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PubMed2004

Mouse testis transcriptome revealed using serial analysis of gene expression.

We applied serial analysis of gene expression (SAGE) to the mouse testis to reveal the global gene expression profile and to identify senescence-dependent changes in that profile. A total of 61,929 SAGE tags, including 19,323 unique tags, were obtained from 3- and 29-month-old BDF1 mice and 14-month-old SAMP1 mice. Genes highly expressed in the testis included those associated with spermatogenesis, protein metabolism, energy metabolism, growth and differentiation, and signal transduction. Testes from old mice of both strains appeared atrophied. Morphological examination of aged testes revealed extremely thin seminiferous epithelia and significantly decreased numbers of spermatids and spermatocytes. Despite the physical deterioration, no gross changes in the gene expression profile were apparent in the testes of old BDF1 mice. However, in 14-month-old SAMP1 mice, protamine 2 gene transcription was approximately 50% lower than in BDF1 mice. This reduction may be associated with the oligozoospermia and early decline in reproductive performance of SAMP1 mice. Our SAGE results are the first quantitative gene expression profile of the mouse testis and provide a reliable transcriptome reference for this organ.

Age Factors↗
PubMedDate not supplied

From the messenger RNA saga to the transcriptome era.

This review attempts to provide an overview of the evolution of the ideas and techniques that prevailed at the beginning of research on ribonucleic acids, until the contemporary era of cellular transcript analysis using DNA biochips and microarrays. Certain applications derived from the use of microarrays and the corresponding analyses of transcriptomes are discussed, particularly concerning diagnosis and prevision of evolution of certain cancers.

Cloning, Molecular↗
PubMed2004

Transcriptome of pituitary adenylate cyclase-activating polypeptide-differentiated PC12 cells.

Addition of pituitary adenylate cyclase-activating polypeptide (PACAP) into the cultured PC12 cells secreted dopamine and promoted neurite outgrowth of the cells, indicating cell differentiation. To characterize the PACAP-differentiated PC12 cell transcriptome, we applied DNA macroarray techniques, using Atlas Rat 1.2 Array membranes (BD Biosciences Clontech) that have 1176 cDNA. RNA samples were harvested from PC12 cells before and at a time of 6 h treatment with 1 nM PACAP, when neuritogenesis was remarkably observed under the condition used. Several genes regulated by PACAP have been associated with neuritogenesis (i.e. villin 2 and tissue plasminogen activator) or cell growth/differentiation (i.e. cyclin or ornitine decarboxylase). Also, cytoskeleton proteins such as actin or tubulin were up-regulated for cell morphology remodeling. A message of vehicle trafficking molecule (synaptotagmin IV) was more remarkably increased (3.95-6.85-fold). Signaling molecules such as small G proteins (rab12, rab16, or ral), IkappaB, or STAT3 were altered by PACAP. It is noteworthy that PACAP inhibited the expression of galanin receptor 2, whose ligand was shown to inhibit tyrosine hydroxylase activity. Thus, in this study the transcriptome of PACAP-differentiated PC12 was established, leading to the elucidation of the molecular mechanism of neuritogenesis by the neuropeptide.

Animals↗
PubMed2006

The cellular response to heat stress in the goby Gillichthys mirabilis: a cDNA microarray and protein-level analysis.

The cellular response to stress relies on the rapid induction of genes encoding proteins involved in preventing and repairing macromolecular damage incurred as a consequence of environmental insult. To increase our understanding of the scope of this response, a cDNA microarray, consisting of 9207 cDNA clones, was used to monitor gene expression changes in the gill and white muscle tissues of a eurythermic fish, Gillichthys mirabilis (Gobiidae) exposed to ecologically relevant heat stress. In each tissue, the induction or repression of over 200 genes was observed. These genes are associated with numerous biological processes, including the maintenance of protein homeostasis, cell cycle control, cytoskeletal reorganization, metabolic regulation and signal transduction, among many others. In both tissues, the molecular chaperones, certain transcription factors and a set of additional genes with various functions were induced in a similar manner; however, the majority of genes displayed tissue-specific responses. In gill, thermal stress induced the expression of the major structural components of the cytoskeleton, whereas these same genes did not respond to heat in muscle. In muscle, many genes involved in promoting cell growth and proliferation were repressed, perhaps to conserve energy for repair and replacement of damaged macromolecules, but a similar repression was not observed in the gill. Many of the observed changes in gene expression were similar to those described in model species whereas many others were unexpected. Measurements of the concentrations of the protein products of selected genes revealed that in each case an induction in mRNA synthesis correlated with an increase in protein production, though the timing and magnitude of the increase in protein was not consistently predicted by mRNA concentration, an important consideration in assessing the condition of the stressed cell using transcriptomic analysis.

Animals↗
PubMed2026

Integrated single-cell and bulk transcriptomic analysis identifies a novel senescent fibroblast subtype associated with poor prognosis in acral melanoma.

BACKGROUND: Acral melanoma (AM) exhibits significant intratumoral heterogeneity, but its tumor microenvironment (TME) and immune regulation remain unclear. This study aims to dissect TME heterogeneity and establish a prognostic model based on key cell subpopulations. METHODS: We collected AM single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data from the Gene Expression Omnibus (GEO) and the Cancer Genome Atlas (TCGA). Unsupervised clustering, CellChat, and Scissor analysis were performed to characterize cellular heterogeneity, cell-cell communication, and prognosis-related cell subpopulations. Kaplan-Meier analysis was used to assess the prognostic value of key genes, which were further validated by multiplex immunohistochemistry (mIHC). RESULTS: In AM, Mel_C2, C7, and C9 with high SEMA6A and KIT expression were strongly linked to poor prognosis. We further identified a senescent fibroblast subpopulation (sCAF_CDKN2A) characterized by high fibroblast senescence signature (FSS) scores. Integrating Scissor analysis of fibroblast subtypes with bulk prognostic data, we identified COL3A1, VCAN, and KIT as prognosis-associated genes upregulated in poor-outcome-related fibroblast subsets. Cell-cell communication analysis revealed that sCAF_CDKN2A engages in an immunosuppressive network, interacting with regulatory T cells (Tregs) via MIF signaling and receiving signals from exhausted CD8+ T cells through PPIA-BSG interactions. Using transcription factor expression patterns from these fibroblast subtypes, we constructed a prognostic model that effectively stratified patients into distinct risk groups with significant differences in overall survival (OS). mIHC confirmed significantly higher protein levels of SEMA6A and COL3A1 in tumor tissues compared to matched normal tissues. CONCLUSIONS: We established a novel prognostic model for AM and identified sCAF_CDKN2A as an immunosuppressive senescent fibroblast subpopulation driving poor prognosis.

Acral melanoma↗
PubMed2004

From masking repeats to identifying functional repeats in the mouse transcriptome.

The back-to-back release of the mouse genome and the functionally annotated RIKEN mouse full-length cDNA collection was an important milestone in mammalian genomics. Yet much of the data remain to be explored in terms of biological effects and mechanisms. For example, interspersed repeats account for 39 per cent of the mouse genome sequence and 11 per cent of representative transcripts. A considerable number of transposable repeat elements are still active and propagating in mouse compared with human. While existing repeat databases and tools assist the classification of repeats or identification of new repeats, there is little bioinformatic support towards exploring the extent and role of repeats in transcriptional variation, modulation of protein function, or gene regulatory events. Since the mouse is used as a model organism to study human genes and their disease associations, this review focuses on information extraction and collation that captures the functional context of repeats in mouse transcripts to facilitate the biological interpretation and extrapolation of findings to the human.

Animals↗
PubMed2005

Complete genome sequence and lytic phase transcription profile of a Coccolithovirus.

The genus Coccolithovirus is a recently discovered group of viruses that infect the globally important marine calcifying microalga Emiliania huxleyi. Among the 472 predicted genes of the 407,339-base pair genome are a variety of unexpected genes, most notably those involved in biosynthesis of ceramide, a sphingolipid known to induce apoptosis. Uniquely for algal viruses, it also contains six RNA polymerase subunits and a novel promoter, suggesting this virus encodes its own transcription machinery. Microarray transcriptomic analysis reveals that 65% of the predicted virus-encoded genes are expressed during lytic infection of E. huxleyi.

Apoptosis↗
PubMed2026

The Role of Small Segmental Duplications in Generating Identical Isoforms Through Alternative Splicing Sites.

Alternative splicing plays a crucial role in expanding proteomic diversity but can also generate identical isoforms under certain conditions. While mutually exclusive splicing of tandem exons has occasionally been reported to produce identical isoforms, the extent to which other splicing events contribute to this phenomenon remains unclear. In this study, we demonstrate that alternative 5' and 3' splice site selection can also lead to the formation of identical isoforms, providing an additional type of splicing event for functional redundancy in transcriptomes. To address this, we analyzed reference genome annotations from 15 plant species, including Arabidopsis thaliana and wheat (Triticum aestivum), obtained from the RefSeq database. Identical isoforms were computationally defined as transcripts with distinct exon-intron structures but identical coding sequences. Our analysis reveals that the majority of alternative 5' and 3' fragments originate from small segmental duplications, suggesting that sequence repetition within gene regions facilitates the emergence of such splicing patterns. We also observed differences in the annotated 5' UTRs of some identical isoforms. However, since the alternative splicing sites themselves were not located within UTRs, these differences may reflect annotation uncertainty rather than genuine AS-derived variation. Given that UTR predictions in reference databases are not always precise, such observations should be interpreted cautiously. Expression analysis using an isoform-specific k-mer approach confirmed that identical isoforms can be differentially regulated. These findings suggest that, beyond expanding protein diversity, alternative splicing can also generate redundant isoforms that are differentially expressed at the RNA level, indicating potential regulatory roles. By elucidating the structural and regulatory factors contributing to the formation and retention of identical isoforms, our study provides new insights into the evolutionary and functional significance of alternative splicing in plants.

Alternative Splicing↗
PubMed2006

Identification and characterization of a novel bovine oocyte-specific secreted protein gene.

The oocyte transcriptome and proteome largely remain a mystery and the important roles of these genes, especially in the bovine, are poorly understood. To better understand specific developmental roles of the bovine oocyte, we sought to characterize a novel oocyte gene. We have sequenced the full-length mRNAs of bovine oocyte-secreted protein 1 (OOSP1) and discovered two splice variants, namely OOSP1_v1 (variant 1) and OOSP1_v2 (variant 2). The OOSP1 gene is located on chromosome 15 and is composed of 5 exons, which span over nearly 7.9 kb. Bovine OOSP1_v1 encodes a predicted protein of 163 aa in length that shares amino acid identity with mouse OOSP1, it also bears a putative signal peptide and is probably glycosylated. Bovine OOSP1_v2 protein bears the same signal peptide as OOSP1_v1 but due to the skipping of exon 2 that introduces a frameshift, it is only 35 aa in length. Expression analysis of both OOSP1 transcripts showed that this gene is exclusively expressed in oocytes, contrasting with the mouse where Oosp1 is also expressed in the spleen and liver. OOSP1_v1 and OOSP1_v2 mRNA expression profiling using real-time PCR revealed that their mRNA levels were high in germinal vesicle (GV) stage oocytes and gradually decreased until the blastocyst stage, at which time they were undetectable. For the first time, we have identified the bovine OOSP1 gene as being one of the few known oocyte-specific markers.

Alternative Splicing↗
PubMed2026

A pro-inflammatory metastasis-associated macrophage subset induces tumor-promoting mesothelial cell conversion in ovarian cancer via IL-1α secretion.

Tumor-associated macrophages (TAMs) are key regulators of the tumor microenvironment, yet the functional specialization of TAM subsets in metastatic progression remains incompletely defined. Here, we characterized distinct TAM populations contributing to tumor-promoting mesothelial cell conversion in high-grade ovarian carcinoma using single-cell RNA sequencing of patient-derived macrophages from ascites (ascTAMs) and omental metastases (omTAMs). TAMs from these anatomical sites were clearly distinguishable by polarization states, with omTAMs exhibiting a mixed M1⁺/M2⁺ phenotype, in contrast to the M1low/M2⁺ profile observed in ascTAMs. Transcriptomic analysis further revealed functional divergence of these subsets. Notably, omTAMs displayed gene signatures associated with mesothelial-to-mesenchymal transition (MMT), a critical process enabling tumor invasion across the peritoneal lining. Functionally, conditioned media from omTAMs, similar to that from classically activated M1 macrophages, induced MMT in primary mesothelial cells via TGFβ and ERK/p38 MAPK signaling pathways. This phenotypic transition enhanced transmesothelial tumor cell invasion. Proteomic analysis identified IL-1α as a key MMT-inducing factor secreted by pro-inflammatory macrophages. Mechanistically, IL-1α cooperates with TGFβ by activating an autocrine TGFβ/TGFBR1 feedback loop in mesothelial cells, thereby amplifying MMT. Consistent with these findings, IL1A expression was enriched in omTAM clusters across independent patient samples and was confirmed by immunohistochemical analysis of clinical samples. From a therapeutic perspective, our study identifies new avenues to counteract the mesothelial reprogramming driven by IL-1α⁺ TAMs, potentially impeding metastatic progression. Created in BioRender. Heidemann, S. (2026) https://BioRender.com/aeu6yd0 .

Female↗
PubMed2026

Airway microbiome diversity, intramucosal bacteria, and spatial immunity in asthmatic adults and controls.

RATIONALE: Asthma is characterized by disruption of the thoracic airway mucosae and loss of microbial diversity. Spatial profiling of the mucosal transcriptome may systematically discover mechanisms for microbial influences on immunity. OBJECTIVES: We investigated relationships between clinical measures, microbial communities, and the host mucosal transcriptome within different strata of bronchial biopsies in subjects with and without asthma. METHODS: We performed bronchoscopy in 65 asthmatic adults and 44 healthy controls, quantifying bacterial operational taxonomic units (OTUs) in bronchial brushings by 16S ribosomal RNA (rRNA) gene amplicon sequences. Biopsy histologic features were scored blind to diagnosis. Following 16S rRNA in situ hybridization of 44 biopsies, bacterial foci were scored in epithelium, basement membrane, and stroma. Global human gene expression was quantified in epithelial and stromal compartments using digital spatial profiling. MEASUREMENTS AND MAIN RESULTS: Clinical asthma was independently predicted by basement membrane abnormalities (BaseMA), endobronchial bacterial diversity, and circulating eosinophil counts, but not by specific OTU abundances. 16S rRNA staining revealed bacteria within epithelium and mucosa of all biopsies. Intramucosal bacteria counts correlated negatively with spatially organized coexpression networks encoding antigen-specific immunity, neutrophil functions, and matrix activation, whereas BaseMA correlated positively with the adaptive immunity module. Eosinophil counts correlated with epithelial bacterial counts and senescence pathways. Clinical asthma was accompanied by upregulation of a regulatory T-cell network. CONCLUSIONS: Asthma and its related phenotypes are accompanied by complex mucosal events that extend beyond eosinophilic pathways. Components of diverse airway microbiota may modify immunity by beneficial interactions within the mucosa.

Humans↗
PubMed2006

Comparasite: a database for comparative study of transcriptomes of parasites defined by full-length cDNAs.

Comparasite is a database for comparative studies of transcriptomes of parasites. In this database, each data is defined by the full-length cDNAs from various apicomplexan parasites. It integrates seven individual databases, Full-Parasites, consisting of numerous full-length cDNA clones that we have produced and sequenced: 12,484 cDNA sequences from Plasmodium falciparum, 11,262 from Plasmodium yoelii, 9633 from Plasmodium vivax, 1518 from Plasmodium berghei, 7400 from Toxoplasma gondii, 5921 from Cryptosporidium parvum and 10,966 from the tapeworm Echinococcus multilocularis. Putatively counterpart gene groups are clustered and comparative analysis of any combination of six apicomplexa species is implemented, such as interspecies comparisons regarding protein motifs (InterPro), predicted subcellular localization signals (PSORT), transmembrane regions (SOSUI) or upstream promoter elements. By specifying keywords and other search conditions, Comparasite retrieves putative counterpart gene groups containing a given feature in common or in a species-specific manner. By enabling multi-faceted comparative analyses of genes of apicomplexa protozoa, monophyletic organisms that have evolved to diversify to parasitize various hosts by adopting complex life cycles, Comparasite should help elucidate the mechanism behind parasitism. Our full-length cDNA databases and Comparasite are accessible from http://fullmal.ims.u-tokyo.ac.jp.

Animals↗
PubMed2006

Cloning and characterization of protease inhibitor-like cDNAs from the Hessian fly mayetiola destructor (SAY).

Analysis of transcriptomes from the salivary glands and midgut of Hessian fly larvae Mayetiola destructor (say) identified a set of diverse cDNAs that encode proteins with a relatively high percentage (over 10%) of cysteinyl residues. Structural comparison of these putative proteins with known sequences in GenBank revealed that the positions of the cysteinyl residues in the identified proteins were highly conserved within a family of proteinase inhibitors despite very little overall sequence similarity. Phylogenetic analysis sorted this set of cDNAs into five different groups. To determine if these cDNAs indeed encode proteinase inhibitors, recombinant proteins were generated with two cDNAs from two different groups. Biochemical analysis of the recombinant proteins against commercial and insect gut proteinases demonstrated that the recombinant proteins are strong proteinase inhibitors with different specificities. Northern blot and real-time PCR analysis revealed that the different genes were expressed at different developmental stages and in different tissues. The overall results indicated that M. destructor contains a complex of genes that code for proteinase inhibitors which may regulate proteinase activities in different regulatory pathways. The GenBank accession numbers for the cDNAs in this paper were DQ232690 to DQ232718.

Amino Acid Sequence↗
PubMed2025

Genomic and stress resistance characterization of Lactiplantibacillus plantarum GX17, a potential probiotic for animal feed applications.

UNLABELLED: Lactobacilli, recognized as beneficial bacteria within the human body, are celebrated for their multifaceted probiotic functions, including the regulation of intestinal flora, enhancement of body immunity, and promotion of nutrient absorption. This study comprehensively analyzed the genotypic and phenotypic characteristics of Lactiplantibacillus plantarum (L. plantarum) strains isolated from the intestines of healthy chicks and assessed their potential as probiotics. The assembled genome consists of 29,521,986 bp, and a total of 1,771 coding sequences (CDSs) were predicted. Based on the entire genome sequence analysis, 50 stress resistance genes and seven virulence factors were identified. The results of the phenotypic experiments showed that the strain had good resistance to high temperature, low temperature, acid, alkali, salt, artificial gastrointestinal fluid, and strong antioxidant capacity. Additionally, transcriptomic analysis confirmed that under stress conditions, the expression levels of key genes were significantly upregulated. Therefore, the phenotypic characteristics of L. plantarum GX17 align well with its genotypic features, demonstrating promising probiotic properties. This strain holds great potential as a probiotic candidate, and further investigation into its beneficial effects on human health is warranted. IMPORTANCE: In humans, Lactiplantibacillus plantarum may synergize with host microbiota to ameliorate dysbiosis-related pathologies, enhance immunomodulation, and facilitate micronutrient bioavailability. For livestock, its application could improve feed conversion ratios, suppress enteric pathogens through competitive exclusion, and mitigate antibiotic overuse, "a critical strategy in One Health frameworks." Further investigations into strain-specific mechanisms (e.g., postbiotic metabolites, quorum sensing regulation) are warranted to translate these genomic-phenotypic advantages into sustainable health solutions across species.

Probiotics↗
PubMed2005

Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals.

BACKGROUND: The expression of gene batteries, genomic units of functionally linked genes which are activated by similar sets of cis- and trans-acting regulators, has been proposed as a major determinant of cell specialization in metazoans. We developed a predictive procedure to screen the mouse and human genomes and transcriptomes for cases of gene-battery-like regulation. RESULTS: In a screen that covered approximately 40 percent of all annotated protein-coding genes, we identified 21 co-expressed gene clusters with statistically supported sharing of cis-regulatory sequence elements. 66 predicted cases of over-represented transcription factor binding motifs were validated against the literature and fell into three categories: (i) previously described cases of gene battery-like regulation, (ii) previously unreported cases of gene battery-like regulation with some support in a limited number of genes, and (iii) predicted cases that currently lack experimental support. The novel predictions include for example Sox 17 and RFX transcription factor binding sites that were detected in approximately 10% of all testis specific genes, and HNF-1 and 4 binding sites that were detected in approximately 30% of all kidney specific genes respectively. The results are publicly available at http://www.wlab.gu.se/lindahl/genebatteries. CONCLUSION: 21 co-expressed gene clusters were enriched for a total of 66 shared cis-regulatory sequence elements. A majority of these predictions represent novel cases of potential co-regulation of functionally coupled proteins. Critical technical parameters were evaluated, and the results and the methods provide a valuable resource for future experimental design.

Amino Acid Motifs↗
PubMed2004

Preparation of planar retinal specimens: verification by histology, mRNA profiling, and proteome analysis.

PURPOSE: Elucidation of the transcriptome and proteome of the normal retina will be difficult since it is comprised of at least 55 different cell types. However the characteristic layered cellular anatomy of the retina makes it amenable to planar sectioning, enabling the generation of enriched retinal cell populations. The aim of this study was to validate a reproducible method for preparing enriched retinal layers from porcine retina. METHODS: The thicknesses of the retinal photoreceptor, inner nuclear and ganglion cell, and fiber layers were determined by routine histology of cross sections of fresh whole retina mounted on polyvinylidene difluoride (PVDF) membrane. Dissected retina (5 mm2) was placed on PVDF membrane and a series of planar cryosections corresponding to the photoreceptor and inner nuclear layer were removed leaving the ganglion cell and fiber layer which was subsequently detached from the membrane. The retinal specimens were stored at -80 degrees C. Representative planar tissue sections were sonicated in ice-chilled 40 mM ammonium bicarbonate pH 7.9 and aliquots removed for RNA extraction. Quantitative RT-PCR was used to analyze the mRNA expression of genes indicative of specific retinal layers. Ammonium bicarbonate protein extracts were centrifuged, lyophilized and prepared for direct liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis using a Waters Q-Tof Ultima. RESULTS: Histological analysis established the parameters for planar cryosectioning: photoreceptor layer (69+/-1.8 microm), outer plexiform (11+/-0.6 microm), inner nuclear layer (28+/-0.5 microm), inner plexiform, ganglion cell and fiber layer (100+/-5.3 microm). Gene expression profiling provided an independent method for validating the respective retinal preparations. For example, glial fibrillary acidic protein (GFAP) was expressed up to 21 fold higher in the inner retinal "ganglion cell enriched" fraction than in the outer retinal "photoreceptor enriched" fraction. The pattern was reversed for blue cone opsin, which was expressed up to 24 fold higher in the "photoreceptor enriched" fraction. Endogenous protein fragments indicative of each layer were identified by mass spectrometry and de novo sequence data obtained. CONCLUSIONS: Combined histological and mRNA expression profiling has confirmed the development of a reproducible method for generating validated porcine retinal layers enriched for specific cell types. Direct proteome analysis detected endogenous peptide fragments of characteristic retinal proteins. Further analysis of these enriched retinal cell preparations will facilitate a more selective investigation of the retinal transcriptome and proteome than studies of the intact retina.

Anatomy, Cross-Sectional↗
PubMed2006

Endogenous retrovirus-related sequences provide an alternative transcript of MCJ genes in human tissues and cancer cells.

The MCJ gene is a member of the DNAJ family, and its transcriptional event is controlled by methylation of the CpG island. In our study, we found LTR33 and LTR7 elements provided an alternative transcript within the MCJ gene. To detect different expression patterns between the originally reported MCJ transcript and the LTR-related transcript, we performed a RT-PCR approach using various human tissues and cancer cells. The original MCJ transcript was detected in human tissues and cancer cells, whereas the LTR-related transcript was only revealed in some cancer cells (HCT106, MCF-3, TE-1, Hela, and CCHM). We also performed a PCR analysis to compare the insertion lineage of the LTR elements with the genomic DNAs of primates, indicating that those LTR33 and LTR7 elements of HERV-H have been integrated into the primate genome at different times. Taken together, we suggest that HERV-related elements trigger transcriptome diversification during primate evolution.

Base Sequence↗