Global Gene Expression Patterns Research Articles

MicroRNAs in cancer metastasis: biological and therapeutic implications.

Cancer metastasis is the primary cause of cancer-related deaths. The seeding of primary tumours at a secondary site is a highly inefficient process requiring substantial alterations in the genetic architecture of cancer cells. These alterations include significant changes in global gene expression patterns. MicroRNAs are small, non-protein coding RNAs which play a central role in regulating gene expression. Here, we focus on microRNA determinants of cancer metastasis and examine microRNA dysregulation in metastatic cancer cells. We dissect the metastatic process in a step-wise manner and summarise the involvement of microRNAs at each step. We also discuss the advantages and limitations of different microRNA-based strategies that have been used to target metastasis in pre-clinical models. Finally, we highlight current clinical trials that use microRNA-based therapies to target advanced or metastatic tumours.

Potential Biomarkers for Parkinson Disease from Functional Enrichment and Bioinformatic Analysis of Global Gene Expression Patterns of Blood and Substantia Nigra Tissues.

The Parkinson disease (PD) is the second most common neurodegenerative disorder affecting the central nervous system and motor functions. The biological complexity of PD is yet to reveal potential targets for intervention or to slow the disease severity. Therefore, this study aimed to compare the fidelity of blood to substantia nigra (SN) tissue gene expression from PD patients to provide a systematic approach to predict role of the key genes of PD pathobiology. Differentially expressed genes (DEGs) from multiple microarray data sets of PD blood and SN tissue from GEO database are identified. Using the theoretical network approach and variety of bioinformatic tools, we prioritized the key genes from DEGs. A total of 540 and 1024 DEGs were identified in blood and SN tissue samples, respectively. Functional pathways closely related to PD such as ERK1 and ERK2 cascades, mitogen-activated protein kinase (MAPK) signaling, Wnt, nuclear factor-κB (NF-κB), and PI3K-Akt signaling were observed by enrichment analysis. Expression patterns of 13 DEGs were similar in both blood and SN tissues. Comprehensive network topological analysis and gene regulatory networks identified additional 10 DEGs functionally connected with molecular mechanisms of PD through the mammalian target of rapamycin (mTOR), autophagy, and AMP-activated protein kinase (AMPK) signaling pathways. Potential drug molecules were identified by chemical-protein network and drug prediction analysis. These potential candidates can be further validated in vitro/in vivo to be used as biomarkers and/or novel drug targets for the PD pathology and/or to arrest or delay the neurodegeneration over the years, respectively.

The Effects of Heat Stress on the Transcriptome of Human Cancer Cells: A Meta-Analysis

Hyperthermia is clinically applied cancer treatment in conjunction with radio- and/or chemotherapy, in which the tumor volume is exposed to supraphysiological temperatures. Since cells can effectively counteract the effects of hyperthermia by protective measures that are commonly known as the heat stress response, the identification of cellular processes that are essential for surviving hyperthermia could lead to novel treatment strategies that improve its therapeutic effects. Here, we apply a meta-analytic approach to 18 datasets that capture hyperthermia-induced transcriptome alterations in nine different human cancer cell lines. We find, in line with previous reports, that hyperthermia affects multiple processes, including protein folding, cell cycle, mitosis, and cell death, and additionally uncover expression changes of genes involved in KRAS signaling, inflammatory responses, TNF-a signaling and epithelial-to-mesenchymal transition (EMT). Interestingly, however, we also find a considerable inter-study variability, and an apparent absence of a 'universal' heat stress response signature, which is likely caused by the differences in experimental conditions. Our results suggest that gene expression alterations after heat stress are driven, to a large extent, by the experimental context, and call for a more extensive, controlled study that examines the effects of key experimental parameters on global gene expression patterns.

Transcriptomic analysis reveals the dynamic changes of transcription factors during early development of chicken embryo

BackgroundThe transition from fertilized egg to embryo in chicken requires activation of hundreds of genes that were mostly inactivated before fertilization, which is accompanied with various biological processes. Undoubtedly, transcription factors (TFs) play important roles in regulating the changes in gene expression pattern observed at early development. However, the contribution of TFs during early embryo development of chicken still remains largely unknown that need to be investigated. Therefore, an understanding of the development of vertebrates would be greatly facilitated by study of the dynamic changes in transcription factors during early chicken embryo.ResultsIn the current study, we selected five early developmental stages in White Leghorn chicken, gallus gallus, for transcriptome analysis, cover 17,478 genes with about 807 million clean reads of RNA-sequencing. We have compared global gene expression patterns of consecutive stages and noted the differences. Comparative analysis of differentially expressed TFs (FDR < 0.05) profiles between neighboring developmental timepoints revealed significantly enriched biological categories associated with differentiation, development and morphogenesis. We also found that Zf-C2H2, Homeobox and bHLH were three dominant transcription factor families that appeared in early embryogenesis. More importantly, a TFs co-expression network was constructed and 16 critical TFs were identified.ConclusionOur findings provide a comprehensive regulatory framework of TFs in chicken early embryo, revealing new insights into alterations of chicken embryonic TF expression and broadening better understanding of TF function in chicken embryogenesis.

Regeneration pattern and genome-wide transcription profile of rhizome axillary buds after perennial rice harvest.

Perennial rice is a new type of rice that allows the harvest of rice for multiple years without growing new seedlings annually. This technology represents a green and sustainable agricultural production mode with many advantages for balancing agricultural ecology and food security. However, the differences in regeneration patterns between perennial and annual rice and the gene regulatory pathways of the apical dominance in axillary bud growth after harvest in perennial rice are still unclear. In this study, perennial rice (PR23) and annual rice (Chugeng28) were used to investigate axillary bud growth patterns before and after apical spike removal. After elimination of apical dominance at different development stages, perennial rice rhizome axillary buds at the compression nodes germinated more rapidly than others and developed into new seedlings. The axillary buds at the high-position nodes in annual rice grew faster than those at other nodes. Furthermore, the global gene expression patterns of PR23 rhizome buds at compression nodes grown for 1, 3, 4, and 5 days after apical spike removal were analyzed by transcriptome sequencing. Compared with the control buds without apical removal, 264, 3,484, 2,095, and 3,398 genes were up-regulated, and 674, 3,484, 1,594, and 1,824 genes were down-regulated in the buds grown for 1, 3, 4, and 5 days after apical spike removal, respectively. Trend analysis of the expressed genes at different time points was performed and co-expression network was constructed to identify key genes in rhizome axillary bud regrowth. The results showed that 85 hub genes involved in 12 co-regulatory networks were mainly enriched in the light system, photosynthesis-antenna protein, plant hormone signal transduction, ABC transporter and metabolic pathways, which suggested that hormone and photosynthetic signals might play important roles in the regulation of rhizome axillary bud regeneration in perennial rice. Overall, this study clarified the differences in the regeneration patterns of axillary buds between perennial and annual rice and provided insight into the complex regulatory networks during the regeneration of rhizome axillary buds in perennial rice.

A Genetic Compensation Phenomenon and Global Gene Expression Changes in Sex-miR-2766-3p Knockout Strain of Spodoptera exigua Hübner (Lepidoptera: Noctuidae).

MicroRNAs (miRNAs) drive the post-transcriptional repression of target mRNAs and play important roles in a variety of biological processes. miR-2766-3p is conserved and abundant in Lepidopteran species and may be involved in a variety of biological activities. In this study, Sex-miR-2766-3p was predicted to potentially bind to the 3' untranslated region (UTR) of cap 'n' collar isoform C (CncC) in Spodoptera exigua, and Sex-miR-2766-3p was confirmed to regulate the expression of SeCncC through screening with a luciferase reporter system. Although CRISPR/Cas9 has been extensively utilized to examine insect gene function, studies of miRNA function are still relatively uncommon. Thus, we employed CRISPR/Cas9 to knock out Sex-miR-2766-3p from S. exigua. However, the expression of SeCncC was not significantly altered in the knockout strain (2766-KO) compared with that of the WHS strain. This result suggested that a miRNA knockout might lack phenotypes because of genetic robustness. Additionally, we used transcriptome analysis to examine how the global gene expression patterns of the Sex-miR-2766-3p knockout strain varied. RNA-seq data revealed 1746 upregulated and 2183 downregulated differentially expressed genes (DEGs) in the 2766-KO strain, which might be the result of Sex-miR-2766-3p loss or DNA lesions as the trigger for transcriptional adaptation. GO function classification and KEGG pathway analyses showed that these DEGs were enriched for terms related to binding, catalytic activity, metabolic process, and signal transduction. Our findings demonstrated that S. exigua could compensate for the missing Sex-miR-2766-3p by maintaining the expression of SeCncC by other pathways.

Acute Myeloid Leukemia with Isolated Trisomy 4 Is Characterized By Frequent Mutations of TET2 and a Distinct DNA Methylation Signature

Background: Trisomy 4 (+4) is a rare cytogenetic abnormality found in less than 1% of acute myeloid leukemia (AML) either as sole abnormality (isolated AML+4, iAML+4) or associated with other genetic lesions. However, iAML+4 is inadequately studied due to its rarity and little is known about its molecular profile. Aim: The aim of this study was to characterize the molecular profile of iAML+4, including gene mutations, gene expression and DNA methylation changes. Methods: For the molecular characterization, we have performed targeted amplicon sequencing (n=68 target genes), gene expression profiling (SCRB-seq) and DNA methylation profiling (Illumina Methylation EPIC arrays) on 11 iAML+4 patients from German AML study groups (AML-CG 1999 and AML-CG 2008) and 105 patients with cytogenetically normal AML (CN-AML). Results: By targeted sequencing, 35 mutations were detected in 11 genes with a median of 3 mutations per patient (range 1-7, Figure 1A). Recurrently mutated genes were TET2 (n=9 patients), NPM1 (n=5) and FLT3-ITD (n=4), DNMT3A (n=2), and WT1 (n=2). Of note, in 8/9 patients with TET2 mutations, a truncating mutation has been detected. Thus, the frequency of truncating TET2 mutations was exceptionally high (8/11; 73%) in iAML+4, as compared to CN-AML with 12/105 patients mutated (11%, P=2.4e-5, Fisher exact test), which is in line with previous findings in the literature. Moreover, 3 patients harbored multiple TET2 mutations. We have further performed targeted amplicon sequencing in 8 AML patients with non-isolated +4, where trisomy 4 was present along with other cytogenetic abnormalities. In non-isolated +4 AML, TET2 mutations were less frequently found, as compared to iAML+4 (2/8, 25%, P=0.07). Gene expression profiling revealed a distinct gene expression pattern in iAML+4 as compared to CN-AML patients. Across all chromosomes, differentially expressed genes were detected; with the highest numbers of overexpressed genes located on chromosome 4, followed by chromosomes 2, 12, 17 and 18, as well as a substantial number of downregulated genes, particularly on chromosomes 11 and 19, indicating a trans-regulatory effect of +4 (Figure 1B). DNA methylation analysis revealed a specific hypermethylation signature among iAML+4 patients, as compared to CN-AML (Figure 1C). A global increase of CpG methylation levels in iAML+4 may be likely due to the high frequency of truncating TET2 mutations, as TET2 is known to be involved in hydroxymethylation of the DNA. However, the hypermethylation signature was confirmed even when comparing iAML+4 to CN-AML within TET2 mutated patient samples, indicating DNA hypermethylation beyond the effect of truncating TET2 mutations. Hierarchical clustering of iAML+4 and CN-AML samples resulted in a separate cluster with a distinct hypermethylation signature, which is strongly enriched for iAML+4 patients. Of note, besides TET2 truncating variants, no additional mutation was found to be enriched in that cluster, indicating that +4 is the major (cyto) genetic driver mediating this pattern. Conclusion: Our comprehensive multi-omics analysis revealed a homogenous molecular profile of iAML+4 with high frequency of truncating TET2 mutations indicating oncogenic cooperativity, a global pattern of differential gene expression as well as a uniform DNA hypermethylation signature, which is generally not associated with truncating TET2 mutations but a specific feature of trisomy 4 in AML. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

MGCEP 1.0: A Genetic-Engineered Marine-Derived Chassis Cell for a Scaled Heterologous Expression Platform of Microbial Bioactive Metabolites.

Marine microorganisms produce a variety of bioactive secondary metabolites, which represent a significant source of novel antibiotics. Heterologous expression is a valuable tool for discovering marine microbial secondary metabolites; however, marine-derived chassis cell is very scarce. Here, we build an efficient plug-and-play marine-derived gene clusters expression platform 1.0 (MGCEP 1.0) by the systematic engineering of the deep-sea-derived Streptomyces atratus SCSIO ZH16. For a proof of concept, four families of microbial bioactive metabolite biosynthetic gene clusters (BGCs), including alkaloids, aminonucleosides, nonribosomal peptides, and polyketides, were efficiently expressed in this platform. Moreover, 19 compounds, including two new angucycline antibiotics, were produced in MGCEP 1.0. Dynamic patterns of global biosynthetic gene expression in MGCEP 1.0 with or without a heterologous gene cluster were revealed at the transcriptome level. The platform MGCEP 1.0 provides new possibilities for expressing microbial secondary metabolites, especially of marine origin.

Transcriptome Analysis Reveals Gene Expression Changes during Repair from Mechanical Wounding in Aquilaria sinensis

Plants repair their mechanical wounds by reprogramming secondary metabolism. However, which genes are reprogrammed during this repair process in Aquilaria sinensis has rarely been studied. Here, we used high-throughput RNA sequencing to explore the changes in the transcriptome of Aquilaria’s xylem, six months after the stem was subjected to mechanical wounding. In total, 1165 transcripts were differentially accumulated, of which 1002 transcripts were increased and 163 were decreased in their abundances (|log2 (fold change)| ≥ 1 and FDR ≤ 0.05). The majority of these genes encode products involved in plant secondary metabolism, transcription regulation, and phytohormone metabolism and signaling. The up-regulated genes were classified into 15 significantly enriched GO terms and were involved in 83 pathways, whereas the down-regulated genes were classified into 5 significantly enriched GO terms and represented 43 pathways. Gene annotation demonstrated that 100 transcripts could encode transcription factors (TFs), such as WRKY, AP2, MYB, and Helix-loop-helix (HLH) TFs. We inferred that the differential expression of TFs, genes associated with plant hormones, phenylpropanoid biosynthesis, and sesquiterpenoid biosynthesis may contribute to the repair of the stem after mechanical wounding in A. sinensis. Using co-expression analysis and prediction of TF binding sites, a TF–gene regulatory network for Aquilaria lignin biosynthesis was constructed. This included the MYB, HLH, WRKY, and AP2 TFs, and the COMT1, 4CLL7, and CCR1 genes. The changes in 10 candidate genes were validated by quantitative reverse-transcription PCR, indicating significant differences between the treated and untreated areas. Our study provides global gene expression patterns under mechanical wounding and would be valuable to further studies on the molecular mechanisms of plant repair in A. sinensis.

Upwelling-level acidification and pH/pCO2 variability moderate effects of ocean acidification on brain gene expression in the temperate surfperch, Embiotoca jacksoni.

Acidification‐induced changes in neurological function have been documented in several tropical marine fishes. Here, we investigate whether similar patterns of neurological impacts are observed in a temperate Pacific fish that naturally experiences regular and often large shifts in environmental pH/pCO2. In two laboratory experiments, we tested the effect of acidification, as well as pH/pCO2 variability, on gene expression in the brain tissue of a common temperate kelp forest/estuarine fish, Embiotoca jacksoni. Experiment 1 employed static pH treatments (target pH = 7.85/7.30), while Experiment 2 incorporated two variable treatments that oscillated around corresponding static treatments with the same mean (target pH = 7.85/7.70) in an eight‐day cycle (amplitude ± 0.15). We found that patterns of global gene expression differed across pH level treatments. Additionally, we identified differential expression of specific genes and enrichment of specific gene sets (GSEA) in comparisons of static pH treatments and in comparisons of static and variable pH treatments of the same mean pH. Importantly, we found that pH/pCO2 variability decreased the number of differentially expressed genes detected between high and low pH treatments, and that interindividual variability in gene expression was greater in variable treatments than static treatments. These results provide important confirmation of neurological impacts of acidification in a temperate fish species and, critically, that natural environmental variability may mediate the impacts of ocean acidification.

Transgenerational effects of co-exposure to cadmium and carbofuran on zebrafish based on biochemical and transcriptomic analyses

The combined toxicity of heavy metals and pesticides to aquatic organisms is still largely unexplored. In this study, we investigated the combined impacts of cadmium (Cd) and carbofuran (CAR) on female zebrafish (F0 generation) and their following F1 generation. Results showed that mixtures of Cd and CAR induced acute synergistic effects on both zebrafish adults of the F0 generation and embryos of the F1 generation. Combined exposure to Cd and CAR could obviously alter the hepatic VTG level of females, and the individual exposures increased the relative mRNA levels of vtg1 and vtg2. Through maternal transmission, co-exposure of Cd and CAR caused toxicity to 4-day-old larvae of the F1 generation, evidenced by the significant changes in T4 and VTG levels, CYP450 activity, and the relative transcriptional levels of genes related to the hormone, oxidative stress, and apoptosis. These effects were also reflected by the global gene expression pattern to 7-day-old larvae of F1 generation using the transcriptomic analysis, and they could also affect energy metabolism. Our results provided a more comprehensive insight into the transgenerational toxic impacts of heavy metal and pesticide mixtures. These findings highlighted that it was highly necessary to consider transgenerational exposures in the ecological risk assessment of chemical mixtures.

Abstract 3861: Microscope-based sorting of highly motile cancer-associated fibroblasts using a photoconvertible fluorescent protein

Abstract In the tumor microenvironment, cancer-associated fibroblasts (CAFs) are known to play key roles in promoting cancer cell invasion and cancer progression. CAFs are also highly invasive compared with normal fibroblasts in a 3-D co-culture system with lung cancer cells. Due to CAF heterogeneity, there are various differences in cell motility even within a CAF population. To classify CAFs according to their motility, we named less motile CAFs as “static CAFs” and more motile CAFs as “motile CAFs”. To separate and isolate these static CAFs and motile CAFs from a 3-D co-culture system, CAFs were transfected with a green-to-red photoconvertible fluorescent protein, Dendra2. Dendra2-transfected CAFs at specific areas (i.e., static or motile CAFs) were UV-irradiated using a confocal microscope. CAFs with red fluorescence were then isolated by flow cytometry and were subjected to RNA sequencing. In gene ontology and gene set enrichment analyses, two types of CAFs showed significant differences in global gene expression patterns. These data suggest that heterogeneous CAFs with different motility have distinct roles in the regulation of various signaling pathways in the tumor microenvironment. Citation Format: Sieun Lee, Young-Ho Ahn. Microscope-based sorting of highly motile cancer-associated fibroblasts using a photoconvertible fluorescent protein [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3861.

Abstract 6016: Patient-derived tumor organoid cultures identify a chemo-resistant sub-population in esophageal squamous cell carcinoma

Abstract Background: Patient-derived xenograft has been a gold standard for cancer modeling. However, low establishment efficiency and high maintenance cost have hindered the development in the field. In recent years, patient-derived tumor organoid culture has been developed as an efficient and economic model to mimic and recapitulate the original tumor tissue, in contrast to conventional cancer cell lines and patient-derived xenografts (Drost &amp; Clevers, 2018). Due to the limited availability of current esophageal squamous cell carcinoma (ESCC) models, we aimed to establish a panel of ESCC patient-derived organoid (PDO) long-term cultures for ESCC study. Results: In the current project, we have established and biobanked a panel of ESCC PDO cultures in vitro from Chinese ESCC treatment-naïve patients undergoing an endoscopic examination or upfront surgery, or patients undergoing neoadjuvant chemoradiotherapy (CRT) followed by surgery in Hong Kong. We also established and maintained PDO-derived xenograft (PDOX) in immunocompromised mice. Immunohistochemical examination confirmed the squamous origin of the established PDOs and PDOXs. Genomic profiling showed consistent mutational landscapes of the established PDO, as compared to ESCC patient profiles. Transcriptomic profiling suggests organoid culture resembles patient tissue samples better than the cell line model in terms of global gene expression patterns. Notably, PDOs from CRT-treated patients show enhanced re-growth after recovery from cisplatin treatment, indicating a candidate cancer stem cell (CSC) sub-population enriched by neoadjuvant CRT. This sub-population can be further enriched in vitro by serial cisplatin treatment and recovery cycles. Conclusions: ESCC PDOs can be efficiently established from highly limited patient tissue samples and maintained long-term in vitro and can be feasibly integrated with mouse model. It preserves the original cell hierarchy and indicates existence of candidate CSC sub-population, which may be targeted therapeutically in future. Reference: Drost J, Clevers H. Organoids in cancer research. Nat Rev Cancer. 2018 Jul; 18(7). Acknowledgment: We acknowledge the Research Grants Council (Theme-based Research Scheme T12-701/17-R to MLL) and the Food and Health Bureau (Health and Medical Research Fund 06171566 to VZY) of Hong Kong Special Administrative Region for funding supports. We acknowledge DSMZ (German Collection of Microorganisms and Cell Culture) for the KYSE cell lines. We acknowledge the University of Hong Kong Faculty of Medicine Core Facility for providing imaging facilities. Citation Format: Valen Z. Yu, Bryan C. Lung, Ian Y. Wong, Claudia L. Wong, Simon Y. Law, Maria L. Lung. Patient-derived tumor organoid cultures identify a chemo-resistant sub-population in esophageal squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6016.

Clinical and Preclinical Evidence for M1 Muscarinic Acetylcholine Receptor Potentiation as a Therapeutic Approach for Rett Syndrome

SummaryRett syndrome (RTT) is a neurodevelopmental disorder that is characterized by developmental regression, loss of communicative ability, stereotyped hand wringing, cognitive impairment, and central apneas, among many other symptoms. RTT is caused by loss-of-function mutations in a methyl-reader known as methyl-CpG-binding protein 2 (MeCP2), a protein that links epigenetic changes on DNA to larger chromatin structure. Historically, target identification for RTT has relied heavily on Mecp2 knockout mice; however, we recently adopted the alternative approach of performing transcriptional profiling in autopsy samples from RTT patients. Through this mechanism, we identified muscarinic acetylcholine receptors (mAChRs) as potential therapeutic targets. Here, we characterized a cohort of 40 temporal cortex samples from individuals with RTT and quantified significantly decreased levels of the M1, M2, M3, and M5 mAChRs subtypes relative to neurotypical controls. Of these four subtypes, M1 expression demonstrated a linear relationship with MeCP2 expression, such that M1 levels were only diminished in contexts where MeCP2 was also significantly decreased. Further, we show that M1 potentiation with the positive allosteric modulator (PAM) VU0453595 (VU595) rescued social preference, spatial memory, and associative memory deficits, as well as decreased apneas in Mecp2+/- mice. VU595’s efficacy on apneas in Mecp2+/- mice was mediated by the facilitation of the transition from inspiration to expiration. Molecular analysis correlated rescue with normalized global gene expression patterns in the brainstem and hippocampus, as well as increased Gsk3β inhibition and NMDA receptor trafficking. Together, these data suggest that M1 PAMs could represent a new class of RTT therapeutics.

Microarray Analysis of the Genomic Effect of Eugenol on Methicillin-Resistant Staphylococcus aureus.

Staphylococcus aureus is a highly adaptive human pathogen responsible for serious hospital- and community-acquired infectious diseases, ranging from skin and soft tissue infections, to complicated and life-threatening conditions such as endocarditis and toxic shock syndrome (TSS). The rapid development of resistance of this organism to available antibiotics over the last few decades has necessitated a constant search for more efficacious antibacterial agents. Eugenol (4-allyl-2-methoxyphenol) belongs to the class of chemical compounds called phenylpropanoids. It is a pure-to-pale yellow, oily liquid substance, mostly extracted as an essential oil from natural products such as clove, cinnamon, nutmeg, basil, and bay leaf. Eugenol has previously been shown to have antimicrobial activity against methicillin-resistant Staphylococcus aureus (MRSA). However, the mechanism of action of eugenol against MRSA has not, as yet, been elucidated; hence, the necessity of this study. Global gene expression patterns in response to challenge from subinhibitory concentrations of eugenol were analysed using the Agilent DNA microarray system to identify genes that can be used as drug targets—most importantly, essential genes involved in unique metabolic pathways elicited for bacterial survival. Transcriptomic analysis of fluctuating genes revealed those involved in amino acid metabolism, fatty acid metabolism, translational, and ribosomal pathways. In amino acid metabolism, for instance, the argC gene encodes for N-acetyl-gamma-glutamyl-phosphate reductase. The argC gene plays an important role in the biosynthesis of arginine from glutamate in the amino acid metabolic pathway. It is the enzyme that catalyses the third step in the latter reaction, and without this process the production of N-acetylglutamate 5-semialdehyde cannot be completed from the NADP-dependent reduction of N-acetyl-5-glutamyl phosphate, which is essential for the survival of some microorganisms and plants. This study enables us to examine complete global transcriptomic responses in MRSA when challenged with eugenol. It reveals novel information with the potential to further benefit the exploratory quest for novel targets against this pathogen, with a view to the development of efficacious antimicrobial agents for the treatment of associated infections.

Cross-Species Analysis Reveals Co-Expressed Genes Regulating Antler Development in Cervidae.

Antlers constitute an interesting model for basic research in regenerative biology. Despite decades of being studied, much is still unknown about the genes related to antler development. Here, we utilized both the genome and antlerogenic periosteum (AP) transcriptome data of four deer species to reveal antler-related genes through cross-species comparative analysis. The results showed that the global gene expression pattern matches the status of antler phenotypes, supporting the fact that the genes expressed in the AP may be related to antler phenotypes. The upregulated genes of the AP in three-antlered deer showed evidence of co-expression, and their protein sequences were highly conserved. These genes were growth related and likely participated in antler development. In contrast, the upregulated genes in antler-less deer (Chinese water deer) were involved mainly in organismal death and growth failure, possibly related to the loss of antlers during evolution. Overall, this study demonstrates that the co-expressed genes in antlered deer may regulate antler development.

Development of a ribosome profiling protocol to study translation in Kluyveromyces marxianus.

Kluyveromyces marxianus is an interesting and important yeast because of particular traits such as thermotolerance and rapid growth, and for applications in food and industrial biotechnology. For both understanding its biology and developing bioprocesses, it is important to understand how K. marxianus responds and adapts to changing environments. For this, a full suite of omics tools to measure and compare global patterns of gene expression and protein synthesis is needed. We report here the development of a ribosome profiling method for K. marxianus, which allows codon resolution of translation on a genome-wide scale by deep sequencing of ribosome locations on mRNAs. To aid in the analysis and sharing of ribosome profiling data, we added the K. marxianus genome as well as transcriptome and ribosome profiling data to the publicly accessible GWIPS-viz and Trips-Viz browsers. Users are able to upload custom ribosome profiling and RNA-Seq data to both browsers, therefore allowing easy analysis and sharing of data. We also provide a set of step-by-step protocols for the experimental and bioinformatic methods that we developed.

In the Absence of YAP, TAZ Contributes to Hepatocyte Adaptation in Chronic Cholestasis in Females

We previously demonstrated that loss of Yes‐associated protein 1 (YAP1) in early liver development (YAP1 KO) leads to an Alagille syndrome‐like phenotype with absence of intrahepatic bile ducts and severe cholestasis accompanied by chronic hepatocyte adaptations to reduce liver injury. We noticed that TAZ, a paralog of YAP1, was significantly upregulated in hepatocytes of YAP1 KO mice and bound to TEAD transcription factors, suggesting compensatory activity in hepatocytes.We next queried the relationship between YAP1 and TAZ by deleting both genes during early liver development using the Foxa3‐Cre promoter, similar to the YAP1 KO mice, resulting in multiple allele combinations. Interestingly, we show that YAP1/TAZ double knock‐out (DKO) mice are embryonic lethal and stillborn, the embryos surviving almost until birth with no grossly visible abnormalities. The liver morphology during development does not show gross abnormalities, suggesting an extrahepatic source of lethality. This suggests that while YAP1 loss has profound impact on biliary development, YAP1 and TAZ together play a co‐dependent critical role in foregut endoderm development yet to be determined.Next, when we examined TAZ heterozygosity in YAP1 KO mice, we found significant embryonic lethality among males, with insufficient samples to analyze a potential cause at this time. However, among females, loss of one copy of TAZ from YAP1 KO mice resulted in a similar gross phenotype to YAP1 KO, with a complete lack of intrahepatic bile ducts resulting in severe chronic cholestatic disease. While serum bilirubin levels were comparable after TAZ heterozygosity, liver transaminases were more elevated than in YAP1 KO alone, suggesting worsening hepatocyte injury. Hepatocyte proliferation levels were not affected by TAZ heterozygosity. Global gene expression patterns as detected by RNA‐sequencing were grossly similar as compared to YAP1 KO mice, although subtle alterations were identified in pathways related to apoptosis, cell division, inflammatory signaling, and metabolism, and we also show that TAZ is needed to regulate canonical YAP1 targets in YAP1 KO hepatocytes such as CTGF and CYR61. We also found significant elevation in serum cholesterol compared to YAP1 KO alone, and xanthomas were observed at later stages on these mice, suggesting worsening metabolic derangements caused by TAZ heterozygosity beyond what was observed in YAP1 KO alone. Interestingly, bile acid profiles in both liver and serum as detected by mass spectrometry showed no difference in YAP1 KO with or without TAZ heterozygosity. Ongoing work aims to further identify the role of TAZ in metabolic adaptations to chronic cholestasis with potential implications for clinical regulation of hypercholesterolemia and long‐term liver metabolic health.

IDENTIFICATION OF GENES REGULATED IN RESPONSE TO Cu EXPOSURE IN Brassica nigra L.

Copper (Cu) is one of the essential trace metals required for plant growth. High amount of Cu in the media inhibits plant growth and is toxic to the plants. Brassica nigra L., a Cu accumulator, can tolerate a high amount of Cu and have specific mechanisms to relocate Cu within the cell compartments and keep the toxic amount of Cu away from the cytoplasm. This study aimed to evaluate the Cu-induced gene expression pattern of B. nigra Diyarbakir ecotype subjected to low Cu treatment. The Arabidopsis ATH1 genome array was used to determine the Cu-induced gene expression in the leaves of B. nigra grown at 25 µM Cu. Ninety-five genes were upregulated, and seventy-two genes were downregulated in the leaves of plants grown under 25 µM Cu. Cu responsive genes, such as glutathione S-transferase, glutathione reductase, heavy metal transporters, natural resistance-associated macrophage proteins, cytochrome p450, MYB-like transcription factor, copper/zinc, and Fe superoxide dismutases, and some protein kinases were highly expressed in the leaves of Cu-treated plants. The present work provides the global gene expression pattern in facultative metallophyte B. nigra, which could serve as a molecular tool for future phytoremediation studies.

Comparative transcriptome analysis of cold-tolerant and -sensitive asparagus bean under chilling stress and recovery.

BackgroundLow temperature is a type of abiotic stress that threatens the growth and yield of asparagus bean. However, the key genes and regulatory pathways involved in low temperature response in this legume are still poorly understood. Methodology. The present study analyzed the transcriptome of seedlings from two asparagus bean cultivars—Dubai bean and Ningjiang 3—using Illumina RNA sequencing (RNA-seq). Correlations between samples were determined by calculating Pearson correlation coefficients (PCC) and principal component analysis (PCA). Differentially expressed genes (DEGs) between two samples were identified using the DESeq package. Transcription factors (TF) prediction, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs were also performed.ResultsPhenotypes and physiological indices indicated that Ningjiang 3 seedlings tolerated cold better than Dubai bean seedlings, in contrast to adult stage. The transcriptome dynamics of the two cultivars were closely compared using Illumina RNA-seq following 0, 3, 12, and 24 h of cold stress at 5 °C and recovery for 3 h at 25 °C room temperature. Global gene expression patterns displayed relatively high correlation between the two cultivars (>0.88), decreasing to 0.79 and 0.81, respectively, at 12 and 24 h of recovery, consistent with the results of principal component analysis. The major transcription factor families identified from differentially expressed genes between the two cultivars included bHLH, NAC, C2H2, MYB, WRKY, and AP2/ERF. The representative GO enrichment terms were protein phosphorylation, photosynthesis, oxidation-reduction process, and cellular glucan metabolic process. Moreover, KEGG analysis of DEGs within each cultivar revealed 36 transcription factors enriched in Dubai bean and Ningjiang 3 seedlings under cold stress.ConclusionsThese results reveal new information that will improve our understanding of the molecular mechanisms underlying the cold stress response of asparagus bean and provide genetic resources for breeding cold-tolerant asparagus bean cultivars.