A signature of Neanderthal introgression on molecular mechanisms of environmental responses

Ancient human migrations led to the settlement of population groups in varied environmental contexts worldwide. The extent to which adaptation to local environments has shaped human genetic diversity is a longstanding question in human evolution. Recent studies have suggested that introgression of archaic alleles in the genome of modern humans may have contributed to adaptation to environmental pressures such as pathogen exposure. Functional genomic studies have demonstrated that variation in gene expression across individuals and in response to environmental perturbations is a main mechanism underlying complex trait variation. We considered gene expression response to in vitro treatments as a molecular phenotype to identify genes and regulatory variants that may have played an important role in adaptations to local environments. We investigated if Neanderthal introgression in the human genome may contribute to the transcriptional response to environmental perturbations. To this end we used eQTLs for genes differentially expressed in a panel of 52 cellular environments, resulting from 5 cell types and 26 treatments, including hormones, vitamins, drugs, and environmental contaminants. We found that SNPs with introgressed Neanderthal alleles (N-SNPs) disrupt binding of transcription factors important for environmental responses, including ionizing radiation and hypoxia, and for glucose metabolism. We identified an enrichment for N-SNPs among eQTLs for genes differentially expressed in response to 8 treatments, including glucocorticoids, caffeine, and vitamin D. Using Massively Parallel Reporter Assays (MPRA) data, we validated the regulatory function of 21 introgressed Neanderthal variants in the human genome, corresponding to 8 eQTLs regulating 15 genes that respond to environmental perturbations. These findings expand the set of environments where archaic introgression may have contributed to adaptations to local environments in modern humans and provide experimental validation for the regulatory function of introgressed variants.

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A signature of Neanderthal introgression on molecular mechanisms of environmental responses

10.1101/2021.03.15.435179 ◽

2021 ◽

Author(s):

Anthony Findley ◽

Xinjun Zhang ◽

Carly Boye ◽

Yen-Lung Lin ◽

Cynthia Kalita ◽

...

Keyword(s):

Gene Expression ◽

Human Genome ◽

Molecular Mechanisms ◽

Differentially Expressed ◽

Regulatory Function ◽

Modern Humans ◽

Gene Expression Response ◽

Environmental Perturbations ◽

Local Environments ◽

Environmental Responses

Ancient human migrations led to the settlement of population groups in varied environmental contexts worldwide. The extent to which adaptation to local environments has shaped human genetic diversity is a longstanding question in human evolution. Recent studies have suggested that introgression of archaic alleles in the genome of modern humans may have contributed to adaptation to environmental pressures such as pathogen exposure. Functional genomic studies have demonstrated that variation in gene expression across individuals and in response to environmental perturbations is a main mechanism underlying complex trait variation. We considered gene expression response to \emph{in vitro} treatments as a molecular phenotype to identify genes and regulatory variants that may have played an important role in adaptations to local environments. We investigated if Neanderthal introgression in the human genome may contribute to the transcriptional response to environmental perturbations. To this end we used eQTLs for genes differentially expressed in a panel of 52 cellular environments, resulting from 5 cell types and 26 treatments, including hormones, vitamins, drugs, and environmental contaminants. We found that SNPs with introgressed Neanderthal alleles (N-SNPs) disrupt binding of transcription factors important for environmental responses, including ionizing radiation and hypoxia, and for glucose metabolism. We identified an enrichment for N-SNPs among eQTLs for genes differentially expressed in response to 8 treatments, including glucocorticoids, caffeine, and vitamin D. Using Massively Parallel Reporter Assays (MPRA) data, we validated the regulatory function of 21 introgressed Neanderthal variants in the human genome, corresponding to 8 eQTLs regulating 15 genes that respond to environmental perturbations. These findings expand the set of environments where archaic introgression may have contributed to adaptations to local environments in modern humans and provide experimental validation for the regulatory function of introgressed variants.

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Impact of aging on gene expression response to x-ray irradiation using mouse blood

Scientific Reports ◽

10.1038/s41598-021-89682-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Constantinos G. Broustas ◽

Axel J. Duval ◽

Sally A. Amundson

Keyword(s):

Gene Expression ◽

Differentially Expressed Genes ◽

Differentially Expressed ◽

X Rays ◽

Gene Expression Response ◽

X Ray ◽

The Impact ◽

Old Mice ◽

Radiation Biodosimetry ◽

Young Mice

AbstractAs a radiation biodosimetry tool, gene expression profiling is being developed using mouse and human peripheral blood models. The impact of dose, dose-rate, and radiation quality has been studied with the goal of predicting radiological tissue injury. In this study, we determined the impact of aging on the gene expression profile of blood from mice exposed to radiation. Young (2 mo) and old (21 mo) male mice were irradiated with 4 Gy x-rays, total RNA was isolated from whole blood 24 h later, and subjected to whole genome microarray analysis. Pathway analysis of differentially expressed genes revealed young mice responded to x-ray exposure by significantly upregulating pathways involved in apoptosis and phagocytosis, a process that eliminates apoptotic cells and preserves tissue homeostasis. In contrast, the functional annotation of senescence was overrepresented among differentially expressed genes from irradiated old mice without enrichment of phagocytosis pathways. Pathways associated with hematologic malignancies were enriched in irradiated old mice compared with irradiated young mice. The fibroblast growth factor signaling pathway was underrepresented in older mice under basal conditions. Similarly, brain-related functions were underrepresented in unirradiated old mice. Thus, age-dependent gene expression differences should be considered when developing gene signatures for use in radiation biodosimetry.

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Insights into the seasonal adaptive mechanisms of Chinese alligators (Alligator sinensis) from transcriptomic analyses

Australian Journal of Zoology ◽

10.1071/zo18005 ◽

2018 ◽

Vol 66 (2) ◽

pp. 93 ◽

Cited By ~ 4

Author(s):

Hongji Sun ◽

Xianbo Zuo ◽

Long Sun ◽

Peng Yan ◽

Fang Zhang ◽

...

Keyword(s):

Gene Expression ◽

Skeletal Muscle ◽

Molecular Mechanisms ◽

Differentially Expressed ◽

Model Organisms ◽

Seasonal Adaptation ◽

Cold Temperatures ◽

Chinese Alligator ◽

Adaptive Mechanisms ◽

Alligator Sinensis

The Chinese alligator (Alligator sinensis) is an endemic and rare species in China, and is considered to be one of the most endangered vertebrates in the world. It is known to hibernate, an energy-saving strategy against cold temperatures and food deprivation. Changes in gene expression during hibernation remain largely unknown. To understand these complex seasonal adaptive mechanisms, we performed a comprehensive survey of differential gene expression in heart, skeletal muscle, and kidney of hibernating and active Chinese alligators using RNA-Sequencing. In total, we identified 4780 genes differentially expressed between the active and hibernating periods. GO and KEGG pathway analysis indicated the likely role of these differentially expressed genes (DEGs). The upregulated DEGs in the active Chinese alligator, CSRP3, MYG and PCKGC, may maintain heart and skeletal muscle contraction, transport and storage of oxygen, and enhance the body’s metabolism, respectively. The upregulated DEGs in the dormant Chinese alligator, ADIPO, CIRBP and TMM27, may improve insulin sensitivity and glucose/lipid metabolism, protect cells against harmful effects of cold temperature and hypoxia, regulate amino acid transport and uptake, and stimulate the proliferation of islet cells and the secretion of insulin. These results provide a foundation for understanding the molecular mechanisms of the seasonal adaptation required for hibernation in Chinese alligators, as well as effective information for other non-model organisms research.

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Insight into Molecular Profile Changes after Skeletal Muscle Contusion Using Microarray and Bioinformatics Analyses

10.21203/rs.3.rs-85830/v1 ◽

2020 ◽

Author(s):

Na Li ◽

Ru-feng Bai ◽

Chun Li ◽

Li-hong Dang ◽

Qiu-xiang Du ◽

...

Keyword(s):

Gene Expression ◽

Network Analysis ◽

Differentially Expressed Genes ◽

Molecular Mechanisms ◽

Expression Profiles ◽

Healing Process ◽

Differentially Expressed ◽

Molecular Profile ◽

Wound Age ◽

Functional Modules

Abstract Background: Muscle trauma frequently occurs in daily life. However, the molecular mechanisms of muscle healing, which partly depend on the extent of the damage, are not well understood. This study aimed to investigate gene expression profiles following mild and severe muscle contusion, and to provide more information about the molecular mechanisms underlying the repair process.Methods: A total of 33 rats were divided randomly into control (n = 3), mild contusion (n = 15), and severe contusion (n = 15) groups; the contusion groups were further divided into five subgroups (1, 3, 24, 48, and 168 h post-injury; n = 3 per subgroup). Then full genome microarray of RNA isolated from muscle tissue was performed to access the gene expression changes during healing process.Results: A total of 2,844 and 2,298 differentially expressed genes were identified in the mild and severe contusion groups, respectively. The analysis of the overlapping differentially expressed genes showed that there are common mechanisms of transcriptomic repair of mild and severe contusion within 48 h post-contusion. This was supported by the results of principal component analysis, hierarchical clustering, and weighted gene co‐expression network analysis of the 1,620 coexpressed genes in mildly and severely contused muscle. From these analyses, we discovered that the gene profiles in functional modules and temporal clusters were similar between the mild and severe contusion groups; moreover, the genes showed time-dependent patterns of expression, which allowed us to identify useful markers of wound age. We then performed an analysis of the functions of genes (including Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway annotation, and protein–protein interaction network analysis) in the functional modules and temporal clusters, and the hub genes in each module–cluster pair were identified. Interestingly, we found that genes downregulated within 24−48 h of the healing process were largely associated with metabolic processes, especially oxidative phosphorylation of reduced nicotinamide adenine dinucleotide phosphate, which has been rarely reported. Conclusions: These results improve our understanding of the molecular mechanisms underlying muscle repair, and provide a basis for further studies of wound age estimation.

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Comparative phosphoproteomic analysis of blast resistant and susceptible rice cultivars in response to salicylic acid

BMC Plant Biology ◽

10.1186/s12870-019-2075-5 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 2

Author(s):

Ranran Sun ◽

Shiwen Qin ◽

Tong Zhang ◽

Zhenzhong Wang ◽

Huaping Li ◽

...

Keyword(s):

Salicylic Acid ◽

Molecular Mechanisms ◽

Defense Responses ◽

Differentially Expressed ◽

Phosphoglycerate Mutase ◽

Regulatory Function ◽

Rice Cultivars ◽

Resistance Response ◽

Basal Resistance ◽

Pathogen Invasion

Abstract Background Salicylic acid (SA) is a significant signaling molecule that induces rice resistance against pathogen invasion. Protein phosphorylation carries out an important regulatory function in plant defense responses, while the global phosphoproteome changes in rice response to SA-mediated defense response has not been reported. In this study, a comparative phosphoproteomic profiling was conducted by two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS) analysis, with two near-isogenic rice cultivars after SA treatment. Results Thirty-seven phosphoprotein spots were differentially expressed after SA treatment, twenty-nine of which were identified by MALDI-TOF/TOF MS, belonging to nine functional categories. Phosphoproteins involved in photosynthesis, antioxidative enzymes, molecular chaperones were similarly expressed in the two cultivars, suggesting SA might alleviate decreases in plant photosynthesis, regulate the antioxidant defense activities, thus improving basal resistance response in both cultivars. Meanwhile, phosphoproteins related to defense, carbohydrate metabolism, protein synthesis and degradation were differentially expressed, suggesting phosphorylation regulation mediated by SA may coordinate complex cellular activities in the two cultivars. Furthermore, the phosphorylation sites of four identified phosphoproteins were verified by NanoLC-MS/MS, and phosphorylated regulation of three enzymes (cinnamoyl-CoA reductase, phosphoglycerate mutase and ascorbate peroxidase) was validated by activity determination. Conclusions Our study suggested that phosphorylation regulation mediated by SA may contribute to the different resistance response of the two cultivars. To our knowledge, this is the first report to measure rice phosphoproteomic changes in response to SA, which provides new insights into molecular mechanisms of SA-induced rice defense.

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Gene expression vs. sequence divergence: comparative transcriptome sequencing among natural Rhinolophus ferrumequinum populations with different acoustic phenotypes

Frontiers in Zoology ◽

10.1186/s12983-019-0336-7 ◽

2019 ◽

Vol 16 (1) ◽

Cited By ~ 1

Author(s):

Hanbo Zhao ◽

Hui Wang ◽

Tong Liu ◽

Sen Liu ◽

Longru Jin ◽

...

Keyword(s):

Gene Expression ◽

Geographic Variation ◽

Molecular Mechanisms ◽

Sequence Divergence ◽

Orthologous Gene ◽

Differentially Expressed ◽

Nucleotide Polymorphisms ◽

Genetic Lineages ◽

Rhinolophus Ferrumequinum ◽

Horseshoe Bat

Abstract Background Although the sensory drive hypothesis can explain the geographic variation in echolocation frequencies of some bat species, the molecular mechanisms underlying this phenomenon are still unclear. The three lineages of greater horseshoe bat (Rhinolophus ferrumequinum) in China (northeast, central-east, and southwest) have significant geographic variation in resting frequencies (RF) of echolocation calls. Because their cochleae have an acoustic fovea that is highly sensitive to a narrow range of frequencies, we reported the transcriptomes of cochleae collected from three genetic lineages of R. ferrumequinum, which is an ideal organism for studying geographic variation in echolocation signals, and tried to understand the mechanisms behind this bat phenomenon by analyzing gene expression and sequence variation. Results A total of 8190 differentially expressed genes (DEGs) were identified. We identified five modules from all DEGs that were significantly related to RF or forearm length (FL). DEGs in the RF-related modules were significantly enriched in the gene categories involved in neural activity, learning, and response to sound. DEGs in the FL-related modules were significantly enriched in the pathways related to muscle and actin functions. Using 21,945 single nucleotide polymorphisms, we identified 18 candidate unigenes associated with hearing, five of which were differentially expressed among the three populations. Additionally, the gene ERBB4, which regulates diverse cellular processes in the inner ear such as cell proliferation and differentiation, was in the largest module. We also found 49 unigenes that were under positive selection from 4105 one-to-one orthologous gene pairs between the three R. ferrumequinum lineages and three other Chiroptera species. Conclusions The variability of gene expression and sequence divergence at the molecular level might provide evidence that can help elucidate the genetic basis of geographic variation in echolocation signals of greater horseshoe bats.

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Microarray analysis of gene expression during early stages of mild and severe cardiac hypertrophy

Physiological Genomics ◽

10.1152/physiolgenomics.00072.2006 ◽

2006 ◽

Vol 27 (3) ◽

pp. 309-317 ◽

Cited By ~ 34

Author(s):

Sudarsan Rajan ◽

Sarah S. Williams ◽

Ganapathy Jagatheesan ◽

Rafeeq P. H. Ahmed ◽

Geraldine Fuller-Bicer ◽

...

Keyword(s):

Gene Expression ◽

Cardiac Hypertrophy ◽

Microarray Analysis ◽

Ventricular Hypertrophy ◽

Molecular Mechanisms ◽

Familial Hypertrophic Cardiomyopathy ◽

Differentially Expressed ◽

Transgenic Mouse Models ◽

Ventricular Tissue ◽

Gene Transcripts

Familial hypertrophic cardiomyopathy (FHC) is a disease characterized by ventricular hypertrophy, fibrosis, and aberrant systolic and/or diastolic function. We previously developed two transgenic mouse models that carry FHC-associated mutations in α-tropomyosin (TM): FHC α-TM175 mice show patchy areas of mild ventricular disorganization and limited hypertrophy, whereas FHC α-TM180 mice exhibit severe hypertrophy and fibrosis and die within 6 mo. To obtain a better understanding of the molecular mechanisms associated with the early onset of cardiac hypertrophy, we conducted a detailed comparative analysis of gene expression in 2.5-mo-old control, FHC α-TM175, and α-TM180 ventricular tissue. Results show that 754 genes (from a total of 22,600) were differentially expressed between the nontransgenic (NTG) and the FHC hearts. There are 178 differentially regulated genes between NTG and the FHC α-TM175 hearts, 388 genes are differentially expressed between NTG and FHC α-TM180 hearts, and 266 genes are differentially expressed between FHC α-TM175 and FHC α-TM180 hearts. Genes that exhibit the largest increase in expression belong to the “secreted/extracellular matrix” category, and those with the most significant decrease in expression are associated with “metabolic enzymes.” Confirmation of the microarray analysis was conducted by quantitative real-time PCR on gene transcripts commonly associated with cardiac hypertrophy.

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PO-046 Gene expression profiling of peripheral blood mononuclear cells in young male trampoline athletes

Exercise Biochemistry Review ◽

10.14428/ebr.v1i3.10113 ◽

2018 ◽

Vol 1 (3) ◽

Author(s):

Li Gao ◽

Yong Jie Yang ◽

En Qi Li ◽

Jia Ning Mao

Keyword(s):

Gene Expression ◽

Differentially Expressed Genes ◽

Bone Health ◽

Expression Profiling ◽

Molecular Mechanisms ◽

Interaction Network ◽

Differentially Expressed ◽

Signal Pathways ◽

Healthy Controls ◽

Mineral Density

Objective Evidence indicates that physical activity influence bone health. However, the molecular mechanisms mediating the beneficial adaptations to exercise are not well understood. The purpose of this study was to examine the differentially expressed genes in PBMC between athletes and healthy controls, and to analyze the important functional genes and signal pathways that cause increased bone mineral density in athletes, in order to further reveal the molecular mechanisms of exercise promoting bone health. Methods Five professional trampoline athletes and five age-matched untrained college students participated in this study. Used the human expression Microarray V4.0 expression profiling chip to detect differentially expressed genes in the two groups, and performed KEGG Pathway analysis and application of STRING database to construct protein interaction Network; Real-Time PCR technology was used to verify the expression of some differential genes. Results Compared with healthy controls, there were significant improvement in lumbar spine bone mineral density, and 236 up-regulated as well as 265 down-regulated in serum samples of athletes. The differentially expressed genes involved 28 signal pathways, such as cell adhesion molecules. Protein interaction network showed that MYC was at the core node position. Real-time PCR results showed that the expression levels of CD40 and ITGα6 genes in the athletes were up-regulated compared with the healthy controls, the detection results were consistent with that of the gene chip. Conclusions The findings highlight that long-term high-intensity trampoline training could induce transcriptional changes in PBMC of the athletes. These data suggest that gene expression fingerprints can serve as a powerful research tool to design novel strategies for monitoring exercise. The findings of the study also provide support for the notion that PBMC could be used as a substitute to study exercise training that affects bone health.

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DOP22 Integrative -omic analysis reveals microbiota mediated molecular mechanisms influencing host mucosal gene expression in Crohn’s Disease

Journal of Crohn s and Colitis ◽

10.1093/ecco-jcc/jjab073.061 ◽

2021 ◽

Vol 15 (Supplement_1) ◽

pp. S061-S062

Author(s):

P Sudhakar ◽

T Andrighetti ◽

S Verstockt ◽

C Caenepeel ◽

M Ferrante ◽

...

Keyword(s):

Gene Expression ◽

Crohn’S Disease ◽

Crohn's Disease ◽

Molecular Mechanisms ◽

Bacterial Species ◽

Differentially Expressed ◽

Mucosal Barrier ◽

Bacterial Proteins ◽

The Impact ◽

Hub Proteins

Abstract Background Mechanistic evidence linking gut microbial changes and host mucosal barrier responses in patients with Crohn’s disease (CD) is lacking. In this study, we used a computational approach to integrate gut microbial and intestinal gene expression in CD patients. Methods Bacterial species, bacterial genes/transcripts with enhanced abundances/transcriptional activity in CD (t-statistic of > 2 and Q-value < 0.05), as well as mucosal (ileum/rectum) differentially expressed genes (DEGs) between CD (n =43) and non-IBD (n=22) subjects were retrieved from the Inflammatory Bowel Disease Meta -Omics Database (IBDMDB). The impact of bacterial proteins on host gene expression was inferred using MicrobioLink, a computational tool for inferring microbe-host interactions. Drug target information was retrieved from OpenTargets. Paired 16S read-outs from stool samples and gene expression data from ileal biopsies in CD patients (n=20) and non-IBD controls (n=15), cross-sectionally collected at our IBD referral center, were used for independent validation. Results Across the 8 identified bacterial species enriched in CD, 3.7% (n= 743) of the orthologous groups were identified as being able to bind to human proteins. Network diffusion analysis uncovered bacterial proteins which could cumulatively modulate the expression of 42% of the genes differentially expressed in the ileum of CD patients. Topological and pathway analysis of the inferred signaling network modulated by the microbiota revealed several key hub proteins and immune-related pathways associated with IL-4, IL-2 and IL-13 signaling, receptor tyrosine-kinases, NFkB, and toll-like receptors including TLR4. Seventy-eight percent of the DEGs in our discovery cohort were also differentially expressed in the validation cohort (R2 = 0.907). Bacterial proteins post-translationally modifying host receptors resulted in the up-regulation of several pro-inflammatory cytokines via critical hub proteins such as NFkB (Figure 1). We observed different levels of locational specificity (from 35 to 61%) for the top regulators such as SPI1, STAT1 and NFKB1in terms of genes regulated by them in ileum and rectum. 24 proteins including ITGA4 and JAK1 from the ileal and rectal signaling networks are existing targets of CD drugs such as vedolizumab and tofacitinib, filgotinib and upadacitinib respectively. Conclusion Our findings outline the potential mechanisms of microbiome-induced host responses and provide insights into designing microbiome-mediated therapies to prevent and/or treat CD.

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Identification of Key Genes and MicroRNAs in Gastric Cancer via miRNA-mRNA Regulatory Network

10.21203/rs.3.rs-32146/v1 ◽

2020 ◽

Author(s):

Chao Huang ◽

Xiaojian Zhu ◽

Jiefeng Zhao ◽

Fanqin Bu ◽

Jun Huang ◽

...

Keyword(s):

Gene Expression ◽

Gastric Cancer ◽

Molecular Markers ◽

Expression Profiling ◽

Regulatory Network ◽

Molecular Mechanisms ◽

Critical Role ◽

Differentially Expressed ◽

Expression Levels ◽

Receptor Interactions

Abstract Background Gastric cancer (GC) is a malignant tumor with high mortality. MicroRNAs (miRNAs) participate in various biological processes and disease pathogenesis by targeting messenger RNA (mRNA). The purpose of this study was to identify potential prognostic molecular markers of GC and to characterize the molecular mechanisms of GC. Methods A gene expression profiling dataset (GSE54129) and miRNA expression profiling dataset (GSE113486) were downloaded from the Gene Expression Omnibus (GEO) database. A miRNA-mRNA interaction network was established. Functional and pathway enrichment analyses were performed for differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) using FunRich, the clusterProfiler package, and DIANA-mirPath. Survival analysis of key molecular markers was performed using the online tool Kaplan-Meier Plotter and the database OncomiR. Finally, experiments were carried out to verify the expression levels and biological functions of a key gene. Results A total of 390 DEMs and 341 DEGs were identified. Ultimately, 45 genes and 31 miRNAs were selected to establish a miRNA-mRNA regulatory network. Four hub genes (ZFPM2, FUT9, NEUROD1 and LIPH) and six miRNAs (hsa-let-7d-5p, hsa-miR-23b-3p, hsa-miR-23a-3p, hsa-miR-133b, hsa-miR-130a-3p and hsa-miR-124-3p) were identified in the network. DEGs and DEMs were associated with ECM-receptor interactions and metabolic pathways. Two genes (ZFPM2 and LIPH) and two miRNAs (hsa-miR-23a-3p and hsa-miR-130a-3p) were observed to be related to the prognosis of GC. ZFPM2 was highly expressed in GC tissues and various GC cell lines and could promote the proliferation, invasion and migration of GC cells. Conclusion The expression levels of ZFPM2, LIPH, hsa-miR-23a-3p and hsa-miR-130a-3p were closely related to the prognosis of GC. ZFPM2 may serve as a potential molecular marker and therapeutic target for GC. ECM receptor interactions and metabolic abnormalities play a critical role in the GC progression.

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