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Results for “expression atlas”

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PubMed2002

Analysis of gene expression in genetic epilepsy-prone rat using a cDNA expression array.

UNLABELLED: Our aim is to search the differential expression genes of genetic epilepsy and establish the groundwork of exploring the pathogenesis of epilepsy on the gene level by using cDNA array technology. METHODS: Gene expression profiles of the cerebral cortex of genetic epilepsy-prone P77PMC rats and normal Wistar rats were established using the Atlas Rat cDNA Expression Array. The difference between gene expression profiles was analyzed using an image analysis instrument. RESULTS: Fifteen genes exhibited a differential expression pattern between the P77PMC rats' and Wistar rats' cerebral cortex, while there maybe many other differential expression genes undiscovered due to having no image analysis software. Among them, the levels of expression of 13 genes were elevated in P77PMC rats as compared to their levels in Wistar rats, in contrast, the levels of expression of two genes were decreased in P77PMC rats. CONCLUSION: There were several differential expression genes between P77PMC rats and Wistar rats. All these genes could play important roles in the pathogenesis of epilepsy.

Animals↗

PubMed2004

GEPIS--quantitative gene expression profiling in normal and cancer tissues.

MOTIVATION: Expression profiling in diverse tissues is fundamental to understanding gene function as well as therapeutic target identification. The vast collection of expressed sequence tags (ESTs) and the associated tissue source information provides an attractive opportunity for studying gene expression. RESULTS: To facilitate EST-based expression analysis, we developed GEPIS (gene expression profiling in silico), a tool that integrates EST and tissue source information to compute gene expression patterns in a large panel of normal and tumor samples. We found EST-based expression patterns to be consistent with published papers as well as our own experimental results. We also built a GEPIS Regional Atlas that depicts expression characteristics of all genes in a selected genomic region. This program can be adapted for large-scale screening for genes with desirable expression patterns, as illustrated by our large-scale mining for tissue- and tumor-specific genes. AVAILABILITY: The email server version of the GEPIS application is freely available at http://share.gene.com/share/gepis. An interactive version of GEPIS will soon be freely available at http://www.cgl.ucsf.edu/Research/genentech/gepis/. The source code, modules, data and gene lists can be downloaded at http://share.gene.com/share/gepis.

Algorithms↗

PubMed2003

Different testicular gene expression patterns in the first spermatogenic cycle of postnatal and vitamin A-deficient rat testis.

Spermatogenesis is a complicated process of germ cell differentiation, involving programmatic expression of diverse cell type- and developmental stage-specific genes. To date, the vitamin-A-deficiency (VAD) rats and postnatal rats are two models commonly used to study spermatogenesis. In the present study, we studied the expression of 1185 known genes in the vitamin-A-deficient and retinol-reinitiated spermatogenesis of rat testis using Clontech Atlas rat cDNA expression arrays. The mRNA expression patterns of post-vitamin-A (PVA) testis on Days 15 and 35 were compared with those of the spermatogenic arrested rat testis on Day 0. About 9% (110/1185) of the genes studied were highly expressed. When compared with VAD rat testis on Day 0, 20 and 31 genes were differentially expressed by a factor of twofold or greater on Days 15 and 35, respectively. Four genes (cytochrome P450 17, sulfated glycoprotein 2, protein kinase inhibitor, and cathepsin L) that play important roles in spermatogenesis were selected and their gene expression patterns were confirmed by semiquantitative reverse transcription-polymerase chain reaction. Comparison of the expression patterns of these genes between PVA-VAD and postnatal rat testis in developmentally matched stages revealed substantial differences during the early stages of spermatogenesis. This discrepancy could be caused by either the presence of arrested but mature somatic cells in the PVA-VAD testis that may contribute to a unique gene expression pattern in this model or the direct effect of retinol on spermatogenesis. Therefore, caution is needed in interpreting the gene expression data using the PVA-VAD and postnatal rat models in studying spermatogenesis in rat testes.

Animals↗

PubMed2002

Changes in WT1 splicing are associated with a specific gene expression profile in Wilms' tumour.

Wilms' tumour (WT) or nephroblastoma is the most frequent kidney cancer in children. In a previous study, we reported alterations to WT1 transcription in 90% of WT tested, with decreased exon 5 +/- isoform ratio being the most frequent alteration (56% of WT). We now report an approach based on cDNA profiling of tumour pools to identify genes likely to be dysregulated in association with a decreased WT1 exon 5 +/- ratio. We compared the expression profiles of pools of tumours classified according to whether this isoform imbalance was present (five tumours) or not (four tumours), using Atlas Cancer cDNA expression arrays. Fourteen of 588 genes tested displayed specific up-regulation (CCND2, PCNA, N-MYC, E2F3, TOP2A, PAK1, DCC and PCDH2) or down-regulation (VEGF, IGFBP5, TIMP3, ARHB, C-FOS and CD9) in the pool of tumours with decreased exon 5 +/- ratio. These results were validated by RT-PCR analysis of four genes (CCND2, PCNA, VEGF and IGFBP5). We extended the analysis of VEGF expression to 51 tumours by real-time RT-PCR and ascertained differential expression of this gene associated with WT1 expression pattern. Moreover, our results suggest that the VEGF expression level may be of prognosis relevance for relapsed patients.

Alternative Splicing↗

PubMed2000

Gene expression profiles of human endometrial cancer samples using a cDNA-expression array technique: assessment of an analysis method.

The recently developed cDNA expression array technique can be used to generate gene-expression fingerprints of tumour specimens. To gain insight into molecular mechanisms involved in the development and progression of cancer, this cDNA expression array technique could be a useful tool, however, no established methods for interpreting the results are yet available. We used the Atlas cancer cDNA expression array (Clontech, USA) for analysing total RNA isolated from four human endometrial carcinoma samples (two cell-lines and two tissue samples), one benign endometrial tissue sample and a human breast cancer cell-line, in order to develop a method for analysing the array data. The obtained gene-expression profiles were highly reproducible. XY-scatterplots and regression analysis of the logarithmic transformed data provided a practical method to analyse the data without the need of preceding normalization. Three genes (Decorin, TIMP3 and Cyclin D1) were identified to be differentially expressed between the benign endometrial tissue sample and the endometrial carcinoma samples (tissue and cell-lines). These three genes may potentially be involved in cancer progression. A higher degree of similarity in gene-expression profile was found between the endometrial samples (tissue and cell-lines) than between the endometrial samples and the breast cancer cell-line, which is indicative for an endometrial tissue-specific gene-expression profile.

DNA, Complementary↗

PubMed2005

cDNA expression array analysis of gene expression in human hepatocarcinoma Hep3B cells induced by BNIPL-1.

Bcl-2/adenovirus E1B 19 kDa interacting protein 2 like-1 (BNIPL-1) is a novel human protein identified in our laboratory, which can interact with Bcl-2 and Cdc42GAP and induce apoptosis via the BNIP-2 and Cdc42GAP homology (BCH) domain. In the present study, we established the Hep3B-Tet-on stable cell line in which expression of BNIPL-1 can be induced by doxycycline. The cell proliferation activity assay showed that the overexpression of BNIPL-1 suppresses Hep3B cell growth in vitro. The differential expression profiles of 588 known genes from BNIPL-1-transfected Hep3B-Tet-on and vector control cells were determined using the Atlas human cDNA expression array. Fifteen genes were differentially expressed between these two cell lines, among which seven genes were up-regulated and eight genes were down-regulated by BINPL-1. Furthermore, the differential expression result was confirmed by semiquantitative RT-PCR. Among these differentially expressed genes, p16INK4, IL-12, TRAIL and the lymphotoxin beta gene involved in growth suppression or cell apoptosis were up-regulated, and PTEN involved in cell proliferation was down-regulated by BNIPL-1. These results suggest that BNIPL-1 might inhibit cell growth though cell cycle arrest and/or apoptotic cell death pathway(s).

Carcinoma, Hepatocellular↗

PubMed2004

Altered gene expression profiles of NIH3T3 cells regulated by human lung cancer associated gene CT120.

CT120, a novel membrane-associated gene implicated in lung carcinogenesis, was previously identified from chromosome 17p13.3 locus, a hot mutation spot involved in human malignancies. In the present study, we further determined that CT120 ectopic expression could promote cell proliferation activity of NIH3T3 cells using MTS assay, and monitored the downstream effects of CT120 in NIH3T3 cells with Atlas mouse cDNA expression arrays. Among 588 known genes, 133 genes were found to be upregulated or downregulated by CT120. Two major signaling pathways involved in cell proliferation, cell survival and anti-apoptosis were overexpressed and activated in response to CT120: One is the Raf/MEK/Erk signal cascades and the other is the PI3K/Akt signal cascades, suggesting that CT120 might contribute, at least in part, to the constitutively activation of Erk and Akt in human lung cancer cells. In addition, some tumor metastasis associated genes cathepsin B, cathepsin D, cathepsin L, MMP-2/TIMP-2 were also upregulated by CT120, upon which CT120 might be involved in tumor invasiveness and metastasis. In addition, CT120 might play an important role in tumor progression through modulating the expression of some candidate "Lung Tumor Progression" genes including B-Raf, Rab-2, BAX, BAG-1, YB-1, and Cdc42.

Animals↗

PubMed2005

Microarray analysis of altered gene expression in murine fibroblasts transformed by nickel(II) to nickel(II)-resistant malignant phenotype.

B200 cells are Ni(II)-transformed mouse BALB/c-3T3 fibroblasts displaying a malignant phenotype and increased resistance to Ni(II) toxicity. In an attempt to find genes whose expression has been altered by the transformation, the Atlas Mouse Stress/Toxicology cDNA Expression Array (Clontech Laboratories, Inc., Palo Alto, CA) was used to analyze the levels of gene expression in both parental and Ni(II)-transformed cells. Comparison of the results revealed a significant up- or downregulation of the expression of 62 of the 588 genes present in the array (approximately 10.5%) in B200 cells. These genes were assigned to different functional groups, including transcription factors and oncogenes (9/14; fractions in parentheses denote the number of up-regulated versus the total number of genes assigned to this group), stress and DNA damage response genes (11/12), growth factors and hormone receptors (6/9), metabolism (7/7), cell adhesion (2/7), cell cycle (3/6), apoptosis (3/4), and cell proliferation (2/3). Among those genes, overexpression of beta-catenin and its downstream targets c-myc and cyclin D1, together with upregulated cyclin G, points at the malignant character of B200 cells. While the increased expression of glutathione (GSH) synthetase, glutathione-S-transferase A4 (GSTA4), and glutathione-S-transferase theta (GSTT), together with high level of several genes responding to oxidative stress, suggests the enforcement of antioxidant defenses in Ni-transformed cells.

Animals↗

PubMed2000

DNA microarray analyses of genes regulated during the differentiation of embryonic stem cells.

Embryonic stem (ES) cells are derived from the inner cell mass of blastocysts, and in response to retinoic acid (RA) are induced to differentiate to form some of the first distinguishable cell types of early mammalian development. This makes ES cells an attractive model system for studying the initial developmental decisions that occur during embryogenesis and the molecular genetics and associated mechanisms underlying these decisions. Additionally, ES cells are of significant interest to those characterizing various gene functions utilizing transgenic and gene-targeting techniques. With the advent of DNA microarray technology, which allows for the study of expression patterns of a large number of genes simultaneously within a cell type, there is an efficient means of gaining critical insights to the expression, regulation, and function of genes involved in mammalian development for which information is not currently available. To this end, we have utilized Clontech's Atlas Mouse cDNA Expression Arrays to examine the expression of 588 known regulatory genes in D3 ES cells and their RA-induced differentiated progeny. We report that nearly 50% of the regulatory genes are expressed in D3 and/or D3-differentiated cells. Of these genes, the steady-state levels of 18 are down-regulated and 61 are up-regulated by a factor of 2.5-fold or greater. These changes in gene expression are highly reproducible and represent changes in the expression of a variety of molecular markers, including: transcription factors, growth factors and their receptors, cytoskeletal and extracellular matrix proteins, cell surface antigens, and intracellular signal transduction modulators and effectors.

Animals↗

PubMed2000

Bone morphogenetic protein 2 (BMP-2) induces sequential changes of Id gene expression in the breast cancer cell line MCF-7.

Bone morphogenetic proteins (BMPs) are involved in the development of various organs including the mammary gland. They are well-regulated and act in a time-, concentration- and cell-type-specific manner. We found that BMP-2 is expressed in primary breast tumor tissue samples and in breast cancer cell lines. Hybridization of labeled cDNA, obtained from the breast cancer cell line MCF-7, against the Atlas human cDNA expression array revealed differential gene expression depending on BMP-2 treatment. The most prominent changes were observed for the helix-loop-helix proteins Id-1, Id-2 and Id-3. Id-1 expression had increased severalfold after 4 h and was even higher after 24 h. Id-2 and Id-3 were more strongly induced after 4 h and showed no further significant change after 24 h. Analysis of cell-cycle distribution revealed a marked increase of the sub-G1 phase after 48 h in serum-deprived cells. In the presence of BMP-2 no change was observed over 48 h indicating that BMP-2 does not induce apoptosis. In addition, expression of caspase-3 was reduced in BMP-2-treated cells after 24 h. In summary, our results clearly indicate that BMP-2 is a susceptibility factor keeping the cells ready for the integration of various other signals for cell progression.

Bone Morphogenetic Protein 2↗

PubMed2026

Pan-cancer Bioinformatics Analysis Combined with Colon Cancer Experimental Validation: A Study on TMED3 as a Diagnostic and Prognostic Biomarker.

Transmembrane Emp24 Protein Transport Domain 3 (TMED3), a member of the p24 protein family, has been implicated in tumor proliferation, invasion, and migration. This study aimed to evaluate the expression patterns, prognostic significance, immune associations, and potential biological functions of TMED3 across multiple cancer types using pan-cancer bioinformatics analysis combined with immunohistochemical (IHC) validation in colon cancer. Multiomics datasets from The Cancer Genome Atlas, Genotype-Tissue Expression, UALCAN, Human Protein Atlas, and cBioPortal databases were analyzed to investigate TMED3 expression and genetic alterations in pan-cancer. Immunohistochemistry was performed to evaluate TMED3 protein expression in colon cancer tissues. Kaplan-Meier survival analysis and Cox regression analysis were used to assess the prognostic value of TMED3. Spearman correlation analysis was conducted to evaluate the associations of TMED3 with tumor mutational burden, microsatellite instability (MSI), immune cell infiltration, and immune checkpoints. Gene Set Enrichment Analysis was performed to investigate potential biological pathways associated with TMED3 in colon cancer. TMED3 expression was elevated in most tumor types and was associated with unfavorable overall survival and disease-specific survival in adrenocortical carcinoma, colon adenocarcinoma, and uveal melanoma. The greatest frequency of TMED3 genetic alterations was identified in mesothelioma, with amplification representing the predominant alteration type. In addition, TMED3 expression showed significant correlations with tumor mutational burden and microsatellite instability in kidney renal clear cell carcinoma, stomach adenocarcinoma, and uterine corpus endometrial carcinoma. TMED3 expression was also associated with immune infiltration and immune checkpoint expression in several tumors. IHC analysis demonstrated increased TMED3 expression in colon cancer tissues compared with normal colon tissues and showed an association with T stage. Functional enrichment analysis identified pathways related to ribosome, antigen processing and presentation, oxidative phosphorylation, and pentose phosphate. These findings indicate that TMED3 may represent a promising biomarker for the diagnosis and prognostic evaluation of colon cancer as well as other tumor types.

Humans↗

PubMed2026

Integrated multi-omics analysis and functional experiments reveals PPAP2C as a potential prognostic biomarker and therapeutic target in breast cancer.

BACKGROUND: This study aims to systematically elucidate the clinical significance and biological function of the phospholipid phosphatase (PLPP) family member (PPAP2C) phosphatidic acid phosphatase type 2C in breast cancer, and to evaluate its potential as a prognostic biomarker and therapeutic target. METHODS: Gene expression data from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), and Cancer Cell Line Encyclopedia (CCLE) databases were integrated to characterize the expression profile of PLPP family members, focusing on PPAP2C in breast cancer. The prognostic value of PPAP2C, initially identified at the mRNA level (TCGA, (METABRIC) Molecular Taxonomy of Breast Cancer International Consortium, Gene Expression Omnibus (GEO)), was confirmed at the protein level by immunohistochemistry (IHC) on tissue microarrays (TMA). The oncogenic functions of PPAP2C were investigated in triple-negative breast cancer (TNBC) cells through CRISPR-Cas9-mediated knockout and ectopic overexpression, with assessment of key phenotypes including proliferation, colony formation, migration, and invasion. In vivo validation was subsequently performed using an MDA-MB-231 xenograft model. RESULTS: PPAP2C exhibits the most significant overexpression pattern across 33 cancer types (upregulated in 16 cancers, downregulated in only 3). Compared with normal tissues, PPAP2C showed specific overexpression in breast cancer tissues and was significantly associated with advanced clinical stages and aggressive subtypes (HER2+ and TNBC). Survival analysis demonstrated that high PPAP2C expression correlated with significantly shorter overall survival and disease-free survival, which was further validated in METABRIC and GEO cohorts. Tissue microarray analysis confirmed higher PPAP2C protein positivity in tumor tissues (94.7%) than in adjacent normal tissues (59.7%), with worse OS and RFS in high-expression groups. Multivariate analysis identified PPAP2C as an independent prognostic factor for OS. Functional experiments revealed that PPAP2C knockout (via 5-bp/1-bp frameshift mutations) suppressed TNBC cell proliferation, colony formation, migration, and invasion, while overexpression enhanced these phenotypes. In vivo studies further demonstrated complete tumor regression in MDA-MB-231 xenografts upon PPAP2C knockout. CONCLUSION: This study identifies PPAP2C as a key oncogenic driver and a robust independent prognostic biomarker in breast cancer. The findings provide compelling evidence that PPAP2C represents a promising therapeutic target, offering a new strategic avenue for precision therapy, particularly for aggressive breast cancer subtypes.

PLPP2↗

PubMed2004

[The gene expression patterns of genetic P77PMC epilepsy-prone rats' hippocampus].

OBJECTIVE: To find out the differentially expressed genes in the hippocampus of the rats with genetic epilepsy so as to lay a foundation for exploring the pathogenesis of epilepsy by means of cDNA array technology. METHODS: Gene expression patterns in the hippocampus of the genetic epilepsy-prone P77PMC rats and normal Wistar rats were established using the alpha-32P-labeled cDNA probes hybridized with the Atlas Rat cDNA Expression Array, and then were analyzed by an image analysis instrument to get the differentially expressed genes. RESULTS: Fifteen genes were found having differential expression patterns in hippocampus between the P77PMC rats and the Wistar rats, while there may be many other differentially expressed genes left undiscovered due to having no appropriate image analysis software. And among the fifteen genes, the expression levels of twelve genes in the P77PMC rats were higher than those in the Wistar rats, while the expression levels of the other three genes were lower. The results of reverse transcription-polymerase chain reaction(RT-PCR) have demonstrated the reliability of cDNA arrays method. CONCLUSION: cDNA array is a powerful tool for identifying differential expression genes of epilepsy on large scales. There are several differentially expressed genes in hippocampus of the P77PMC rats and the Wistar rats. All these identified genes could play potentially important roles in the pathogenesis of epilepsy.

Animals↗

PubMed2004

Gene expression profiling of bone cells on smooth and rough titanium surfaces.

Titanium (Ti) and Ti alloys are widely used as dental and orthopaedic implants, but the effects of the surface characteristics of these materials on the response of cells and target tissues is not well understood. The present study has therefore examined the effects of a rough Ti (RT) and a smooth Ti (ST) surface on human bone cells in vitro. Scanning electron microscopy showed attachment and spreading of cells on both surfaces. Expression profiling using ATLAS gene arrays showed marked differences in gene responses after 3 h of culture. A number of osteoblast genes were identified as "roughness response" genes on the basis of changes in expression on the RT compared with the ST surfaces. The surface roughness of Ti was thus found to have a profound effect on the profile of genes expressed by the bone cells, and suggests that improvements in the biological activity and possibly the clinical efficacy of these materials could be achieved by selective regulation of gene expression mediated by controlled modification of Ti surface.

Adult↗

PubMed2004

Expression patterns of cell cycle and apoptosis-related genes in a multidrug-resistant human colon carcinoma cell line.

BACKGROUND: An in vitro multidrug resistance (MDR) system from a human colonic cancer cell line (SW620-MDR) has been established. To further study the mechanisms at molecular level and prevention of multidrug resistance in clinical practice, it was demonstrated that the expressions of several apoptosis-related and cell cycle regulator genes were changed in the cells. METHODS: A multidrug-resistant colonic cell line (SW620-MDR) was established, and the Atlas human cDNA expression array was used for studying the pattern of gene expression in this cell line. Furthermore, Northern hybridization or real-time PCR analysis confirmed the pattern of gene expression. RESULTS: In the SW620-MDR cell line the pro-apoptosis genes, CASP4, BIK, PDCD2, and TACE were expressed with decreased levels, and the antiapoptosis genes CD27-L and IGFBP2 were over-expressed. Furthermore, the cell cycle regulator genes such as CDK6, CCND1, CDC27HS, CDC16HS, Wee1Hu, MAPKK1, and IGFBP6 were expressed with decreased levels in the drug-resistant cell line. CONCLUSIONS: It is worthwhile investigating whether the differentially expressed pattern of the aforementioned genes exists in the drug-resistant cancer specimens, and to further understand their functions in the cancer drug-resistance mechanism.

Apoptosis↗

PubMed2026

Pan-cancer characterization of HMGA1 reveals its oncogenic role in tumor microenvironment and stemness: functional validation in pancreatic cancer migration and invasion.

BACKGROUND: HMGA1 is a chromatin-associated oncogenic factor implicated in tumor progression, epithelial-mesenchymal transition (EMT), stemness, and metastasis. However, its pan-cancer expression and prognostic patterns, epigenetic activation, and relationship with malignant-cell stemness/plasticity and tumor microenvironment (TME) remodeling in pancreatic adenocarcinoma (PAAD) remain incompletely defined. This study aimed to systematically characterize HMGA1 across cancers and clarify its clinical and biological relevance in PAAD. METHODS: Pan-cancer transcriptomic, clinical, genetic, methylation, immune, and stemness data were integrated from multiple public databases. PAAD single-cell RNA sequencing data were analyzed to localize HMGA1 expression, infer malignant-cell pseudotime, calculate a stemness module score, and assess ligand-receptor communication using CellChat. Public HMGA1-knockdown RNA sequencing data were reanalyzed to evaluate transcriptional remodeling. The Cancer Genome Atlas (TCGA)-PAAD expression and methylation data were used to assess TME-remodeling, immune-suppression, stemness/plasticity, cytokine/chemokine, checkpoint, and promoter-methylation features. HMGA1 expression and function were further examined using immunohistochemistry (IHC), quantitative real-time polymerase chain reaction, Western blotting, wound-healing assays, and Transwell migration and invasion assays. RESULTS: HMGA1 was upregulated in most tumor types, and high expression was associated with unfavorable survival in multiple cancers, including PAAD. In PAAD, HMGA1 was enriched in malignant epithelial cells and positively correlated with pseudotime (Spearman's rho =0.594), while the stemness module score increased along pseudotime (rho =0.748). HMGA1-high malignant cells showed markedly stronger CellChat-inferred outgoing communication, predominantly involving extracellular matrix (ECM)-receptor, adhesion-related, and selected immunomodulatory ligand-receptor axes. HMGA1 knockdown was associated with broad remodeling of EMT, TGF-β, Hedgehog, IL6/JAK/STAT3, KRAS, and cancer stem cell/stemness-related programs rather than uniform suppression of these programs. HMGA1 promoter methylation was inversely correlated with HMGA1 expression (rho =-0.633) and the TME-remodeling score (rho =-0.347). HMGA1 was associated with selected mediators, including PPIA, PLAU, ANXA1, LGALS9, TGFB1, CD276, and CD47, but not with a generalized checkpoint-high phenotype. Functionally, HMGA1 knockdown significantly reduced pancreatic cancer (PC) cell migration and invasion. CONCLUSIONS: These findings support an association-based model in which promoter hypomethylation-associated HMGA1 activation is linked to malignant epithelial stemness/plasticity, ECM/adhesion-dominant TME remodeling, selected immunomodulatory programs, and aggressive PAAD phenotypes. Further mechanistic and clinical validation is required before HMGA1 can be used for therapeutic stratification or immunotherapy-response prediction.

HMGA1↗

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↗

PubMed2026

Integrative pan-cancer analysis of transferrin reveals context-dependent prognostic associations and links to immune and metabolic disease-related programs.

BACKGROUND: Iron metabolism is closely linked to tumor biology, yet the pan-cancer significance of transferrin (TF), the major circulating iron-transport protein, remains insufficiently defined. Although TF has been implicated in cancer-related processes, its prognostic relevance, immune associations, and broader disease-related transcriptional context have not been systematically characterized across tumor types. OBJECTIVE: This study aimed to perform an integrative pan-cancer analysis of TF to characterize its expression patterns, clinical associations, immune context, pathway features, and pharmacogenomic correlations, and to explore whether TF-related signals extend to selected metabolic and chronic organ injury settings. METHODS: We used multiple public databases, including The Cancer Genome Atlas (TCGA), Human Protein Atlas (HPA), Gene Expression Omnibus (GEO), and Cancer Cell Line Encyclopedia (CCLE), to integrate transcriptomic, proteomic, and clinical data across 33 tumor types and selected non-malignant conditions. TF expression was evaluated across normal tissues, tumors, and cell lines, followed by survival analysis, immune infiltration analysis, TMB/MSI and methylation assessment, pathway enrichment, and drug-response correlation. Independent GEO cohorts of non-alcoholic steatohepatitis (NASH), heart failure (HF), and liver cirrhosis (LC) were used for cross-disease extension. Selected findings were further explored in OA/PA-treated hepatocytes, 786-O renal carcinoma cells, and AC16 cardiomyocytes. RESULTS: TF showed pronounced tissue specificity and cancer-type-dependent dysregulation. Across pan-cancer cohorts, the most consistent adverse survival associations were observed in kidney renal clear cell carcinoma (KIRC) and stomach adenocarcinoma (STAD), where TF remained associated with overall survival (OS) in multivariable analyses. TF expression was also correlated with cancer-type-specific immune infiltration patterns and selected drug-response profiles. Across independent NASH, HF, and LC datasets, TF expression was elevated and TF-associated pathways partially overlapped with those observed in cancer. In vitro experiments provided preliminary support that TF modulation is associated with proliferative phenotypes in KIRC cells and stress- and metabolism-related phenotypes in hepatocyte and cardiomyocyte models. CONCLUSION: These findings support TF as a context-dependent biomarker candidate in cancer, with the most consistent prognostic relevance observed in KIRC and STAD. Rather than establishing a unified mechanism across diseases, this study provides an integrative framework suggesting that TF is associated with malignant behavior, immune context, and selected metabolic stress-related programs, and warrants further mechanistic investigation.

Iron metabolism↗