagenesis screen would greatly facilitate research in addressing the importance of these clusters. Here we use the 'local hopping' phenomenon of a DNA-type transposon, Sleeping Beauty (SB), for region-specific saturation mutagenesis. A transgenic mouse containing both transposon (acts as a mutagen) and transposase (recognizes and mobilizes the transposon) was bred for germ-cell transposition events, allowing us to generate many mutant mice. All genes within a 4-Mb region of the original donor site were mutated by SB, indicating the potential of this system for functional genomic studies within a specific chromosomal region.

Animals↗
PubMed2006

The application of laser microdissection to in planta gene expression profiling of the maize anthracnose stalk rot fungus Colletotrichum graminicola.

Laser microdissection (LM) offers a potential means for deep sampling of a fungal plant-pathogen transcriptome during the infection process using whole-genome DNA microarrays. The use of a fluorescent protein-expressing fungus can greatly facilitate the identification of fungal structures for LM sampling. However, fixation methods that preserve both tissue histology and protein fluorescence, and that also yield RNA of suitable quality for microarray applications, have not been reported. We developed a microwave-accelerated acetone fixation, paraffin-embedding method that fulfills these requirements and used it to prepare mature maize stalk tissues infected with an Anemonia majano cyan fluorescent protein-expressing isolate of the anthracnose stalk rot fungus Colletotrichum graminicola. We successfully used LM to isolate individual maize cells associated with C. graminicola hyphae at an early stage of infection. The LM-derived RNA, after two-round linear amplification, was of sufficient quality and quantity for global expression profiling using a fungal microarray. Comparing replicated LM samples representing an early stage of stalk cell infection with samples from in vitro-germinated conidia, we identified 437 and 370 C. graminicola genes showing significant up- or downregulation, respectively. We confirmed the differential expression of several representative transcripts by quantitative reverse-transcriptase polymerase chain reaction (RT-PCR) and documented extensive overlap of this dataset with a PCR-subtraction library enriched for C. graminicola transcripts in planta. Our results demonstrate that LM is feasible for in planta pathogen expression profiling and can reveal clues about fungal genes involved in pathogenesis. The method in this report may be advantageous for visualizing a variety of cellular features that depend on a high degree of histochemical preservation and RNA integrity prior to LM.

Acetone↗
PubMed2004

Combined effects of blood and temperature shift on Borrelia burgdorferi gene expression as determined by whole genome DNA array.

Borrelia burgdorferi undergoes differential gene expression during transmission from its tick vector to a vertebrate host. The addition of blood to a spirochete culture at 35 degrees C for 48 h had a dramatic effect on gene expression of this organism. Utilizing B. burgdorferi whole genome DNA arrays, we compared the transcriptomes of the spirochetes following a 2-day temperature shift with blood and without blood. Using combined data from three independent RNA isolations we demonstrated that the addition of blood led to a differential expression of 154 genes. Of these, 75 genes were upregulated, with 49 (65%) of them encoded on plasmids. Blood supplementation of cultures also resulted in the downregulation of 79 genes, where 56 (70%) were plasmid encoded. We verified our results by reverse transcriptase PCR of several genes in both flat and feeding ticks. In the 2-day experiment we observed the effect that exposure to increased temperature and blood combined had on B. burgdorferi gene expression at this crucial time when the spirochetes begin to move from the vector to a new vertebrate host. These changes, among others, coincide with the upregulation of the chemotaxis and sensing regulons, of the lp38-encoded ABC transporter, of proteases capable of remodeling the outer surface of the spirochetes, and of the recombination genes of cp32 as a transient or initial part of the stress response of the phage. These are all functions that could cause or facilitate the changes that spirochetes undergo following a blood meal in the tick.

Animals↗
PubMed2006

The iron-regulated transcriptome and proteome of Neisseria meningitidis serogroup C.

Restricting bacterial growth by iron-chelating proteins that reduce iron availability in mucosal secretions and body fluids belongs to basic mechanisms of innate immunity. Most pathogens and commensals thus developed gene regulons responding to iron concentration and encoding iron acquisition systems and genes involved in host colonization and virulence. Here, we analyzed the steady-state composition of the iron-regulated proteome and transcriptome of an invasive serogroup C clinical isolate of Neisseria meningitidis. The proteome of meningococci grown under iron-depleted and iron-replete conditions was analyzed by 2-DE and proteins exhibiting significantly altered expression were identified by MALDI-TOF MS analysis. In parallel, total RNA was isolated from the same cultures and iron-regulated genes were identified using whole-genome DNA microarrays. The proteome and the transcriptome were found to overlap by only 19 iron-regulated genes/proteins, with 111 genes/proteins being significantly up-regulated in iron-replete cultures and 130 genes/proteins being up-regulated during iron starvation, respectively. Comparisons with published transcriptomic data for N. meningitidis serogroup B, moreover, indicate that expression of up to 20% of all meningococcal genes can be subject to regulation in function of iron availability.

Deferoxamine↗
PubMed2003

Transcriptome-based antigen identification for Neisseria meningitidis.

The identification of suitable antigens is crucial to successful vaccine development based on subunit approaches. While many methods exist for the identification of vaccine candidates which are surface-exposed or secreted, immunogenic and conserved, contain B and T cell epitopes, most of these have a major drawback: they do not yield any information on whether the antigen is indeed expressed by the pathogen during infection. However, DNA microarrays offer a novel tool for the investigation of the transcriptional activity of all genes of a pathogenic microorganism under in vivo conditions. Employing whole genome DNA microarrays, we have analyzed the transcriptome of Neisseria meningitidis serogroup B bacteria during different stages of infection, i.e. exposure to human serum and the interaction with human epithelial and endothelial cells. Combined with data derived from genome-based approaches (such as reverse vaccinology) and immunogenicity studies, this novel transcriptome-based antigen identification should reveal ideal vaccine candidates against serogroup B meningococcal infection.

Antigens, Bacterial↗
PubMed2006

Bioinformatics for cancer management in the post-genome era.

Human cancer is caused by multiple factors, such as genetic predisposition, chronic persistent inflammation, environmental factors, life style, and aging. Dysregulated proliferation, dysregulated adhesion, resistance to apoptosis, resistance to senescence, and resistance to anti-cancer drugs are features of cancer cells. Accumulation of multiple epigenetic changes and genetic alterations of cancer-associated genes during multi-stage carcinogenesis results in more malignant phenotypes. Post-genome science is characterized by omics data related to genome, transcriptome, proteome, metabolome, interactome, and epigenome as well as by high-throughput technology, such as whole-genome tiling oligonucleotide array, array CGH with 32,433 overlapping BAC clones, transcriptome microarray, mass spectrometry, tissue-based expression array, and cell-based transfection array. Benchtop oncology supplies Desktop oncology with large amounts of omics data produced by high-throughput technology. Desktop oncology establishes knowledge on cancer-related biomarkers, such as predisposition markers, diagnostic markers, prognostic markers, and therapeutic markers, by using bioinformatics and human intelligence of experts for data mining and text mining. Bedside oncology applies the knowledge established by Desktop oncology to determine therapeutics for cancer patients. Antibody drugs (Trastuzumab/Herceptin, Cetuximab/Erbitux, Bevacizumab/Avastin, et cetera), small molecule inhibitors for tyrosine kinases (Gefitinib/Iressa, Erlotinib/Tarceva, Imatinib/Gleevec, et cetera), conventional cytotoxic drugs, and anti-hormonal drugs are used for cancer chemotherapy. Biomarker monitoring contributes to therapeutic optional choice and drug dosage determination for cancer patients. Knowledge on biomarkers is feedforwarded from desktop to bedside in the translational research, and then biomarker monitoring is feedbacked from bedside to desktop in the reverse translational research. Desktop oncology is indispensable for cancer research in the post-genome era. Combination of genetic screening for cancer predisposition in the general population and precise selection of therapeutic options during cancer management could contribute to the realization of personalized prevention and to dramatically improve the prognosis of cancer patients in the future.

Antineoplastic Agents↗
PubMed2004

Transcriptome and genome conservation of alternative splicing events in humans and mice.

Combining mRNA and EST data in splicing graphs with whole genome alignments, we discover alternative splicing events that are conserved in both human and mouse transcriptomes. 1,964 of 19,156 (10%) loci examined contain one or more such alternative splicing events, with 2,698 total events. These events represent a lower bound on the amount of alternative splicing in the human genome. Also, as these alternative splicing events are conserved between the human and mouse transcriptomes they should be enriched for functionally significant alternative splicing events, free from much of the noise found in the EST libraries. Further classification of these alternative splicing events reveals that 1,037 (38.4%) are due to exon skipping, 497 (18.4%) are due to alternative 3' splice sites, 214 (7.9%) are due to alternative 5' splice sites, 75 (2.8%) are due to intron retention and the other 875 (32.4%) are due to other, more complicated, alternative splicing events. In addition, genomic sequences nearby these alternative splicing events display increased sequence conservation. Both the alternatively spliced exons and the proximal intron show increased levels of genomic conservation relative to constitutively spliced exons. For exon skipping events both intron regions flanking the exon are conserved while for alternative 5' and 3' splicing events the conservation is greater near the alternative splice site.

Algorithms↗