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Aging is a universal and progressive process involving the deterioration of physiological functions and the accumulation of cellular damage. Gene regulation programs influence how phenotypes respond to environmental and intrinsic changes during aging. Although several factors, including sex, are known to impact this process, the underlying mechanisms remain incompletely understood. Here, we investigate the functional organization patterns of skeletal muscle genes across different sexes and ages using gene co-expression networks (GCNs) to explore their influence on aging. We constructed GCNs for three different age groups for male and female samples, analyzed topological similarities and differences, inferred significant associated processes for each network, and constructed null models to provide statistically robust results. We found that each network is topologically and functionally distinct, with young women having the most associated processes, likely due to reproductive tasks. The functional organization and modularity of genes decline with age, starting from middle age, potentially leading to age-related deterioration. Women maintain better gene functional organization throughout life compared to men, especially in processes like macroautophagy and sarcomere organization. The study suggests that the loss of gene co-expression could be a universal aging marker. This research offers insights into how gene organization changes with age and sex, providing a complementary method to analyze aging.
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Oil palm (Elaeis guineensis Jacq.) is a highly productive crop economically significant for food, cosmetics, and biofuels. Abiotic stresses such as low water availability, salt accumulation, and high temperatures severely impact oil palm growth, physiology, and yield by restricting water flux among soil, plants, and the environment. While drought stress's physiological and biochemical effects on oil palm have been extensively studied, the molecular mechanisms underlying drought stress tolerance remain unclear. Under water deficit conditions, this study investigates two commercial E. guineensis cultivars, IRHO 7001 and IRHO 2501. Water deficit adversely affected the physiology of both cultivars, with IRHO 2501 being more severely impacted. After several days of water deficit, there was a 40% reduction in photosynthetic rate (A) for IRHO 7001 and a 58% decrease in IRHO 2501. Further into the drought conditions, there was a 75% reduction in A for IRHO 7001 and a 91% drop in IRHO 2501. Both cultivars reacted to the drought stress conditions by closing stomata and reducing the transpiration rate. Despite these differences, no significant variations were observed between the cultivars in stomatal conductance, transpiration, or instantaneous leaf-level water use efficiency. This indicates that IRHO 7001 is more tolerant to drought stress than IRHO 2501. A differential gene expression and network analysis was conducted to elucidate the differential responses of the cultivars. The DESeq2 algorithm identified 502 differentially expressed genes (DEGs). The gene coexpression network for IRHO 7001 comprised 274 DEGs and 46 predicted HUB genes, whereas IRHO 2501's network included 249 DEGs and 3 HUB genes. RT-qPCR validation of 15 DEGs confirmed the RNA-Seq data. The transcriptomic profiles and gene coexpression network analysis revealed a set of DEGs and HUB genes associated with regulatory and transcriptional functions. Notably, the zinc finger protein ZAT11 and linoleate 13S-lipoxygenase 2-1 (LOX2.1) were overexpressed in IRHO 2501 but under-expressed in IRHO 7001. Additionally, phytohormone crosstalk was identified as a central component in the response and adaptation of oil palm to drought stress.
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Arecaceae , Secas , Regulação da Expressão Gênica de Plantas , Estresse Fisiológico , Transcriptoma , Estresse Fisiológico/genética , Arecaceae/genética , Arecaceae/fisiologia , Arecaceae/metabolismo , Perfilação da Expressão Gênica , Fotossíntese/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismoRESUMO
Breast cancer, characterized by its complexity and diversity, presents significant challenges in understanding its underlying biology. In this study, we employed gene co-expression network analysis to investigate the gene composition and functional patterns in breast cancer subtypes and normal breast tissue. Our objective was to elucidate the detailed immunological features distinguishing these tumors at the transcriptional level and to explore their implications for diagnosis and treatment. The analysis identified nine distinct gene module clusters, each representing unique transcriptional signatures within breast cancer subtypes and normal tissue. Interestingly, while some clusters exhibited high similarity in gene composition between normal tissue and certain subtypes, others showed lower similarity and shared traits. These clusters provided insights into the immune responses within breast cancer subtypes, revealing diverse immunological functions, including innate and adaptive immune responses. Our findings contribute to a deeper understanding of the molecular mechanisms underlying breast cancer subtypes and highlight their unique characteristics. The immunological signatures identified in this study hold potential implications for diagnostic and therapeutic strategies. Additionally, the network-based approach introduced herein presents a valuable framework for understanding the complexities of other diseases and elucidating their underlying biology.
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Neoplasias da Mama , Perfilação da Expressão Gênica , Regulação Neoplásica da Expressão Gênica , Redes Reguladoras de Genes , Inflamação , Humanos , Neoplasias da Mama/genética , Neoplasias da Mama/imunologia , Feminino , Inflamação/imunologia , Inflamação/genética , Transcriptoma , Biomarcadores Tumorais/genéticaRESUMO
This study investigated how gene expression is affected by dietary fatty acids (FA) by using pigs as a reliable model for studying human diseases that involve lipid metabolism. This includes changes in FA composition in the liver, blood serum parameters and overall metabolic pathways. RNA-Seq data from 32 pigs were analyzed using Weighted Gene Co-expression Network Analysis (WGCNA). Our aim was to identify changes in blood serum parameters and gene expression between diets containing 3% soybean oil (SOY3.0) and a standard pig production diet containing 1.5% soybean oil (SOY1.5). Significantly, both the SOY1.5 and SOY3.0 groups showed significant modules, with a higher number of co-expressed modules identified in the SOY3.0 group. Correlated modules and specific features were identified, including enriched terms and pathways such as the histone acetyltransferase complex, type I diabetes mellitus pathway, cholesterol metabolism, and metabolic pathways in SOY1.5, and pathways related to neurodegeneration and Alzheimer's disease in SOY3.0. The variation in co-expression observed for HDL in the groups analyzed suggests different regulatory patterns in response to the higher concentration of soybean oil. Key genes co-expressed with metabolic processes indicative of diseases such as Alzheimer's was also identified, as well as genes related to lipid transport and energy metabolism, including CCL5, PNISR, DEGS1. These findings are important for understanding the genetic and metabolic responses to dietary variation and contribute to the development of more precise nutritional strategies.
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In reproductive technologies, uncovering the molecular aspects of oocyte and embryo competence under different conditions is crucial for refining protocols and enhancing efficiency. RNA-seq generates high-throughput data and provides transcriptomes that can undergo additional computational analyses. This study presented the transcriptomic profiles of in vitro matured oocytes and blastocysts produced in vitro from buffalo crossbred (Bubalus bubalis), coupled with gene co-expression and module preservation analysis. Cumulus Oophorus Complexes, obtained from slaughterhouse-derived ovaries, were subjected to in vitro maturation to yield metaphase II oocytes (616) or followed in vitro fertilization and culture to yield blastocysts for sequencing (526). Oocyte maturation (72%, ±3.34 sd) and embryo development (21.3%, ±4.18 sd) rates were obtained from three in vitro embryo production routines following standard protocols. Sequencing of 410 metaphase II oocytes and 70 hatched blastocysts (grade 1 and 2) identified a total of 13,976 genes, with 62% being ubiquitously expressed (8,649). Among them, the differentially expressed genes (4,153) and the strongly variable genes with the higher expression (fold-change above 11) were highlighted in oocytes (BMP15, UCHL1, WEE1, NLRPs, KPNA7, ZP2, and ZP4) and blastocysts (APOA1, KRT18, ANXA2, S100A14, SLC34A2, PRSS8 and ANXA2) as representative indicators of molecular quality. Additionally, genes exclusively found in oocytes (224) and blastocysts (2,200) with specific biological functions were identified. Gene co-expression network and module preservation analysis revealed strong preservation of functional modules related to exosome components, steroid metabolism, cell proliferation, and morphogenesis. However, cell cycle and amino acid transport modules exhibited weak preservation, which may reflect differences in embryo development kinetics and the activation of cell signaling pathways between buffalo and bovine. This comprehensive transcriptomic profile serves as a valuable resource for assessing the molecular quality of buffalo oocytes and embryos in future in vitro embryo production assays.
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Cystic echinococcosis (CE) is a zoonotic disease caused by the tapeworm Echinococcus granulosus sensu lato (s.l). In the intermediate host, this disease is characterized by the growth of cysts in viscera such as liver and lungs, inside of which the parasite develops to the next infective stage known as protoscoleces. There are records that the infected viscera affect the development and morphology of E. granulosus s.l. protoscolex in hosts such as buffalo or humans. However, the molecular mechanisms that drive these differences remains unknown. Weighted gene co-expression network analysis (WGCNA) using a set of RNAseq data obtained from E. granulosus sensu stricto (s.s.) protoscoleces found in liver and lung cysts reveals 34 modules in protoscoleces of liver origin, of which 12 have differential co-expression from protoscoleces of lung origin. Three of these twelve modules contain hub genes related to immune evasion: tegument antigen, tegumental protein, ubiquitin hydrolase isozyme L3, COP9 signalosome complex subunit 3, tetraspanin CD9 antigen, and the methyl-CpG-binding protein Mbd2. Also, two of the twelve modules contain only hypothetical proteins with unknown orthology, which means that there are a group of unknown function proteins co-expressed inside the protoscolex of liver CE cyst origin. This is the first evidence of gene expression differences in protoscoleces from CE cysts found in different viscera, with co-expression networks that are exclusive to protoscoleces from liver CE cyst samples. This should be considered in the control strategies of CE, as intermediate hosts can harbor CE cysts in liver, lungs, or both organs simultaneously.
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Cistos , Equinococose , Echinococcus granulosus , Humanos , Animais , Echinococcus granulosus/genética , Evasão da Resposta Imune , Genótipo , Equinococose/genética , Equinococose/parasitologiaRESUMO
Bud Rot, caused by Phytophthora palmivora, is considered one of the main diseases affecting African oil palm (Elaeis guineensis). In this study, we investigated the in vitro molecular dynamics of the pathogen-host interaction by analyzing gene expression profiles from oil palm genotypes that were either susceptible or resistant to the disease. We observed distinct interactions of P. palmivora with resistant and susceptible oil palms through co-expression network analysis. When interacting with susceptible genotypes, P. palmivora exhibited upregulation of carbohydrate and sulfate transport genes. These genes demonstrated co-expression with apoplastic and cytoplasmic effectors, including cell wall degrading enzymes, elicitins, and RxLR motif effectors. The pathogen manipulated susceptible oil palm materials, exacerbating the response and compromising the phenylpropanoid pathway, ultimately leading to susceptibility. In contrast, resistant materials exhibited control over their response through putative Heat Shock Proteins (HSP) that maintained homeostasis between primary metabolism and biotic defense. Co-expressed genes related to flavonoids, WRKY transcripts, lectin-type receptors, and LRR receptors may play important roles in pathogen control. Overall, the study provides new knowledge of the molecular mechanisms underlying the interaction between E. guineensis and P. palmivora, which can contribute to controlling Bud Rot in oil palms and gives new insights into the interactions of P. palmivora with their hosts.
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Osteoporosis is a systemic bone disease characterized by low bone mineral density and bone microstructure damage, resulting in increased bone fragility and fracture risk. The present study aimed to identify key genes and functionally enriched pathways in osteoporotic patients. Weighted Gene Co-expression Network Analysis (WGCNA) was applied to microarray datasets of blood samples of osteoporotic patients from the Sao Paulo Ageing & Health [SPAH] study (26 osteoporotic samples and 31 normal samples) to construct co-expression networks and identify hub gene. The results showed that HDGF, AP2M1, DNAJC6, TMEM183B, MFSD2B, IGKV1-5, IGKV1-8, IGKV3-7, IGKV3D-11, and IGKV1D-42 are genes which were associated with the disease status of osteoporosis. Differentially expressed genes are enriched in proteasomal protein catabolic process, ubiquitin ligase complex, and ubiquitin-like protein transferase activity. Functional enrichment analysis demonstrated that genes in the tan module were enriched in immune-related functions, indicating that the immune system plays a critical role in osteoporosis. Validation assay demonstrated that the HDGF, AP2M1, TMEM183B, and MFSD2B levels were decreased in osteoporosis samples compared with healthy controls, while the levels of IGKV1-5, IGKV1-8, and IGKV1D-42 were increased in osteoporosis samples compared with healthy controls. In conclusion, our data identified and validated the association of HDGF, AP2M1, TMEM183B, MFSD2B, IGKV1-5, IGKV1-8, and IGKV1D-42 with osteoporosis in elderly women. These results suggest that these transcripts have potential clinical significance and may help to explain the molecular mechanisms and biological functions of osteoporosis.
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Perfilação da Expressão Gênica , Osteoporose , Humanos , Feminino , Idoso , Brasil , Perfilação da Expressão Gênica/métodos , Osteoporose/genética , Expressão GênicaRESUMO
Fungal pathogens can have devastating effects on global crop production, leading to annual economic losses ranging from 10% to 23%. In light of climate change-related challenges, researchers anticipate an increase in fungal infections as a result of shifting environmental conditions. However, plants have developed intricate molecular mechanisms for effective defense against fungal attacks. Understanding these mechanisms is essential to the development of new strategies for protecting crops from multiple fungi threats. Public omics databases provide valuable resources for research on plant-pathogen interactions; however, integrating data from different studies can be challenging due to experimental variation. In this study, we aimed to identify the core genes that defend against the pathogenic fungi Colletotrichum higginsianum and Botrytis cinerea in Arabidopsis thaliana. Using a custom framework to control batch effects and construct Gene Co-expression Networks in publicly available RNA-seq dataset from infected A. thaliana plants, we successfully identified a gene module that was responsive to both pathogens. We also performed gene annotation to reveal the roles of previously unknown protein-coding genes in plant defenses against fungal infections. This research demonstrates the potential of publicly available RNA-seq data for identifying the core genes involved in defending against multiple fungal pathogens.
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Proteínas de Arabidopsis , Arabidopsis , Micoses , Arabidopsis/genética , Arabidopsis/microbiologia , RNA-Seq , Proteínas de Arabidopsis/genética , Plantas/genéticaRESUMO
Tropical forage grasses, particularly those belonging to the Urochloa genus, play a crucial role in cattle production and serve as the main food source for animals in tropical and subtropical regions. The majority of these species are apomictic and tetraploid, highlighting the significance of U. ruziziensis, a sexual diploid species that can be tetraploidized for use in interspecific crosses with apomictic species. As a means to support breeding programs, our study investigates the feasibility of genome-wide family prediction in U. ruziziensis families to predict agronomic traits. Fifty half-sibling families were assessed for green matter yield, dry matter yield, regrowth capacity, leaf dry matter, and stem dry matter across different clippings established in contrasting seasons with varying available water capacity. Genotyping was performed using a genotyping-by-sequencing approach based on DNA samples from family pools. In addition to conventional genomic prediction methods, machine learning and feature selection algorithms were employed to reduce the necessary number of markers for prediction and enhance predictive accuracy across phenotypes. To explore the regulation of agronomic traits, our study evaluated the significance of selected markers for prediction using a tree-based approach, potentially linking these regions to quantitative trait loci (QTLs). In a multiomic approach, genes from the species transcriptome were mapped and correlated to those markers. A gene coexpression network was modeled with gene expression estimates from a diverse set of U. ruziziensis genotypes, enabling a comprehensive investigation of molecular mechanisms associated with these regions. The heritabilities of the evaluated traits ranged from 0.44 to 0.92. A total of 28,106 filtered SNPs were used to predict phenotypic measurements, achieving a mean predictive ability of 0.762. By employing feature selection techniques, we could reduce the dimensionality of SNP datasets, revealing potential genotype-phenotype associations. The functional annotation of genes near these markers revealed associations with auxin transport and biosynthesis of lignin, flavonol, and folic acid. Further exploration with the gene coexpression network uncovered associations with DNA metabolism, stress response, and circadian rhythm. These genes and regions represent important targets for expanding our understanding of the metabolic regulation of agronomic traits and offer valuable insights applicable to species breeding. Our work represents an innovative contribution to molecular breeding techniques for tropical forages, presenting a viable marker-assisted breeding approach and identifying target regions for future molecular studies on these agronomic traits.
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Breast cancer encompasses a diverse array of subtypes, each exhibiting distinct clinical characteristics and treatment responses. Unraveling the underlying regulatory mechanisms that govern gene expression patterns in these subtypes is essential for advancing our understanding of breast cancer biology. Gene co-expression networks (GCNs) help us identify groups of genes that work in coordination. Previous research has revealed a marked reduction in the interaction of genes located on different chromosomes within GCNs for breast cancer, as well as for lung, kidney, and hematopoietic cancers. However, the reasons behind why genes on the same chromosome often co-express remain unclear. In this study, we investigate the role of transcription factors in shaping gene co-expression networks within the four main breast cancer subtypes: Luminal A, Luminal B, HER2+, and Basal, along with normal breast tissue. We identify communities within each GCN and calculate the transcription factors that may regulate these communities, comparing the results across different phenotypes. Our findings indicate that, in general, regulatory behavior is to a large extent similar among breast cancer molecular subtypes and even in healthy networks. This suggests that transcription factor motif usage does not fully determine long-range co-expression patterns. Specific transcription factor motifs, such as CCGGAAG, appear frequently across all phenotypes, even involving multiple highly connected transcription factors. Additionally, certain transcription factors exhibit unique actions in specific subtypes but with limited influence. Our research demonstrates that the loss of inter-chromosomal co-expression is not solely attributable to transcription factor regulation. Although the exact mechanism responsible for this phenomenon remains elusive, this work contributes to a better understanding of gene expression regulatory programs in breast cancer.
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Neoplasias da Mama , Humanos , Feminino , Neoplasias da Mama/genética , Fatores de Transcrição/genética , Mama , Cromossomos , Regulação Neoplásica da Expressão GênicaRESUMO
Climate-change-induced temperature fluctuations pose a significant threat to crop production, particularly in the Southern Hemisphere. This study investigates the transcriptome and physiological responses of rapeseed to post-flowering temperature increases, providing valuable insights into the molecular mechanisms underlying rapeseed tolerance to heat stress. Two rapeseed genotypes, Lumen and Solar, were assessed under control and heat stress conditions in field experiments conducted in Valdivia, Chile. Results showed that seed yield and seed number were negatively affected by heat stress, with genotype-specific responses. Lumen exhibited an average of 9.3% seed yield reduction, whereas Solar showed a 28.7% reduction. RNA-seq analysis of siliques and seeds revealed tissue-specific responses to heat stress, with siliques being more sensitive to temperature stress. Hierarchical clustering analysis identified distinct gene clusters reflecting different aspects of heat stress adaptation in siliques, with a role for protein folding in maintaining silique development and seed quality under high-temperature conditions. In seeds, three distinct patterns of heat-responsive gene expression were observed, with genes involved in protein folding and response to heat showing genotype-specific expression. Gene coexpression network analysis revealed major modules for rapeseed yield and quality, as well as the trade-off between seed number and seed weight. Overall, this study contributes to understanding the molecular mechanisms underlying rapeseed tolerance to heat stress and can inform crop improvement strategies targeting yield optimization under changing environmental conditions.
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Brassica napus , Brassica rapa , Brassica napus/genética , Transcriptoma , Temperatura , Brassica rapa/genética , Genótipo , Sementes/metabolismoRESUMO
[This corrects the article DOI: 10.3389/fgene.2023.1209416.].
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The cognitive effects of nicotine are linked to persistent modifications in extended neural systems that regulate cognitive and emotional processes, and these changes occur during development. Additionally, acute stress has modulatory effects on cognition that involve broad neural systems and can be influenced by prior environmental challenges. The effects of nicotine and stress may be interconnected, leading to modifications in a network of shared brain substrates. Here, we explored the interaction between nicotine and stress by evaluating the effects of acute stress exposure in spatial memory retrieval for animals pretreated with nicotine during adolescence or adulthood. Adolescent (35 days old) and adult (70 days old) male Wistar rats were treated for 21 days with one daily subcutaneous injection of nicotine 0.14 mg/ml (free base). 30 days after the last injection, rats were trained in the Barnes maze and tested 24 h later, half the rats were tested under regular conditions, and half of them were exposed to 1 h of restraining stress before the retrieval test, and brain samples were collected and c-Fos immunopositive cells were stained. Prolonged nicotine withdrawal or acute stress improved spatial memory retrieval. Acute stress in nicotine pretreated adults impaired spatial memory retrieval. Nicotine exposure during early adulthood resulted in long-lasting brain adaptations that amplified emotional responses to acute stress after prolonged drug withdrawal.
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Nicotina , Síndrome de Abstinência a Substâncias , Ratos , Masculino , Animais , Nicotina/farmacologia , Memória Espacial , Ratos Wistar , Encéfalo/metabolismo , Síndrome de Abstinência a Substâncias/metabolismoRESUMO
Renal carcinomas are a group of malignant tumors often originating in the cells lining the small tubes in the kidney responsible for filtering waste from the blood and urine production. Kidney tumors arise from the uncontrolled growth of cells in the kidneys and are responsible for a large share of global cancer-related morbidity and mortality. Understanding the molecular mechanisms driving renal carcinoma progression results crucial for the development of targeted therapies leading to an improvement of patient outcomes. Epigenetic mechanisms such as DNA methylation are known factors underlying the development of several cancer types. There is solid experimental evidence of relevant biological functions modulated by methylation-related genes, associated with the progression of different carcinomas. Those mechanisms can often be associated to different epigenetic marks, such as DNA methylation sites or chromatin conformation patterns. Currently, there is no definitive method to establish clear relations between genetic and epigenetic factors that influence the progression of cancer. Here, we developed a data-driven method to find methylation-related genes, so we could find relevant bonds between gene co-expression and methylation-wide-genome regulation patterns able to drive biological processes during the progression of clear cell renal carcinoma (ccRC). With this approach, we found out genes such as ITK oncogene that appear hypomethylated during all four stages of ccRC progression and are strongly involved in immune response functions. Also, we found out relevant tumor suppressor genes such as RAB25 hypermethylated, thus potentially avoiding repressed functions in the AKT signaling pathway during the evolution of ccRC. Our results have relevant implications to further understand some epigenetic-genetic-affected roles underlying the progression of renal cancer.
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Neuroblastoma represents a neoplastic expansion of neural crest cells in the developing sympathetic nervous system and is childhood's most common extracranial solid tumor. The heterogeneity of gene expression in different types of cancer is well-documented, and genetic features of neuroblastoma have been described by classification, development stage, malignancy, and progression of tumors. Here, we aim to analyze RNA sequencing datasets, publicly available in the GDC data portal, of neuroblastoma tumor samples from various patients and compare them with normal adrenal gland tissue from the GTEx data portal to elucidate the gene expression profile and regulation networks they share. Our results from the differential expression, weighted correlation network, and functional enrichment analyses that we performed with the count data from neuroblastoma and standard normal gland samples indicate that the analysis of transcriptome data from 58 patients diagnosed with high-risk neuroblastoma shares the expression pattern of 104 genes. More importantly, our analyses identify the co-expression relationship and the role of these genes in multiple biological processes and signaling pathways strongly associated with this disease phenotype. Our approach proposes a group of genes and their biological functions to be further investigated as essential molecules and possible therapeutic targets of neuroblastoma regardless of the etiology of individual tumors.
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Fungal plant diseases are a major threat to food security worldwide. Current efforts to identify and list loci involved in different biological processes are more complicated than originally thought, even when complete genome assemblies are available. Despite numerous experimental and computational efforts to characterize gene functions in plants, about ~40% of protein-coding genes in the model plant Arabidopsis thaliana L. are still not categorized in the Gene Ontology (GO) Biological Process (BP) annotation. In non-model organisms, such as sunflower (Helianthus annuus L.), the number of BP term annotations is far fewer, ~22%. In the current study, we performed gene co-expression network analysis using eight terabytes of public transcriptome datasets and expression-based functional prediction to categorize and identify loci involved in the response to fungal pathogens. We were able to construct a reference gene network of healthy green tissue (GreenGCN) and a gene network of healthy and stressed root tissues (RootGCN). Both networks achieved robust, high-quality scores on the metrics of guilt-by-association and selective constraints versus gene connectivity. We were able to identify eight modules enriched in defense functions, of which two out of the three modules in the RootGCN were also conserved in the GreenGCN, suggesting similar defense-related expression patterns. We identified 16 WRKY genes involved in defense related functions and 65 previously uncharacterized loci now linked to defense response. In addition, we identified and classified 122 loci previously identified within QTLs or near candidate loci reported in GWAS studies of disease resistance in sunflower linked to defense response. All in all, we have implemented a valuable strategy to better describe genes within specific biological processes.
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This research elucidates the dynamic expression of expansin genes during the wheat grain (Triticum aestivum L.) development process using comprehensive meta-analysis and experimental validation. We leveraged RNA-seq data from multiple public databases, applying stringent criteria for selection, and identified 60,852 differentially expressed genes across developmental stages. From this pool, 28,558 DEGs were found to exhibit significant temporal regulation in at least two different datasets and were enriched for processes integral to grain development such as carbohydrate metabolism and cell wall organization. Notably, 30% of the 241 known expansin genes showed differential expression during grain growth. Hierarchical clustering and expression level analysis revealed temporal regulation and distinct contributions of expansin subfamilies during the early stages of grain development. Further analysis using co-expression networks underscored the significance of expansin genes, revealing their substantial co-expression with genes involved in cell wall modification. Finally, qPCR validation and grain morphological analysis under field conditions indicated a significant negative correlation between the expression of select expansin genes, and grain size and weight. This study illuminates the potential role of expansin genes in wheat grain development and provides new avenues for targeted genetic improvements in wheat.
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This perspective highlights the potential of individualized networks as a novel strategy for studying complex diseases through patient stratification, enabling advancements in precision medicine. We emphasize the impact of interpatient heterogeneity resulting from genetic and environmental factors and discuss how individualized networks improve our ability to develop treatments and enhance diagnostics. Integrating system biology, combining multimodal information such as genomic and clinical data has reached a tipping point, allowing the inference of biological networks at a single-individual resolution. This approach generates a specific biological network per sample, representing the individual from which the sample originated. The availability of individualized networks enables applications in personalized medicine, such as identifying malfunctions and selecting tailored treatments. In essence, reliable, individualized networks can expedite research progress in understanding drug response variability by modeling heterogeneity among individuals and enabling the personalized selection of pharmacological targets for treatment. Therefore, developing diverse and cost-effective approaches for generating these networks is crucial for widespread application in clinical services.
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BACKGROUND: The solubilization of aluminum ions (Al3+) that results from soil acidity (pH < 5.5) is a limiting factor in oil palm yield. Al can be uptaken by the plant roots affecting DNA replication and cell division and triggering root morphological alterations, nutrient and water deprivation. In different oil palm-producing countries, oil palm is planted in acidic soils, representing a challenge for achieving high productivity. Several studies have reported the morphological, physiological, and biochemical oil palm mechanisms in response to Al-stress. However, the molecular mechanisms are just partially understood. RESULTS: Differential gene expression and network analysis of four contrasting oil palm genotypes (IRHO 7001, CTR 3-0-12, CR 10-0-2, and CD 19 - 12) exposed to Al-stress helped to identify a set of genes and modules involved in oil palm early response to the metal. Networks including the ABA-independent transcription factors DREB1F and NAC and the calcium sensor Calmodulin-like (CML) that could induce the expression of internal detoxifying enzymes GRXC1, PER15, ROMT, ZSS1, BBI, and HS1 against Al-stress were identified. Also, some gene networks pinpoint the role of secondary metabolites like polyphenols, sesquiterpenoids, and antimicrobial components in reducing oxidative stress in oil palm seedlings. STOP1 expression could be the first step of the induction of common Al-response genes as an external detoxification mechanism mediated by ABA-dependent pathways. CONCLUSIONS: Twelve hub genes were validated in this study, supporting the reliability of the experimental design and network analysis. Differential expression analysis and systems biology approaches provide a better understanding of the molecular network mechanisms of the response to aluminum stress in oil palm roots. These findings settled a basis for further functional characterization of candidate genes associated with Al-stress in oil palm.