High throughput gene expression profiling: a molecular approach to integrative physiology

The role of nanomedicine and artificial intelligence in cancer health care: individual applications and emerging integrations-a narrative review

Cancer remains one of the deadliest diseases globally, significantly impacting patients' quality of life. Addressing the rising incidence of cancer deaths necessitates innovative approaches such as nanomedicine and artificial intelligence (AI). The convergence of nanomedicine and AI represents a transformative frontier in cancer healthcare, promising unprecedented advancements in diagnosis, treatment, and patient management. This narrative review explores the distinct applications of nanomedicine and AI in oncology, alongside their synergistic potential. Nanomedicine leverages nanoparticles for targeted drug delivery, enhancing therapeutic efficacy while minimizing adverse effects. Concurrently, AI algorithms facilitate early cancer detection, personalized treatment planning, and predictive analytics, thereby optimizing clinical outcomes. Emerging integrations of these technologies could transform cancer care by facilitating precise, personalized, and adaptive treatment strategies. This review synthesizes current research, highlights innovative individual applications, and discusses the emerging integrations of nanomedicine and AI in oncology. The goal is to provide a comprehensive understanding of how these cutting-edge technologies can collaboratively improve cancer diagnosis, treatment, and patient prognosis.

A Decade in a Systematic Review: The Evolution and Impact of Cell Painting

High-content image-based assays have fueled significant discoveries in the life sciences in the past decade (2013-2023), including novel insights into disease etiology, mechanism of action, new therapeutics, and toxicology predictions. Here, we systematically review the substantial methodological advancements and applications of Cell Painting. Advancements include improvements in the Cell Painting protocol, assay adaptations for different types of perturbations and applications, and improved methodologies for feature extraction, quality control, and batch effect correction. Moreover, machine learning methods recently surpassed classical approaches in their ability to extract biologically useful information from Cell Painting images. Cell Painting data have been used alone or in combination with other - omics data to decipher the mechanism of action of a compound, its toxicity profile, and many other biological effects. Overall, key methodological advances have expanded Cell Painting's ability to capture cellular responses to various perturbations. Future advances will likely lie in advancing computational and experimental techniques, developing new publicly available datasets, and integrating them with other high-content data types.

A Decade in a Systematic Review: The Evolution and Impact of Cell Painting

High-content image-based assays have fueled significant discoveries in the life sciences in the past decade (2013-2023), including novel insights into disease etiology, mechanism of action, new therapeutics, and toxicology predictions. Here, we systematically review the substantial methodological advancements and applications of Cell Painting. Advancements include improvements in the Cell Painting protocol, assay adaptations for different types of perturbations and applications, and improved methodologies for feature extraction, quality control, and batch effect correction. Moreover, machine learning methods recently surpassed classical approaches in their ability to extract biologically useful information from Cell Painting images. Cell Painting data have been used alone or in combination with other -omics data to decipher the mechanism of action of a compound, its toxicity profile, and many other biological effects. Overall, key methodological advances have expanded Cell Painting's ability to capture cellular responses to various perturbations. Future advances will likely lie in advancing computational and experimental techniques, developing new publicly available datasets, and integrating them with other high-content data types.

Molecular and epigenetic mechanisms governing ocular surface squamous neoplasia: opportunities for diagnostics

INTRODUCTION

Ocular surface squamous neoplasia (OSSN) is the most common ocular malignancy; the pathophysiology is influenced by molecular, genetic, and epigenetic mechanisms. The incidence of OSSN is associated with the anatomy and physiology of the ocular surface, limbal stem cell configuration, limbal vulnerability, cancer stem cells, dysplasia, neoplasia, angiogenesis, invasion, and metastasis. The key etiological factors involved are human papillomavirus (HPV), human immunodeficiency virus (HIV), immunosuppression, p53 tumor suppressor gene, hypovitaminosis A, and failure of Deoxyribonucleic acid (DNA) repair mechanisms.

AREAS COVERED

This special report is a focussed attempt to understand the molecular mechanism, genetic and epigenetic mechanism, and diagnostic modalities for OSSN.

EXPERT OPINION

While these mechanisms contribute to genome instability, promoter-specific hypermethylation might facilitate and promote tumor formation by silencing tumor suppressor genes. OSSN understanding has improved with increased literature available on various genetic, molecular, and epigenetic mechanisms, although the exact genetic and epigenetic mechanisms still need to be elucidated. It is important to note that the molecular mechanisms of OSSN can vary among individuals, and further research is required to elucidate the underlying processes fully. Understanding these mechanisms is crucial for the development of targeted therapies and improved management of OSSN.

Gene network profiling in muscle-invasive bladder cancer: A systematic review and meta-analysis

BACKGROUND

Determining meta-analysis of transcriptional profiling of muscle-invasive bladder cancer (MIBC) through Gene Expression Omnibus (GEO) datasets has not been investigated. This study aims to define gene expression profiles in MIBC and to identify potential candidate genes and pathways.

OBJECTIVES

To review and evaluate gene expression studies in MIBC through publicly available RNA sequencing (RNA-Seq) and microarray data in order to identify potential prognostic and therapeutic targets for MIBC.

METHODS

A systematic literature search of the Ovid MEDLINE, PubMed, and Wiley Cochrane Central Register of Controlled Trials databases was performed using the terms "gene," "gene expression," and "bladder cancer" January 1, 1990 through March 2021 focused on populations with MIBC.

RESULTS

In the final analysis, GEO datasets were included. Fixed effect model was employed in the meta-analysis. Gene networking connections and gene-set functional analyses of the identified genes as differentially expressed in MIBC were performed using ImaGEO and GeneMANIA software. A heatmap for the upregulated and downregulated genes was generated along with the correlated pathways.

CONCLUSION

A total of 9 genes were reported in this analysis. Six genes were reported as upregulated (ProTα, SPINT1, UBE2E1, RAB25, KPNB1, HDAC1) and 3 genes as downregulated (NUP188, IPO13, NUP124). Genes were found to be involved in "ubiquitin mediated proteolysis," "protein processing in endoplasmic reticulum," "transcriptional misregulation in cancer," and "RNA transport" pathways.

Gene Interaction Network Analysis Reveals IFI44L as a Drug Target in Rheumatoid Arthritis and Periodontitis

Simple Summary

In spite of substantial investigation, the biological link between periodontitis and rheumatoid arthritis remains unexplained. This study intended to correlate periodontitis and rheumatoid arthritis gene expression patterns to find shared targets for both the disease. We identified the differentially expressed genes (DEGs) in periodontitis and rheumatoid arthritis. The network was built by integrating DEGs and ranking the genes using GeneMANIA. FINDSITEcomb2.0 was used to find a possible inhibitor for the top-ranked gene. Further, the binding effectiveness and protein-ligand complex stability were then determined by molecular docking and molecular dynamics. The network analysis showed IFI44L as a highly ranking gene implicated in most immunological pathways. A virtual screening of 6507 compounds revealed vemurafenib as the best candidate for the IFI44L target. Molecular docking and molecular dynamics modelling revealed the stability of the IFI44L-vemurafenib complex, which suggest IFI44L is potential target and vemurafenib could be the better candidate to treat both diseases.

Abstract

Objective: Despite extensive research on periodontitis and rheumatoid arthritis, the underlying molecular connectivity between these condition remains largely unknown. This research aimed to integrate periodontitis and rheumatoid arthritis gene expression profiles to identify interconnecting genes and focus to develop a common lead molecule against these inflammatory conditions. Materials and Methods: Differentially expressed genes (DEGs) of periodontitis and rheumatoid arthritis were identified from the datasets retrieved from the Gene Expression Omnibus database. The network was constructed by merging DEGs, and the interconnecting genes were identified and ranked using GeneMANIA. For the selected top ranked gene, the potential inhibitor was searched using FINDSITE^comb2.0. Subsequently, the molecular docking and molecular dynamics were performed to determine the binding efficiency and protein-ligand complex stability, respectively. Results: From the network analysis, IFN-induced protein 44-like (IFI44L) was identified as a top ranked gene involved in most of the immunological pathway. With further virtual screening of 6507 molecules, vemurafenib was identified to be the best fit against the IFI44L target. The binding energy and stability of IFI44L with vemurafenib were investigated using molecular docking and molecular dynamics simulation. Docking results show binding energy of −7.7 Kcal/mol, and the simulation results show stability till 100 ns. Conclusions: The identified IFI44L may represent a common drug target for periodontitis and rheumatoid arthritis. Vemurafenib could be a potent anti-inflammatory drug for both diseases.

Identification of Candidate Biomarkers for Idiopathic Thrombocytopenic Purpura by Bioinformatics Analysis of Microarray Data

Idiopathic Thrombocytopenic Purpura (ITP) is a multifactorial disease with decreased count of platelet that can lead to bruising and bleeding manifestations. This study was intended to identify critical genes associated with chronic ITP. The gene expression profile GSE46922 was downloaded from the Gene Expression Omnibus database to recognize Differentially Expressed Genes (DEGs) by R software. Gene ontology and pathway analyses were performed by DAVID. The biological network was constructed using the Cytoscape. Molecular Complex Detection (MCODE) was applied for detecting module analysis. Transcription factors were identified by the PANTHER classification system database and the gene regulatory network was constructed by Cytoscape. One hundred thirty-two DEGs were screened from comparison newly diagnosed ITP than chronic ITP. Biological process analysis revealed that the DEGs were enriched in terms of positive regulation of autophagy and prohibiting apoptosis in the chronic phase. KEGG pathway analysis showed that the DEGs were enriched in the ErbB signaling pathway, mRNA surveillance pathway, Estrogen signaling pathway, and Notch signaling pathway. Additionally, the biological network was established, and five modules were extracted from the network. ARRB1, VIM, SF1, BUB3, GRK5, and RHOG were detected as hub genes that also belonged to the modules. SF1 also was identified as a hub-TF gene. To sum up, microarray data analysis could perform a panel of genes that provides new clues for diagnosing chronic ITP.

Expression of the ZIP/SLC39A transporters in β-cells: a systematic review and integration of multiple datasets

BACKGROUND

Pancreatic β-cells require a constant supply of zinc to maintain normal insulin secretory function. Following co-exocytosis with insulin, zinc is replenished via the Zrt- and Irt-like (ZIP; SLC39A) family of transporters. However the ZIP paralogues of particular importance for zinc uptake, and associations with β-cell function and Type 2 Diabetes remain largely unexplored. We retrieved and statistically analysed publically available microarray and RNA-seq datasets to perform a systematic review on the expression of β-cell SLC39A paralogues. We complemented results with experimental data on expression profiling of human islets and mouse β-cell derived MIN6 cells, and compared transcriptomic and proteomic sequence conservation between human, mouse and rat.

RESULTS

The 14 ZIP paralogues have 73-98% amino sequence conservation between human and rodents. We identified 18 datasets for β-cell SLC39A analysis, which compared relative expression to non-β-cells, and expression in response to PDX-1 activity, cytokines, glucose and type 2 diabetic status. Published expression data demonstrate enrichment of transcripts for ZIP7 and ZIP9 transporters within rodent β-cells and of ZIP6, ZIP7 and ZIP14 within human β-cells, with ZIP1 most differentially expressed in response to cytokines and PDX-1 within rodent, and ZIP6 in response to diabetic status in human and glucose in rat. Our qPCR expression profiling data indicate that SLC39A6, -9, -13, and - 14 are the highest expressed paralogues in human β-cells and Slc39a6 and -7 in MIN6 cells.

CONCLUSIONS

Our systematic review, expression profiling and sequence alignment reveal similarities and potentially important differences in ZIP complements between human and rodent β-cells. We identify ZIP6, ZIP7, ZIP9, ZIP13 and ZIP14 in human and rodent and ZIP1 in rodent as potentially biologically important for β-cell zinc trafficking. We propose ZIP6 and ZIP7 are key functional orthologues in human and rodent β-cells and highlight these zinc importers as important targets for exploring associations between zinc status and normal physiology of β-cells and their decline in Type 2 Diabetes.

Characterization of the kidney transcriptome of the long-haired mouse Abrothrix hirta (Rodentia, Sigmodontinae) and comparison with that of the olive mouse A. olivacea

To understand how small mammals cope with the challenge of water homeostasis is a matter of interest for ecologists and evolutionary biologists. Here we take a step towards the understanding of the transcriptomic functional response of kidney using as a model the long-haired mouse (Abrothrix hirta) a species that distributes across Patagonian steppes and Austral temperate rainforests in Argentina and Chile. Specifically, we i) characterize the renal transcriptome of A. hirta, and ii) compare it with that-already available-of the co-generic and co-distributed A. olivacea. Renal mRNA transcripts from 16 specimens of A. hirta from natural populations were analyzed. Over 500 million Illumina paired-end reads were assembled de novo under two approaches, an individual assembly for each specimen, and a single in-silico normalized joint assembly including all reads from all specimens. The total number of annotated genes was similar with both strategies: an average of 14,956 in individual assemblies and 14,410 in the joint assembly. Overall, 15,463 distinct genes express in the kidney of A. hirta. Transcriptomes of A. hirta and A. olivacea were similar in terms of gene abundance and composition: 95.6% of the genes of A. hirta were also found in A. olivacea making their functional profiles also similar. However, differences in the transcriptome of these two species were observed in the set of highly expressed genes, in terms of private genes for each species and the functional profiles of highly expressed genes. As part of the novel transcriptome characterization, we provide distinct gene lists with their functional annotation that would constitute the basis for further research on these or any other species of the subfamily Sigmodontinae, which includes about 400 living species distributed from Tierra del Fuego to southern United States.

High-throughput gene expression profiling of opioid-induced alterations in discrete brain areas

Whole-genome screening methods are unique approach to search for novel genes and molecular pathways involved in drug action. High-throughput profiling allows the gene expression levels of tens of thousands of transcripts to be measured simultaneously. Here, we describe transcriptional profiling in a specific area of the brain using DNA microarrays and next-generation sequencing.

Epigenomics of hypertension

Multiple genes and pathways are involved in the pathogenesis of hypertension. Epigenomic studies of hypertension are beginning to emerge and hold great promise of providing novel insights into the mechanisms underlying hypertension. Epigenetic marks or mediators including DNA methylation, histone modifications, and noncoding RNA can be studied at a genome or near-genome scale using epigenomic approaches. At the single gene level, several studies have identified changes in epigenetic modifications in genes expressed in the kidney that correlate with the development of hypertension. Systematic analysis and integration of epigenetic marks at the genome-wide scale, demonstration of cellular and physiological roles of specific epigenetic modifications, and investigation of inheritance are among the major challenges and opportunities for future epigenomic and epigenetic studies of hypertension.

Differential changes in TGF-β/BMP signaling pathway in the right ventricular myocardium of newborns with hypoplastic left heart syndrome

BACKGROUND

Hypoplastic left heart syndrome (HLHS) is characterized by underdevelopment of the left ventricle (LV) and increased biomechanical stress on the right ventricle (RV) from single ventricle physiology. Despite the clinical significance, the signaling pathways active during RV remodeling and disease progression are not known. To address this, we examined differential changes in expression of genes associated with transforming growth factor-beta (TGF-beta)/bone morphogenetic protein (BMP) signaling in RV tissue isolated from HLHS patients relative to RV and LV tissue from control subjects.

METHODS AND RESULTS

Quantitative real-time polymerase chain reaction was used to detect changes in expression of 84 genes involved in TGF-beta/BMP-mediated cardiac development, cell growth, and differentiation in RV tissue collected from 6 neonates with HLHS undergoing stage 1 Norwood procedure (age, 1-7 days; mean, 4 days) and RV and LV tissue obtained from 5 infants with noncardiac pathology (age range, 1-135 days: mean, 85 days) that served as controls. Analysis of gene expression profiles between control-LV and control-RV revealed significant depression of TGF-beta/BMP signaling in RV compared with LV. Of the 84 genes analyzed, 38 were differentially expressed between HLHS-RV and control-RV, whereas only 22 compared with control-LV. Significant changes were observed in: tissue remodeling genes including Activin receptor type IIA (ACVR2A) (+2.13) and Activin receptor-like kinase 1 (ACVRL1) (+2.22); and cell survival, growth, and differentiation genes including CDC25A (+2.18), p21 (-3.64), p15 (+2.15), BMP5 (+4.58), BMP3 (+2.16), GDF3 (+8.59), NODAL (+2.32), and BMP binding endothelial regulator (BMPER) (+4.58). The most significant changes common to HLHS-RV versus control-RV and control-LV sample groups is observed for Anti müllerian hormone receptor 2 (AMHR2) (+18.79 control-RV, +3.38 control-LV), and the BMP antagonist Inhibin alpha (INHA) (+11.47 control-RV, +5.73 control-LV).

CONCLUSIONS

Although this descriptive study does not allow cause-effect inferences, our results suggest changes in cardiac development pathways and upregulation of genes associated with cell growth and differentiation in the neonatal RV of children with HLHS. These molecular profiles are more closely related to those observed in the normal LV rather than normal RV at similar maturational age. This work provides the basis for future mechanistic studies to elucidate the molecular mechanisms regulating RV remodeling in HLHS.

MicroRNA: a new frontier in kidney and blood pressure research

MicroRNA (miRNA) has emerged rapidly as a major new direction in many fields of research including kidney and blood pressure research. A mammalian genome encodes several hundred miRNAs. These miRNAs potentially regulate the expression of thousands of proteins. miRNA expression profiles differ substantially between the kidney and other organs as well as between kidney regions. miRNAs may be functionally important in models of diabetic nephropathy, podocyte development, and polycystic disease. miRNAs may be involved in the regulation of arterial blood pressure, including possible involvement in genetic elements of hypertension. Studies of miRNAs could generate diagnostic biomarkers for kidney disease and new mechanistic insights into the complex regulatory networks underlying kidney disease and hypertension. Further progress in the understanding of miRNA biogenesis and action and technical improvements for target identification and miRNA manipulation will be important for studying miRNAs in renal function and blood pressure regulation.

Reuse of cDNA microarrays hybridized with cRNA by stripping with RNase H

DNA microarrays are powerful tools for global analysis of gene transcript expression. However, their high cost and the need for replication have limited their use. Here, we report a new stripping technique applicable to microarrays hybridized with cRNA with RNase H that is reproducible, leaving the DNA oligonucleotide probes intact and available for adding two additional uses. A Pearson correlation was used to assess the agreement between the first-round hybridization and the second- and third-round hybridizations. Significant correlations (R2, 0.9893 and 0.975; P < 0.001) were observed among virgin arrays and stripped arrays hybridized with the same sample. Additionally, statistical class comparison analysis globally indicated that there were essentially no differences detected following three hybridizations. Dye-swapped microarrays produced similar results. However, arrays stripped with RNase H exhibited decreased efficiency of hybridization signal with increasing use. In the present study, the oligonucleotide microarrays can be used three times.

Renal medullary 11 beta-hydroxysteroid dehydrogenase type 1 in Dahl salt-sensitive hypertension

The Dahl salt-sensitive rat is a widely used model of human salt-sensitive forms of hypertension. The kidney plays an important role in the pathogenesis of Dahl salt-sensitive hypertension, but the molecular mechanisms involved remain a subject of intensive investigation. Gene expression profiling studies suggested that 11 beta-hydroxysteroid dehydrogenase type 1 might be dysregulated in the renal medulla of Dahl salt-sensitive rats. Additional analysis confirmed that renal medullary expression of 11 beta-hydroxysteroid dehydrogenase type 1 was downregulated by a high-salt diet in SS-13BN rats, a consomic rat strain with reduced blood pressure salt sensitivity, but not in Dahl salt-sensitive rats. 11 beta-Hydroxysteroid dehydrogenase type 1 is known to convert inactive 11-dehydrocorticosterone to active corticosterone. The urinary corticosterone/11-dehydrocorticosterone ratio as well as urinary excretion of corticosterone was higher in Dahl salt-sensitive rats than in SS-13BN rats. Knockdown of renal medullary 11 beta-hydroxysteroid dehydrogenase type 1 with small-interfering RNA attenuated the early phase of salt-induced hypertension in Dahl salt-sensitive rats and reduced urinary excretion of corticosterone. Knockdown of 11 beta-hydroxysteroid dehydrogenase type 1 did not affect blood pressure in SS-13BN rats. Long-term attenuation of salt-induced hypertension was achieved with small hairpin RNA targeting renal medullary 11 beta-hydroxysteroid dehydrogenase type 1. In summary, we have demonstrated that suppression of 11 beta-hydroxysteroid dehydrogenase type 1 expression in the renal medulla attenuates salt-induced hypertension in Dahl salt-sensitive rats.

High perfusion pressure accelerates renal injury in salt-sensitive hypertension

Renal injury in the Dahl salt-sensitive rat mimics human salt-sensitive forms of hypertension that are particularly prevalent in black individuals, but the mechanisms that lead to the development of this injury are incompletely understood. We studied the impact of renal perfusion pressure (RPP) on the development of renal injury in this model. During the development of salt-induced hypertension over 2 wk, the RPP to the left kidney was maintained at control levels (125 +/- 2 mmHg) by continuous servocontrol inflation of an aortic balloon implanted between the renal arteries; during the same period, the RPP to the right kidney rose to 164 +/- 8 mmHg. After 2 wk of a 4% salt diet, DNA microarray and real-time PCR identified genes related to fibrosis and epithelial-to-mesenchymal transition in the kidneys exposed to hypertension. The increased RPP to the right kidney accounted for differences in renal injury between the two kidneys, measured by percentage of injured cortical and juxtamedullary glomeruli, quantified proteinaceous casts, number of ED-1-positive cells per glomerular tuft area, and interstitial fibrosis. Interlobular arteriolar injury was not increased in the kidney exposed to elevated pressure but was reduced in the control kidney. We conclude that elevations of RPP contribute significantly to the fibrosis and epithelial-to-mesenchymal transition found in the early phases of hypertension in the salt-sensitive rat.

Renal regional proteomes in young Dahl salt-sensitive rats

We performed an extensive proteomic analysis of the Dahl model of salt-sensitive hypertension. The consomic SS-13(BN) rat, genetically similar to the Dahl salt-sensitive rat, while exhibiting a significant amelioration of salt-induced hypertension, was used as a control. Proteomic analysis, using differential in-gel electrophoresis and mass spectrometry techniques, was performed in the renal cortex and the renal medulla of 6-week-old SS and SS-13(BN) rats before significant differences in blood pressure were developed between the 2 strains of rat. Several dozen proteins were identified as differentially expressed between SS and SS-13(BN) rats fed the 0.4% NaCl diet or switched to the 4% NaCl diet for 3 days (n=4). The identified proteins were involved in cellular functions or structures including signal transduction, energy metabolism, and the cytoskeleton. The proteomic analysis and subsequent Western blotting indicated that heterogeneous nuclear ribonucleoprotein K in the renal medulla was upregulated by the 4% NaCl diet in SS-13(BN) rats but downregulated in SS rats. The level of angiotensinogen mRNA in the renal medulla was regulated in an opposite manner. Silencing of heterogeneous nuclear ribonucleoprotein K resulted in an upregulation of angiotensinogen in cultured human kidney cells. In summary, we identified significant differences in kidney regional proteomic profiles between SS and SS-13(BN) rats and demonstrated a potential role of heterogeneous nuclear ribonucleoprotein K in the regulation of angiotensinogen expression in the renal medulla.

From the genome sequence to the proteome and back: evaluation of E. coli genome annotation with a 2-D gel-based proteomics approach

The ambition of systems biology to understand complex biological systems at the molecular level implies that we need to have a concrete and correct understanding of each molecular entity and its function. However, even for the best-studied organism, Escherichia coli, a large number of proteins have never been identified and characterised from wild-type cells, and/or await unravelling of their biological role. Instead, the ORF models for these proteins have been predicted by suitable algorithms and/or through comparison with known, homologous proteins from other organisms, approaches which may be prone to error. In the present study, we used a combination of 2-DE, MALDI-TOF-MS and PMF to identify 1151 different proteins in E. coli K12 JM109. Comparison of the experimental with the theoretical Mr and pI values (4000 experimental values each) allowed the identification of numerous proteins with incorrect or incomplete ORF annotations in the current E. coli genome databases. Several inconsistencies in genome annotation were verified experimentally, and up to 55 candidates await further investigation. Our findings demonstrate how an up-to-date 2-D gel-based proteomics approach can be used for improving the annotation of prokaryotic genomes. They also highlight the need for harmonization among the different E. coli genome databases.

Integrative pathway knowledge bases as a tool for systems molecular medicine

There exists a sense of urgency to begin to generate a cohesive assembly of biomedical knowledge as the pace of knowledge accumulation accelerates. The urgency is in part driven by the emergence of systems molecular medicine that emphasizes the combination of systems analysis and molecular dissection in the future of medical practice and research. A potentially powerful approach is to build integrative pathway knowledge bases that link organ systems function with molecules.

Gene expression microarrays and respiratory muscles

The routine measurement of the expression of tens of thousands of gene transcripts, simultaneously, is a defining advance of the last decade which has been made possible by microarray technology. Using this very powerful approach, a pattern has emerged from a number of studies that suggest a molecular niche for the diaphragm which is quite different from that occupied by limb muscle. All indications are that this is true not only in regard to differential gene transcription patterns in healthy muscles but also in the changes in transcription occurring in association with different diseases. Furthermore, respiratory muscle mounts a rich gene expression response to a number of disturbances, be they primary genetic defects (e.g. various types of muscular dystrophies) or non-genetic perturbations (e.g. controlled mechanical ventilation). Large numbers of genes undergo altered levels of transcription, ranging from tens to hundreds (typical) to thousands. These genes are involved in diverse cellular processes, such as contraction, intermediate metabolism, oxidative stress, apoptosis and cellular adhesion. Functional groups of genes identified as having changed expression differ in many respects from one disease to another. Previously identified pathways of muscle injury and repair are often perturbed to greater extents than previously anticipated, and processes not previously suspected of having important roles in the pathophysiology of specific disorders have been identified. Elucidation of these under-appreciated molecular events may lead to novel therapeutic interventions based on disrupting the downstream adverse consequences of the primary event or facilitating events which ameliorate the injury and/or promote muscle healing.

The genetic dissection of essential hypertension

QTL mapping in humans and rats has identified hundreds of blood-pressure-related phenotypes and genomic regions; the next daunting task is gene identification and validation. The development of novel rat model systems that mimic many elements of the human disease, coupled with advances in the genomic and informatic infrastructure for rats, promise to revolutionize the hunt for genes that determine susceptibility to hypertension. Furthermore, methods are evolving that should enable the identification of candidate genes in human populations. Together with the computational reconstruction of regulatory networks, these methods provide opportunities to significantly advance our understanding of the underlying aetiology of hypertension.

Physiological oxygenation status is required for fully differentiated phenotype in kidney cortex proximal tubules

Hypoxia has been suspected to trigger transdifferentiation of renal tubular cells into myofibroblasts in an epithelial-to-mesenchymal transition (EMT) process. To determine the functional networks potentially altered by hypoxia, rat renal tubule suspensions were incubated under three conditions of oxygenation ranging from normoxia (lactate uptake) to severe hypoxia (lactate production). Transcriptome changes after 4 h were analyzed on a high scale by restriction fragment differential display. Among 1,533 transcripts found, 42% were maximally expressed under severe hypoxia and 8% under mild hypoxia (Po2 = 48 mmHg), suggesting two different levels of oxygen sensing. Normoxia was required for full expression of the proximal tubule-specific transcripts 25-hydroxyvitamin D 1-hydroxylase ( Cyp27b1) and l-pyruvate kinase ( Pklr), transcripts involved in tissue cohesion such as fibronectin ( Fn1) and N-cadherin ( Cdh2), and non-muscle-type myosin transcripts. Mild hypoxia increased myogenin transcript level. Conversely, severe hypoxia increased transcripts involved in extracellular matrix remodeling, those of muscle-type myosins, and others involved in creatine phosphate synthesis and lactate transport ( Slc16a7). Accordingly, microscopy showed loss of tubule aggregation under hypoxia, without tubular disruption. Hypoxia also increased the levels of kidney-specific transcripts normally restricted to the less oxygenated medullary zone and others specific for the distal part of the nephron. We conclude that extensive oxygen supply to the kidney tubule favors expression of its differentiated functions specifically in the proximal tubule, whose embryonic origin is mesenchymal. The phenotype changes could potentially permit transient adaptation to hypoxia but also favor pathological processes such as tissue invasion.

Post-genomic approaches to understanding the mechanisms of environmentally induced phenotypic plasticity

Post-genomic techniques offer new and detailed insights into the mechanisms underpinning all biological processes, including phenotypic plasticity and environmentally relevant phenotypes. Although they require access to genomic resources it is now possible to create these for species of comparative or environmental interest even within a modest research project. Here we describe an open transcript screen for genes responding to environmental cold that might account for the acquired cold-specific phenotype in all its complex manifestations. Construction of a cDNA microarray led to a survey of transcript expression levels in seven tissues of carp, as a function of time,and three different extents of cooling. The resulting data delineated a common stress response found in all tissues that comprises genes involved in cellular homeostasis, including energy charge, ATP turnover, protein turnover and stress protein production. These genes respond to kinds of perturbation other than cold and probably form part of a more general stress response common to other species. We also defined tissue-specific response patterns of transcript regulation whose main characteristics were investigated by a profiling technique based on categorisation of gene function. These genes underpin the highly tissue-specific pattern of physiological adaptations observed in the cold-acclimated fish. As a result we have identified a large number of candidate gene targets with which to investigate adaptive responses to environmental challenge.

Hypertension, kidney, and transgenics: a fresh perspective

In this review, we outline the application and contribution of transgenic technology to establishing the genetic basis of blood pressure regulation and its dysfunction. Apart from a small number of examples where high blood pressure is the result of single gene mutation, essential hypertension is the sum of interactions between multiple environmental and genetic factors. Candidate genes can be identified by a variety of means including linkage analysis, quantitative trait locus analysis, association studies, and genome-wide scans. To test the validity of candidate genes, it is valuable to model hypertension in laboratory animals. Animal models generated through selective breeding strategies are often complex, and the underlying mechanism of hypertension is not clear. A complementary strategy has been the use of transgenic technology. Here one gene can be selectively, tissue specifically, or developmentally overexpressed, knocked down, or knocked out. Although resulting phenotypes may still be complicated, the underlying genetic perturbation is a starting point for identifying interactions that lead to hypertension. We recognize that the development and maintenance of hypertension may involve many systems including the vascular, cardiac, and central nervous systems. However, given the central role of the kidney in normal and abnormal blood pressure regulation, we intend to limit our review to models with a broadly renal perspective.

Role of endothelial cell apoptosis in regulation of skeletal muscle angiogenesis during high and low salt intake

Angiogenesis, under normal conditions, is a tightly regulated balance between pro- and antiangiogenic factors. The goal of this study was to investigate the mechanisms involved in the control of the skeletal muscle angiogenic response induced by electrical stimulation during the suppression of plasma renin activity (PRA) with a high-salt diet. Rats fed 0.4% or 4% salt diets were exposed to electrical stimulation for 7 days. The tibialis anterior (TA) muscles from stimulated and unstimulated hindlimbs were removed and prepared for gene expression analysis, CD31-terminal deoxynucleotide transferase-mediated dUTP nick-end labeling (TUNEL) double-staining assay, and Bcl-2 and Bax protein expression by Western blot. Rats fed a low-salt diet showed a dramatic angiogenesis response in the stimulated limb compared with the unstimulated limb. This angiogenesis response was significantly attenuated when rats were placed on a high-salt diet. Microarray analysis showed that in the stimulated limb of rats fed a low-salt diet many genes related to angiogenesis were upregulated. In contrast, in rats fed a high-salt diet most of the genes upregulated in the stimulated limb function in apoptosis and cell cycle arrest. Endothelial cell apoptosis, as analyzed by CD31-TUNEL staining, increased by fourfold in the stimulated limb compared with the unstimulated limb. There was also a 48% decrease in the Bcl-2-to-Bax ratio in stimulated compared with unstimulated limbs of rats fed a high-salt diet, confirming severe apoptosis. This study suggests that the increase in endothelial cell apoptosis in TA muscle might contribute to the attenuation of angiogenesis response observed in rats fed a high-salt diet.

Microarray analysis of the differential effects of open and laparoscopic surgery on murine splenic T-cells

BACKGROUND

Surgical trauma depresses cell-mediated immunity of a duration and magnitude proportional to the degree of injury. However, the cellular mechanism underlying this effect is poorly understood. Microarrays were used to survey gene expression in murine splenic T-cells after pneumoperitoneum and laparotomy.

METHODS

C3H/HeJ mice were assigned randomly to undergo anesthesia alone, sham laparotomy, or CO(2) pneumoperitoneum and sacrificed 12 or 24 hours later. RNA was isolated from purified splenic T-cells and hybridized to Affymetrix oligonucleotide microarrays.

RESULTS

Relative to anesthesia, 116 genes after pneumoperitoneum and 398 genes after laparotomy showed a > or =2-fold change in expression at 12 hours. One hundred thirty-two genes after pneumoperitoneum and 157 genes after laparotomy met those criteria at 24 hours. Comparing surgical modalities, 177 genes were increased and 15 decreased > or =2-fold after laparotomy relative to pneumoperitoneum at 12 hours, compared with 44 and 5 genes respectively at 24 hours. Expression changes for 8 genes were validated by quantitative real-time polymerase chain reaction.

CONCLUSIONS

Laparotomy and pneumoperitoneum alter splenic T-cell gene expression, with the most extensive changes occurring 12 hours after laparotomy. This study is one of the first comprehensive genomic studies of the molecular effects of surgical manipulation on immune function. The genes identified are potential targets for modulating the immune response to surgery.

Transcriptional profiling of tissue plasticity: role of shifts in gene expression and technical limitations

Reprogramming of gene expression has been recognized as a main instructive modality for the adjustments of tissues to various kinds of stress. The recent application of gene expression profiling has provided a powerful tool to elucidate the molecular pathways underlying such tissue remodeling. However, the biological interpretations of expression profiling results critically depend on normalization of transcript signals to mRNA standards before statistical evaluation. A hypothesis is proposed whereby the “fluctuating nature” of gene expression represents an inherent limitation of the test system used to quantify RNA levels. Misinterpretation of gene expression data occurs when RNA quantities are normalized to a subset of mRNAs that are subject to strong regulation. The contention of contradictory biological outcomes using different RNA-normalization schemes is demonstrated in two models of skeletal muscle plasticity with data from custom-designed microarrays and biochemical and ultrastructural evidence for correspondingly altered RNA content and nucleolar activity. The prevalence of these biological constraints is underlined by a literature survey in different models of tissue plasticity with emphasis on the unique malleability of skeletal muscle. Finally, recommendations on the optimal experimental layout are given to control biological and technical variability in microarray and RT-PCR studies. It is proposed to approach normalization of transcript signals by measuring total RNA and DNA content per sample weight and by correcting for concurrently estimated endogenous standards such as major ribosomal RNAs and spiked RNA and DNA species. This allows for later conversion to diverse tissue-relevant references and should improve the physiological interpretations of phenotypic plasticity.

Transcriptome analysis and kidney research: Toward systems biology

An enormous amount of data has been generated in kidney research using transcriptome analysis techniques. In this review article, we first describe briefly the principles and major characteristics of several of these techniques. We then summarize the progress in kidney research that has been made by using transcriptome analysis, emphasizing the experience gained and the lessons learned. Several technical issues regarding DNA microarray are highlighted because of the rapidly increased use of this technology. It appears clear from this brief survey that transcriptome analysis is an effective and important tool for question-driven exploratory science. To further enhance the power of this and other high throughput, as well as conventional approaches, in future studies of the kidney, we propose a multidimensional systems biology paradigm that integrates investigation at multiple levels of biologic regulation toward the goal of achieving a global understanding of physiology and pathophysiology.

Biomarkers in molecular medicine: cancer detection and diagnosis

In spite of advances in diagnostics and therapeutics, cancer remains the second leading cause of death in the U.S. Successful cancer treatment depends not only on better therapies but also on improved methods to assess an individual's risk of developing cancer and to detect cancers at early stages when they can be more effectively treated. Current cancer diagnostic imaging methods are labor-intensive and expensive, especially for screening large asymptomatic populations. Effective screening strategies depend on methods that are noninvasive and detect cancers in their early stages of development. There is increasing interest and enthusiasm in molecular markers as tools for cancer detection and prognosis. It is hoped that newly discovered cancer biomarkers and advances in high-throughput technologies would revolutionize cancer therapies by improving cancer risk assessment, early detection, diagnosis, prognosis, and monitoring therapeutic response. These biomarkers will be used either as stand-alone tests or to complement existing imaging methods.

Tissue-specific transcriptome responses in rats with early streptozotocin-induced diabetes

The understanding of common and tissue-specific molecular alterations in diabetes, particularly at early stages, is limited and fragmental. In the present study, we systematically compared transcriptome responses in four important diabetic target tissues in rats with 2 wk of streptozotocin (STZ)-induced diabetes. At this stage of diabetes, the skeletal muscle exhibited the highest transcriptome sensitivity to the STZ treatment with nearly 17% of the transcriptome being altered (false discovery rate, 1.6%) compared with approximately 3% in the cardiac left ventricle, renal cortex, and retina. Similarity in transcriptome response among tissues was low, with the highest similarity being 2.2% between skeletal muscle and the left ventricle. Several biological processes or cellular components, such as lipid metabolism in the left ventricle and collagen in the renal cortex, were significantly overrepresented in the responsive genes than in the entire array. Particularly interesting cases of common or tissue-specific regulation included decorin and CD36, which were upregulated in several tissues, and serum/glucocorticoid-regulated kinase and four and a half LIM domains 2, which were upregulated only in the renal cortex. Further biochemical analyses indicated that the thiol and oxidative stress pathway was altered in a tissue-specific manner at several levels including transcript abundance, content of reduced thiols, and lipid peroxidation, providing an example of the potential biological relevance of tissue-specific transcript regulation. These results provided a transcriptome-wide view of the molecular alterations across several key tissues in early diabetes. It appears that both common pathways and, perhaps more importantly, tissue-specific mechanisms are involved in the adaptation to diabetes or the initiation of diabetic complications.

Neurogenomics: at the intersection of neurobiology and genome sciences

Neurogenomics is the study of how the genome as a whole contributes to the evolution, development, structure and function of the nervous system. It includes investigations of how genome products (transcriptomes and proteomes) vary in time and space. Neurogenomics differs markedly from the application of genome sciences to other systems, particularly in the spatial category, because anatomy and connectivity are paramount to our understanding of function in the nervous system. We focus here on some of the influences of genomics and its associated technologies on neuroscience. We discuss comparative genomics, gene expression atlases of the brain, network genetics and applications to behavioral phenotypes, and consider the culture, organization and funding of genome-scale projects.

Effect of high glucose on gene expression in mesangial cells: upregulation of the thiol pathway is an adaptational response

Pathological alterations in glomerular mesangial cells play a critical role in the development of diabetic nephropathy, the leading cause of end-stage renal disease. Molecular mechanisms mediating such alterations, however, remain to be fully understood. The present study first examined the effect of high glucose on the mRNA expression profile in rat mesangial cells using cDNA microarray. Based on variation-weighted criteria and with a false discovery rate of 4.3%, 459 of 17,664 cDNA elements examined were found to be upregulated and 151 downregulated by exposure to 25 mM d-glucose for 5 days. A large number of differentially expressed genes belonged to several functional categories, indicating high glucose had a profound effect on mesangial cell proliferation, protein synthesis, energy metabolism, and, somewhat unexpectedly, protein sorting and the cytoskeleton. Interestingly, several thiol antioxidative genes (glutathione peroxidase 1, peroxiredoxin 6, and thioredoxin 2) were found by microarray and confirmed by real-time PCR to be upregulated by high glucose. These changes suggested that the oxidative stress known to be induced in mesangial cells by high glucose might be buffered by upregulation of the thiol antioxidative pathway. Upregulation of thiol antioxidative genes also occurred in high-glucose-treated human mesangial cells and in glomeruli isolated from rats after 1 wk of streptozotocin-induced diabetes, but not in human proximal tubule cells. High glucose slightly increased lipid peroxidation and decreased the amount of reduced thiols in rat and human mesangial cells. Disruption of the thiol antioxidative pathway by two different thiol-oxidizing agents resulted in a three- to fivefold increase in high-glucose-induced lipid peroxidation. In summary, the present study provided a global view of the short-term effect of high glucose on mesangial cells at the level of mRNA expression and identified the upregulation of the thiol antioxidative pathway as an adaptational response of mesangial cells to high glucose.